xtools.normalizer.5.2.1.source-code.Miriam.xml Maven / Gradle / Ivy
<?xml version="1.0" encoding="UTF-8"?>
<!-- Export of Identifiers.org's Registry (full) -->
<!-- Generated: Tue, 24 Apr 2018 14:23:08 GMT -->
<!-- http://identifiers.org/registry/ -->
<!--Igor R. manually fixed date, data-version format (for JAXB unmarshaling to work)-->
<!--and also removed ambiguous "KEGG" synonym from KEGG Compound, et al. collections!-->
<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2018-04-24T14:41:47+00:00" data-version="2018-04-20T13:10:26+00:00">
<datatype id="MIR:00000001" pattern="^\d+$" restricted="true" obsolete="true" replacement="MIR:00000010">
<comment>BIND doesn't exist any more and its successor (BOND) is not open-access. Bulk downloads of BIND data (http://bond.unleashedinformatics.com/downloads/data/BIND/data/datasets/taxon/xml/) and a PSI-MI 2.5 translation (http://download.baderlab.org/BINDTranslation/) are available.</comment>
<name>BIND</name>
<synonyms>
<synonym>Biomolecular Interaction Network Database</synonym>
</synonyms>
<definition>BIND is a database of protein-protein interactions. This data-resource is not open-access.</definition>
<uris>
<uri type="URN">urn:miriam:bind</uri>
<uri type="URL">http://identifiers.org/bind/</uri>
<uri type="URL" deprecated="true">http://www.bind.ca/</uri>
</uris>
<namespace>bind</namespace>
<resources>
<resource id="MIR:00100008" state="unknown" reliability="0">
<dataResource>http://www.bind.ca/</dataResource>
<dataEntry>http://www.bind.ca/Action?identifier=bindid&idsearch=$id</dataEntry>
<dataInfo>BIND (Biomolecular Interaction Network Database)</dataInfo>
<dataInstitution>Unleashed Informatics</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>May not be exploited for any commercial purpose without express written consent (BOND).</statement>
<link desc="license">http://thomsonreuters.com/terms_of_use/</link>
</restriction>
<restriction type="6" desc="Collection subset">
<statement>This data is a subset of that found in BOND {MIR:00900214}.</statement>
<link desc="sources">http://bond.unleashedinformatics.com/Action?pg=23299</link>
</restriction>
</restrictions>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>rule</element>
<element>reaction</element>
<element>event</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000002" pattern="^CHEBI:\d+$">
<name>ChEBI</name>
<definition>Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.</definition>
<uris>
<uri type="URN">urn:miriam:chebi</uri>
<uri type="URL">http://identifiers.org/chebi/</uri>
<uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/CHEBI</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.chebi/</uri>
<uri type="URL" deprecated="true">http://www.ebi.ac.uk/chebi/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.chebi</uri>
</uris>
<namespace>chebi</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19854951</documentation>
<documentation type="PMID">urn:miriam:pubmed:19496059</documentation>
<documentation type="PMID">urn:miriam:pubmed:17932057</documentation>
<documentation type="PMID">urn:miriam:pubmed:22065232</documentation>
<documentation type="PMID">urn:miriam:pubmed:23180789</documentation>
</documentations>
<resources>
<resource id="MIR:00100009" state="up" reliability="97" primary="true">
<dataResource>http://www.ebi.ac.uk/chebi/</dataResource>
<dataEntityExample>CHEBI:36927</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id</dataEntry>
<dataInfo>ChEBI (Chemical Entities of Biological Interest)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100158" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/chebi</dataResource>
<dataEntityExample>CHEBI:36927</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/chebi/terms?obo_id=$id</dataEntry>
<dataInfo>ChEBI through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100565" state="up" reliability="94">
<dataResource>http://bioportal.bioontology.org/ontologies/CHEBI</dataResource>
<dataEntityExample>CHEBI:36927</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/CHEBI/$id</dataEntry>
<dataInfo>ChEBI through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>metabolite</tag>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000003" pattern="^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$" restricted="true">
<name>Ensembl</name>
<definition>Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.</definition>
<uris>
<uri type="URN">urn:miriam:ensembl</uri>
<uri type="URL">http://identifiers.org/ensembl/</uri>
<uri type="URL" deprecated="true">http://www.ensembl.org/</uri>
</uris>
<namespace>ensembl</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381931</documentation>
</documentations>
<resources>
<resource id="MIR:00100011" state="up" reliability="99" primary="true">
<dataResource>http://www.ensembl.org/</dataResource>
<dataEntityExample>ENSG00000139618</dataEntityExample>
<dataEntry>http://www.ensembl.org/id/$id</dataEntry>
<dataInfo>Ensembl at Sanger/EMBL-EBI</dataInfo>
<dataInstitution>Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100561" state="down" reliability="99">
<dataResource>http://uswest.ensembl.org/</dataResource>
<dataEntityExample>ENSG00000139618</dataEntityExample>
<dataEntry>http://uswest.ensembl.org/id/$id</dataEntry>
<dataInfo>Ensembl US West mirror</dataInfo>
<dataInstitution></dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100562" state="up" reliability="99">
<dataResource>http://useast.ensembl.org/</dataResource>
<dataEntityExample>ENSG00000139618</dataEntityExample>
<dataEntry>http://useast.ensembl.org/id/$id</dataEntry>
<dataInfo>Ensembl US East mirror</dataInfo>
<dataInstitution></dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100563" state="up" reliability="99">
<dataResource>http://asia.ensembl.org/</dataResource>
<dataEntityExample>ENSG00000139618</dataEntityExample>
<dataEntry>http://asia.ensembl.org/id/$id</dataEntry>
<dataInfo>Ensembl Asia mirror</dataInfo>
<dataInstitution></dataInstitution>
<dataLocation>Singapore</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="2" desc="Data aggregation">
<statement>While Ensembl data is nominally restricted to vertebrate species, it also includes out groups (Dorsophila, Saccharomyces and C. elegans) used in comparative analysis. These species can also be referenced through Ensembl Genomes datasets.</statement>
<link desc="Ensembl overlap">http://www.ensemblgenomes.org/info/data_access</link>
</restriction>
<restriction type="9" desc="Identifier multiplicity">
<statement>This data collection uses some 'outlier' organisms, to normalise its dataset, which are not intended to be referenced directly in this collection. In addition, those outlier organisms may be referenced using non-standard identifiers. We recommend that human data be accessed using identifiers beginning with 'ENS', and outlier organisms be referenced through the appropriate collection: WormBase (http://identifiers.org/wormbase/), SGD (http://identifiers.org/sgd/) or FlyBase (http://identifiers.org/flybase/).</statement>
</restriction>
</restrictions>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
<tag>nucleotide</tag>
<tag>schema.org</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000004" pattern="^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$">
<name>Enzyme Nomenclature</name>
<synonyms>
<synonym>Enzyme Classification</synonym>
<synonym>EC code</synonym>
<synonym>EC</synonym>
</synonyms>
<definition>The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.</definition>
<uris>
<uri type="URN">urn:miriam:ec-code</uri>
<uri type="URL">http://identifiers.org/ec-code/</uri>
<uri type="URN" deprecated="true">urn:lsid:ec-code.org</uri>
<uri type="URL" deprecated="true">http://www.ec-code.org/</uri>
<uri type="URL" deprecated="true">http://www.ebi.ac.uk/IntEnz/</uri>
</uris>
<namespace>ec-code</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:10812475</documentation>
<documentation type="URL">http://www.chem.qmul.ac.uk/iubmb/enzyme/</documentation>
</documentations>
<resources>
<resource id="MIR:00100001" state="up" reliability="99">
<dataResource>http://www.ebi.ac.uk/intenz/</dataResource>
<dataEntityExample>1.1.1.1</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id</dataEntry>
<dataInfo>IntEnZ (Integrated relational Enzyme database)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100002" state="up" reliability="99">
<dataResource>http://www.genome.jp/dbget-bin/www_bfind?enzyme</dataResource>
<dataEntityExample>1.1.1.1</dataEntityExample>
<dataEntry>http://www.genome.jp/dbget-bin/www_bget?ec:$id</dataEntry>
<dataInfo>KEGG Ligand Database for Enzyme Nomenclature</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
<resource id="MIR:00100003" state="down" reliability="96">
<dataResource>http://enzyme.expasy.org/</dataResource>
<dataEntityExample>1.1.1.1</dataEntityExample>
<dataEntry>http://enzyme.expasy.org/EC/$id</dataEntry>
<dataInfo>Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
<resource id="MIR:00100308" state="up" reliability="100">
<dataResource>http://www.enzyme-database.org/</dataResource>
<dataEntityExample>1.1.1.1</dataEntityExample>
<dataEntry>http://www.enzyme-database.org/query.php?ec=$id</dataEntry>
<dataInfo>ExploreEnz at Trinity College</dataInfo>
<dataInstitution>Trinity College, Dublin</dataInstitution>
<dataLocation>Ireland</dataLocation>
</resource>
<resource id="MIR:00100835" state="unknown" reliability="0">
<dataResource>https://www.ebi.ac.uk/enzymeportal</dataResource>
<dataEntityExample>1.1.1.1</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/enzymeportal/search/ec/$id</dataEntry>
<dataInfo>Enzyme Portal through EMBL-EBI</dataInfo>
<dataInstitution>Enzyme Portal at European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>enzyme</tag>
<tag>protein</tag>
<tag>taxonomy</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
<element>event</element>
<element>rule</element>
<element>species</element>
</elements>
</format>
<format name="CellML">
<elements>
<element>component</element>
<element>reaction</element>
</elements>
</format>
<format name="BioPAX">
<elements>
<element>catalysis</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000005" pattern="^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$">
<name>UniProt Knowledgebase</name>
<synonyms>
<synonym>UniProtKB</synonym>
<synonym>UniProt</synonym>
<synonym>Protein Knowledgebase</synonym>
<synonym>UniProt-TrEMBL</synonym>
<synonym>UniProt/TrEMBL</synonym>
<synonym>UniProtKB/Swiss-Prot</synonym>
</synonyms>
<definition>The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.</definition>
<uris>
<uri type="URN">urn:miriam:uniprot</uri>
<uri type="URL">http://identifiers.org/uniprot/</uri>
<uri type="URN" deprecated="true">urn:lsid:uniprot.org:uniprot</uri>
<uri type="URL" deprecated="true">http://www.uniprot.org/</uri>
<uri type="URN" deprecated="true">urn:lsid:uniprot.org</uri>
</uris>
<namespace>uniprot</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381842</documentation>
<documentation type="PMID">urn:miriam:pubmed:23161681</documentation>
</documentations>
<resources>
<resource id="MIR:00100164" state="up" reliability="99" primary="true">
<dataResource>http://www.uniprot.org/</dataResource>
<dataEntityExample>P0DP23</dataEntityExample>
<dataEntry>http://purl.uniprot.org/uniprot/$id</dataEntry>
<dataInfo>Universal Protein Resource using Persistent URL system</dataInfo>
<dataInstitution>UniProt Consortium</dataInstitution>
<dataLocation></dataLocation>
</resource>
<resource id="MIR:00100330" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/protein/</dataResource>
<dataEntityExample>P0DP23</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/protein/$id</dataEntry>
<dataInfo>UniProt through NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100004" obsolete="true">
<dataResource>http://www.ebi.uniprot.org/</dataResource>
<dataEntityExample>P62158</dataEntityExample>
<dataEntry>http://www.ebi.uniprot.org/entry/$id</dataEntry>
<dataInfo>Universal Protein Resource</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100027" obsolete="true">
<dataResource>http://www.pir.uniprot.org/</dataResource>
<dataEntityExample>P62158</dataEntityExample>
<dataEntry>http://www.pir.uniprot.org/cgi-bin/upEntry?id=$id</dataEntry>
<dataInfo>Universal Protein Resource</dataInfo>
<dataInstitution>Georgetown University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100031" obsolete="true">
<dataResource>http://www.expasy.uniprot.org/</dataResource>
<dataEntityExample>P62158</dataEntityExample>
<dataEntry>http://us.expasy.org/uniprot/$id</dataEntry>
<dataInfo>Universal Protein Resource, ExPASy (Expert Protein Analysis System)</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
<resource id="MIR:00100134" obsolete="true">
<dataResource>http://www.uniprot.org/</dataResource>
<dataEntityExample>P0DP23</dataEntityExample>
<dataEntry>http://www.uniprot.org/uniprot/$id</dataEntry>
<dataInfo>Universal Protein Resource</dataInfo>
<dataInstitution>UniProt Consortium</dataInstitution>
<dataLocation>USA, UK and Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>speciesType</element>
<element>parameter</element>
</elements>
</format>
<format name="BioPAX">
<elements>
<element>physicalEntity</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000006" pattern="^\d+$">
<name>Taxonomy</name>
<synonyms>
<synonym>NEWT</synonym>
<synonym>NCBI taxonomy</synonym>
</synonyms>
<definition>The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.</definition>
<uris>
<uri type="URN">urn:miriam:taxonomy</uri>
<uri type="URL">http://identifiers.org/taxonomy/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/taxonomy</uri>
<uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/NCBITaxon</uri>
<uri type="URL" deprecated="true">http://www.uniprot.org/taxonomy/</uri>
<uri type="URL" deprecated="true">http://www.taxonomy.org/</uri>
<uri type="URL" deprecated="true">http://www.ncbi.nlm.nih.gov/Taxonomy/</uri>
</uris>
<namespace>taxonomy</namespace>
<documentations>
<documentation type="URL">http://www.ncbi.nlm.nih.gov/books/NBK53758/</documentation>
</documentations>
<resources>
<resource id="MIR:00100007" state="up" reliability="99" primary="true">
<dataResource>http://www.ncbi.nlm.nih.gov/Taxonomy/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$id</dataEntry>
<dataInfo>NCBI Taxonomy</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100019" state="up" reliability="100">
<dataResource>http://www.uniprot.org/taxonomy/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://purl.uniprot.org/taxonomy/$id</dataEntry>
<dataInfo>Taxonomy through UniProt PURL</dataInfo>
<dataInstitution>UniProt Consortium</dataInstitution>
<dataLocation>USA, UK and Switzerland</dataLocation>
</resource>
<resource id="MIR:00100299" state="probably up" reliability="99">
<dataResource>http://www.ebi.ac.uk/ena/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/Taxon:$id</dataEntry>
<dataInfo>European Nucleotide Archive (ENA)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100507" state="up" reliability="85">
<dataResource>http://bioportal.bioontology.org/ontologies/NCBITAXON</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/NCBITAXON/$id</dataEntry>
<dataInfo>BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100695" state="down" reliability="83">
<dataResource>http://taxonomy.bio2rdf.org/fct/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://taxonomy.bio2rdf.org/describe/?url=http://bio2rdf.org/taxonomy:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
<resource id="MIR:00100770" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/ncbitaxon/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms?short_form=NCBITaxon_$id</dataEntry>
<dataInfo>NCBI Taxonomy through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>taxonomy</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000007" pattern="^((BIOMD|MODEL)\d{10})|(BMID\d{12})$">
<name>BioModels Database</name>
<synonyms>
<synonym>BioModels</synonym>
</synonyms>
<definition>BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.</definition>
<uris>
<uri type="URN">urn:miriam:biomodels.db</uri>
<uri type="URL">http://identifiers.org/biomodels.db/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/biomodels</uri>
<uri type="URL" deprecated="true">http://www.ebi.ac.uk/biomodels/</uri>
</uris>
<namespace>biomodels.db</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381960</documentation>
<documentation type="PMID">urn:miriam:pubmed:20587024</documentation>
<documentation type="PMID">urn:miriam:pubmed:25414348</documentation>
<documentation type="PMID">urn:miriam:pubmed:25182954</documentation>
<documentation type="DOI">urn:miriam:doi:10.1002%2Fpsp4.3</documentation>
</documentations>
<resources>
<resource id="MIR:00100006" state="up" reliability="99" primary="true">
<dataResource>http://www.ebi.ac.uk/biomodels/</dataResource>
<dataEntityExample>BIOMD0000000048</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/biomodels-main/$id</dataEntry>
<dataInfo>BioModels Database</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100107" state="up" reliability="82">
<dataResource>http://biomodels.caltech.edu/</dataResource>
<dataEntityExample>BIOMD0000000048</dataEntityExample>
<dataEntry>http://biomodels.caltech.edu/$id</dataEntry>
<dataInfo>Caltech mirror</dataInfo>
<dataInstitution>California Institute of Technology</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100674" state="down" reliability="33">
<dataResource>http://cu.biomodels.bio2rdf.org/fct/</dataResource>
<dataEntityExample>BIOMD0000000048</dataEntityExample>
<dataEntry>http://cu.biomodels.bio2rdf.org/describe/?url=http://bio2rdf.org/biomodels:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
<resource id="MIR:00100855" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>BIOMD0000000048</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/biomodels/$id</dataEntry>
<dataInfo>BioModels through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>model</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000008" pattern="^MIR:000\d{5}$">
<name>MIRIAM Registry collection</name>
<synonyms>
<synonym>MIRIAM Resources</synonym>
<synonym>MIRIAM</synonym>
</synonyms>
<definition>MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.</definition>
<uris>
<uri type="URN">urn:miriam:miriam.collection</uri>
<uri type="URL">http://identifiers.org/miriam.collection/</uri>
<uri type="URL" deprecated="true">http://www.biomodels.net/MIRIAM/</uri>
<uri type="URN" deprecated="true">urn:miriam:miriam</uri>
<uri type="URL" deprecated="true">http://biomodels.net/MIRIAM/</uri>
<uri type="URN" deprecated="true">urn:miriam:miriam.datatype</uri>
</uris>
<namespace>miriam.collection</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18078503</documentation>
<documentation type="PMID">urn:miriam:pubmed:16333295</documentation>
</documentations>
<resources>
<resource id="MIR:00100005" state="up" reliability="99">
<dataResource>http://www.ebi.ac.uk/miriam/</dataResource>
<dataEntityExample>MIR:00000008</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/miriam/main/$id</dataEntry>
<dataInfo>MIRIAM Resources (data collection)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>registry</tag>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000009" pattern="^[A-Z]\d+(\.[-\d+])?$">
<name>ICD</name>
<definition>The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes.</definition>
<uris>
<uri type="URN">urn:miriam:icd</uri>
<uri type="URL">http://identifiers.org/icd/</uri>
<uri type="URL" deprecated="true">http://www.who.int/classifications/icd/</uri>
</uris>
<namespace>icd</namespace>
<documentations>
<documentation type="URL">http://www.who.int/classifications/icd/en/</documentation>
</documentations>
<resources>
<resource id="MIR:00100016" state="probably up" reliability="99">
<dataResource>http://www.who.int/classifications/icd/en/</dataResource>
<dataEntityExample>C34</dataEntityExample>
<dataEntry>http://apps.who.int/classifications/icd10/browse/2010/en#/$id</dataEntry>
<dataInfo>International Statistical Classification of Diseases and Related Health Problems</dataInfo>
<dataInstitution>German Institute of Medical Documentation and Information</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
<tag>schema.org</tag>
<tag>taxonomy</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000010" pattern="^EBI\-[0-9]+$">
<name>IntAct</name>
<definition>IntAct provides a freely available, open source database system and analysis tools for protein interaction data.</definition>
<uris>
<uri type="URN">urn:miriam:intact</uri>
<uri type="URL">http://identifiers.org/intact/</uri>
<uri type="URL" deprecated="true">http://www.ebi.ac.uk/intact/</uri>
</uris>
<namespace>intact</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681455</documentation>
<documentation type="PMID">urn:miriam:pubmed:17145710</documentation>
</documentations>
<resources>
<resource id="MIR:00100017" state="up" reliability="97" primary="true">
<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
<dataEntityExample>EBI-2307691</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/intact/interaction/$id</dataEntry>
<dataInfo>IntAct at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
<element>event</element>
<element>rule</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000011" pattern="^IPR\d{6}$">
<name>InterPro</name>
<definition>InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.</definition>
<uris>
<uri type="URN">urn:miriam:interpro</uri>
<uri type="URL">http://identifiers.org/interpro/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/interpro</uri>
<uri type="URL" deprecated="true">http://purl.uniprot.org/interpro/</uri>
<uri type="URL" deprecated="true">http://www.ebi.ac.uk/interpro/</uri>
</uris>
<namespace>interpro</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608177</documentation>
</documentations>
<resources>
<resource id="MIR:00100018" state="up" reliability="98" primary="true">
<dataResource>http://www.ebi.ac.uk/interpro/</dataResource>
<dataEntityExample>IPR000100</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/interpro/entry/$id</dataEntry>
<dataInfo>InterPro</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100697" state="down" reliability="23">
<dataResource>http://interpro.bio2rdf.org/fct/</dataResource>
<dataEntityExample>IPR000100</dataEntityExample>
<dataEntry>http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000012" pattern="^\w{2,4}\d{5}$">
<name>KEGG Pathway</name>
<!--<synonyms>-->
<!--<synonym>KEGG</synonym>-->
<!--</synonyms>-->
<definition>KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.pathway</uri>
<uri type="URL">http://identifiers.org/kegg.pathway/</uri>
<uri type="URL" deprecated="true">http://www.genome.jp/kegg/pathway/</uri>
</uris>
<namespace>kegg.pathway</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22700311</documentation>
</documentations>
<resources>
<resource id="MIR:00100020" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/pathway.html</dataResource>
<dataEntityExample>hsa00620</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG PATHWAY Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>rule</element>
<element>reaction</element>
<element>event</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000013" pattern="^C\d+$">
<name>KEGG Compound</name>
<!--<synonyms>-->
<!--<synonym>KEGG</synonym>-->
<!--</synonyms>-->
<definition>KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.compound</uri>
<uri type="URL">http://identifiers.org/kegg.compound/</uri>
<uri type="URL" deprecated="true">http://www.genome.jp/kegg/compound/</uri>
</uris>
<namespace>kegg.compound</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22700311</documentation>
</documentations>
<resources>
<resource id="MIR:00100021" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/ligand.html</dataResource>
<dataEntityExample>C12345</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG LIGAND Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>metabolite</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000014" pattern="^R\d+$">
<name>KEGG Reaction</name>
<!--<synonyms>-->
<!--<synonym>KEGG</synonym>-->
<!--</synonyms>-->
<definition>KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.reaction</uri>
<uri type="URL">http://identifiers.org/kegg.reaction/</uri>
<uri type="URL" deprecated="true">http://www.genome.jp/kegg/reaction/</uri>
</uris>
<namespace>kegg.reaction</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22700311</documentation>
</documentations>
<resources>
<resource id="MIR:00100022" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/reaction/</dataResource>
<dataEntityExample>R00100</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG Reaction Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>reaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
<element>event</element>
<element>rule</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000015" pattern="^\d+$">
<name>PubMed</name>
<definition>PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.</definition>
<uris>
<uri type="URN">urn:miriam:pubmed</uri>
<uri type="URL">http://identifiers.org/pubmed/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/pubmed</uri>
<uri type="URL" deprecated="true">http://linkedlifedata.com/resource/pubmed/id/</uri>
<uri type="URL" deprecated="true">http://www.ncbi.nlm.nih.gov/PubMed/</uri>
<uri type="URL" deprecated="true">http://www.pubmed.gov/</uri>
</uris>
<namespace>pubmed</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381840</documentation>
</documentations>
<resources>
<resource id="MIR:00100023" state="up" reliability="99" primary="true">
<dataResource>http://www.ncbi.nlm.nih.gov/PubMed/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/pubmed/$id</dataEntry>
<dataInfo>NCBI PubMed</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100064" state="up" reliability="98">
<dataResource>http://www.hubmed.org/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://www.hubmed.org/display.cgi?uids=$id</dataEntry>
<dataInfo>HubMed</dataInfo>
<dataInstitution>Alfred D. Eaton</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
<resource id="MIR:00100497" state="up" reliability="99">
<dataResource>http://europepmc.org/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://europepmc.org/abstract/MED/$id</dataEntry>
<dataInfo>Europe PMC</dataInfo>
<dataInstitution>Europe PubMed Central partners</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100702" state="down" reliability="13">
<dataResource>http://pubmed.bio2rdf.org/fct</dataResource>
<dataEntityExample>23735196</dataEntityExample>
<dataEntry>http://pubmed.bio2rdf.org/describe/?url=http://bio2rdf.org/pubmed:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
<resource id="MIR:00100745" state="up" reliability="88">
<dataResource>http://linkedlifedata.com/</dataResource>
<dataEntityExample>23735196</dataEntityExample>
<dataEntry>http://linkedlifedata.com/resource/pubmed/id/$id</dataEntry>
<dataInfo>PubMed through Linkedlife data</dataInfo>
<dataInstitution>Linkedlifedata, Ontotext, Sofia</dataInstitution>
<dataLocation>Bulgaria</dataLocation>
</resource>
<resource id="MIR:00100028" obsolete="true">
<dataResource>http://www.ebi.ac.uk/Databases/MEDLINE/medline.html</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-view+MedlineFull+[medline-PMID:$id]</dataEntry>
<dataInfo>PubMed through SRS@EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100032" obsolete="true">
<dataResource>http://www.ebi.ac.uk/citexplore/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/citexplore/citationDetails.do?dataSource=MED&externalId=$id</dataEntry>
<dataInfo>CiteXplore</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100462" obsolete="true">
<dataResource>http://ukpmc.ac.uk/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://ukpmc.ac.uk/abstract/MED/$id</dataEntry>
<dataInfo>PubMed through UK PubMed Central</dataInfo>
<dataInstitution>UKPMC Funders Group</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>bibliography</tag>
<tag>schema.org</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>species</element>
<element>reaction</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000016" pattern="^[*#+%^]?\d{6}$">
<name>OMIM</name>
<synonyms>
<synonym>Online Mendelian Inheritance in Man</synonym>
<synonym>Mendelian Inheritance in Man</synonym>
<synonym>MIM</synonym>
</synonyms>
<definition>Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.</definition>
<uris>
<uri type="URN">urn:miriam:omim</uri>
<uri type="URL">http://identifiers.org/omim/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/omim</uri>
<uri type="URL" deprecated="true">http://www.ncbi.nlm.nih.gov/OMIM/</uri>
</uris>
<namespace>omim</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608251</documentation>
</documentations>
<resources>
<resource id="MIR:00100024" state="up" reliability="99" primary="true">
<dataResource>http://omim.org/</dataResource>
<dataEntityExample>603903</dataEntityExample>
<dataEntry>http://omim.org/entry/$id</dataEntry>
<dataInfo>OMIM at John Hopkins</dataInfo>
<dataInstitution>Johns Hopkins University, Baltimore, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100694" state="down" reliability="84">
<dataResource>http://omim.bio2rdf.org/fct</dataResource>
<dataEntityExample>603903</dataEntityExample>
<dataEntry>http://omim.bio2rdf.org/describe/?url=http://bio2rdf.org/omim:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
<resource id="MIR:00100777" state="up" reliability="100">
<dataResource>http://mirror.omim.org/</dataResource>
<dataEntityExample>603903</dataEntityExample>
<dataEntry>http://mirror.omim.org/entry/$id</dataEntry>
<dataInfo>OMIM mirror at John Hopkins</dataInfo>
<dataInstitution>Johns Hopkins University, Baltimore, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100480" obsolete="true">
<dataResource>http://us-east.omim.org/</dataResource>
<dataEntityExample>603903</dataEntityExample>
<dataEntry>http://us-east.omim.org/entry/$id</dataEntry>
<dataInfo>OMIM (East Coast mirror)</dataInfo>
<dataInstitution>OMIM, Virgina</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100481" obsolete="true">
<dataResource>http://europe.omim.org/</dataResource>
<dataEntityExample>603903</dataEntityExample>
<dataEntry>http://europe.omim.org/entry/$id</dataEntry>
<dataInfo>OMIM (EBI mirror)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>disorder</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000017" pattern="^PIRSF\d{6}$">
<name>PIRSF</name>
<synonyms>
<synonym>Protein Information Resource</synonym>
</synonyms>
<definition>The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.</definition>
<uris>
<uri type="URN">urn:miriam:pirsf</uri>
<uri type="URL">http://identifiers.org/pirsf/</uri>
<uri type="URL" deprecated="true">http://pir.georgetown.edu/pirsf/</uri>
</uris>
<namespace>pirsf</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681371</documentation>
</documentations>
<resources>
<resource id="MIR:00100025" state="up" reliability="99">
<dataResource>http://pir.georgetown.edu/</dataResource>
<dataEntityExample>PIRSF000100</dataEntityExample>
<dataEntry>http://pir.georgetown.edu/cgi-bin/ipcSF?id=$id</dataEntry>
<dataInfo>PIRSF</dataInfo>
<dataInstitution>Georgetown University Medical Center</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000018" pattern="(^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$)|(^REACT_\d+(\.\d+)?$)">
<name>Reactome</name>
<synonyms>
<synonym>Reactome Stable ID</synonym>
</synonyms>
<definition>The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.</definition>
<uris>
<uri type="URN">urn:miriam:reactome</uri>
<uri type="URL">http://identifiers.org/reactome/</uri>
<uri type="URL" deprecated="true">http://www.reactome.org/</uri>
</uris>
<namespace>reactome</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24243840</documentation>
</documentations>
<resources>
<resource id="MIR:00100026" state="probably up" reliability="97">
<dataResource>http://www.reactome.org/</dataResource>
<dataEntityExample>R-HSA-201451</dataEntityExample>
<dataEntry>http://reactome.org/content/detail/$id</dataEntry>
<dataInfo>Reactome, a curated knowledgebase of biological pathways</dataInfo>
<dataInstitution>Ontario Institute for Cancer Research, NYU Medical School, Cold Spring Harbor Laboratory and European Bioinformatics Institute</dataInstitution>
<dataLocation>Canada / USA / UK</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>pathway</tag>
<tag>reaction</tag>
<tag>schema.org</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>rule</element>
<element>reaction</element>
<element>event</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000019" pattern="^(doi\:)?\d{2}\.\d{4}.*$">
<name>DOI</name>
<synonyms>
<synonym>Digital Object Identifier</synonym>
</synonyms>
<definition>The Digital Object Identifier System is for identifying content objects in the digital environment.</definition>
<uris>
<uri type="URN">urn:miriam:doi</uri>
<uri type="URL">http://identifiers.org/doi/</uri>
<uri type="URL" deprecated="true">http://www.doi.org/</uri>
</uris>
<namespace>doi</namespace>
<resources>
<resource id="MIR:00100010" state="down" reliability="94" primary="true">
<dataResource>http://www.doi.org/</dataResource>
<dataEntityExample>10.1038/nbt1156</dataEntityExample>
<dataEntry>http://doi.org/$id</dataEntry>
<dataInfo>Digital Object Identifier</dataInfo>
<dataInstitution>International DOI Foundation</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
<resource id="MIR:00100065" obsolete="true">
<dataResource>http://www.handle.net/index.html</dataResource>
<dataEntityExample>10.1038/nbt1156</dataEntityExample>
<dataEntry>http://hdl.handle.net/$id</dataEntry>
<dataInfo>CNRI DOI Resolver</dataInfo>
<dataInstitution>Corporation for National Research Initiatives</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100751" obsolete="true">
<dataResource>http://doai.io/</dataResource>
<dataEntityExample>10.1038/nbt1156</dataEntityExample>
<dataEntry>http://doai.io/$id</dataEntry>
<dataInfo>DOAI (Digital Open Access Identifier) at CAPSH</dataInfo>
<dataInstitution>CAPSH (Committee for the Accessibility of Publications in Sciences and Humanities), Paris</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>bibliography</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>species</element>
<element>reaction</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000020" pattern="^[0-9][A-Za-z0-9]{3}$">
<name>Protein Data Bank</name>
<synonyms>
<synonym>PDB</synonym>
</synonyms>
<definition>The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.</definition>
<uris>
<uri type="URN">urn:miriam:pdb</uri>
<uri type="URL">http://identifiers.org/pdb/</uri>
<uri type="URL" deprecated="true">http://www.pdb.org/</uri>
</uris>
<namespace>pdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17142228</documentation>
<documentation type="PMID">urn:miriam:pubmed:10592235</documentation>
</documentations>
<resources>
<resource id="MIR:00100029" state="up" reliability="99">
<dataResource>http://www.pdb.org/</dataResource>
<dataEntityExample>2gc4</dataEntityExample>
<dataEntry>http://www.rcsb.org/pdb/explore/explore.do?structureId=$id</dataEntry>
<dataInfo>RCSB PDB</dataInfo>
<dataInstitution>Rutgers, The State University of New Jersey</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100037" state="up" reliability="99">
<dataResource>http://www.pdbe.org/</dataResource>
<dataEntityExample>2gc4</dataEntityExample>
<dataEntry>http://www.pdbe.org/$id</dataEntry>
<dataInfo>Protein Databank in Europe (PDBe)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100096" state="up" reliability="99">
<dataResource>http://www.proteopedia.org/</dataResource>
<dataEntityExample>2gc4</dataEntityExample>
<dataEntry>http://proteopedia.org/wiki/index.php/$id</dataEntry>
<dataInfo>Proteopedia</dataInfo>
<dataInstitution>Weizmann Institute of Science</dataInstitution>
<dataLocation>Israel</dataLocation>
</resource>
<resource id="MIR:00100165" state="up" reliability="95">
<dataResource>http://www.pdbj.org/</dataResource>
<dataEntityExample>2gc4</dataEntityExample>
<dataEntry>http://pdbj.org/mine/summary/$id</dataEntry>
<dataInfo>Protein Data Bank Japan (PDBj)</dataInfo>
<dataInstitution>Institute for Protein Research, Osaka University</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
<resource id="MIR:00100166" state="up" reliability="99">
<dataResource>http://www.ebi.ac.uk/pdbsum/</dataResource>
<dataEntityExample>2gc4</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/pdbsum/$id</dataEntry>
<dataInfo>Protein Databank through PDBsum</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000021" pattern="^[0-9A-Za-z]+:\d+:\d{1,5}(\.\d)?$" obsolete="true" replacement="">
<comment>The EBI stopped providing this service.</comment>
<name>CluSTr</name>
<definition>The CluSTr database offers an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons (Smith-Waterman) between protein sequences.</definition>
<uris>
<uri type="URN">urn:miriam:clustr</uri>
<uri type="URL">http://identifiers.org/clustr/</uri>
<uri type="URL" deprecated="true">http://www.ebi.ac.uk/clustr/</uri>
</uris>
<namespace>clustr</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15961444</documentation>
<documentation type="URL">http://www.ebi.ac.uk/clustr/documentation.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100030" obsolete="true">
<dataResource>http://www.ebi.ac.uk/clustr/</dataResource>
<dataEntityExample>HUMAN:55140:308.6</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/clustr-srv/CCluster?interpro=yes&cluster_varid=$id</dataEntry>
<dataInfo>CluSTr Database</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000022" pattern="^GO:\d{7}$">
<name>Gene Ontology</name>
<synonyms>
<synonym>GO</synonym>
</synonyms>
<definition>The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.</definition>
<uris>
<uri type="URN">urn:miriam:go</uri>
<uri type="URL">http://identifiers.org/go/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/go</uri>
<uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/GO</uri>
<uri type="URL" deprecated="true">http://www.geneontology.org/</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.go/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.go</uri>
</uris>
<namespace>go</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681407</documentation>
<documentation type="PMID">urn:miriam:pubmed:10802651</documentation>
</documentations>
<resources>
<resource id="MIR:00100012" state="down" reliability="92">
<dataResource>http://www.ebi.ac.uk/QuickGO/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/QuickGO/GTerm?id=$id</dataEntry>
<dataInfo>QuickGO (Gene Ontology browser)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100013" state="up" reliability="98" primary="true">
<dataResource>http://amigo.geneontology.org/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://amigo.geneontology.org/amigo/term/$id</dataEntry>
<dataInfo>AmiGO 2</dataInfo>
<dataInstitution>The Gene Ontology Consortium</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100015" state="down" reliability="89">
<dataResource>http://www.informatics.jax.org/searches/GO_form.shtml</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://www.informatics.jax.org/searches/GO.cgi?id=$id</dataEntry>
<dataInfo>GO Browser</dataInfo>
<dataInstitution>The Jackson Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100237" state="up" reliability="95">
<dataResource>http://bioportal.bioontology.org/ontologies/GO</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/GO/$id</dataEntry>
<dataInfo>GO through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100585" state="up" reliability="98">
<dataResource>http://www.pantherdb.org/</dataResource>
<dataEntityExample>GO:0000003</dataEntityExample>
<dataEntry>http://www.pantherdb.org/panther/category.do?categoryAcc=$id</dataEntry>
<dataInfo>GO through PANTHER</dataInfo>
<dataInstitution>Keck School of Medicine, University of Southern California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100675" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/go</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id</dataEntry>
<dataInfo>GO through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100014" obsolete="true">
<dataResource>http://ep.ebi.ac.uk/EP/GO/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://www.bioinf.ebc.ee/EP/EP/GO/?Q=$id</dataEntry>
<dataInfo>EP:GO, Browser and analysis for Gene Ontology</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100659" obsolete="true">
<dataResource>http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/$id</dataEntry>
<dataInfo>GO through Amigo2 (prototype)</dataInfo>
<dataInstitution>Berkeley Bioinformatics Open-source Projects, Lawrence Berkeley National Lab, Berkeley, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>compartment</element>
<element>species</element>
<element>rule</element>
<element>reaction</element>
<element>event</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000023" pattern="^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$" restricted="true">
<name>SGD</name>
<synonyms>
<synonym>Saccharomyces Genome Database</synonym>
</synonyms>
<definition>The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.</definition>
<uris>
<uri type="URN">urn:miriam:sgd</uri>
<uri type="URL">http://identifiers.org/sgd/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/sgd</uri>
<uri type="URL" deprecated="true">http://www.yeastgenome.org/</uri>
</uris>
<namespace>sgd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681421</documentation>
</documentations>
<resources>
<resource id="MIR:00100033" state="down" reliability="93" primary="true">
<dataResource>http://www.yeastgenome.org/</dataResource>
<dataEntityExample>S000003909</dataEntityExample>
<dataEntry>http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=$id</dataEntry>
<dataInfo>SGD</dataInfo>
<dataInstitution>Stanford University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100703" state="down" reliability="82">
<dataResource>http://sgd.bio2rdf.org/fct</dataResource>
<dataEntityExample>S000003909</dataEntityExample>
<dataEntry>http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="9" desc="Identifier multiplicity">
<statement>This data collection can be referenced through two different identifier patterns. We recommend the use of identifiers of the form 'S\d+'.</statement>
<link desc="SGD identifiers nomenclature">http://www.yeastgenome.org/help/community/nomenclature-conventions</link>
</restriction>
</restrictions>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000024" pattern="^SBO:\d{7}$">
<name>Systems Biology Ontology</name>
<synonyms>
<synonym>SBO</synonym>
</synonyms>
<definition>The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.</definition>
<uris>
<uri type="URN">urn:miriam:sbo</uri>
<uri type="URL">http://identifiers.org/sbo/</uri>
<uri type="URN" deprecated="true">urn:miriam:biomodels.sbo</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.sbo</uri>
<uri type="URL" deprecated="true">http://www.biomodels.net/SBO/</uri>
<uri type="URL" deprecated="true">http://biomodels.net/SBO/</uri>
</uris>
<namespace>sbo</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17118155</documentation>
</documentations>
<resources>
<resource id="MIR:00100034" state="up" reliability="99" primary="true">
<dataResource>http://www.ebi.ac.uk/sbo/</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/sbo/main/$id</dataEntry>
<dataInfo>SBO</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100176" state="up" reliability="98">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/sbo</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/sbo/terms?obo_id=$id</dataEntry>
<dataInfo>SBO through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100242" state="up" reliability="88">
<dataResource>http://bioportal.bioontology.org/ontologies/SBO</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/SBO/$id</dataEntry>
<dataInfo>SBO through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>compartment</element>
<element>event</element>
<element>model</element>
<element>parameter</element>
<element>reaction</element>
<element>rule</element>
<element>species</element>
<element>speciesType</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000025" pattern="^D\d+$">
<name>KEGG Drug</name>
<!--<synonyms>-->
<!--<synonym>KEGG</synonym>-->
<!--</synonyms>-->
<definition>KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.drug</uri>
<uri type="URL">http://identifiers.org/kegg.drug/</uri>
<uri type="URL" deprecated="true">http://www.genome.jp/kegg/drug/</uri>
</uris>
<namespace>kegg.drug</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381885</documentation>
</documentations>
<resources>
<resource id="MIR:00100035" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/drug/</dataResource>
<dataEntityExample>D00123</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG DRUG Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>drug</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000026" pattern="^G\d+$">
<name>KEGG Glycan</name>
<!--<synonyms>-->
<!--<synonym>KEGG</synonym>-->
<!--</synonyms>-->
<definition>KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.glycan</uri>
<uri type="URL">http://identifiers.org/kegg.glycan/</uri>
<uri type="URL" deprecated="true">http://www.genome.jp/kegg/glycan/</uri>
</uris>
<namespace>kegg.glycan</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16014746</documentation>
</documentations>
<resources>
<resource id="MIR:00100036" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/glycan/</dataResource>
<dataEntityExample>G00123</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG GLYCAN Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>polysaccharide</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000027" pattern="^(WBGene\d{8}|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$" restricted="true">
<name>WormBase</name>
<definition>WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references genes.</definition>
<uris>
<uri type="URN">urn:miriam:wormbase</uri>
<uri type="URL">http://identifiers.org/wormbase/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/wormbase</uri>
<uri type="URL" deprecated="true">http://www.wormbase.org/</uri>
</uris>
<namespace>wormbase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11125056</documentation>
<documentation type="PMID">urn:miriam:pubmed:17099234</documentation>
<documentation type="PMID">urn:miriam:pubmed:17099225</documentation>
<documentation type="PMID">urn:miriam:pubmed:16988424</documentation>
<documentation type="PMID">urn:miriam:pubmed:16381915</documentation>
<documentation type="PMID">urn:miriam:pubmed:16232125</documentation>
<documentation type="PMID">urn:miriam:pubmed:15608221</documentation>
<documentation type="PMID">urn:miriam:pubmed:15489338</documentation>
<documentation type="PMID">urn:miriam:pubmed:14681445</documentation>
<documentation type="PMID">urn:miriam:pubmed:12519966</documentation>
</documentations>
<resources>
<resource id="MIR:00100038" state="up" reliability="99" primary="true">
<dataResource>http://www.wormbase.org/</dataResource>
<dataEntityExample>WBGene00000001</dataEntityExample>
<dataEntry>http://www.wormbase.org/db/gene/gene?name=$id;class=Gene</dataEntry>
<dataInfo>WormBase (Master)</dataInfo>
<dataInstitution>Cold Spring Harbor Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100704" state="down" reliability="83">
<dataResource>http://wormbase.bio2rdf.org/fct</dataResource>
<dataEntityExample>WBGene00000001</dataEntityExample>
<dataEntry>http://wormbase.bio2rdf.org/describe/?url=http://bio2rdf.org/wormbase:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
<resource id="MIR:00100039" obsolete="true">
<dataResource>http://wormbase.sanger.ac.uk/</dataResource>
<dataEntityExample>WBGene00000001</dataEntityExample>
<dataEntry>http://wormbase.sanger.ac.uk/db/gene/gene?name=$id;class=Gene</dataEntry>
<dataInfo>Sanger WormBase Mirror</dataInfo>
<dataInstitution>Wellcome Trust Sanger Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
<resource id="MIR:00100040" obsolete="true">
<dataResource>http://imbb.wormbase.org/</dataResource>
<dataEntityExample>WBGene00000001</dataEntityExample>
<dataEntry>http://imbb.wormbase.org/db/gene/gene?name=$id;class=Gene</dataEntry>
<dataInfo>WormBase Mirror in Crete</dataInfo>
<dataInstitution>Institute of Molecular Biology and Biotechnology</dataInstitution>
<dataLocation>Greece</dataLocation>
</resource>
<resource id="MIR:00100041" obsolete="true">
<dataResource>http://caltech.wormbase.org/</dataResource>
<dataEntityExample>WBGene00000001</dataEntityExample>
<dataEntry>http://caltech.wormbase.org/db/gene/gene?name=$id;class=Gene</dataEntry>
<dataInfo>Caltech WormBase Mirror</dataInfo>
<dataInstitution>California Institute of Technology</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100042" obsolete="true">
<dataResource>http://crfb-3.univ-mrs.fr/</dataResource>
<dataEntityExample>WBGene00000001</dataEntityExample>
<dataEntry>http://crfb-3.univ-mrs.fr/db/gene/gene?name=$id;class=Gene</dataEntry>
<dataInfo>WormBase Mirror at Marseille-Nice Genopole</dataInfo>
<dataInstitution>Marseille-Nice Genopole</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="9" desc="Identifier multiplicity">
<statement>This data collection's records can be referenced through two different identifier patterns. We recommend the use of identifiers of the form 'WBGene\d{8}'.</statement>
<link desc="WormBase nomenclature">http://www.wormbase.org/about/userguide/nomenclature</link>
</restriction>
</restrictions>
<tags>
<tag>expression</tag>
<tag>genome</tag>
<tag>nucleotide</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000028" pattern="^PF\d{5}$">
<name>Pfam</name>
<synonyms>
<synonym>Protein Family Database</synonym>
</synonyms>
<definition>The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.</definition>
<uris>
<uri type="URN">urn:miriam:pfam</uri>
<uri type="URL">http://identifiers.org/pfam/</uri>
<uri type="URL" deprecated="true">http://pfam.org/</uri>
</uris>
<namespace>pfam</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:9847196</documentation>
<documentation type="PMID">urn:miriam:pubmed:14681378</documentation>
<documentation type="PMID">urn:miriam:pubmed:11752314</documentation>
<documentation type="PMID">urn:miriam:pubmed:10592242</documentation>
<documentation type="PMID">urn:miriam:pubmed:9399864</documentation>
<documentation type="PMID">urn:miriam:pubmed:9223186</documentation>
</documentations>
<resources>
<resource id="MIR:00100685" state="up" reliability="99" primary="true">
<dataResource>http://pfam.xfam.org/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.xfam.org/family/$id</dataEntry>
<dataInfo>Pfam at EMBL-EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100043" obsolete="true">
<dataResource>http://pfam.sanger.ac.uk/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.sanger.ac.uk/family/$id/</dataEntry>
<dataInfo>Sanger Pfam Mirror</dataInfo>
<dataInstitution>Wellcome Trust Sanger Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
<resource id="MIR:00100044" obsolete="true">
<dataResource>http://pfam.sbc.su.se/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.sbc.su.se/family/$id</dataEntry>
<dataInfo>Sweden Pfam Mirror</dataInfo>
<dataInstitution>Karolinska Institutet</dataInstitution>
<dataLocation>Sweden</dataLocation>
</resource>
<resource id="MIR:00100045" obsolete="true">
<dataResource>http://pfam.janelia.org/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.janelia.org/family/$id</dataEntry>
<dataInfo>Janelia Farm Research Campus Pfam Mirror</dataInfo>
<dataInstitution>Howard Hughes Medical Institute</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100046" obsolete="true">
<dataResource>http://pfam.jouy.inra.fr/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.jouy.inra.fr/cgi-bin/getdesc?acc=$id</dataEntry>
<dataInfo>INRA Pfam Mirror</dataInfo>
<dataInstitution>Institut National de la Recherche Agronomique</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
<resource id="MIR:00100047" obsolete="true">
<dataResource>http://pfam.ccbb.re.kr/index.shtml</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.ccbb.re.kr/cgi-bin/getdesc?acc=$id</dataEntry>
<dataInfo>CCBB Pfam Mirror</dataInfo>
<dataInstitution>Center for Computational Biology and Bioinformatics</dataInstitution>
<dataLocation>Korea</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
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<tag>genome</tag>
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<synonym>PubChem CID</synonym>
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<definition>PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.</definition>
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<uri type="URN">urn:miriam:arxiv</uri>
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<uri type="URL" deprecated="true">http://arxiv.org/</uri>
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<uri type="URN">urn:miriam:arrayexpress</uri>
<uri type="URL">http://identifiers.org/arrayexpress/</uri>
<uri type="URL" deprecated="true">http://arrayexpress.org/</uri>
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<synonym>MGI</synonym>
<synonym>Mouse Genome Informatics</synonym>
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<definition>The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.</definition>
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<definition>The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.</definition>
<uris>
<uri type="URN">urn:miriam:mint</uri>
<uri type="URL">http://identifiers.org/mint/</uri>
</uris>
<namespace>mint</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17135203</documentation>
</documentations>
<resources>
<resource id="MIR:00100070" state="down" reliability="76">
<dataResource>http://mint.bio.uniroma2.it/mint/</dataResource>
<dataEntityExample>MINT-10000</dataEntityExample>
<dataEntry>http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id</dataEntry>
<dataInfo>The Molecular INTeraction database (MINT)</dataInfo>
<dataInstitution>University of Rome Tor Vergata, Rome</dataInstitution>
<dataLocation>Italy</dataLocation>
</resource>
<resource id="MIR:00100654" state="up" reliability="92">
<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
<dataEntityExample>MINT-7905142</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/intact/query/interaction_id:$id</dataEntry>
<dataInfo>MINT subset through IntAct</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000043" pattern="^IPI\d{8}$" obsolete="true" replacement="MIR:00000005">
<comment>As of April 2013, this collection is no longer maintained. An ftp archive is available at ftp://ftp.ebi.ac.uk/pub/databases/IPI.</comment>
<name>IPI</name>
<synonyms>
<synonym>International Protein Index</synonym>
</synonyms>
<definition>The International Protein Index (IPI) provides complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases</definition>
<uris>
<uri type="URN">urn:miriam:ipi</uri>
<uri type="URL">http://identifiers.org/ipi/</uri>
</uris>
<namespace>ipi</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15221759</documentation>
</documentations>
<resources>
<resource id="MIR:00100071" state="down" reliability="85">
<dataResource>http://www.ebi.ac.uk/IPI</dataResource>
<dataEntityExample>IPI00000001</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ipi&id=$id&format=default&style=html</dataEntry>
<dataInfo>IPI (International Protein Index)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000044" pattern="^DIP(\:)?\-\d{1,}[ENXS]$">
<name>Database of Interacting Proteins</name>
<synonyms>
<synonym>DIP</synonym>
</synonyms>
<definition>The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions</definition>
<uris>
<uri type="URN">urn:miriam:dip</uri>
<uri type="URL">http://identifiers.org/dip/</uri>
</uris>
<namespace>dip</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681454</documentation>
</documentations>
<resources>
<resource id="MIR:00100072" state="up" reliability="99">
<dataResource>http://dip.doe-mbi.ucla.edu/</dataResource>
<dataEntityExample>DIP-743N</dataEntityExample>
<dataEntry>http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id</dataEntry>
<dataInfo>Database of interacting proteins</dataInfo>
<dataInstitution>UCLA</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000045" pattern="A\d{6}$">
<name>Signaling Gateway</name>
<synonyms>
<synonym>SGMP</synonym>
<synonym>Signaling Gateway Molecule Pages</synonym>
<synonym>AfCS</synonym>
<synonym>UCSD Signaling Gateway Molecule Pages</synonym>
<synonym>UCSD - Molecule Pages</synonym>
</synonyms>
<definition>The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.</definition>
<uris>
<uri type="URN">urn:miriam:signaling-gateway</uri>
<uri type="URL">http://identifiers.org/signaling-gateway/</uri>
</uris>
<namespace>signaling-gateway</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17965093</documentation>
<documentation type="PMID">urn:miriam:pubmed:12478304</documentation>
<documentation type="PMID">urn:miriam:pubmed:21505029</documentation>
</documentations>
<resources>
<resource id="MIR:00100073" state="up" reliability="98">
<dataResource>http://www.signaling-gateway.org/molecule</dataResource>
<dataEntityExample>A001094</dataEntityExample>
<dataEntry>http://www.signaling-gateway.org/molecule/query?afcsid=$id</dataEntry>
<dataInfo>Signaling Gateway Molecule Pages</dataInfo>
<dataInstitution>UC San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>mammalian</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000046" pattern="^AA\d{4}$">
<name>RESID</name>
<definition>The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.</definition>
<uris>
<uri type="URN">urn:miriam:resid</uri>
<uri type="URL">http://identifiers.org/resid/</uri>
</uris>
<namespace>resid</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15174124</documentation>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkg038</documentation>
</documentations>
<resources>
<resource id="MIR:00100653" state="up" reliability="99" primary="true">
<dataResource>http://pir0.georgetown.edu/resid/</dataResource>
<dataEntityExample>AA0001</dataEntityExample>
<dataEntry>http://pir0.georgetown.edu/cgi-bin/resid?id=$id</dataEntry>
<dataInfo>RESID at Georgetown University</dataInfo>
<dataInstitution>Georgetown University Medical Center, Washington</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100074" obsolete="true">
<dataResource>http://www.ebi.ac.uk/RESID/</dataResource>
<dataEntityExample>AA0001</dataEntityExample>
<dataEntry>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id']</dataEntry>
<dataInfo>RESID</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000047" pattern="^\d{4,7}$">
<name>Rat Genome Database</name>
<synonyms>
<synonym>RGD</synonym>
</synonyms>
<definition>Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes.</definition>
<uris>
<uri type="URN">urn:miriam:rgd</uri>
<uri type="URL">http://identifiers.org/rgd/</uri>
</uris>
<namespace>rgd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17151068</documentation>
</documentations>
<resources>
<resource id="MIR:00100075" state="up" reliability="99">
<dataResource>http://rgd.mcw.edu/</dataResource>
<dataEntityExample>2018</dataEntityExample>
<dataEntry>http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id</dataEntry>
<dataInfo>Rat Genome Database</dataInfo>
<dataInstitution>Medical College of Wisconsin</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>annotation</tag>
<tag>disease</tag>
<tag>eukaryotic</tag>
<tag>gene</tag>
<tag>genome</tag>
<tag>mammalian</tag>
<tag>nucleotide</tag>
<tag>pathway</tag>
<tag>phenotype</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000048" pattern="^AASequence:\d{10}$">
<name>TAIR Protein</name>
<definition>The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept</definition>
<uris>
<uri type="URN">urn:miriam:tair.protein</uri>
<uri type="URL">http://identifiers.org/tair.protein/</uri>
</uris>
<namespace>tair.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12444417</documentation>
</documentations>
<resources>
<resource id="MIR:00100076" state="up" reliability="98">
<dataResource>http://arabidopsis.org/index.jsp</dataResource>
<dataEntityExample>AASequence:1009107926</dataEntityExample>
<dataEntry>http://arabidopsis.org/servlets/TairObject?accession=$id</dataEntry>
<dataInfo>The Arabidopsis Information Resource (TAIR) Protein</dataInfo>
<dataInstitution>Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
<tag>plant</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000049" pattern="^Gene:\d{7}$">
<name>TAIR Gene</name>
<definition>The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus.</definition>
<uris>
<uri type="URN">urn:miriam:tair.gene</uri>
<uri type="URL">http://identifiers.org/tair.gene/</uri>
</uris>
<namespace>tair.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12444417</documentation>
</documentations>
<resources>
<resource id="MIR:00100077" state="up" reliability="98">
<dataResource>http://arabidopsis.org/index.jsp</dataResource>
<dataEntityExample>Gene:2200934</dataEntityExample>
<dataEntry>http://arabidopsis.org/servlets/TairObject?accession=$id</dataEntry>
<dataInfo>The Arabidopsis Information Resource (TAIR) Gene</dataInfo>
<dataInstitution>Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>gene</tag>
<tag>genome</tag>
<tag>nucleotide</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000050" pattern="^Locus:\d{7}$">
<name>TAIR Locus</name>
<definition>The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.</definition>
<uris>
<uri type="URN">urn:miriam:tair.locus</uri>
<uri type="URL">http://identifiers.org/tair.locus/</uri>
</uris>
<namespace>tair.locus</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12444417</documentation>
</documentations>
<resources>
<resource id="MIR:00100078" state="up" reliability="86">
<dataResource>http://arabidopsis.org/index.jsp</dataResource>
<dataEntityExample>Locus:2200950</dataEntityExample>
<dataEntry>http://www.arabidopsis.org/servlets/TairObject?accession=$id</dataEntry>
<dataInfo>The Arabidopsis Information Resource (TAIR) Locus</dataInfo>
<dataInstitution>Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000051" pattern="^HMDB\d+$">
<name>HMDB</name>
<synonyms>
<synonym>Human Metabolome Database</synonym>
</synonyms>
<definition>The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.</definition>
<uris>
<uri type="URN">urn:miriam:hmdb</uri>
<uri type="URL">http://identifiers.org/hmdb/</uri>
<uri type="URL" deprecated="true">http://www.hmdb.ca/</uri>
</uris>
<namespace>hmdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17202168</documentation>
</documentations>
<resources>
<resource id="MIR:00100079" state="up" reliability="99">
<dataResource>http://www.hmdb.ca/</dataResource>
<dataEntityExample>HMDB00001</dataEntityExample>
<dataEntry>http://www.hmdb.ca/metabolites/$id</dataEntry>
<dataInfo>The Human Metabolome Database</dataInfo>
<dataInstitution>University of Alberta, Edmonton, AB</dataInstitution>
<dataLocation>Canada </dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>human</tag>
<tag>metabolite</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000052" pattern="^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$">
<name>LIPID MAPS</name>
<synonyms>
<synonym>LMSD</synonym>
</synonyms>
<definition>The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.</definition>
<uris>
<uri type="URN">urn:miriam:lipidmaps</uri>
<uri type="URL">http://identifiers.org/lipidmaps/</uri>
</uris>
<namespace>lipidmaps</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17098933</documentation>
<documentation type="PMID">urn:miriam:pubmed:15722563</documentation>
</documentations>
<resources>
<resource id="MIR:00100080" state="up" reliability="99">
<dataResource>http://www.lipidmaps.org</dataResource>
<dataEntityExample>LMPR0102010012</dataEntityExample>
<dataEntry>http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$id</dataEntry>
<dataInfo>Department of Bioengineering and the San Diego Supercomputer Center</dataInfo>
<dataInstitution>University of California, San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>lipid</tag>
<tag>structure</tag>
<tag>taxonomy</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000053" pattern="^PAp[0-9]{8}$">
<name>PeptideAtlas</name>
<definition>The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.</definition>
<uris>
<uri type="URN">urn:miriam:peptideatlas</uri>
<uri type="URL">http://identifiers.org/peptideatlas/</uri>
</uris>
<namespace>peptideatlas</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18451766</documentation>
</documentations>
<resources>
<resource id="MIR:00100081" state="up" reliability="98" primary="true">
<dataResource>http://www.peptideatlas.org/</dataResource>
<dataEntityExample>PAp00000009</dataEntityExample>
<dataEntry>https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$id</dataEntry>
<dataInfo>PeptideAtlas at ISB</dataInfo>
<dataInstitution>Institute for Systems Biology, Seattle</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>mass spectrometry</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000054" pattern="^G(PL|SM|SE|DS)\d+$">
<name>GEO</name>
<synonyms>
<synonym>Gene Expression Omnibus</synonym>
</synonyms>
<definition>The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.</definition>
<uris>
<uri type="URN">urn:miriam:geo</uri>
<uri type="URL">http://identifiers.org/geo/</uri>
</uris>
<namespace>geo</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11752295</documentation>
</documentations>
<resources>
<resource id="MIR:00100082" state="down" reliability="92">
<dataResource>http://www.ncbi.nlm.nih.gov/geo/</dataResource>
<dataEntityExample>GDS1234</dataEntityExample>
<dataEntry>https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$id</dataEntry>
<dataInfo>Gene Expression Omnibus at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>microarray</tag>
<tag>nucleotide</tag>
</tags>
</datatype>
<datatype id="MIR:00000055" pattern="ECO:\d{7}$">
<name>Evidence Code Ontology</name>
<synonyms>
<synonym>ECO</synonym>
</synonyms>
<definition>Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.</definition>
<uris>
<uri type="URN">urn:miriam:eco</uri>
<uri type="URL">http://identifiers.org/eco/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.eco</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.eco/</uri>
</uris>
<namespace>eco</namespace>
<documentations>
<documentation type="URL">http://www.geneontology.org/GO.evidence.shtml</documentation>
</documentations>
<resources>
<resource id="MIR:00100083" state="down" reliability="81">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/eco</dataResource>
<dataEntityExample>ECO:0000006</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=$id</dataEntry>
<dataInfo>Evidence Codes via the Ontology Lookup Service (OLS)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100235" state="down" reliability="73">
<dataResource>http://bioportal.bioontology.org/ontologies/ECO</dataResource>
<dataEntityExample>ECO:0000006</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/ECO/$id</dataEntry>
<dataInfo>Evidence Code Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
</tags>
</datatype>
<datatype id="MIR:00000056" pattern="^MOD:\d{5}">
<name>Protein Modification Ontology</name>
<synonyms>
<synonym>PSI-MOD</synonym>
<synonym>MOD</synonym>
</synonyms>
<definition>The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.</definition>
<uris>
<uri type="URN">urn:miriam:mod</uri>
<uri type="URL">http://identifiers.org/mod/</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.psi-mod/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.psi-mod</uri>
<uri type="URN" deprecated="true">urn:miriam:psimod</uri>
</uris>
<namespace>mod</namespace>
<documentations>
<documentation type="URL">http://psidev.sourceforge.net/mod/data/PSI-MOD.obo</documentation>
</documentations>
<resources>
<resource id="MIR:00100084" state="up" reliability="98">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/mod</dataResource>
<dataEntityExample>MOD:00001</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=$id</dataEntry>
<dataInfo>Protein modifications ontology via the Ontology Lookup Service (OLS)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100239" state="up" reliability="98">
<dataResource>http://bioportal.bioontology.org/ontologies/PSIMOD</dataResource>
<dataEntityExample>MOD:00001</dataEntityExample>
<dataEntry>http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=$id</dataEntry>
<dataInfo>Protein modifications ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000057" pattern="^PWY\w{2}\-\d{3}$">
<name>Saccharomyces genome database pathways</name>
<definition>Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD).</definition>
<uris>
<uri type="URN">urn:miriam:sgd.pathways</uri>
<uri type="URL">http://identifiers.org/sgd.pathways/</uri>
</uris>
<namespace>sgd.pathways</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681421</documentation>
</documentations>
<resources>
<resource id="MIR:00100085" state="up" reliability="97">
<dataResource>http://pathway.yeastgenome.org/</dataResource>
<dataEntityExample>PWY3O-214</dataEntityExample>
<dataEntry>http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$id</dataEntry>
<dataInfo>Saccharomyces cerevisiae pathways at SGD.</dataInfo>
<dataInstitution>SGD, Stanford University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>pathway</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000058" pattern="^\d+$">
<name>BioGRID</name>
<definition>BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.</definition>
<uris>
<uri type="URN">urn:miriam:biogrid</uri>
<uri type="URL">http://identifiers.org/biogrid/</uri>
</uris>
<namespace>biogrid</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381927</documentation>
</documentations>
<resources>
<resource id="MIR:00100086" state="down" reliability="83">
<dataResource>http://thebiogrid.org/</dataResource>
<dataEntityExample>31623</dataEntityExample>
<dataEntry>http://thebiogrid.org/$id</dataEntry>
<dataInfo>BioGRID database of physical and genetic interactions</dataInfo>
<dataInstitution>Ontario Cancer Institute</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000059" pattern="^[SCTAGMNU]\d{2}\.([AB]\d{2}|\d{3})$">
<name>MEROPS</name>
<definition>The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.</definition>
<uris>
<uri type="URN">urn:miriam:merops</uri>
<uri type="URL">http://identifiers.org/merops/</uri>
</uris>
<namespace>merops</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17991683</documentation>
</documentations>
<resources>
<resource id="MIR:00100087" state="down" reliability="89">
<dataResource>http://merops.sanger.ac.uk/index.htm</dataResource>
<dataEntityExample>S01.001</dataEntityExample>
<dataEntry>http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$id</dataEntry>
<dataInfo>MEROPS database at Sanger Institute</dataInfo>
<dataInstitution>Wellcome Trust Sanger Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
</resources>
<tags>
<tag>enzyme</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000060" pattern="^PTHR\d{5}(\:SF\d{1,3})?$">
<name>PANTHER Family</name>
<definition>The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families.</definition>
<uris>
<uri type="URN">urn:miriam:panther.family</uri>
<uri type="URL">http://identifiers.org/panther.family/</uri>
<uri type="URN" deprecated="true">urn:miriam:panther</uri>
</uris>
<namespace>panther.family</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12952881</documentation>
</documentations>
<resources>
<resource id="MIR:00100088" state="probably up" reliability="97">
<dataResource>http://www.pantherdb.org/</dataResource>
<dataEntityExample>PTHR12345</dataEntityExample>
<dataEntry>http://www.pantherdb.org/panther/family.do?clsAccession=$id</dataEntry>
<dataInfo>PANTHER Family at USC (Los Angeles)</dataInfo>
<dataInstitution>Keck School of Medicine, University of Southern California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000061" pattern="^PR\d{5}$">
<name>PRINTS</name>
<synonyms>
<synonym>SPRINT</synonym>
</synonyms>
<definition>PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.</definition>
<uris>
<uri type="URN">urn:miriam:prints</uri>
<uri type="URL">http://identifiers.org/prints/</uri>
<uri type="URN" deprecated="true">urn:miriam:sprint</uri>
</uris>
<namespace>prints</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:10592232</documentation>
</documentations>
<resources>
<resource id="MIR:00100089" state="up" reliability="97">
<dataResource>http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/</dataResource>
<dataEntityExample>PR00001</dataEntityExample>
<dataEntry>http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$id&display_opts=Prints&category=None&queryform=false&regexpr=off</dataEntry>
<dataInfo>PRINTS through SPRINT</dataInfo>
<dataInstitution>University of Manchester</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000062" pattern="^(\w){3}$">
<name>Ligand Expo</name>
<synonyms>
<synonym>Ligand Depot</synonym>
</synonyms>
<definition>Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.</definition>
<uris>
<uri type="URN">urn:miriam:ligandexpo</uri>
<uri type="URL">http://identifiers.org/ligandexpo/</uri>
</uris>
<namespace>ligandexpo</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15059838</documentation>
</documentations>
<resources>
<resource id="MIR:00100090" state="up" reliability="97">
<dataResource>http://ligand-depot.rutgers.edu/index.html</dataResource>
<dataEntityExample>ABC</dataEntityExample>
<dataEntry>http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$id&operation=ccid</dataEntry>
<dataInfo>Ligand Expo at RutgersRCSB PDB</dataInfo>
<dataInstitution>Rutgers, The State University of New Jersey</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100615" state="up" reliability="98">
<dataResource>http://ligand-expo.rcsb.org/</dataResource>
<dataEntityExample>ABC</dataEntityExample>
<dataEntry>http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$id&operation=ccid</dataEntry>
<dataInfo>Ligand Expo at Rutgers</dataInfo>
<dataInstitution>Rutgers, The State University of New Jersey</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000063" pattern="^mge:\d+$">
<name>Aclame</name>
<definition>ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.</definition>
<uris>
<uri type="URN">urn:miriam:aclame</uri>
<uri type="URL">http://identifiers.org/aclame/</uri>
</uris>
<namespace>aclame</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681355</documentation>
</documentations>
<resources>
<resource id="MIR:00100091" state="up" reliability="95">
<dataResource>http://aclame.ulb.ac.be/</dataResource>
<dataEntityExample>mge:2</dataEntityExample>
<dataEntry>http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=$id</dataEntry>
<dataInfo>Aclame database of mobile genetic elements</dataInfo>
<dataInstitution>Service de Conformation de Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles</dataInstitution>
<dataLocation>Belgium</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000064" pattern="^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$">
<name>ISBN</name>
<definition>The International Standard Book Number (ISBN) is for identifying printed books.</definition>
<uris>
<uri type="URN">urn:miriam:isbn</uri>
<uri type="URL">http://identifiers.org/isbn/</uri>
</uris>
<namespace>isbn</namespace>
<documentations>
<documentation type="URL">http://www.worldcat.org/whatis/default.jsp</documentation>
</documentations>
<resources>
<resource id="MIR:00100092" state="down" reliability="92">
<dataResource>http://isbndb.com/</dataResource>
<dataEntityExample>9781584885658</dataEntityExample>
<dataEntry>http://isbndb.com/search-all.html?kw=$id</dataEntry>
<dataInfo>ISBNDB - ISBN Database</dataInfo>
<dataInstitution>ISNBdb project, San Gabriel, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100093" state="down" reliability="87">
<dataResource>http://www.worldcat.org/</dataResource>
<dataEntityExample>9781584885658</dataEntityExample>
<dataEntry>http://www.worldcat.org/isbn/$id</dataEntry>
<dataInfo>ISBN database at WorldCat</dataInfo>
<dataInstitution>OCLC Online Computer Library Center, Inc. Ohio</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>bibliography</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>species</element>
<element>parameter</element>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000065" pattern="^\d+$">
<name>PRIDE</name>
<definition>The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays.</definition>
<uris>
<uri type="URN">urn:miriam:pride</uri>
<uri type="URL">http://identifiers.org/pride/</uri>
</uris>
<namespace>pride</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381953</documentation>
<documentation type="PMID">urn:miriam:pubmed:16041671</documentation>
<documentation type="PMID">urn:miriam:pubmed:18033805</documentation>
<documentation type="PMID">urn:miriam:pubmed:18428683</documentation>
</documentations>
<resources>
<resource id="MIR:00100094" state="up" reliability="97" primary="true">
<dataResource>http://www.ebi.ac.uk/pride/</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/pride/archive/assays/$id</dataEntry>
<dataInfo>PRIDE at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000066" pattern="^B\d{5}$">
<name>3DMET</name>
<definition>3DMET is a database collecting three-dimensional structures of natural metabolites.</definition>
<uris>
<uri type="URN">urn:miriam:3dmet</uri>
<uri type="URL">http://identifiers.org/3dmet/</uri>
</uris>
<namespace>3dmet</namespace>
<documentations>
<documentation type="URL">http://www.jsbi.org/journal/GIW04/GIW04P058.pdf</documentation>
<documentation type="URL">http://pubs.acs.org/doi/ipdf/10.1021/ci300309k</documentation>
</documentations>
<resources>
<resource id="MIR:00100095" state="down" reliability="95">
<dataResource>http://www.3dmet.dna.affrc.go.jp/</dataResource>
<dataEntityExample>B00162</dataEntityExample>
<dataEntry>http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$id</dataEntry>
<dataInfo>3DMET database</dataInfo>
<dataInstitution>Bioinformatics Research Unit, National Institute of Agrobiological Sciences</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>metabolite</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000067" pattern="^FMA:\d+$">
<name>FMA</name>
<synonyms>
<synonym>Foundational Model of Anatomy Ontology</synonym>
</synonyms>
<definition>The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.</definition>
<uris>
<uri type="URN">urn:miriam:fma</uri>
<uri type="URL">http://identifiers.org/fma/</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.fma/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.fma</uri>
</uris>
<namespace>fma</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17271570</documentation>
</documentations>
<resources>
<resource id="MIR:00100097" state="up" reliability="98">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/fma/</dataResource>
<dataEntityExample>FMA:67112</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=$id</dataEntry>
<dataInfo>Foundational Model of Anatomy via Ontology Lookup Service (OLS)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100236" state="up" reliability="95">
<dataResource>http://bioportal.bioontology.org/ontologies/FMA</dataResource>
<dataEntityExample>FMA:67112</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/FMA_subset/$id</dataEntry>
<dataInfo>Foundational Model of Anatomy through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>compartment</element>
<element>model</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000068" pattern="^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$">
<name>MatrixDB</name>
<definition>MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations.</definition>
<uris>
<uri type="URN">urn:miriam:matrixdb.association</uri>
<uri type="URL">http://identifiers.org/matrixdb.association/</uri>
</uris>
<namespace>matrixdb.association</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19147664</documentation>
</documentations>
<resources>
<resource id="MIR:00100098" state="down" reliability="87" primary="true">
<dataResource>http://matrixdb.univ-lyon1.fr/</dataResource>
<dataEntityExample>P00747__P07355</dataEntityExample>
<dataEntry>http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$id&class=Association</dataEntry>
<dataInfo>MatrixDB Association</dataInfo>
<dataInstitution>Institut de Biologie et Chimie des Protéines, Lyon University</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>lipid</tag>
<tag>polysaccharide</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000069" pattern="^\d+$">
<name>NCBI Gene</name>
<synonyms>
<synonym>Entrez Gene</synonym>
</synonyms>
<definition>Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis.</definition>
<uris>
<uri type="URN">urn:miriam:ncbigene</uri>
<uri type="URL">http://identifiers.org/ncbigene/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/ncbigene</uri>
<uri type="URN" deprecated="true">urn:miriam:ncbi.gene</uri>
<uri type="URN" deprecated="true">urn:miriam:entrez.gene</uri>
</uris>
<namespace>ncbigene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608257</documentation>
</documentations>
<resources>
<resource id="MIR:00100099" state="up" reliability="99" primary="true">
<dataResource>http://www.ncbi.nlm.nih.gov/gene</dataResource>
<dataEntityExample>100010</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/gene/$id</dataEntry>
<dataInfo>Entrez Gene (NCBI)</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100693" state="down" reliability="83">
<dataResource>http://ncbigene.bio2rdf.org/fct</dataResource>
<dataEntityExample>100010</dataEntityExample>
<dataEntry>http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000070" pattern="^\w+:[\w\d\.-]*$">
<name>KEGG Genes</name>
<!--<synonyms>-->
<!--<synonym>KEGG</synonym>-->
<!--</synonyms>-->
<definition>KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.genes</uri>
<uri type="URL">http://identifiers.org/kegg.genes/</uri>
<uri type="URL" deprecated="true">http://www.genome.jp/kegg/genes/</uri>
</uris>
<namespace>kegg.genes</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381885</documentation>
</documentations>
<resources>
<resource id="MIR:00100100" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/genes.html</dataResource>
<dataEntityExample>syn:ssr3451</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG GENES Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000071" pattern="^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$">
<name>BRENDA</name>
<definition>BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.</definition>
<uris>
<uri type="URN">urn:miriam:brenda</uri>
<uri type="URL">http://identifiers.org/brenda/</uri>
</uris>
<namespace>brenda</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18984617</documentation>
</documentations>
<resources>
<resource id="MIR:00100101" state="up" reliability="99">
<dataResource>http://www.brenda-enzymes.org/</dataResource>
<dataEntityExample>1.1.1.1</dataEntityExample>
<dataEntry>http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$id</dataEntry>
<dataInfo>Brenda enzyme database</dataInfo>
<dataInstitution>Technical University Braunschweig, Institute for Bioinformatics and Biochemistry</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>enzyme</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000072" pattern="^\d+$">
<name>PubChem-bioassay</name>
<definition>PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results.</definition>
<uris>
<uri type="URN">urn:miriam:pubchem.bioassay</uri>
<uri type="URL">http://identifiers.org/pubchem.bioassay/</uri>
</uris>
<namespace>pubchem.bioassay</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17170002</documentation>
</documentations>
<resources>
<resource id="MIR:00100102" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay </dataResource>
<dataEntityExample>1018</dataEntityExample>
<dataEntry>http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$id</dataEntry>
<dataInfo>PubChem Bioassay at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000073" pattern="^\d+$" restricted="true">
<name>Pathway Commons</name>
<definition>Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.</definition>
<uris>
<uri type="URN">urn:miriam:pathwaycommons</uri>
<uri type="URL">http://identifiers.org/pathwaycommons/</uri>
</uris>
<namespace>pathwaycommons</namespace>
<documentations>
<documentation type="URL">http://www.pathwaycommons.org/pc/</documentation>
</documentations>
<resources>
<resource id="MIR:00100103" state="up" reliability="95">
<dataResource>http://www.pathwaycommons.org/pc/</dataResource>
<dataEntityExample>485991</dataEntityExample>
<dataEntry>http://www.pathwaycommons.org/pc/record2.do?id=$id</dataEntry>
<dataInfo>Pathway Commons</dataInfo>
<dataInstitution>Memorial Sloan-Kettering Cancer Center</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="4" desc="Identifier instability">
<statement>Interaction and pathway identifiers are not stable, and can vary between releases.</statement>
<link desc="faq link">http://www.pathwaycommons.org/pc/faq.do#general</link>
</restriction>
</restrictions>
<tags>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000074" pattern="^HBG\d+$">
<name>HOVERGEN</name>
<definition>HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.</definition>
<uris>
<uri type="URN">urn:miriam:hovergen</uri>
<uri type="URL">http://identifiers.org/hovergen/</uri>
</uris>
<namespace>hovergen</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15713731</documentation>
</documentations>
<resources>
<resource id="MIR:00100104" state="up" reliability="96">
<dataResource>http://pbil.univ-lyon1.fr/databases/hovergen.php</dataResource>
<dataEntityExample>HBG004341</dataEntityExample>
<dataEntry>http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$id&db=HOVERGEN</dataEntry>
<dataInfo>Hovergen</dataInfo>
<dataInstitution>Laboratoire de Biométrie, Génétique et Biologie des Populations</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000075" pattern="^\d+$">
<name>Melanoma Molecular Map Project Biomaps</name>
<synonyms>
<synonym>MMMP Biomaps</synonym>
</synonyms>
<definition>A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.</definition>
<uris>
<uri type="URN">urn:miriam:mmmp:biomaps</uri>
<uri type="URL">http://identifiers.org/biomaps/</uri>
</uris>
<namespace>biomaps</namespace>
<documentations>
<documentation type="URL">http://www.mmmp.org/MMMP/import.mmmp?page=aims_org.mmmp</documentation>
</documentations>
<resources>
<resource id="MIR:00100105" state="up" reliability="95">
<dataResource>http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp</dataResource>
<dataEntityExample>37</dataEntityExample>
<dataEntry>http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$id</dataEntry>
<dataInfo>main webpage</dataInfo>
<dataInstitution>Melanoma Molecular Map Project</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<tags>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000076" pattern="WP\d{1,5}(\_r\d+)?$">
<name>WikiPathways</name>
<definition>WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style.
All content is under the Creative Commons Attribution 3.0 Unported license.</definition>
<uris>
<uri type="URN">urn:miriam:wikipathways</uri>
<uri type="URL">http://identifiers.org/wikipathways/</uri>
</uris>
<namespace>wikipathways</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18651794</documentation>
</documentations>
<resources>
<resource id="MIR:00100106" state="down" reliability="93">
<dataResource>http://www.wikipathways.org/</dataResource>
<dataEntityExample>WP100</dataEntityExample>
<dataEntry>http://www.wikipathways.org/instance/$id</dataEntry>
<dataInfo>Wikipathways</dataInfo>
<dataInstitution>BiGCaT Bioinformatics (University of Maastricht) and Conklin Lab (UCSF).</dataInstitution>
<dataLocation>Holland and USA</dataLocation>
</resource>
</resources>
<tags>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000077" pattern="^M\d{4}$">
<name>MACiE</name>
<definition>MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.</definition>
<uris>
<uri type="URN">urn:miriam:macie</uri>
<uri type="URL">http://identifiers.org/macie/</uri>
</uris>
<namespace>macie</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17082206</documentation>
</documentations>
<resources>
<resource id="MIR:00100108" state="up" reliability="99" primary="true">
<dataResource>http://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html</dataResource>
<dataEntityExample>M0001</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$id</dataEntry>
<dataInfo>MACiE database of mechanisms, annotation and classification in enzymes</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>enzyme</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000078" pattern="MI\d{7}">
<name>miRBase Sequence</name>
<definition>The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).</definition>
<uris>
<uri type="URN">urn:miriam:mirbase</uri>
<uri type="URL">http://identifiers.org/mirbase/</uri>
</uris>
<namespace>mirbase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681370</documentation>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkj112</documentation>
</documentations>
<resources>
<resource id="MIR:00100135" state="up" reliability="99">
<dataResource>http://www.mirbase.org/</dataResource>
<dataEntityExample>MI0000001</dataEntityExample>
<dataEntry>http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id</dataEntry>
<dataInfo>miRBase Sequence Database</dataInfo>
<dataInstitution>Faculty of Life Sciences, University of Manchester </dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100109" obsolete="true">
<dataResource>http://microrna.sanger.ac.uk/</dataResource>
<dataEntityExample>MI0000001</dataEntityExample>
<dataEntry>http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc=$id</dataEntry>
<dataInfo>miRBase Sequence Database</dataInfo>
<dataInstitution>University of Manchester and Wellcome Trust Sanger institute</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000079" pattern="ZDB\-GENE\-\d+\-\d+">
<name>ZFIN Gene</name>
<definition>ZFIN serves as the zebrafish model organism database. This collection references gene information.</definition>
<uris>
<uri type="URN">urn:miriam:zfin</uri>
<uri type="URL">http://identifiers.org/zfin/</uri>
</uris>
<namespace>zfin</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17991680</documentation>
</documentations>
<resources>
<resource id="MIR:00100110" state="up" reliability="97">
<dataResource>http://zfin.org</dataResource>
<dataEntityExample>ZDB-GENE-041118-11</dataEntityExample>
<dataEntry>http://zfin.org/$id</dataEntry>
<dataInfo>ZFIN Expression at University of Oregon</dataInfo>
<dataInstitution>Zebrafish Information Network, University of Oregon</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000080" pattern="^((HGNC|hgnc):)?\d{1,5}$">
<name>HGNC</name>
<synonyms>
<synonym>HUGO Gene Nomenclature Committee</synonym>
</synonyms>
<definition>The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database.</definition>
<uris>
<uri type="URN">urn:miriam:hgnc</uri>
<uri type="URL">http://identifiers.org/hgnc/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/hgnc</uri>
</uris>
<namespace>hgnc</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17984084</documentation>
<documentation type="PMID">urn:miriam:pubmed:20929869</documentation>
<documentation type="PMID">urn:miriam:pubmed:23161694</documentation>
</documentations>
<resources>
<resource id="MIR:00100111" state="up" reliability="97" primary="true">
<dataResource>http://www.genenames.org</dataResource>
<dataEntityExample>2674</dataEntityExample>
<dataEntry>http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$id</dataEntry>
<dataInfo>HUGO Genome Nomenclature Committee</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100698" state="down" reliability="82">
<dataResource>http://hgnc.bio2rdf.org/fct</dataResource>
<dataEntityExample>hgnc:2674</dataEntityExample>
<dataEntry>http://hgnc.bio2rdf.org/describe/?url=http://bio2rdf.org/$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>human</tag>
<tag>schema.org</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000081" pattern="^SO:\d{7}$">
<name>Sequence Ontology</name>
<synonyms>
<synonym>SO</synonym>
<synonym>Sequence Types and Features</synonym>
</synonyms>
<definition>The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.</definition>
<uris>
<uri type="URN">urn:miriam:so</uri>
<uri type="URL">http://identifiers.org/so/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.so</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.so/</uri>
</uris>
<namespace>so</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15892872</documentation>
</documentations>
<resources>
<resource id="MIR:00100112" state="up" reliability="96">
<dataResource>http://www.sequenceontology.org/</dataResource>
<dataEntityExample>SO:0000704</dataEntityExample>
<dataEntry>http://www.sequenceontology.org/miso/current_release/term/$id</dataEntry>
<dataInfo>Sequence Ontology</dataInfo>
<dataInstitution>Department of Molecular and Cellular Biology, University of California, Berkeley</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100241" state="up" reliability="93">
<dataResource>http://bioportal.bioontology.org/ontologies/SO</dataResource>
<dataEntityExample>SO:0000704</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/SO/$id</dataEntry>
<dataInfo>Sequence Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100628" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/so</dataResource>
<dataEntityExample>SO:0000704</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=$id</dataEntry>
<dataInfo>Sequence Ontology through Ontology Lookup Service (OLS)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000082" pattern="^\d{5}$">
<name>Rhea</name>
<definition>Rhea is a manually annotated reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest), providing detailed information about structure, formulae and charge. It is populated with the reactions found in the EC list, IntEnz and ENZYME databases), as well as other biochemical reactions, including those that are often termed "spontaneous".</definition>
<uris>
<uri type="URN">urn:miriam:rhea</uri>
<uri type="URL">http://identifiers.org/rhea/</uri>
</uris>
<namespace>rhea</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:25332395</documentation>
<documentation type="URL">http://www.rhea-db.org/documentation</documentation>
</documentations>
<resources>
<resource id="MIR:00100113" state="up" reliability="98" primary="true">
<dataResource>http://www.rhea-db.org/</dataResource>
<dataEntityExample>12345</dataEntityExample>
<dataEntry>http://www.rhea-db.org/reaction?id=$id</dataEntry>
<dataInfo>Rhea</dataInfo>
<dataInstitution>European Bioinformatics Institute and Swiss Institute of Bioinformatics</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>reaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000083" pattern="^UPA\d{5}$">
<name>Unipathway</name>
<definition>UniPathway is a manually curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled vocabulary to describe the role of a protein in a metabolic pathway.</definition>
<uris>
<uri type="URN">urn:miriam:unipathway</uri>
<uri type="URL">http://identifiers.org/unipathway/</uri>
</uris>
<namespace>unipathway</namespace>
<documentations>
<documentation type="URL">http://precedings.nature.com/documents/3214/version/1</documentation>
</documentations>
<resources>
<resource id="MIR:00100114" state="down" reliability="73">
<dataResource>http://www.grenoble.prabi.fr/obiwarehouse/unipathway</dataResource>
<dataEntityExample>UPA00206</dataEntityExample>
<dataEntry>http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id</dataEntry>
<dataInfo>UniPathway</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics (SIB) and French National Institute for Research in Computer Science and Control</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000084" pattern="^CHEMBL\d+$">
<name>ChEMBL compound</name>
<definition>ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.</definition>
<uris>
<uri type="URN">urn:miriam:chembl.compound</uri>
<uri type="URL">http://identifiers.org/chembl.compound/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/chembl</uri>
</uris>
<namespace>chembl.compound</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19194660</documentation>
<documentation type="URL">https://github.com/egonw/chembl.rdf</documentation>
</documentations>
<resources>
<resource id="MIR:00100115" state="up" reliability="99" primary="true">
<dataResource>https://www.ebi.ac.uk/chembldb/</dataResource>
<dataEntityExample>CHEMBL308052</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/chembl/compound/inspect/$id</dataEntry>
<dataInfo>ChEMBL compound database at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100484" state="up" reliability="99">
<dataResource>https://github.com/egonw/chembl.rdf</dataResource>
<dataEntityExample>CHEMBL308052</dataEntityExample>
<dataEntry>http://linkedchemistry.info/chembl/chemblid/$id</dataEntry>
<dataInfo>ChEMBL compound RDF</dataInfo>
<dataInstitution>Maastricht University</dataInstitution>
<dataLocation>The Netherlands</dataLocation>
</resource>
<resource id="MIR:00100744" state="down" reliability="98">
<dataResource>https://www.ebi.ac.uk/rdf/services/chembl/</dataResource>
<dataEntityExample>CHEMBL308052</dataEntityExample>
<dataEntry>http://rdf.ebi.ac.uk/resource/chembl/molecule/$id</dataEntry>
<dataInfo>ChEMBL compound RDF through EBI RDF Platform</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>metabolite</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000085" pattern="^CHEMBL\d+$">
<name>ChEMBL target</name>
<definition>ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.</definition>
<uris>
<uri type="URN">urn:miriam:chembl.target</uri>
<uri type="URL">http://identifiers.org/chembl.target/</uri>
</uris>
<namespace>chembl.target</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19194660</documentation>
<documentation type="URL">https://github.com/egonw/chembl.rdf</documentation>
</documentations>
<resources>
<resource id="MIR:00100116" state="up" reliability="99" primary="true">
<dataResource>https://www.ebi.ac.uk/chembldb/</dataResource>
<dataEntityExample>CHEMBL3467</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/chembl/target/inspect/$id</dataEntry>
<dataInfo>ChEMBL targets database at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100485" state="up" reliability="99">
<dataResource>https://github.com/egonw/chembl.rdf</dataResource>
<dataEntityExample>CHEMBL3467</dataEntityExample>
<dataEntry>http://linkedchemistry.info/chembl/chemblid/$id</dataEntry>
<dataInfo>ChEMBL target RDF</dataInfo>
<dataInstitution>Maastricht University</dataInstitution>
<dataLocation>The Netherlands</dataLocation>
</resource>
<resource id="MIR:00100743" state="down" reliability="98">
<dataResource>http://rdf.ebi.ac.uk/resource/chembl/</dataResource>
<dataEntityExample>CHEMBL3467</dataEntityExample>
<dataEntry>http://rdf.ebi.ac.uk/resource/chembl/target/$id</dataEntry>
<dataInfo>ChEMBL target RDF through EBI RDF Platform</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>parameter</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000086" pattern="^\d+$">
<name>SABIO-RK Kinetic Record</name>
<definition>SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information.</definition>
<uris>
<uri type="URN">urn:miriam:sabiork.kineticrecord</uri>
<uri type="URL">http://identifiers.org/sabiork.kineticrecord/</uri>
</uris>
<namespace>sabiork.kineticrecord</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17822389</documentation>
<documentation type="DOI">urn:miriam:doi:10.1007%2F11799511_9</documentation>
<documentation type="DOI">urn:miriam:doi:10.2390%2Fbiecoll-jib-2007-49</documentation>
<documentation type="DOI">urn:miriam:doi:10.1186%2F1752-0509-1-S1-S6</documentation>
<documentation type="DOI">urn:miriam:doi:10.1186%2F1752-0509-1-S1-P4</documentation>
</documentations>
<resources>
<resource id="MIR:00100117" state="probably up" reliability="98">
<dataResource>http://sabiork.h-its.org/</dataResource>
<dataEntityExample>5046</dataEntityExample>
<dataEntry>http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$id</dataEntry>
<dataInfo>SABIO-RK Reaction Kinetics Database - Kinetic Dataset</dataInfo>
<dataInstitution>Heidelberg Institute for Theoretical Studies (HITS gGmbH)</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>kinetics</tag>
<tag>reaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>parameter</element>
<element>reaction</element>
<element>kineticLaw</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000087" pattern="^\w+$">
<name>Ligand-Gated Ion Channel database</name>
<synonyms>
<synonym>LGICdb</synonym>
</synonyms>
<definition>The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.</definition>
<uris>
<uri type="URN">urn:miriam:lgic</uri>
<uri type="URL">http://identifiers.org/lgic/</uri>
</uris>
<namespace>lgic</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:9847222</documentation>
</documentations>
<resources>
<resource id="MIR:00100118" state="up" reliability="99">
<dataResource>http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php</dataResource>
<dataEntityExample>5HT3Arano</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$id.php</dataEntry>
<dataInfo>Ligand-Gated Ion Channel database at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>protein</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000088" pattern="^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$">
<name>Anatomical Therapeutic Chemical</name>
<synonyms>
<synonym>ATC</synonym>
</synonyms>
<definition>The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.</definition>
<uris>
<uri type="URN">urn:miriam:atc</uri>
<uri type="URL">http://identifiers.org/atc/</uri>
</uris>
<namespace>atc</namespace>
<documentations>
<documentation type="URL">http://www.whocc.no/atc_ddd_publications/guidelines/</documentation>
</documentations>
<resources>
<resource id="MIR:00100119" state="down" reliability="83">
<dataResource>http://www.whocc.no/atc_ddd_index/</dataResource>
<dataEntityExample>A10BA02</dataEntityExample>
<dataEntry>http://www.whocc.no/atc_ddd_index/?code=$id</dataEntry>
<dataInfo>Anatomical Therapeutic Chemical Index at WHO</dataInfo>
<dataInstitution>World Health Organisation</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>drug</tag>
</tags>
<annotation>
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<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000089" pattern="^PA\d+$" restricted="true">
<name>PharmGKB Pathways</name>
<definition>The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.
PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.</definition>
<uris>
<uri type="URN">urn:miriam:pharmgkb.pathways</uri>
<uri type="URL">http://identifiers.org/pharmgkb.pathways/</uri>
</uris>
<namespace>pharmgkb.pathways</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11908751</documentation>
<documentation type="PMID">urn:miriam:pubmed:22103613</documentation>
</documentations>
<resources>
<resource id="MIR:00100120" state="down" reliability="79">
<dataResource>http://www.pharmgkb.org/</dataResource>
<dataEntityExample>PA146123006</dataEntityExample>
<dataEntry>http://www.pharmgkb.org/pathway/$id</dataEntry>
<dataInfo>PharmGKB at Stanford</dataInfo>
<dataInstitution>Department of Genetics, School of Medicine, Stanford University, Stanford, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The data may be used for research purposes only.</statement>
<link desc="terms and conditions of data use">http://www.pharmgkb.org/home/policies/web-data.jsp</link>
</restriction>
</restrictions>
<tags>
<tag>pathway</tag>
<tag>pharmacogenomics</tag>
</tags>
</datatype>
<datatype id="MIR:00000090" pattern="^PA\d+$" restricted="true">
<name>PharmGKB Disease</name>
<definition>The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.</definition>
<uris>
<uri type="URN">urn:miriam:pharmgkb.disease</uri>
<uri type="URL">http://identifiers.org/pharmgkb.disease/</uri>
</uris>
<namespace>pharmgkb.disease</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11908751</documentation>
<documentation type="PMID">urn:miriam:pubmed:22103613</documentation>
</documentations>
<resources>
<resource id="MIR:00100121" state="down" reliability="79">
<dataResource>http://www.pharmgkb.org/</dataResource>
<dataEntityExample>PA447218</dataEntityExample>
<dataEntry>http://www.pharmgkb.org/disease/$id</dataEntry>
<dataInfo>PharmGKB Disease at Stanford</dataInfo>
<dataInstitution>Department of Genetics, School of Medicine, Stanford University, Stanford, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The data may be used for research purposes only.</statement>
<link desc="terms and conditions of data use">http://www.pharmgkb.org/home/policies/web-data.jsp</link>
</restriction>
</restrictions>
<tags>
<tag>pharmacogenomics</tag>
</tags>
<annotation>
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<elements>
<element>model</element>
</elements>
</format>
</annotation>
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<datatype id="MIR:00000091" pattern="^PA\d+$" restricted="true">
<name>PharmGKB Drug</name>
<definition>The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.</definition>
<uris>
<uri type="URN">urn:miriam:pharmgkb.drug</uri>
<uri type="URL">http://identifiers.org/pharmgkb.drug/</uri>
</uris>
<namespace>pharmgkb.drug</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11908751</documentation>
<documentation type="PMID">urn:miriam:pubmed:22103613</documentation>
</documentations>
<resources>
<resource id="MIR:00100122" state="down" reliability="79">
<dataResource>http://www.pharmgkb.org/</dataResource>
<dataEntityExample>PA448710</dataEntityExample>
<dataEntry>http://www.pharmgkb.org/drug/$id</dataEntry>
<dataInfo>PharmGKB Drug at Stanford</dataInfo>
<dataInstitution>Department of Genetics, School of Medicine, Stanford University, Stanford, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The data may be used for research purposes only.</statement>
<link desc="terms and conditions of data use">http://www.pharmgkb.org/home/policies/web-data.jsp</link>
</restriction>
</restrictions>
<tags>
<tag>drug</tag>
<tag>pharmacogenomics</tag>
</tags>
</datatype>
<datatype id="MIR:00000092" pattern="^DAP\d+$">
<name>TTD Drug</name>
<synonyms>
<synonym>Therapeutic Target Database</synonym>
</synonyms>
<definition>The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.</definition>
<uris>
<uri type="URN">urn:miriam:ttd.drug</uri>
<uri type="URL">http://identifiers.org/ttd.drug/</uri>
</uris>
<namespace>ttd.drug</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11752352</documentation>
<documentation type="PMID">urn:miriam:pubmed:24265219</documentation>
</documentations>
<resources>
<resource id="MIR:00100123" state="up" reliability="90">
<dataResource>http://bidd.nus.edu.sg/group/ttd/ttd.asp</dataResource>
<dataEntityExample>DAP000773</dataEntityExample>
<dataEntry>http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$id</dataEntry>
<dataInfo>Therapeutic Target Database Drug</dataInfo>
<dataInstitution>Computational Science Department, National University of Singapore</dataInstitution>
<dataLocation>Singapore</dataLocation>
</resource>
</resources>
<tags>
<tag>drug</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000093" pattern="^TTDS\d+$">
<name>TTD Target</name>
<definition>The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.</definition>
<uris>
<uri type="URN">urn:miriam:ttd.target</uri>
<uri type="URL">http://identifiers.org/ttd.target/</uri>
</uris>
<namespace>ttd.target</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11752352</documentation>
<documentation type="PMID">urn:miriam:pubmed:24265219</documentation>
</documentations>
<resources>
<resource id="MIR:00100124" state="up" reliability="90">
<dataResource>http://bidd.nus.edu.sg/group/ttd/ttd.asp</dataResource>
<dataEntityExample>TTDS00056</dataEntityExample>
<dataEntry>http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$id</dataEntry>
<dataInfo>Therapeutic Target Database Target</dataInfo>
<dataInstitution>Computational Science Department, National University of Singapore</dataInstitution>
<dataLocation>Singapore</dataLocation>
</resource>
</resources>
<tags>
<tag>drug</tag>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000094" pattern="^\d+$">
<name>NeuronDB</name>
<definition>NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.</definition>
<uris>
<uri type="URN">urn:miriam:neurondb</uri>
<uri type="URL">http://identifiers.org/neurondb/</uri>
</uris>
<namespace>neurondb</namespace>
<documentations>
<documentation type="URL">http://senselab.med.yale.edu/NeuronDB/default.asp</documentation>
</documentations>
<resources>
<resource id="MIR:00100125" state="down" reliability="83">
<dataResource>http://senselab.med.yale.edu/NeuronDB/</dataResource>
<dataEntityExample>265</dataEntityExample>
<dataEntry>http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$id</dataEntry>
<dataInfo>NeuronDB at SenseLab</dataInfo>
<dataInstitution>Yale University School of Medicine</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>neuroscience</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>compartment</element>
<element>species</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000095" pattern="^\w+$">
<name>NeuroMorpho</name>
<definition>NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons.</definition>
<uris>
<uri type="URN">urn:miriam:neuromorpho</uri>
<uri type="URL">http://identifiers.org/neuromorpho/</uri>
</uris>
<namespace>neuromorpho</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16552417</documentation>
</documentations>
<resources>
<resource id="MIR:00100126" state="up" reliability="97">
<dataResource>http://neuromorpho.org/index.jsp</dataResource>
<dataEntityExample>Rosa2</dataEntityExample>
<dataEntry>http://neuromorpho.org/neuron_info.jsp?neuron_name=$id</dataEntry>
<dataInfo>NeuroMorpho</dataInfo>
<dataInstitution>Krasnow Institute, Virginia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>neuroscience</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>compartment</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000096" pattern="^\d+$">
<name>ChemIDplus</name>
<definition>ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.</definition>
<uris>
<uri type="URN">urn:miriam:chemidplus</uri>
<uri type="URL">http://identifiers.org/chemidplus/</uri>
</uris>
<namespace>chemidplus</namespace>
<documentations>
<documentation type="URL">http://www.nlm.nih.gov/pubs/factsheets/chemidplusfs.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100127" state="probably up" reliability="99">
<dataResource>http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp</dataResource>
<dataEntityExample>000057272</dataEntityExample>
<dataEntry>http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id</dataEntry>
<dataInfo>ChemIDplus at National Library of Medicine</dataInfo>
<dataInstitution>National Library of Medicine, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>parameter</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000097" pattern="^\d+$">
<name>BioSystems</name>
<definition>The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.</definition>
<uris>
<uri type="URN">urn:miriam:biosystems</uri>
<uri type="URL">http://identifiers.org/biosystems/</uri>
</uris>
<namespace>biosystems</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19854944</documentation>
</documentations>
<resources>
<resource id="MIR:00100128" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/biosystems/</dataResource>
<dataEntityExample>001</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/biosystems/$id</dataEntry>
<dataInfo>BioSystems database at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>pathway</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>reaction</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000098" pattern="^[CD]\d+$">
<name>CTD Chemical</name>
<definition>The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.</definition>
<uris>
<uri type="URN">urn:miriam:ctd.chemical</uri>
<uri type="URL">http://identifiers.org/ctd.chemical/</uri>
</uris>
<namespace>ctd.chemical</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16675512</documentation>
</documentations>
<resources>
<resource id="MIR:00100129" state="up" reliability="99">
<dataResource>http://ctdbase.org/</dataResource>
<dataEntityExample>D001151</dataEntityExample>
<dataEntry>http://ctdbase.org/detail.go?type=chem&acc=$id</dataEntry>
<dataInfo>Comparative Toxicogenomics Database (Chemical)</dataInfo>
<dataInstitution>The Mount Desert Island Biological Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>pharmacogenomics</tag>
</tags>
</datatype>
<datatype id="MIR:00000099" pattern="^D\d+$">
<name>CTD Disease</name>
<definition>The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.</definition>
<uris>
<uri type="URN">urn:miriam:ctd.disease</uri>
<uri type="URL">http://identifiers.org/ctd.disease/</uri>
</uris>
<namespace>ctd.disease</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16675512</documentation>
</documentations>
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<resource id="MIR:00100130" state="up" reliability="99">
<dataResource>http://ctdbase.org/</dataResource>
<dataEntityExample>D053716</dataEntityExample>
<dataEntry>http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$id</dataEntry>
<dataInfo>Comparative Toxicogenomics Database (Disease)</dataInfo>
<dataInstitution>The Mount Desert Island Biological Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
<tag>pharmacogenomics</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000100" pattern="^\d+$">
<name>CTD Gene</name>
<definition>The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.</definition>
<uris>
<uri type="URN">urn:miriam:ctd.gene</uri>
<uri type="URL">http://identifiers.org/ctd.gene/</uri>
</uris>
<namespace>ctd.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16675512</documentation>
</documentations>
<resources>
<resource id="MIR:00100131" state="up" reliability="99">
<dataResource>http://ctdbase.org/</dataResource>
<dataEntityExample>101</dataEntityExample>
<dataEntry>http://ctdbase.org/detail.go?type=gene&acc=$id</dataEntry>
<dataInfo>Comparative Toxicogenomics Database (Gene)</dataInfo>
<dataInstitution>The Mount Desert Island Biological Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>pharmacogenomics</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000101" pattern="^\d+$">
<name>BioNumbers</name>
<definition>BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data.
</definition>
<uris>
<uri type="URN">urn:miriam:bionumbers</uri>
<uri type="URL">http://identifiers.org/bionumbers/</uri>
</uris>
<namespace>bionumbers</namespace>
<documentations>
<documentation type="URL">http://www.bionumbers.hms.harvard.edu/aboutus.aspx</documentation>
</documentations>
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<dataResource>http://www.bionumbers.hms.harvard.edu/search.aspx</dataResource>
<dataEntityExample>104674</dataEntityExample>
<dataEntry>http://www.bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=$id&ver=1</dataEntry>
<dataInfo>BioNumbers database</dataInfo>
<dataInstitution>Weizmann Institute</dataInstitution>
<dataLocation>Israel</dataLocation>
</resource>
</resources>
<tags>
<tag>registry</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000102" pattern="^DB\d{5}$">
<name>DrugBank</name>
<definition>The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.</definition>
<uris>
<uri type="URN">urn:miriam:drugbank</uri>
<uri type="URL">http://identifiers.org/drugbank/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/drugbank</uri>
</uris>
<namespace>drugbank</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381955</documentation>
</documentations>
<resources>
<resource id="MIR:00100133" state="up" reliability="99" primary="true">
<dataResource>http://www.drugbank.ca/</dataResource>
<dataEntityExample>DB00001</dataEntityExample>
<dataEntry>http://www.drugbank.ca/drugs/$id</dataEntry>
<dataInfo>DrugBank drug information</dataInfo>
<dataInstitution>Departments of Computing Science & Biological Sciences, University of Alberta</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
<resource id="MIR:00100691" state="down" reliability="84">
<dataResource>http://drugbank.bio2rdf.org/fct/</dataResource>
<dataEntityExample>DB00001</dataEntityExample>
<dataEntry>http://drugbank.bio2rdf.org/describe/?url=http://bio2rdf.org/drugbank:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<tags>
<tag>drug</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000103" pattern="^T3D\d+$">
<name>T3DB</name>
<synonyms>
<synonym>Toxin and Toxin Target Database</synonym>
</synonyms>
<definition>Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.</definition>
<uris>
<uri type="URN">urn:miriam:t3db</uri>
<uri type="URL">http://identifiers.org/t3db/</uri>
</uris>
<namespace>t3db</namespace>
<documentations>
<documentation type="URL">http://www.t3db.org/about#cite</documentation>
</documentations>
<resources>
<resource id="MIR:00100136" state="up" reliability="99">
<dataResource>http://www.t3db.org/</dataResource>
<dataEntityExample>T3D0001</dataEntityExample>
<dataEntry>http://www.t3db.org/toxins/$id</dataEntry>
<dataInfo>Toxin and Toxin Target Database</dataInfo>
<dataInstitution>University of Alberta</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>drug</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000104" pattern="^SMP\d{5}$">
<name>Small Molecule Pathway Database</name>
<synonyms>
<synonym>SMPDB</synonym>
</synonyms>
<definition>The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.</definition>
<uris>
<uri type="URN">urn:miriam:smpdb</uri>
<uri type="URL">http://identifiers.org/smpdb/</uri>
</uris>
<namespace>smpdb</namespace>
<documentations>
<documentation type="URL">http://www.smpdb.ca/</documentation>
</documentations>
<resources>
<resource id="MIR:00100137" state="up" reliability="90">
<dataResource>http://www.smpdb.ca/pathways</dataResource>
<dataEntityExample>SMP00001</dataEntityExample>
<dataEntry>http://smpdb.ca/view/$id</dataEntry>
<dataInfo>Small Molecule Pathway Database</dataInfo>
<dataInstitution>University of Alberta, Edmonton, AB</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>human</tag>
<tag>metabolite</tag>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000105" pattern="^\d{5}$">
<name>PhosphoSite Protein</name>
<synonyms>
<synonym>PhosphoSitePlus</synonym>
</synonyms>
<definition>PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.</definition>
<uris>
<uri type="URN">urn:miriam:phosphosite.protein</uri>
<uri type="URL">http://identifiers.org/phosphosite.protein/</uri>
<uri type="URN" deprecated="true">urn:miriam:phosphosite</uri>
</uris>
<namespace>phosphosite.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12478304</documentation>
</documentations>
<resources>
<resource id="MIR:00100138" state="down" reliability="96">
<dataResource>http://www.phosphosite.org/homeAction.do</dataResource>
<dataEntityExample>12300</dataEntityExample>
<dataEntry>http://www.phosphosite.org/proteinAction.do?id=$id</dataEntry>
<dataInfo>PhosphoSite</dataInfo>
<dataInstitution>Cell Signaling Technology, Inc.</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>mammalian</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000106" pattern="^[\w\d\.-]*$">
<name>GeneDB</name>
<definition>GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.</definition>
<uris>
<uri type="URN">urn:miriam:genedb</uri>
<uri type="URL">http://identifiers.org/genedb/</uri>
</uris>
<namespace>genedb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681429</documentation>
</documentations>
<resources>
<resource id="MIR:00100139" state="up" reliability="98">
<dataResource>http://www.genedb.org/</dataResource>
<dataEntityExample>Cj1536c</dataEntityExample>
<dataEntry>http://www.genedb.org/gene/$id</dataEntry>
<dataInfo>GeneDB at Sanger Institute</dataInfo>
<dataInstitution>Pathogen Genomics, Sanger Institute and European Bioinformatics Institute</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000107" pattern="^TEDDY_\d{7}$">
<name>TEDDY</name>
<definition>The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.</definition>
<uris>
<uri type="URN">urn:miriam:biomodels.teddy</uri>
<uri type="URL">http://identifiers.org/biomodels.teddy/</uri>
<uri type="URN" deprecated="true">urn:miriam:teddy</uri>
</uris>
<namespace>biomodels.teddy</namespace>
<documentations>
<documentation type="URL">http://teddyontology.sourceforge.net/</documentation>
</documentations>
<resources>
<resource id="MIR:00100140" state="up" reliability="95">
<dataResource>http://teddyontology.sourceforge.net/</dataResource>
<dataEntityExample>TEDDY_0000066</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/TEDDY/$id</dataEntry>
<dataInfo>TEDDY through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100761" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/teddy</dataResource>
<dataEntityExample>TEDDY_0000066</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/teddy/terms?short_form=$id</dataEntry>
<dataInfo>TEDDY though OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
</datatype>
<datatype id="MIR:00000108" pattern="^KISAO_\d+$">
<name>KiSAO</name>
<synonyms>
<synonym>Kinetic Simulation Algorithm Ontology</synonym>
</synonyms>
<definition>The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment.</definition>
<uris>
<uri type="URN">urn:miriam:biomodels.kisao</uri>
<uri type="URL">http://identifiers.org/biomodels.kisao/</uri>
</uris>
<namespace>biomodels.kisao</namespace>
<documentations>
<documentation type="URL">http://www.ebi.ac.uk/compneur-srv/kisao/</documentation>
</documentations>
<resources>
<resource id="MIR:00100141" state="up" reliability="97">
<dataResource>http://bioportal.bioontology.org/ontologies/KISAO</dataResource>
<dataEntityExample>KISAO_0000057</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/KISAO/kisao:$id</dataEntry>
<dataInfo>KiSAO via NCBO's Bioportal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100757" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/kisao</dataResource>
<dataEntityExample>KISAO_0000057</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/kisao/terms?short_form=$id</dataEntry>
<dataInfo>KiSAO through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000109" pattern="^MI:\d{4}$" restricted="true">
<name>Molecular Interactions Ontology</name>
<synonyms>
<synonym>MI</synonym>
</synonyms>
<definition>The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.</definition>
<uris>
<uri type="URN">urn:miriam:psimi</uri>
<uri type="URL">http://identifiers.org/psimi/</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.mi/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.mi</uri>
</uris>
<namespace>psimi</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14755292</documentation>
</documentations>
<resources>
<resource id="MIR:00100142" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/mi</dataResource>
<dataEntityExample>MI:0308</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=$id</dataEntry>
<dataInfo>Molecular Interactions Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100564" obsolete="true">
<dataResource>http://bioportal.bioontology.org/ontologies/PPIO</dataResource>
<dataEntityExample>MI:0308</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/PPIO/$id</dataEntry>
<dataInfo>PSI Molecular Interactions Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="6" desc="Collection subset">
<statement>This collection is a subset of the information in the 'Protein Affinity Reagents' (PSI-PAR) collection [MIR:00000533], which should be used in preference.</statement>
<link desc="Documentation of overlap with Protein Affinity Reagents collection.">http://www.psidev.info/psi-par#cv</link>
</restriction>
</restrictions>
<tags>
<tag>interaction</tag>
<tag>ontology</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>event</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000110" pattern="^CL:\d{7}$">
<name>Cell Type Ontology</name>
<synonyms>
<synonym>Cell Ontology</synonym>
<synonym>CL</synonym>
</synonyms>
<definition>The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.</definition>
<uris>
<uri type="URN">urn:miriam:cl</uri>
<uri type="URL">http://identifiers.org/cl/</uri>
<uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/CL</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.clo/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.clo</uri>
</uris>
<namespace>cl</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15693950</documentation>
</documentations>
<resources>
<resource id="MIR:00100143" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/cl</dataResource>
<dataEntityExample>CL:0000232</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=$id</dataEntry>
<dataInfo>Cell Type Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100234" state="up" reliability="95">
<dataResource>http://bioportal.bioontology.org/ontologies/CL</dataResource>
<dataEntityExample>CL:0000232</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/CL/$id</dataEntry>
<dataInfo>Cell Type Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000111" pattern="^BTO:\d{7}$">
<name>Brenda Tissue Ontology</name>
<synonyms>
<synonym>BTO</synonym>
</synonyms>
<definition>The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.</definition>
<uris>
<uri type="URN">urn:miriam:bto</uri>
<uri type="URL">http://identifiers.org/bto/</uri>
<uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/BTO</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.bto/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.bto</uri>
</uris>
<namespace>bto</namespace>
<documentations>
<documentation type="URL">http://www.brenda-enzymes.info/</documentation>
</documentations>
<resources>
<resource id="MIR:00100144" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/bto</dataResource>
<dataEntityExample>BTO:0000146</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=$id</dataEntry>
<dataInfo>Brenda Tissue Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100233" state="up" reliability="95">
<dataResource>http://bioportal.bioontology.org/ontologies/BTO</dataResource>
<dataEntityExample>BTO:0000146</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/BTO/$id</dataEntry>
<dataInfo>Brenda Tissue Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>compartment</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000112" pattern="^PATO:\d{7}$">
<name>PATO</name>
<definition>PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.</definition>
<uris>
<uri type="URN">urn:miriam:pato</uri>
<uri type="URL">http://identifiers.org/pato/</uri>
<uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/PATO</uri>
<uri type="URL" deprecated="true">http://purl.org/obo/owl/PATO</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.pato/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.pato</uri>
</uris>
<namespace>pato</namespace>
<documentations>
<documentation type="URL">http://obofoundry.org/wiki/index.php/PATO:About</documentation>
</documentations>
<resources>
<resource id="MIR:00100145" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/pato</dataResource>
<dataEntityExample>PATO:0001998</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=$id</dataEntry>
<dataInfo>PATO through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100238" state="up" reliability="95">
<dataResource>http://bioportal.bioontology.org/ontologies/PATO</dataResource>
<dataEntityExample>PATO:0001998</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/PATO/$id</dataEntry>
<dataInfo>PATO through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>parameter</element>
<element>model</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000113" pattern="^\w{3}$">
<name>Chemical Component Dictionary</name>
<synonyms>
<synonym>PDBeChem</synonym>
<synonym>PDB-CCD</synonym>
</synonyms>
<definition>The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.</definition>
<uris>
<uri type="URN">urn:miriam:pdb-ccd</uri>
<uri type="URL">http://identifiers.org/pdb-ccd/</uri>
</uris>
<namespace>pdb-ccd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14634627</documentation>
</documentations>
<resources>
<resource id="MIR:00100146" state="up" reliability="99">
<dataResource>http://www.ebi.ac.uk/pdbe-srv/pdbechem/</dataResource>
<dataEntityExample>AB0</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id</dataEntry>
<dataInfo>Protein Data Bank Chemical Component Dictionary at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>classification</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000114" pattern="^\d+$">
<name>GlycomeDB</name>
<definition>GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.</definition>
<uris>
<uri type="URN">urn:miriam:glycomedb</uri>
<uri type="URL">http://identifiers.org/glycomedb/</uri>
</uris>
<namespace>glycomedb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19759275</documentation>
</documentations>
<resources>
<resource id="MIR:00100147" state="down" reliability="85">
<dataResource>http://www.glycome-db.org/showMenu.action?major=database</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://www.glycome-db.org/database/showStructure.action?glycomeId=$id</dataEntry>
<dataInfo>GlycomeDB carbohydrate structure database</dataInfo>
<dataInstitution>German Cancer Research Center, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000115" pattern="^\w+\d+$">
<name>LipidBank</name>
<definition>LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.</definition>
<uris>
<uri type="URN">urn:miriam:lipidbank</uri>
<uri type="URL">http://identifiers.org/lipidbank/</uri>
</uris>
<namespace>lipidbank</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12058481</documentation>
</documentations>
<resources>
<resource id="MIR:00100148" state="up" reliability="99">
<dataResource>http://lipidbank.jp/index.html</dataResource>
<dataEntityExample>BBA0001</dataEntityExample>
<dataEntry>http://lipidbank.jp/cgi-bin/detail.cgi?id=$id</dataEntry>
<dataInfo>LipidBank the Lipid database</dataInfo>
<dataInstitution>Department of Computational Biology, University of Tokyo, Tokyo</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>lipid</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000116" pattern="^K\d+$">
<name>KEGG Orthology</name>
<!--<synonyms>-->
<!--<synonym>KEGG</synonym>-->
<!--</synonyms>-->
<definition>KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.orthology</uri>
<uri type="URL">http://identifiers.org/kegg.orthology/</uri>
</uris>
<namespace>kegg.orthology</namespace>
<documentations>
<documentation type="URL">http://www.genome.jp/kegg/ko.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100149" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/ko.html</dataResource>
<dataEntityExample>K00001</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG Orthology Database</dataInfo>
<dataInstitution>Department of Computational Biology, University of Tokyo, Tokyo</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000117" pattern="^PD\d+$">
<name>ProDom</name>
<definition>ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.</definition>
<uris>
<uri type="URN">urn:miriam:prodom</uri>
<uri type="URL">http://identifiers.org/prodom/</uri>
</uris>
<namespace>prodom</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608179</documentation>
</documentations>
<resources>
<resource id="MIR:00100150" state="up" reliability="93">
<dataResource>http://prodom.prabi.fr/prodom/current/html/home.php</dataResource>
<dataEntityExample>PD10000</dataEntityExample>
<dataEntry>http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$id</dataEntry>
<dataInfo>ProDom Protein Domain Database</dataInfo>
<dataInstitution>Laboratoire des Interactions Plantes-Microorganismes, INRA/CNRS</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000118" pattern="^SM\d{5}$">
<name>SMART</name>
<definition>The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.</definition>
<uris>
<uri type="URN">urn:miriam:smart</uri>
<uri type="URL">http://identifiers.org/smart/</uri>
</uris>
<namespace>smart</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:9847187</documentation>
</documentations>
<resources>
<resource id="MIR:00100151" state="up" reliability="99">
<dataResource>http://smart.embl-heidelberg.de/</dataResource>
<dataEntityExample>SM00015</dataEntityExample>
<dataEntry>http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id</dataEntry>
<dataInfo>SMART (Simple Modular Architecture Research Tool)</dataInfo>
<dataInstitution>EMBL, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>gene</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000119" pattern="^(cd)?\d{5}$">
<name>Conserved Domain Database</name>
<synonyms>
<synonym>CDD</synonym>
</synonyms>
<definition>The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.</definition>
<uris>
<uri type="URN">urn:miriam:cdd</uri>
<uri type="URL">http://identifiers.org/cdd/</uri>
</uris>
<namespace>cdd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18984618</documentation>
</documentations>
<resources>
<resource id="MIR:00100152" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd</dataResource>
<dataEntityExample>cd00400</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$id</dataEntry>
<dataInfo>Conserved Domain Database at NCBI</dataInfo>
<dataInstitution>National Library of Medicine, National Institutes of Health, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000120" pattern="^RO_\d+{7}$">
<name>Relation Ontology</name>
<definition>The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.</definition>
<uris>
<uri type="URN">urn:miriam:ro</uri>
<uri type="URL">http://identifiers.org/ro/</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.ro/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.ro</uri>
</uris>
<namespace>ro</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15892874</documentation>
</documentations>
<resources>
<resource id="MIR:00100764" state="up" reliability="97">
<dataResource>http://obofoundry.org/ontology/ro.html</dataResource>
<dataEntityExample>RO_0002533</dataEntityExample>
<dataEntry>http://purl.obolibrary.org/obo/$id</dataEntry>
<dataInfo>OBO Relation Ontology through OntoBee</dataInfo>
<dataInstitution>University of Michigan Medical School (MI), Lawrence Berkeley National Laboratory (CA) and Science Commons (MA)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100767" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/ro</dataResource>
<dataEntityExample>RO_0002533</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/ro/terms?short_form=$id</dataEntry>
<dataInfo>OBO Relation Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100153" obsolete="true">
<dataResource>http://www.obofoundry.org/ro/</dataResource>
<dataEntityExample>OBO_REL:is_a</dataEntityExample>
<dataEntry>http://www.obofoundry.org/ro/#$id</dataEntry>
<dataInfo>OBO Relation Ontology</dataInfo>
<dataInstitution>Institute for Formal Ontology and Medical Information Science, Saarbrücken</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
</datatype>
<datatype id="MIR:00000121" pattern="^\d{1,5}$">
<name>Molecular Modeling Database</name>
<synonyms>
<synonym>MMDB</synonym>
<synonym>Entrez Structure</synonym>
</synonyms>
<definition>The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.</definition>
<uris>
<uri type="URN">urn:miriam:mmdb</uri>
<uri type="URL">http://identifiers.org/mmdb/</uri>
</uris>
<namespace>mmdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17135201</documentation>
</documentations>
<resources>
<resource id="MIR:00100154" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure</dataResource>
<dataEntityExample>50885</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$id</dataEntry>
<dataInfo>MMDB at NCBI</dataInfo>
<dataInstitution>National Library of Medicine, National Institutes of Health, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000122" pattern="^IM-\d+(-?)(\d+?)$">
<name>IMEx</name>
<definition>The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.</definition>
<uris>
<uri type="URN">urn:miriam:imex</uri>
<uri type="URL">http://identifiers.org/imex/</uri>
</uris>
<namespace>imex</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17893861</documentation>
</documentations>
<resources>
<resource id="MIR:00100155" state="up" reliability="96">
<dataResource>http://www.imexconsortium.org/</dataResource>
<dataEntityExample>IM-19210-3</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$id</dataEntry>
<dataInfo>IMEx Consortium running at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100663" state="up" reliability="97">
<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
<dataEntityExample>IM-19210-3</dataEntityExample>
<dataEntry>https://imexcentral.org/icentral/imex/rec/$id</dataEntry>
<dataInfo>IMEx Consortium though Intact</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000123" pattern="^\d+$">
<name>iRefWeb</name>
<definition>iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.</definition>
<uris>
<uri type="URN">urn:miriam:irefweb</uri>
<uri type="URL">http://identifiers.org/irefweb/</uri>
</uris>
<namespace>irefweb</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1186%2F1471-2105-9-405</documentation>
<documentation type="URL">http://irefindex.uio.no/wiki/iRefIndex</documentation>
</documentations>
<resources>
<resource id="MIR:00100156" state="up" reliability="98">
<dataResource>http://wodaklab.org/iRefWeb/</dataResource>
<dataEntityExample>617102</dataEntityExample>
<dataEntry>http://wodaklab.org/iRefWeb/interaction/show/$id</dataEntry>
<dataInfo>iRefWeb Protein Interaction Reference Index</dataInfo>
<dataInstitution>Wodak Lab, Hospital for Sick Children, Toronto</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000124" pattern="^\d+$">
<name>Microbial Protein Interaction Database</name>
<synonyms>
<synonym>MPID</synonym>
</synonyms>
<definition>The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.</definition>
<uris>
<uri type="URN">urn:miriam:mpid</uri>
<uri type="URL">http://identifiers.org/mpid/</uri>
</uris>
<namespace>mpid</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18556668</documentation>
</documentations>
<resources>
<resource id="MIR:00100157" state="down" reliability="85">
<dataResource>http://www.jcvi.org/mpidb/about.php</dataResource>
<dataEntityExample>172</dataEntityExample>
<dataEntry>http://www.jcvi.org/mpidb/experiment.php?interaction_id=$id</dataEntry>
<dataInfo>Microbial Protein Interaction Database</dataInfo>
<dataInstitution>J. Craig Venter Institute, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100655" state="up" reliability="99">
<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
<dataEntityExample>1776</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$id</dataEntry>
<dataInfo>Microbial Protein Interaction Database subset through IntAct</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>microbial</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000125" pattern="^\d+$">
<name>PhosphoSite Residue</name>
<definition>PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.</definition>
<uris>
<uri type="URN">urn:miriam:phosphosite.residue</uri>
<uri type="URL">http://identifiers.org/phosphosite.residue/</uri>
</uris>
<namespace>phosphosite.residue</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12478304</documentation>
</documentations>
<resources>
<resource id="MIR:00100159" state="up" reliability="99">
<dataResource>http://www.phosphosite.org/homeAction.do</dataResource>
<dataEntityExample>2842</dataEntityExample>
<dataEntry>http://www.phosphosite.org/siteAction.do?id=$id</dataEntry>
<dataInfo>PhosphoSite Residue</dataInfo>
<dataInstitution>Cell Signaling Technology, Inc.</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000126" pattern="^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$">
<name>NeuroLex</name>
<synonyms>
<synonym>BIRNLex</synonym>
<synonym>NIFSTD</synonym>
</synonyms>
<definition>The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex).</definition>
<uris>
<uri type="URN">urn:miriam:neurolex</uri>
<uri type="URL">http://identifiers.org/neurolex/</uri>
</uris>
<namespace>neurolex</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18975148</documentation>
</documentations>
<resources>
<resource id="MIR:00100160" state="down" reliability="91" primary="true">
<dataResource>http://www.neurolex.org/wiki/Main_Page</dataResource>
<dataEntityExample>Birnlex_721</dataEntityExample>
<dataEntry>http://www.neurolex.org/wiki/$id</dataEntry>
<dataInfo>NeuroLex Neuroscience Lexicon</dataInfo>
<dataInstitution>Department of Neuroscience, University of California, San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100183" state="up" reliability="97">
<dataResource>http://bioportal.bioontology.org/ontologies/BIRNLEX</dataResource>
<dataEntityExample>birnlex_1672</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/BIRNLEX/$id</dataEntry>
<dataInfo>NeuroLex through NCBO's BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>controlled vocabulary</tag>
<tag>neuroscience</tag>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000127" pattern="(^OBI:\d{7}$)|(^OBI_\d{7}$)">
<name>Ontology for Biomedical Investigations</name>
<synonyms>
<synonym>OBI</synonym>
</synonyms>
<definition>The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).</definition>
<uris>
<uri type="URN">urn:miriam:obi</uri>
<uri type="URL">http://identifiers.org/obi/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.obi</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.obi/</uri>
</uris>
<namespace>obi</namespace>
<documentations>
<documentation type="URL">http://www.jbiomedsem.com/content/1/S1/S7</documentation>
<documentation type="URL">http://purl.obolibrary.org/obo/obi</documentation>
</documentations>
<resources>
<resource id="MIR:00100162" state="up" reliability="91" primary="true">
<dataResource>http://www.ontobee.org/</dataResource>
<dataEntityExample>OBI_0000070</dataEntityExample>
<dataEntry>http://purl.obolibrary.org/obo/$id</dataEntry>
<dataInfo>OBI through Ontobee</dataInfo>
<dataInstitution>University of Michigan Medical School (MI), awrence Berkeley National Laboratory (CA) and Science Commons (MA)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100177" state="probably up" reliability="68">
<dataResource>http://bioportal.bioontology.org/ontologies/OBI</dataResource>
<dataEntityExample>OBI:0000070</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/OBI/$id</dataEntry>
<dataInfo>Ontology for Biomedical Investigations through Bioportal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100760" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/obi</dataResource>
<dataEntityExample>OBI:0000070</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/obi/terms?obo_id=$id</dataEntry>
<dataInfo>OBI through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100161" obsolete="true">
<dataResource>http://obi-ontology.org/page/Main_Page</dataResource>
<dataEntityExample>OBI:0000225</dataEntityExample>
<dataEntry>http://ashby.csail.mit.edu/cgi-bin/obiterm?ref=$id</dataEntry>
<dataInfo>OBI at MIT</dataInfo>
<dataInstitution>Massachusetts Institute of Technology (MIT)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100759" obsolete="true">
<dataResource>https://www.ebi.ac.uk/ols/beta/ontologies/obi</dataResource>
<dataEntityExample>OBI:0000070</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/beta/ontologies/obi/terms?obo_id=$id</dataEntry>
<dataInfo>OBI through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000128" pattern="^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$">
<name>SABIO-RK EC Record</name>
<synonyms>
<synonym>SABIO-RK Enzyme Classification Record</synonym>
</synonyms>
<definition>SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data.</definition>
<uris>
<uri type="URN">urn:miriam:sabiork.ec</uri>
<uri type="URL">http://identifiers.org/sabiork.ec/</uri>
</uris>
<namespace>sabiork.ec</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17822389</documentation>
<documentation type="DOI">urn:miriam:doi:10.2390%2Fbiecoll-jib-2007-49</documentation>
<documentation type="DOI">urn:miriam:doi:10.1186%2F1752-0509-1-S1-S6</documentation>
<documentation type="DOI">urn:miriam:doi:10.1007%2F11799511_9</documentation>
<documentation type="DOI">urn:miriam:doi:10.1186%2F1752-0509-1-S1-P4</documentation>
</documentations>
<resources>
<resource id="MIR:00100163" state="probably up" reliability="98">
<dataResource>http://sabiork.h-its.org/</dataResource>
<dataEntityExample>2.7.1.1</dataEntityExample>
<dataEntry>http://sabiork.h-its.org/newSearch?q=ecnumber:$id</dataEntry>
<dataInfo>SABIO-RK Reaction Kinetics Database - Enzyme Classification (EC)</dataInfo>
<dataInstitution>Heidelberg Institute for Theoretical Studies (HITS gGmbH)</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>enzyme</tag>
<tag>kinetics</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
<element>event</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000129" pattern="^OPB_\d+$">
<name>Ontology of Physics for Biology</name>
<synonyms>
<synonym>OPB</synonym>
</synonyms>
<definition>The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.</definition>
<uris>
<uri type="URN">urn:miriam:opb</uri>
<uri type="URL">http://identifiers.org/opb/</uri>
</uris>
<namespace>opb</namespace>
<documentations>
<documentation type="URL">http://sig.biostr.washington.edu/projects/biosim/opb-intro.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100167" state="down" reliability="61">
<dataResource>http://bioportal.bioontology.org/ontologies/OPB</dataResource>
<dataEntityExample>OPB_00573</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$id</dataEntry>
<dataInfo>Ontology of Physics for Biology through Bioportal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>parameter</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000130" pattern="^\w+$">
<name>JWS Online</name>
<synonyms>
<synonym>JWS</synonym>
</synonyms>
<definition>JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.</definition>
<uris>
<uri type="URN">urn:miriam:jws</uri>
<uri type="URL">http://identifiers.org/jws/</uri>
</uris>
<namespace>jws</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15072998</documentation>
</documentations>
<resources>
<resource id="MIR:00100168" state="up" reliability="95">
<dataResource>http://jjj.biochem.sun.ac.za/models/</dataResource>
<dataEntityExample>curien</dataEntityExample>
<dataEntry>http://jjj.biochem.sun.ac.za/models/$id/</dataEntry>
<dataInfo>JWS Online Model Repository at Stellenbosch</dataInfo>
<dataInstitution>Department of Biochemistry, Stellenbosch University</dataInstitution>
<dataLocation>South Africa</dataLocation>
</resource>
<resource id="MIR:00100169" state="down" reliability="71">
<dataResource>http://jjj.bio.vu.nl/models/</dataResource>
<dataEntityExample>curien</dataEntityExample>
<dataEntry>http://jjj.bio.vu.nl/models/$id/</dataEntry>
<dataInfo>JWS Online Model Repository at Amsterdam</dataInfo>
<dataInstitution>University of Amsterdam</dataInstitution>
<dataLocation>Netherlands</dataLocation>
</resource>
<resource id="MIR:00100170" state="up" reliability="76">
<dataResource>http://jjj.mib.ac.uk/index.html</dataResource>
<dataEntityExample>curien</dataEntityExample>
<dataEntry>http://jjj.mib.ac.uk/models/$id</dataEntry>
<dataInfo>JWS Online Model Repository at Manchester</dataInfo>
<dataInstitution>Manchester Interdisciplinary Biocentre, University of Manchester</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>model</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000131" pattern="^\d+$">
<name>ModelDB</name>
<definition>ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.</definition>
<uris>
<uri type="URN">urn:miriam:modeldb</uri>
<uri type="URL">http://identifiers.org/modeldb/</uri>
</uris>
<namespace>modeldb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15055399</documentation>
</documentations>
<resources>
<resource id="MIR:00100171" state="up" reliability="98">
<dataResource>http://senselab.med.yale.edu/ModelDB/</dataResource>
<dataEntityExample>45539</dataEntityExample>
<dataEntry>http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$id</dataEntry>
<dataInfo>ModelDB at SenseLab</dataInfo>
<dataInstitution>Yale University School of Medicine</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>model</tag>
<tag>neuroscience</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000132" pattern="^BSU\d{5}$">
<name>SubtiWiki</name>
<definition>SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein.
Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon.</definition>
<uris>
<uri type="URN">urn:miriam:subtiwiki</uri>
<uri type="URL">http://identifiers.org/subtiwiki/</uri>
</uris>
<namespace>subtiwiki</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19959575</documentation>
<documentation type="PMID">urn:miriam:pubmed:20157485</documentation>
</documentations>
<resources>
<resource id="MIR:00100172" state="up" reliability="99">
<dataResource>http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page</dataResource>
<dataEntityExample>BSU29180</dataEntityExample>
<dataEntry>http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id</dataEntry>
<dataInfo>SubtiWiki website</dataInfo>
<dataInstitution>University of Göttingen, Department for General Microbiology</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>genome</tag>
<tag>microbial</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000133" pattern="^\w+$">
<name>NCI Pathway Interaction Database: Pathway</name>
<synonyms>
<synonym>NCI_Nature</synonym>
<synonym>PID</synonym>
<synonym>Pathway Interaction Database NCI-Nature Curated Data</synonym>
<synonym>NCI-Nature PID</synonym>
<synonym>NCI-Nature Pathway Interaction Database</synonym>
<synonym>NCI_Nature curated</synonym>
</synonyms>
<definition>The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information.</definition>
<uris>
<uri type="URN">urn:miriam:pid.pathway</uri>
<uri type="URL">http://identifiers.org/pid.pathway/</uri>
</uris>
<namespace>pid.pathway</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18832364</documentation>
</documentations>
<resources>
<resource id="MIR:00100173" state="down" reliability="69">
<dataResource>http://pid.nci.nih.gov/</dataResource>
<dataEntityExample>pi3kcipathway</dataEntityExample>
<dataEntry>http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$id</dataEntry>
<dataInfo>NCI Pathway Interaction Database (Pathway)</dataInfo>
<dataInstitution>National Cancer Institute, Rockville, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>interaction</tag>
<tag>pathway</tag>
</tags>
</datatype>
<datatype id="MIR:00000134" pattern="^\d+$">
<name>Database of Quantitative Cellular Signaling: Model</name>
<synonyms>
<synonym>DOQCS Model</synonym>
</synonyms>
<definition>The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models.</definition>
<uris>
<uri type="URN">urn:miriam:doqcs.model</uri>
<uri type="URL">http://identifiers.org/doqcs.model/</uri>
</uris>
<namespace>doqcs.model</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12584128</documentation>
</documentations>
<resources>
<resource id="MIR:00100174" state="up" reliability="96">
<dataResource>http://doqcs.ncbs.res.in/</dataResource>
<dataEntityExample>57</dataEntityExample>
<dataEntry>http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$id</dataEntry>
<dataInfo>Database of Quantitative Cellular Signaling (DOQCS) - Model Access</dataInfo>
<dataInstitution>National Centre for Biological Sciences, Bangalore</dataInstitution>
<dataLocation>India</dataLocation>
</resource>
</resources>
<tags>
<tag>model</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000135" pattern="^\d+$">
<name>Database of Quantitative Cellular Signaling: Pathway</name>
<synonyms>
<synonym>DOQCS Pathway</synonym>
</synonyms>
<definition>The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways.</definition>
<uris>
<uri type="URN">urn:miriam:doqcs.pathway</uri>
<uri type="URL">http://identifiers.org/doqcs.pathway/</uri>
</uris>
<namespace>doqcs.pathway</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12584128</documentation>
</documentations>
<resources>
<resource id="MIR:00100175" state="up" reliability="96">
<dataResource>http://doqcs.ncbs.res.in/</dataResource>
<dataEntityExample>131</dataEntityExample>
<dataEntry>http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$id</dataEntry>
<dataInfo>Database of Quantitative Cellular Signaling (DOQCS) - Pathway Access</dataInfo>
<dataInstitution>National Centre for Biological Sciences, Bangalore</dataInstitution>
<dataLocation>India</dataLocation>
</resource>
</resources>
<tags>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000136" pattern="^UO:\d{7}?">
<name>Unit Ontology</name>
<synonyms>
<synonym>UO</synonym>
</synonyms>
<definition>Ontology of standardized units</definition>
<uris>
<uri type="URN">urn:miriam:uo</uri>
<uri type="URL">http://identifiers.org/uo/</uri>
<uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/UO</uri>
<uri type="URL" deprecated="true">http://identifiers.org/unit/</uri>
<uri type="URN" deprecated="true">urn:miriam:unit</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.unit</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.unit/</uri>
</uris>
<namespace>uo</namespace>
<resources>
<resource id="MIR:00100178" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/uo</dataResource>
<dataEntityExample>UO:0000080</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=$id</dataEntry>
<dataInfo>Unit Ontology via Ontology Lookup Service</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100243" state="up" reliability="97">
<dataResource>http://bioportal.bioontology.org/ontologies/UO</dataResource>
<dataEntityExample>UO:0000080</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/UO/$id</dataEntry>
<dataInfo>Unit Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
</datatype>
<datatype id="MIR:00000137" pattern="^NCT\d{8}$">
<name>ClinicalTrials.gov</name>
<synonyms>
<synonym>NCT</synonym>
</synonyms>
<definition>ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries</definition>
<uris>
<uri type="URN">urn:miriam:clinicaltrials</uri>
<uri type="URL">http://identifiers.org/clinicaltrials/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/clinicaltrials</uri>
</uris>
<namespace>clinicaltrials</namespace>
<documentations>
<documentation type="URL">http://clinicaltrials.gov/ct2/info/about</documentation>
</documentations>
<resources>
<resource id="MIR:00100179" state="up" reliability="92" primary="true">
<dataResource>http://clinicaltrials.gov/</dataResource>
<dataEntityExample>NCT00222573</dataEntityExample>
<dataEntry>http://clinicaltrials.gov/ct2/show/$id</dataEntry>
<dataInfo>ClinicalTrials.gov at NIH</dataInfo>
<dataInstitution>National Library of Medicine and ClinicalTrials.gov, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100692" state="down" reliability="82">
<dataResource>http://clinicaltrials.bio2rdf.org/fct</dataResource>
<dataEntityExample>NCT00222573</dataEntityExample>
<dataEntry>http://clinicaltrials.bio2rdf.org/describe/?url=http://bio2rdf.org/clinicaltrials:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
<tag>disorder</tag>
<tag>human</tag>
<tag>pharmacogenomics</tag>
</tags>
</datatype>
<datatype id="MIR:00000138" pattern="^\d+$">
<name>ChemSpider</name>
<definition>ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.</definition>
<uris>
<uri type="URN">urn:miriam:chemspider</uri>
<uri type="URL">http://identifiers.org/chemspider/</uri>
</uris>
<namespace>chemspider</namespace>
<documentations>
<documentation type="URL">http://www.chemspider.com/About.aspx</documentation>
</documentations>
<resources>
<resource id="MIR:00100180" state="up" reliability="99">
<dataResource>http://www.chemspider.com/</dataResource>
<dataEntityExample>56586</dataEntityExample>
<dataEntry>http://www.chemspider.com/Chemical-Structure.$id.html</dataEntry>
<dataInfo>ChemSpider at RSC</dataInfo>
<dataInstitution>Royal Society of Chemistry, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000139" pattern="^C\d+$">
<name>NCIt</name>
<synonyms>
<synonym>NCI thesaurus</synonym>
<synonym>National Cancer Institute Thesaurus</synonym>
</synonyms>
<definition>NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code.</definition>
<uris>
<uri type="URN">urn:miriam:ncit</uri>
<uri type="URL">http://identifiers.org/ncit/</uri>
</uris>
<namespace>ncit</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19789731</documentation>
<documentation type="URL">http://ncit.nci.nih.gov/ncitbrowser/pages/help.jsf</documentation>
</documentations>
<resources>
<resource id="MIR:00100181" state="probably up" reliability="58">
<dataResource>http://ncit.nci.nih.gov/</dataResource>
<dataEntityExample>C80519</dataEntityExample>
<dataEntry>http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$id</dataEntry>
<dataInfo>NCIt at National Cancer Institute</dataInfo>
<dataInstitution>National Cancer Institute, Center for Bioinformatics, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100868" state="unknown" reliability="0">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/ncit</dataResource>
<dataEntityExample>C16353</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/ncit/terms?short_form=NCIT_$id</dataEntry>
<dataInfo>NCIt through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>controlled vocabulary</tag>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>compartment</element>
<element>species</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000140" pattern="^\d+$">
<name>BioCatalogue</name>
<definition>The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all.</definition>
<uris>
<uri type="URN">urn:miriam:biocatalogue.service</uri>
<uri type="URL">http://identifiers.org/biocatalogue.service/</uri>
</uris>
<namespace>biocatalogue.service</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20484378</documentation>
<documentation type="URL">http://www.biocatalogue.org/wiki/</documentation>
</documentations>
<resources>
<resource id="MIR:00100182" state="up" reliability="94">
<dataResource>http://www.biocatalogue.org/</dataResource>
<dataEntityExample>614</dataEntityExample>
<dataEntry>https://www.biocatalogue.org/services/$id</dataEntry>
<dataInfo>BioCatalogue at EMBL-EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>registry</tag>
</tags>
</datatype>
<datatype id="MIR:00000141" pattern="^PR\:P?\d+$">
<name>Protein Ontology</name>
<definition>The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies.</definition>
<uris>
<uri type="URN">urn:miriam:pr</uri>
<uri type="URL">http://identifiers.org/pr/</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.pr/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.pr</uri>
</uris>
<namespace>pr</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18047702</documentation>
<documentation type="URL">https://pir5.georgetown.edu/wiki/PRO</documentation>
</documentations>
<resources>
<resource id="MIR:00100184" state="down" reliability="93">
<dataResource>http://pir.georgetown.edu/pro/pro.shtml</dataResource>
<dataEntityExample>PR:000000024</dataEntityExample>
<dataEntry>http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=$id</dataEntry>
<dataInfo>Protein Ontology at Georgetown</dataInfo>
<dataInstitution>Georgetown University Medical Center, Washington</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100240" state="up" reliability="87">
<dataResource>http://bioportal.bioontology.org/ontologies/PR</dataResource>
<dataEntityExample>PR:000000024</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/PR/$id</dataEntry>
<dataInfo>Protein Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100755" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/pr</dataResource>
<dataEntityExample>PR:000000024</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/pr/terms?obo_id=$id</dataEntry>
<dataInfo>Protein Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>speciesType</element>
</elements>
</format>
<format name="BioPAX">
<elements>
<element>physicalEntity</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000142" pattern="^\d+$">
<name>OMIA</name>
<synonyms>
<synonym>Online Mendelian Inheritance in Animals</synonym>
</synonyms>
<definition>Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse).</definition>
<uris>
<uri type="URN">urn:miriam:omia</uri>
<uri type="URL">http://identifiers.org/omia/</uri>
</uris>
<namespace>omia</namespace>
<documentations>
<documentation type="URL">http://omia.angis.org.au/</documentation>
</documentations>
<resources>
<resource id="MIR:00100185" state="up" reliability="99">
<dataResource>http://omia.angis.org.au/</dataResource>
<dataEntityExample>1000</dataEntityExample>
<dataEntry>http://omia.angis.org.au/$id/</dataEntry>
<dataInfo>OMIA at University of Sydney</dataInfo>
<dataInstitution>Reprogen, Faculty of Veterinary Science, University of Sydney</dataInstitution>
<dataLocation>Australia</dataLocation>
</resource>
<resource id="MIR:00100186" obsolete="true">
<dataResource>http://www.ncbi.nlm.nih.gov/sites/entrez?db=omia</dataResource>
<dataEntityExample>1000</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=omia&dopt=Detailed&list_uids=$id</dataEntry>
<dataInfo>OMIA at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>disorder</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000143" pattern="^\d+$">
<name>ChemBank</name>
<definition>ChemBank stores small molecule information, as well as measurements derived from cells and other biological assay systems treated with small molecules.</definition>
<uris>
<uri type="URN">urn:miriam:chembank</uri>
<uri type="URL">http://identifiers.org/chembank/</uri>
</uris>
<namespace>chembank</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17947324</documentation>
</documentations>
<resources>
<resource id="MIR:00100187" state="up" reliability="98">
<dataResource>http://chembank.broadinstitute.org/</dataResource>
<dataEntityExample>1000000</dataEntityExample>
<dataEntry>http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$id</dataEntry>
<dataInfo>ChemBank at Broad Institute</dataInfo>
<dataInstitution>Broad Institute of Harvard and MIT, Cambridge, MA</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>metabolite</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000144" pattern="^[0-9][A-Za-z0-9]{3}$">
<name>CSA</name>
<synonyms>
<synonym>Catalytic Site Atlas</synonym>
</synonyms>
<definition>The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.</definition>
<uris>
<uri type="URN">urn:miriam:csa</uri>
<uri type="URL">http://identifiers.org/csa/</uri>
</uris>
<namespace>csa</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681376</documentation>
</documentations>
<resources>
<resource id="MIR:00100188" state="up" reliability="97">
<dataResource>http://www.ebi.ac.uk/thornton-srv/databases/CSA/</dataResource>
<dataEntityExample>1a05</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$id</dataEntry>
<dataInfo>CSA at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000145" pattern="^CAL\d{7}$">
<name>Candida Genome Database</name>
<synonyms>
<synonym>CGD</synonym>
</synonyms>
<definition>The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.</definition>
<uris>
<uri type="URN">urn:miriam:cgd</uri>
<uri type="URL">http://identifiers.org/cgd/</uri>
</uris>
<namespace>cgd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608216</documentation>
</documentations>
<resources>
<resource id="MIR:00100189" state="up" reliability="99">
<dataResource>http://www.candidagenome.org/</dataResource>
<dataEntityExample>CAL0003079</dataEntityExample>
<dataEntry>http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$id</dataEntry>
<dataInfo>Candida Genome Database at Stanford University</dataInfo>
<dataInstitution>Stanford University,</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>parameter</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000146" pattern="^casent\d+(\-D\d+)?$">
<name>AntWeb</name>
<definition>AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.</definition>
<uris>
<uri type="URN">urn:miriam:antweb</uri>
<uri type="URL">http://identifiers.org/antweb/</uri>
</uris>
<namespace>antweb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12867945</documentation>
</documentations>
<resources>
<resource id="MIR:00100190" state="up" reliability="96">
<dataResource>http://www.antweb.org/</dataResource>
<dataEntityExample>casent0106247</dataEntityExample>
<dataEntry>http://www.antweb.org/specimen.do?name=$id</dataEntry>
<dataInfo>AntWeb at California Academy of Sciences</dataInfo>
<dataInstitution>California Academy of Sciences, Goldengate Park, San Francisco</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000147" pattern="PMC\d+">
<name>PMC International</name>
<synonyms>
<synonym>PubMed Central</synonym>
<synonym>PMCI</synonym>
</synonyms>
<definition>PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.</definition>
<uris>
<uri type="URN">urn:miriam:pmc</uri>
<uri type="URL">http://identifiers.org/pmc/</uri>
</uris>
<namespace>pmc</namespace>
<resources>
<resource id="MIR:00100191" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/pmc/</dataResource>
<dataEntityExample>PMC3084216</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/pmc/articles/$id/?tool=pubmed</dataEntry>
<dataInfo>PubMed Central</dataInfo>
<dataInstitution>NCBI</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100498" state="up" reliability="99" primary="true">
<dataResource>http://europepmc.org/</dataResource>
<dataEntityExample>PMC3084216</dataEntityExample>
<dataEntry>http://europepmc.org/articles/$id</dataEntry>
<dataInfo>Europe PMC</dataInfo>
<dataInstitution>Europe PubMed Central partners</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100747" state="down" reliability="90">
<dataResource>http://pubmedcentralcanada.ca/pmcc</dataResource>
<dataEntityExample>PMC3084216</dataEntityExample>
<dataEntry>http://pubmedcentralcanada.ca/pmcc/articles/$id</dataEntry>
<dataInfo>PubMedCentral Canada</dataInfo>
<dataInstitution>Canadian Institute of Health, Ottawa</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
<resource id="MIR:00100192" obsolete="true">
<dataResource>http://ukpmc.ac.uk/</dataResource>
<dataEntityExample>PMC3084216</dataEntityExample>
<dataEntry>http://ukpmc.ac.uk/articles/$id</dataEntry>
<dataInfo>PMC through UK PubMed Central</dataInfo>
<dataInstitution>UKPMC Funders Group</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>bibliography</tag>
<tag>schema.org</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>parameter</element>
<element>reaction</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000148" pattern="^EDI_\d+$">
<name>AmoebaDB</name>
<definition>AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.</definition>
<uris>
<uri type="URN">urn:miriam:amoebadb</uri>
<uri type="URL">http://identifiers.org/amoebadb/</uri>
</uris>
<namespace>amoebadb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19914931</documentation>
</documentations>
<resources>
<resource id="MIR:00100193" state="down" reliability="77">
<dataResource>http://amoebadb.org/amoeba/</dataResource>
<dataEntityExample>EDI_244000</dataEntityExample>
<dataEntry>http://amoebadb.org/amoeba/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id</dataEntry>
<dataInfo>AmoebaDB at EuPathDB</dataInfo>
<dataInstitution>Center for Tropical & Emerging Global Diseases, University of Georgia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
</tags>
</datatype>
<datatype id="MIR:00000149" pattern="^\w+">
<name>CryptoDB</name>
<definition>CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.</definition>
<uris>
<uri type="URN">urn:miriam:cryptodb</uri>
<uri type="URL">http://identifiers.org/cryptodb/</uri>
</uris>
<namespace>cryptodb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381902</documentation>
</documentations>
<resources>
<resource id="MIR:00100194" state="down" reliability="76">
<dataResource>http://cryptodb.org/cryptodb/</dataResource>
<dataEntityExample>cgd7_230</dataEntityExample>
<dataEntry>http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id</dataEntry>
<dataInfo>CryptoDB at EuPathDB</dataInfo>
<dataInstitution>Center for Tropical & Emerging Global Diseases, University of Georgia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000150" pattern="^\w+$">
<name>PlasmoDB</name>
<definition>AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.</definition>
<uris>
<uri type="URN">urn:miriam:plasmodb</uri>
<uri type="URL">http://identifiers.org/plasmodb/</uri>
</uris>
<namespace>plasmodb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18957442</documentation>
</documentations>
<resources>
<resource id="MIR:00100195" state="down" reliability="76">
<dataResource>http://plasmodb.org/plasmo/</dataResource>
<dataEntityExample>PF11_0344</dataEntityExample>
<dataEntry>http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id</dataEntry>
<dataInfo>PlasmoDB at EuPathDB</dataInfo>
<dataInstitution>Center for Tropical & Emerging Global Diseases, University of Georgia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000151" pattern="^\w+$">
<name>GiardiaDB</name>
<definition>GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.</definition>
<uris>
<uri type="URN">urn:miriam:giardiadb</uri>
<uri type="URL">http://identifiers.org/giardiadb/</uri>
</uris>
<namespace>giardiadb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18824479</documentation>
</documentations>
<resources>
<resource id="MIR:00100196" state="down" reliability="77">
<dataResource>http://giardiadb.org/giardiadb/</dataResource>
<dataEntityExample>GL50803_102438</dataEntityExample>
<dataEntry>http://giardiadb.org/giardiadb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id</dataEntry>
<dataInfo>GiardiaDB at EuPathDB</dataInfo>
<dataInstitution>Center for Tropical & Emerging Global Diseases, University of Georgia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000152" pattern="^\w+$">
<name>MicrosporidiaDB</name>
<definition>MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.</definition>
<uris>
<uri type="URN">urn:miriam:microsporidia</uri>
<uri type="URL">http://identifiers.org/microsporidia/</uri>
</uris>
<namespace>microsporidia</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19914931</documentation>
</documentations>
<resources>
<resource id="MIR:00100197" state="down" reliability="77">
<dataResource>http://microsporidiadb.org/micro/</dataResource>
<dataEntityExample>ECU03_0820i</dataEntityExample>
<dataEntry>http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id</dataEntry>
<dataInfo>MicrosporidiaDB at EuPathDB</dataInfo>
<dataInstitution>Center for Tropical & Emerging Global Diseases, University of Georgia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000153" pattern="^\w+$">
<name>ToxoDB</name>
<definition>ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.</definition>
<uris>
<uri type="URN">urn:miriam:toxoplasma</uri>
<uri type="URL">http://identifiers.org/toxoplasma/</uri>
</uris>
<namespace>toxoplasma</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18003657</documentation>
</documentations>
<resources>
<resource id="MIR:00100198" state="down" reliability="76">
<dataResource>http://toxodb.org/toxo/</dataResource>
<dataEntityExample>TGME49_053730</dataEntityExample>
<dataEntry>http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id</dataEntry>
<dataInfo>ToxoDB at EuPathDB</dataInfo>
<dataInstitution>Center for Tropical & Emerging Global Diseases, University of Georgia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000154" pattern="^\w+$">
<name>TrichDB</name>
<definition>TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.</definition>
<uris>
<uri type="URN">urn:miriam:trichdb</uri>
<uri type="URL">http://identifiers.org/trichdb/</uri>
</uris>
<namespace>trichdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18824479</documentation>
</documentations>
<resources>
<resource id="MIR:00100199" state="down" reliability="76">
<dataResource>http://trichdb.org/trichdb/</dataResource>
<dataEntityExample>TVAG_386080</dataEntityExample>
<dataEntry>http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id</dataEntry>
<dataInfo>TrichDB at EuPathDB</dataInfo>
<dataInstitution>Center for Tropical & Emerging Global Diseases, University of Georgia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000155" pattern="^\w+(\.)?\w+(\.)?\w+">
<name>TriTrypDB</name>
<synonyms>
<synonym>Kinetoplastid Genomics Resource</synonym>
</synonyms>
<definition>TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.</definition>
<uris>
<uri type="URN">urn:miriam:tritrypdb</uri>
<uri type="URL">http://identifiers.org/tritrypdb/</uri>
</uris>
<namespace>tritrypdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19843604</documentation>
</documentations>
<resources>
<resource id="MIR:00100200" state="down" reliability="69">
<dataResource>http://tritrypdb.org/tritrypdb/</dataResource>
<dataEntityExample>Tb927.8.620</dataEntityExample>
<dataEntry>http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id</dataEntry>
<dataInfo>TriTrypDB at EuPathDB</dataInfo>
<dataInstitution>Wellcome Trust Sanger Institute, Hinxton</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000156" pattern="^\w+$">
<name>BDGP insertion DB</name>
<synonyms>
<synonym>BDGP gene disruption</synonym>
</synonyms>
<definition>BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.</definition>
<uris>
<uri type="URN">urn:miriam:bdgp.insertion</uri>
<uri type="URL">http://identifiers.org/bdgp.insertion/</uri>
</uris>
<namespace>bdgp.insertion</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15238527</documentation>
</documentations>
<resources>
<resource id="MIR:00100201" state="up" reliability="94">
<dataResource>http://flypush.imgen.bcm.tmc.edu/pscreen/</dataResource>
<dataEntityExample>KG09531</dataEntityExample>
<dataEntry>http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$id</dataEntry>
<dataInfo>BDGP Gene Disruption Project</dataInfo>
<dataInstitution>Baylor College of Medicine, Texas</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000157" pattern="^TC\d+$">
<name>BeetleBase</name>
<definition>BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications.</definition>
<uris>
<uri type="URN">urn:miriam:beetlebase</uri>
<uri type="URL">http://identifiers.org/beetlebase/</uri>
</uris>
<namespace>beetlebase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19820115</documentation>
</documentations>
<resources>
<resource id="MIR:00100202" state="up" reliability="87">
<dataResource>http://beetlebase.org/</dataResource>
<dataEntityExample>TC010103</dataEntityExample>
<dataEntry>http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$id</dataEntry>
<dataInfo>BeetleBase at Kansas State University</dataInfo>
<dataInstitution>Bioinformatics Center, Kansas State University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000158" pattern="^\d+$">
<name>BOLD Taxonomy</name>
<definition>The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.</definition>
<uris>
<uri type="URN">urn:miriam:bold.taxonomy</uri>
<uri type="URL">http://identifiers.org/bold.taxonomy/</uri>
</uris>
<namespace>bold.taxonomy</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18784790</documentation>
</documentations>
<resources>
<resource id="MIR:00100203" state="up" reliability="99">
<dataResource>http://www.boldsystems.org/</dataResource>
<dataEntityExample>27267</dataEntityExample>
<dataEntry>http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$id</dataEntry>
<dataInfo>BOLD taxonomy browser</dataInfo>
<dataInstitution>Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000159" pattern="^([A-Z]+)?\d+(\.\d+)?$">
<name>dbEST</name>
<synonyms>
<synonym>Database of Expressed Sequence Tags</synonym>
<synonym>NCBI EST</synonym>
</synonyms>
<definition>The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.</definition>
<uris>
<uri type="URN">urn:miriam:dbest</uri>
<uri type="URL">http://identifiers.org/dbest/</uri>
</uris>
<namespace>dbest</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:8401577</documentation>
</documentations>
<resources>
<resource id="MIR:00100204" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/nucest</dataResource>
<dataEntityExample>BP100000</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/nucest/$id</dataEntry>
<dataInfo>dbEST at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100331" state="probably up" reliability="99">
<dataResource>http://www.ebi.ac.uk/ena</dataResource>
<dataEntityExample>BP100000.1</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/$id</dataEntry>
<dataInfo>dbEST through European Nucleotide Archive (ENA)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100651" state="up" reliability="97">
<dataResource>http://www.ddbj.nig.ac.jp/</dataResource>
<dataEntityExample>BP100000</dataEntityExample>
<dataEntry>http://getentry.ddbj.nig.ac.jp/getentry/na/$id</dataEntry>
<dataInfo>dbEST through DNA Data Bank of Japan (DDBJ)</dataInfo>
<dataInstitution>DNA Data Bank of Japan, Mishima, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000160" pattern="^\d+$">
<name>dbProbe</name>
<definition>The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.</definition>
<uris>
<uri type="URN">urn:miriam:dbprobe</uri>
<uri type="URL">http://identifiers.org/dbprobe/</uri>
</uris>
<namespace>dbprobe</namespace>
<documentations>
<documentation type="URL">http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/UsingProbeDB.shtml</documentation>
</documentations>
<resources>
<resource id="MIR:00100205" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe</dataResource>
<dataEntityExample>1000000</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/probe/?term=$id</dataEntry>
<dataInfo>dbProbe at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000161" pattern="^rs\d+$">
<name>dbSNP</name>
<definition>The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.</definition>
<uris>
<uri type="URN">urn:miriam:dbsnp</uri>
<uri type="URL">http://identifiers.org/dbsnp/</uri>
</uris>
<namespace>dbsnp</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11125122</documentation>
</documentations>
<resources>
<resource id="MIR:00100206" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp</dataResource>
<dataEntityExample>121909098</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$id</dataEntry>
<dataInfo>dbSNP at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000162" pattern="^\d+$">
<name>UniSTS</name>
<synonyms>
<synonym>dbSTS</synonym>
</synonyms>
<definition>UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.</definition>
<uris>
<uri type="URN">urn:miriam:unists</uri>
<uri type="URL">http://identifiers.org/unists/</uri>
</uris>
<namespace>unists</namespace>
<documentations>
<documentation type="URL">http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists</documentation>
</documentations>
<resources>
<resource id="MIR:00100207" state="up" reliability="95">
<dataResource>http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists</dataResource>
<dataEntityExample>456789</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$id</dataEntry>
<dataInfo>UniSTS at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000163" pattern="^EG\d+$">
<name>EcoGene</name>
<definition>The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.</definition>
<uris>
<uri type="URN">urn:miriam:ecogene</uri>
<uri type="URL">http://identifiers.org/ecogene/</uri>
</uris>
<namespace>ecogene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:10592181</documentation>
<documentation type="PMID">urn:miriam:pubmed:23197660</documentation>
</documentations>
<resources>
<resource id="MIR:00100208" state="up" reliability="91" primary="true">
<dataResource>http://ecogene.org/</dataResource>
<dataEntityExample>EG10173</dataEntityExample>
<dataEntry>http://www.ecogene.org/gene/$id</dataEntry>
<dataInfo>EcoGene at University of Miami</dataInfo>
<dataInstitution>Miller School of Medicine, University of Miami</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100209" obsolete="true">
<dataResource>http://maxd.cs.purdue.edu:9455</dataResource>
<dataEntityExample>EG10173</dataEntityExample>
<dataEntry>http://maxd.cs.purdue.edu:9455/geneInfo.php?eg_id=$id</dataEntry>
<dataInfo>EcoGene at Purdue University</dataInfo>
<dataInstitution>Purdue University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000164" pattern="^\w+$">
<name>GABI</name>
<synonyms>
<synonym>GABI PD</synonym>
</synonyms>
<definition>GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.</definition>
<uris>
<uri type="URN">urn:miriam:gabi</uri>
<uri type="URL">http://identifiers.org/gabi/</uri>
</uris>
<namespace>gabi</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18812395</documentation>
</documentations>
<resources>
<resource id="MIR:00100210" state="up" reliability="90" primary="true">
<dataResource>http://www.gabipd.org/</dataResource>
<dataEntityExample>2679240</dataEntityExample>
<dataEntry>http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$id&Mode=ShowBioObject</dataEntry>
<dataInfo>GABI at Max Planck</dataInfo>
<dataInstitution>Max Planck Institute of Molecular Plant Physiology, Berlin</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>genome</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000165" pattern="^\d+$">
<name>GreenGenes</name>
<definition>A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.</definition>
<uris>
<uri type="URN">urn:miriam:greengenes</uri>
<uri type="URL">http://identifiers.org/greengenes/</uri>
</uris>
<namespace>greengenes</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16820507</documentation>
</documentations>
<resources>
<resource id="MIR:00100211" state="down" reliability="86">
<dataResource>http://greengenes.lbl.gov/</dataResource>
<dataEntityExample>100000</dataEntityExample>
<dataEntry>http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$id</dataEntry>
<dataInfo>GreenGenes at Lawrence Berkeley</dataInfo>
<dataInstitution>Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000166" pattern="^\d+$">
<name>GRIN Plant Taxonomy</name>
<synonyms>
<synonym>GRIN Taxonomy for Plants</synonym>
<synonym>Germplasm Resources Information Network Plant Taxonomy</synonym>
</synonyms>
<definition>GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.</definition>
<uris>
<uri type="URN">urn:miriam:grin.taxonomy</uri>
<uri type="URL">http://identifiers.org/grin.taxonomy/</uri>
</uris>
<namespace>grin.taxonomy</namespace>
<documentations>
<documentation type="URL">http://www.ars-grin.gov/cgi-bin/npgs/html/paper.pl?language=en</documentation>
</documentations>
<resources>
<resource id="MIR:00100212" state="down" reliability="86">
<dataResource>http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en</dataResource>
<dataEntityExample>19333</dataEntityExample>
<dataEntry>http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$id</dataEntry>
<dataInfo>GRIN at Maryland</dataInfo>
<dataInstitution>National Germplasm Resources Laboratory, Beltsville, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>plant</tag>
<tag>taxonomy</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000167" pattern="^HIX\d{7}(\.\d+)?$">
<name>H-InvDb Locus</name>
<definition>H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.</definition>
<uris>
<uri type="URN">urn:miriam:hinv.locus</uri>
<uri type="URL">http://identifiers.org/hinv.locus/</uri>
</uris>
<namespace>hinv.locus</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19933760</documentation>
</documentations>
<resources>
<resource id="MIR:00100213" state="down" reliability="98">
<dataResource>http://h-invitational.jp/hinv/ahg-db/index.jsp</dataResource>
<dataEntityExample>HIX0004394</dataEntityExample>
<dataEntry>http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$id</dataEntry>
<dataInfo>H-Invitational Locus View at BIRC</dataInfo>
<dataInstitution>BIRC, Tokyo</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000168" pattern="^HIT\d{9}(\.\d+)?$">
<name>H-InvDb Transcript</name>
<definition>H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.</definition>
<uris>
<uri type="URN">urn:miriam:hinv.transcript</uri>
<uri type="URL">http://identifiers.org/hinv.transcript/</uri>
</uris>
<namespace>hinv.transcript</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19933760</documentation>
</documentations>
<resources>
<resource id="MIR:00100214" state="down" reliability="98">
<dataResource>http://h-invitational.jp/hinv/ahg-db/index.jsp</dataResource>
<dataEntityExample>HIT000195363</dataEntityExample>
<dataEntry>http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$id</dataEntry>
<dataInfo>H-Invitational Transcript View at BIRC</dataInfo>
<dataInstitution>BIRC, Tokyo</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000169" pattern="^HIP\d{9}(\.\d+)?$">
<name>H-InvDb Protein</name>
<definition>H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.</definition>
<uris>
<uri type="URN">urn:miriam:hinv.protein</uri>
<uri type="URL">http://identifiers.org/hinv.protein/</uri>
</uris>
<namespace>hinv.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19933760</documentation>
</documentations>
<resources>
<resource id="MIR:00100215" state="down" reliability="99">
<dataResource>http://h-invitational.jp/hinv/ahg-db/index.jsp</dataResource>
<dataEntityExample>HIP000030660</dataEntityExample>
<dataEntry>http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$id</dataEntry>
<dataInfo>H-Invitational Protein View at BIRC</dataInfo>
<dataInstitution>BIRC, Tokyo</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000170" pattern="^SEQF\d+$">
<name>HOMD Sequence Metainformation</name>
<synonyms>
<synonym>Human Oral Microbiome Database</synonym>
</synonyms>
<definition>The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.</definition>
<uris>
<uri type="URN">urn:miriam:homd.seq</uri>
<uri type="URL">http://identifiers.org/homd.seq/</uri>
</uris>
<namespace>homd.seq</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20624719</documentation>
</documentations>
<resources>
<resource id="MIR:00100216" state="up" reliability="99">
<dataResource>http://www.homd.org/index.php</dataResource>
<dataEntityExample>SEQF1003</dataEntityExample>
<dataEntry>http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$id</dataEntry>
<dataInfo>HOMD sequence metainformation at The Forsyth Institute</dataInfo>
<dataInstitution>The Forsyth Institute, Boston</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000171" pattern="^\d+$">
<name>HOMD Taxonomy</name>
<definition>The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.</definition>
<uris>
<uri type="URN">urn:miriam:homd.taxon</uri>
<uri type="URL">http://identifiers.org/homd.taxon/</uri>
</uris>
<namespace>homd.taxon</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20624719</documentation>
</documentations>
<resources>
<resource id="MIR:00100217" state="up" reliability="99">
<dataResource>http://www.homd.org/index.php</dataResource>
<dataEntityExample>811</dataEntityExample>
<dataEntry>http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$id&view=dynamic</dataEntry>
<dataInfo>HOMD taxon information at The Forsyth Institute</dataInfo>
<dataInstitution>The Forsyth Institute, Boston</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>microbial</tag>
<tag>taxonomy</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000172" pattern="^\w+(\_)?\d+(\.\d+)?$">
<name>IRD Segment Sequence</name>
<synonyms>
<synonym>Influenza Research Database Segment</synonym>
</synonyms>
<definition>Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).</definition>
<uris>
<uri type="URN">urn:miriam:ird.segment</uri>
<uri type="URL">http://identifiers.org/ird.segment/</uri>
</uris>
<namespace>ird.segment</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17965094</documentation>
</documentations>
<resources>
<resource id="MIR:00100218" state="up" reliability="96">
<dataResource>http://www.fludb.org/</dataResource>
<dataEntityExample>CY077097</dataEntityExample>
<dataEntry>http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$id</dataEntry>
<dataInfo>IRD at BioHealthBase</dataInfo>
<dataInstitution>Southwestern Medical Center, University of Texas, Dallas</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000173" pattern="^IS\w+(\-\d)?$">
<name>ISFinder</name>
<synonyms>
<synonym>Insertion Sequence Finder</synonym>
</synonyms>
<definition>ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.</definition>
<uris>
<uri type="URN">urn:miriam:isfinder</uri>
<uri type="URL">http://identifiers.org/isfinder/</uri>
</uris>
<namespace>isfinder</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381877</documentation>
</documentations>
<resources>
<resource id="MIR:00100219" state="down" reliability="75">
<dataResource>http://www-is.biotoul.fr/i</dataResource>
<dataEntityExample>ISA1083-2</dataEntityExample>
<dataEntry>https://www-is.biotoul.fr/scripts/ficheIS.php?name=$id</dataEntry>
<dataInfo>IS Finder at CNRS</dataInfo>
<dataInstitution>Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, Toulouse</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>sequence</tag>
</tags>
</datatype>
<datatype id="MIR:00000174" pattern="^\d+$">
<name>Japan Collection of Microorganisms</name>
<synonyms>
<synonym>JCM</synonym>
</synonyms>
<definition>The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.</definition>
<uris>
<uri type="URN">urn:miriam:jcm</uri>
<uri type="URL">http://identifiers.org/jcm/</uri>
</uris>
<namespace>jcm</namespace>
<documentations>
<documentation type="URL">http://www.jcm.riken.go.jp/JCM/aboutJCM.shtml</documentation>
</documentations>
<resources>
<resource id="MIR:00100220" state="down" reliability="86">
<dataResource>http://www.jcm.riken.go.jp/</dataResource>
<dataEntityExample>17254</dataEntityExample>
<dataEntry>http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$id</dataEntry>
<dataInfo>JCM at RIKEN BioResource Center</dataInfo>
<dataInstitution>RIKEN BioResource Center, Ibaraki</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>microbial</tag>
<tag>strain</tag>
</tags>
</datatype>
<datatype id="MIR:00000175" pattern="^\d+$" restricted="true">
<name>Integrated Microbial Genomes Taxon</name>
<synonyms>
<synonym>IMG Taxon</synonym>
</synonyms>
<definition>The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.</definition>
<uris>
<uri type="URN">urn:miriam:img.taxon</uri>
<uri type="URL">http://identifiers.org/img.taxon/</uri>
</uris>
<namespace>img.taxon</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17933782</documentation>
</documentations>
<resources>
<resource id="MIR:00100221" state="restricted access" reliability="94">
<dataResource>http://img.jgi.doe.gov/</dataResource>
<dataEntityExample>648028003</dataEntityExample>
<dataEntry>http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$id</dataEntry>
<dataInfo>Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory</dataInfo>
<dataInstitution>Lawrence Berkeley National Laboratory, Berkeley</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>Access to this collection requires registration for an account.</statement>
<link desc="registration link">https://img.jgi.doe.gov/cgi-bin/submit/request.cgi</link>
</restriction>
</restrictions>
<tags>
<tag>genome</tag>
<tag>taxonomy</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000176" pattern="^\d+$" restricted="true">
<name>Integrated Microbial Genomes Gene</name>
<definition>The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.</definition>
<uris>
<uri type="URN">urn:miriam:img.gene</uri>
<uri type="URL">http://identifiers.org/img.gene/</uri>
</uris>
<namespace>img.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17933782</documentation>
</documentations>
<resources>
<resource id="MIR:00100222" state="restricted access" reliability="94">
<dataResource>http://img.jgi.doe.gov/</dataResource>
<dataEntityExample>638309541</dataEntityExample>
<dataEntry>http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$id</dataEntry>
<dataInfo>Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory</dataInfo>
<dataInstitution>Lawrence Berkeley National Laboratory, Berkeley</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>Access to this collection requires registration for an account.</statement>
<link desc="registration link">https://img.jgi.doe.gov/cgi-bin/submit/request.cgi</link>
</restriction>
</restrictions>
<tags>
<tag>gene</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000177" pattern="^\d+$">
<name>MaizeGDB Locus</name>
<definition>MaizeGDB is the maize research community's central repository for genetics and genomics information.</definition>
<uris>
<uri type="URN">urn:miriam:maizegdb.locus</uri>
<uri type="URL">http://identifiers.org/maizegdb.locus/</uri>
</uris>
<namespace>maizegdb.locus</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18769488</documentation>
</documentations>
<resources>
<resource id="MIR:00100223" state="probably up" reliability="85">
<dataResource>http://www.maizegdb.org/</dataResource>
<dataEntityExample>25011</dataEntityExample>
<dataEntry>http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$id</dataEntry>
<dataInfo>MaizeGDB at Missouri</dataInfo>
<dataInstitution>Division of Plant Sciences, Missouri</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000178" pattern="^\d+$">
<name>MycoBank</name>
<definition>MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.</definition>
<uris>
<uri type="URN">urn:miriam:mycobank</uri>
<uri type="URL">http://identifiers.org/mycobank/</uri>
</uris>
<namespace>mycobank</namespace>
<documentations>
<documentation type="URL">http://www.mycobank.org/Help.aspx</documentation>
</documentations>
<resources>
<resource id="MIR:00100224" state="up" reliability="98">
<dataResource>http://www.mycobank.org/</dataResource>
<dataEntityExample>349124</dataEntityExample>
<dataEntry>http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$id</dataEntry>
<dataInfo>MycoBank at Fungal Biodiversity Centre</dataInfo>
<dataInstitution>CBS-KNAW Fungal Biodiversity Centre, Utrecht</dataInstitution>
<dataLocation>Netherlands</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000179" pattern="^\d+$">
<name>NITE Biological Research Center Catalogue</name>
<synonyms>
<synonym>NBRC Catalogue</synonym>
</synonyms>
<definition>NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information.</definition>
<uris>
<uri type="URN">urn:miriam:nbrc</uri>
<uri type="URL">http://identifiers.org/nbrc/</uri>
</uris>
<namespace>nbrc</namespace>
<documentations>
<documentation type="URL">http://www.bio.nite.go.jp/pamphlet/e/nbrc-e.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100225" state="up" reliability="98">
<dataResource>http://www.nbrc.nite.go.jp/e/index.html</dataResource>
<dataEntityExample>00001234</dataEntityExample>
<dataEntry>http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$id</dataEntry>
<dataInfo>NBRC Catalogue at National Institute of Technology Evaluation</dataInfo>
<dataInstitution>National Institute of Technology Evaluation, Tokyo</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>microbial</tag>
<tag>strain</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000180" pattern="^P\w+$">
<name>Pseudomonas Genome Database</name>
<synonyms>
<synonym>PGD</synonym>
<synonym>Pseudocap</synonym>
</synonyms>
<definition>The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.</definition>
<uris>
<uri type="URN">urn:miriam:pseudomonas</uri>
<uri type="URL">http://identifiers.org/pseudomonas/</uri>
</uris>
<namespace>pseudomonas</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18978025</documentation>
</documentations>
<resources>
<resource id="MIR:00100226" state="down" reliability="78">
<dataResource>http://www.pseudomonas.com/</dataResource>
<dataEntityExample>PSEEN0001</dataEntityExample>
<dataEntry>http://v2.pseudomonas.com/getAnnotation.do?locusID=$id</dataEntry>
<dataInfo>Pseudomonas Genome Database at Simon Fraser University</dataInfo>
<dataInstitution>Simon Fraser University, British Columbia</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>microbial</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000181" pattern="^\d+$">
<name>Gramene protein</name>
<definition>Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.</definition>
<uris>
<uri type="URN">urn:miriam:gramene.protein</uri>
<uri type="URL">http://identifiers.org/gramene.protein/</uri>
</uris>
<namespace>gramene.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21076153</documentation>
</documentations>
<resources>
<resource id="MIR:00100227" state="up" reliability="99">
<dataResource>http://www.gramene.org/</dataResource>
<dataEntityExample>78073</dataEntityExample>
<dataEntry>http://www.gramene.org/db/protein/protein_search?protein_id=$id</dataEntry>
<dataInfo>Gramene Protein at Cold Spring Harbor</dataInfo>
<dataInstitution>Cold Spring Harbor Laboratory, New York</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>genome</tag>
<tag>plant</tag>
<tag>sequence</tag>
</tags>
</datatype>
<datatype id="MIR:00000182" pattern="^GR\:\d+$">
<name>Gramene genes</name>
<definition>Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.</definition>
<uris>
<uri type="URN">urn:miriam:gramene.gene</uri>
<uri type="URL">http://identifiers.org/gramene.gene/</uri>
</uris>
<namespace>gramene.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21076153</documentation>
</documentations>
<resources>
<resource id="MIR:00100228" state="up" reliability="98">
<dataResource>http://www.gramene.org/</dataResource>
<dataEntityExample>GR:0080039</dataEntityExample>
<dataEntry>http://www.gramene.org/db/genes/search_gene?acc=$id</dataEntry>
<dataInfo>Gramene Genes at Cold Spring Harbor</dataInfo>
<dataInstitution>Cold Spring Harbor Laboratory, New York</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>genome</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000183" pattern="^GR\_tax\:\d+$">
<name>Gramene Taxonomy</name>
<definition>Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.</definition>
<uris>
<uri type="URN">urn:miriam:gramene.taxonomy</uri>
<uri type="URL">http://identifiers.org/gramene.taxonomy/</uri>
</uris>
<namespace>gramene.taxonomy</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21076153</documentation>
</documentations>
<resources>
<resource id="MIR:00100229" state="up" reliability="99">
<dataResource>http://www.gramene.org/</dataResource>
<dataEntityExample>GR_tax:013681</dataEntityExample>
<dataEntry>http://www.gramene.org/db/ontology/search?id=$id</dataEntry>
<dataInfo>Gramene Taxonomy at Cold Spring Harbor</dataInfo>
<dataInstitution>Cold Spring Harbor Laboratory, New York</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>plant</tag>
<tag>taxonomy</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000184" pattern="^\w+$">
<name>Gramene QTL</name>
<definition>Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.</definition>
<uris>
<uri type="URN">urn:miriam:gramene.qtl</uri>
<uri type="URL">http://identifiers.org/gramene.qtl/</uri>
</uris>
<namespace>gramene.qtl</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21076153</documentation>
</documentations>
<resources>
<resource id="MIR:00100230" state="up" reliability="99">
<dataResource>http://www.gramene.org/</dataResource>
<dataEntityExample>CQG5</dataEntityExample>
<dataEntry>http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$id</dataEntry>
<dataInfo>Gramene Quantitative Trait Loci at Cold Spring Harbor</dataInfo>
<dataInstitution>Cold Spring Harbor Laboratory, New York</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>genome</tag>
<tag>phenotype</tag>
<tag>plant</tag>
</tags>
</datatype>
<datatype id="MIR:00000185" pattern="^\d+$">
<name>Sol Genomics Network</name>
<synonyms>
<synonym>SGN</synonym>
</synonyms>
<definition>The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.</definition>
<uris>
<uri type="URN">urn:miriam:sgn</uri>
<uri type="URL">http://identifiers.org/sgn/</uri>
</uris>
<namespace>sgn</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20935049</documentation>
</documentations>
<resources>
<resource id="MIR:00100231" state="down" reliability="61">
<dataResource>http://solgenomics.net/</dataResource>
<dataEntityExample>0001</dataEntityExample>
<dataEntry>http://solgenomics.net/phenome/locus_display.pl?locus_id=$id</dataEntry>
<dataInfo>Sol Genomics Network at Boyce Thompson Institute for Plant Research</dataInfo>
<dataInstitution>Boyce Thompson Institute for Plant Research, New York</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000186" pattern="^(XB-GENE-)?\d+$">
<name>Xenbase</name>
<definition>Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.</definition>
<uris>
<uri type="URN">urn:miriam:xenbase</uri>
<uri type="URL">http://identifiers.org/xenbase/</uri>
</uris>
<namespace>xenbase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19884130</documentation>
</documentations>
<resources>
<resource id="MIR:00100232" state="up" reliability="98">
<dataResource>http://www.xenbase.org/</dataResource>
<dataEntityExample>922462</dataEntityExample>
<dataEntry>http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=$id</dataEntry>
<dataInfo>Xenbase at University of Calgary</dataInfo>
<dataInstitution>Department of Biological Sciences, University of Calgary, Alberta</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>parameter</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000187" pattern="^\d+$">
<name>BioPortal</name>
<definition>BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.</definition>
<uris>
<uri type="URN">urn:miriam:bioportal</uri>
<uri type="URL">http://identifiers.org/bioportal/</uri>
</uris>
<namespace>bioportal</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19483092</documentation>
</documentations>
<resources>
<resource id="MIR:00100244" state="up" reliability="99">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>1046</dataEntityExample>
<dataEntry>http://bioportal.bioontology.org/ontologies/$id</dataEntry>
<dataInfo>BioPortal at National Center for Biomedical Ontology</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
<tag>registry</tag>
</tags>
</datatype>
<datatype id="MIR:00000188" pattern="^MIR:001\d{5}$">
<name>MIRIAM Registry resource</name>
<definition>MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.</definition>
<uris>
<uri type="URN">urn:miriam:miriam.resource</uri>
<uri type="URL">http://identifiers.org/miriam.resource/</uri>
</uris>
<namespace>miriam.resource</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18078503</documentation>
</documentations>
<resources>
<resource id="MIR:00100245" state="up" reliability="99">
<dataResource>http://www.ebi.ac.uk/miriam/</dataResource>
<dataEntityExample>MIR:00100005</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/miriam/main/resources/$id</dataEntry>
<dataInfo>MIRIAM Registry (resources)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000189" pattern="^(data|topic|operation|format)\_\d{4}$">
<name>EDAM Ontology</name>
<synonyms>
<synonym>EMBRACE Data and Methods Ontology</synonym>
</synonyms>
<definition>EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).</definition>
<uris>
<uri type="URN">urn:miriam:edam</uri>
<uri type="URL">http://identifiers.org/edam/</uri>
<uri type="URL" deprecated="true">http://edamontology.org/</uri>
</uris>
<namespace>edam</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23479348</documentation>
<documentation type="URL">http://edamontology.sourceforge.net/</documentation>
</documentations>
<resources>
<resource id="MIR:00100536" state="up" reliability="96">
<dataResource>http://bioportal.bioontology.org/ontologies/EDAM</dataResource>
<dataEntityExample>data_1664</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/EDAM/$id</dataEntry>
<dataInfo>EDAM through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100762" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/edam</dataResource>
<dataEntityExample>data_1664</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/edam/terms?short_form=$id</dataEntry>
<dataInfo>EDAM through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100246" obsolete="true">
<dataResource>https://www.ebi.ac.uk/ontology-lookup/</dataResource>
<dataEntityExample>1664</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ontology-lookup/?termId=EDAM_data:$id</dataEntry>
<dataInfo>EDAM via OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
</datatype>
<datatype id="MIR:00000190" pattern="^PM\d{7}">
<name>Protein Model Database</name>
<synonyms>
<synonym>PMDB</synonym>
</synonyms>
<definition>The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.</definition>
<uris>
<uri type="URN">urn:miriam:pmdb</uri>
<uri type="URL">http://identifiers.org/pmdb/</uri>
</uris>
<namespace>pmdb</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkj105</documentation>
</documentations>
<resources>
<resource id="MIR:00100247" state="up" reliability="81">
<dataResource>https://bioinformatics.cineca.it/PMDB/</dataResource>
<dataEntityExample>PM0012345</dataEntityExample>
<dataEntry>https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$id</dataEntry>
<dataInfo>Protein Model Database at University of Rome</dataInfo>
<dataInstitution>CASPUR and Biocomputing group, Department of Biochemical Sciences, University of Rome, Rome</dataInstitution>
<dataLocation>Italy</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000191" pattern="^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$" restricted="true" obsolete="true" replacement="MIR:00000005">
<comment>This collection is no longer maintained.</comment>
<name>2D-PAGE protein</name>
<synonyms>
<synonym>2D-PAGE E. coli</synonym>
</synonyms>
<definition>2DBase of Escherichia coli stores 2D polyacrylamide gel electrophoresis and mass spectrometry proteome data for E. coli. This collection references a subset of Uniprot, and contains general information about the protein record.</definition>
<uris>
<uri type="URN">urn:miriam:2d-page.protein</uri>
<uri type="URL">http://identifiers.org/2d-page.protein/</uri>
</uris>
<namespace>2d-page.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17904107</documentation>
</documentations>
<resources>
<resource id="MIR:00100248" state="down" reliability="31">
<dataResource>http://2dbase.techfak.uni-bielefeld.de/</dataResource>
<dataEntityExample>P39172</dataEntityExample>
<dataEntry>http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?ac=$id</dataEntry>
<dataInfo>2D-Page at Bielefeld</dataInfo>
<dataInstitution>Graduate School in Bioinformatics and Genome Research, University of Bielefeld,</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="5" desc="Collection maintenance">
<statement>The long term stability of this collection is questionable. Users are advised to find an alternative source of information.</statement>
</restriction>
</restrictions>
<tags>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000192" pattern="^AGR\w+$" obsolete="true" replacement="">
<comment>This service is obsolete and has been dismissed.</comment>
<name>AGD</name>
<synonyms>
<synonym>Ashbya Genome Database</synonym>
</synonyms>
<definition>AGD 3.0 is a genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from the fungi Ashbya gossypii and Saccharomyces cerevisiae.</definition>
<uris>
<uri type="URN">urn:miriam:agd</uri>
<uri type="URL">http://identifiers.org/agd/</uri>
</uris>
<namespace>agd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15001715</documentation>
</documentations>
<resources>
<resource id="MIR:00100249" state="down" reliability="89">
<dataResource>http://agd.vital-it.ch/</dataResource>
<dataEntityExample>AGR144C</dataEntityExample>
<dataEntry>http://agd.vital-it.ch/Ashbya_gossypii/geneview?gene=$id</dataEntry>
<dataInfo>AGD at Basel</dataInfo>
<dataInstitution>Biozentrum der Universität Basel, Basel</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>microarray</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000193" pattern="^AS\d{6}$">
<name>ArachnoServer</name>
<definition>ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.</definition>
<uris>
<uri type="URN">urn:miriam:arachnoserver</uri>
<uri type="URL">http://identifiers.org/arachnoserver/</uri>
</uris>
<namespace>arachnoserver</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21036864</documentation>
</documentations>
<resources>
<resource id="MIR:00100250" state="up" reliability="97">
<dataResource>http://www.arachnoserver.org/</dataResource>
<dataEntityExample>AS000060</dataEntityExample>
<dataEntry>http://www.arachnoserver.org/toxincard.html?id=$id</dataEntry>
<dataInfo>ArachnoServer at Brisbane</dataInfo>
<dataInstitution>Institute for Molecular Bioscience, The University of Queensland, Brisbane</dataInstitution>
<dataLocation>Australia</dataLocation>
</resource>
</resources>
<tags>
<tag>drug</tag>
<tag>sequence</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000194" pattern="^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$" restricted="true">
<name>BioCyc</name>
<definition>BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.</definition>
<uris>
<uri type="URN">urn:miriam:biocyc</uri>
<uri type="URL">http://identifiers.org/biocyc/</uri>
</uris>
<namespace>biocyc</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16246909</documentation>
</documentations>
<resources>
<resource id="MIR:00100251" state="up" reliability="83">
<dataResource>http://biocyc.org</dataResource>
<dataEntityExample>ECOLI:CYT-D-UBIOX-CPLX</dataEntityExample>
<dataEntry>http://biocyc.org/getid?id=$id</dataEntry>
<dataInfo>BioCyc at SRI International</dataInfo>
<dataInstitution>Bioinformatics Research Group, SRI International, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="2" desc="Data aggregation">
<statement>BioCyc is a collection of 1690 Pathway/Genome Databases.</statement>
<link desc="BioCyc introduction">http://biocyc.org/intro.shtml</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
<tag>genome</tag>
<tag>pathway</tag>
<tag>reaction</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000195" pattern="^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$">
<name>CAZy</name>
<synonyms>
<synonym>Carbohydrate-Active enzYmes</synonym>
</synonyms>
<definition>The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features.</definition>
<uris>
<uri type="URN">urn:miriam:cazy</uri>
<uri type="URL">http://identifiers.org/cazy/</uri>
</uris>
<namespace>cazy</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18838391</documentation>
</documentations>
<resources>
<resource id="MIR:00100252" state="up" reliability="99">
<dataResource>http://www.cazy.org/</dataResource>
<dataEntityExample>GT10</dataEntityExample>
<dataEntry>http://www.cazy.org/$id.html</dataEntry>
<dataInfo>CAZy at CNRS</dataInfo>
<dataInstitution>Architecture et Fonction des Macromolécules Biologiques, CNRS, Marseille</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>polysaccharide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000196" pattern="^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$">
<name>GOA</name>
<synonyms>
<synonym>Gene Ontology Annotation</synonym>
<synonym>UniProtKB-GOA</synonym>
</synonyms>
<definition>The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.</definition>
<uris>
<uri type="URN">urn:miriam:goa</uri>
<uri type="URL">http://identifiers.org/goa/</uri>
</uris>
<namespace>goa</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18957448</documentation>
</documentations>
<resources>
<resource id="MIR:00100253" state="down" reliability="88">
<dataResource>http://www.ebi.ac.uk/GOA/</dataResource>
<dataEntityExample>P12345</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/QuickGO/GProtein?ac=$id</dataEntry>
<dataInfo>GOA through QuickGO</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>annotation</tag>
<tag>ontology</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000197" pattern="^\d+$">
<name>PaleoDB</name>
<synonyms>
<synonym>Paleobiology database</synonym>
</synonyms>
<definition>The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.</definition>
<uris>
<uri type="URN">urn:miriam:paleodb</uri>
<uri type="URL">http://identifiers.org/paleodb/</uri>
</uris>
<namespace>paleodb</namespace>
<documentations>
<documentation type="URL">http://paleodb.org/cgi-bin/bridge.pl?a=displayPage&page=paleodbFAQ</documentation>
</documentations>
<resources>
<resource id="MIR:00100254" state="up" reliability="99">
<dataResource>http://paleodb.org/</dataResource>
<dataEntityExample>83088</dataEntityExample>
<dataEntry>http://fossilworks.org/?a=taxonInfo&taxon_no=$id</dataEntry>
<dataInfo>PaleoDB at Macquarie University</dataInfo>
<dataInstitution>Macquarie University, Sydney</dataInstitution>
<dataLocation>Australia</dataLocation>
</resource>
<resource id="MIR:00100255" obsolete="true">
<dataResource>http://museumu03.museumwww.naturkundemuseum-berlin.de/</dataResource>
<dataEntityExample>83088</dataEntityExample>
<dataEntry>http://museumu03.museumwww.naturkundemuseum-berlin.de/cgi-bin/bridge.pl?a=basicTaxonInfo&taxon_no=$id</dataEntry>
<dataInfo>PaleoDB at Museum für Naturkunde</dataInfo>
<dataInstitution>Museum für Naturkunde, Berlin</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
<resource id="MIR:00100256" obsolete="true">
<dataResource>http://paleodb.geology.wisc.edu/</dataResource>
<dataEntityExample>83088</dataEntityExample>
<dataEntry>http://paleodb.geology.wisc.edu/cgi-bin/bridge.pl?a=basicTaxonInfo&taxon_no=$id</dataEntry>
<dataInfo>PaleoDB at University of Wisconsin</dataInfo>
<dataInstitution>University of Wisconsin, Madison</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>taxonomy</tag>
</tags>
</datatype>
<datatype id="MIR:00000198" pattern="^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$">
<name>Compulyeast</name>
<synonyms>
<synonym>Compluyeast-2D-DB</synonym>
</synonyms>
<definition>Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.</definition>
<uris>
<uri type="URN">urn:miriam:compulyeast</uri>
<uri type="URL">http://identifiers.org/compulyeast/</uri>
</uris>
<namespace>compulyeast</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18617148</documentation>
</documentations>
<resources>
<resource id="MIR:00100257" state="down" reliability="73">
<dataResource>http://compluyeast2dpage.dacya.ucm.es/</dataResource>
<dataEntityExample>O08709</dataEntityExample>
<dataEntry>http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$id</dataEntry>
<dataInfo>Compluyeast database at Universidad Complutense Madrid</dataInfo>
<dataInstitution>Department Microbiology II, Universidad Complutense Madrid, Madrid</dataInstitution>
<dataLocation>Spain</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000199" pattern="^DP\d{5}$">
<name>DisProt</name>
<definition>The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.</definition>
<uris>
<uri type="URN">urn:miriam:disprot</uri>
<uri type="URL">http://identifiers.org/disprot/</uri>
</uris>
<namespace>disprot</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17145717</documentation>
</documentations>
<resources>
<resource id="MIR:00100258" state="probably up" reliability="99">
<dataResource>http://www.disprot.org/</dataResource>
<dataEntityExample>DP00003</dataEntityExample>
<dataEntry>http://www.disprot.org/$id</dataEntry>
<dataInfo>DisProt at Indiana University</dataInfo>
<dataInstitution>Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000200" pattern="^EB\d+$">
<name>EchoBASE</name>
<definition>EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.</definition>
<uris>
<uri type="URN">urn:miriam:echobase</uri>
<uri type="URL">http://identifiers.org/echobase/</uri>
</uris>
<namespace>echobase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608209</documentation>
</documentations>
<resources>
<resource id="MIR:00100259" state="down" reliability="88">
<dataResource>http://www.york.ac.uk/</dataResource>
<dataEntityExample>EB0170</dataEntityExample>
<dataEntry>http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$id</dataEntry>
<dataInfo>EchoBASE at the University of York</dataInfo>
<dataInstitution>Department of Biology (Area 10), University of York, York</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>genome</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000201" pattern="^\w+$">
<name>eggNOG</name>
<definition>eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).</definition>
<uris>
<uri type="URN">urn:miriam:eggnog</uri>
<uri type="URL">http://identifiers.org/eggnog/</uri>
</uris>
<namespace>eggnog</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19900971</documentation>
</documentations>
<resources>
<resource id="MIR:00100260" state="up" reliability="97">
<dataResource>http://eggnog.embl.de/version_3.0/</dataResource>
<dataEntityExample>veNOG12876</dataEntityExample>
<dataEntry>http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$id</dataEntry>
<dataInfo>eggNOG Version 3 at European Molecular Biology Laboratory</dataInfo>
<dataInstitution>European Molecular Biology Laboratory, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
<resource id="MIR:00100298" obsolete="true">
<dataResource>http://eggnog.embl.de/version_2/</dataResource>
<dataEntityExample>veNOG12876</dataEntityExample>
<dataEntry>http://eggnog.embl.de/cgi_bin/display_single_node.pl?node=$id</dataEntry>
<dataInfo>eggNOG Version 2 at European Molecular Biology Laboratory</dataInfo>
<dataInstitution>European Molecular Biology Laboratory, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000202" pattern="^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$">
<name>Ensembl Bacteria</name>
<synonyms>
<synonym>Ensembl Genomes Bacteria</synonym>
</synonyms>
<definition>Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes.</definition>
<uris>
<uri type="URN">urn:miriam:ensembl.bacteria</uri>
<uri type="URL">http://identifiers.org/ensembl.bacteria/</uri>
</uris>
<namespace>ensembl.bacteria</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19884133</documentation>
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<resources>
<resource id="MIR:00100261" state="up" reliability="94">
<dataResource>http://bacteria.ensembl.org/</dataResource>
<dataEntityExample>MU9_3181</dataEntityExample>
<dataEntry>http://bacteria.ensembl.org/id/$id</dataEntry>
<dataInfo>Ensembl Bacteria at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000203" pattern="^\w+$">
<name>Ensembl Protists</name>
<synonyms>
<synonym>Ensembl Genomes Protists</synonym>
</synonyms>
<definition>Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes.</definition>
<uris>
<uri type="URN">urn:miriam:ensembl.protist</uri>
<uri type="URL">http://identifiers.org/ensembl.protist/</uri>
</uris>
<namespace>ensembl.protist</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19884133</documentation>
</documentations>
<resources>
<resource id="MIR:00100262" state="down" reliability="73">
<dataResource>http://protists.ensembl.org</dataResource>
<dataEntityExample>PFC0120w</dataEntityExample>
<dataEntry>http://protists.ensembl.org/id/$id</dataEntry>
<dataInfo>Ensembl Protists at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000204" pattern="^\w+(\.)?\d+$">
<name>Ensembl Metazoa</name>
<synonyms>
<synonym>Ensembl Genomes Metazoa</synonym>
</synonyms>
<definition>Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes.</definition>
<uris>
<uri type="URN">urn:miriam:ensembl.metazoa</uri>
<uri type="URL">http://identifiers.org/ensembl.metazoa/</uri>
</uris>
<namespace>ensembl.metazoa</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19884133</documentation>
</documentations>
<resources>
<resource id="MIR:00100263" state="up" reliability="96">
<dataResource>http://metazoa.ensembl.org/</dataResource>
<dataEntityExample>FBtr0084214</dataEntityExample>
<dataEntry>http://metazoa.ensembl.org/id/$id</dataEntry>
<dataInfo>Enzembl Metazoa at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000205" pattern="^\w+(\.\d+)?(\.\d+)?$">
<name>Ensembl Plants</name>
<synonyms>
<synonym>Ensembl Genomes Plants</synonym>
</synonyms>
<definition>Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes.</definition>
<uris>
<uri type="URN">urn:miriam:ensembl.plant</uri>
<uri type="URL">http://identifiers.org/ensembl.plant/</uri>
</uris>
<namespace>ensembl.plant</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19884133</documentation>
</documentations>
<resources>
<resource id="MIR:00100264" state="up" reliability="88">
<dataResource>http://plants.ensembl.org/</dataResource>
<dataEntityExample>AT1G73965</dataEntityExample>
<dataEntry>http://plants.ensembl.org/id/$id</dataEntry>
<dataInfo>Enzembl Plants at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000206" pattern="^[A-Z-a-z0-9]+$">
<name>Ensembl Fungi</name>
<synonyms>
<synonym>Ensembl Genomes Fungi</synonym>
</synonyms>
<definition>Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.</definition>
<uris>
<uri type="URN">urn:miriam:ensembl.fungi</uri>
<uri type="URL">http://identifiers.org/ensembl.fungi/</uri>
</uris>
<namespace>ensembl.fungi</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19884133</documentation>
</documentations>
<resources>
<resource id="MIR:00100265" state="down" reliability="73">
<dataResource>http://fungi.ensembl.org/</dataResource>
<dataEntityExample>CADAFLAT00006211</dataEntityExample>
<dataEntry>http://fungi.ensembl.org/id/$id</dataEntry>
<dataInfo>Enzembl Fungi at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000207" pattern="^M\d{5}$">
<name>HCVDB</name>
<synonyms>
<synonym>euHCVDB</synonym>
</synonyms>
<definition>the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses.</definition>
<uris>
<uri type="URN">urn:miriam:hcvdb</uri>
<uri type="URL">http://identifiers.org/hcvdb/</uri>
</uris>
<namespace>hcvdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17142229</documentation>
</documentations>
<resources>
<resource id="MIR:00100266" state="up" reliability="75">
<dataResource>http://euhcvdb.ibcp.fr/euHCVdb/</dataResource>
<dataEntityExample>M58335</dataEntityExample>
<dataEntry>https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$id</dataEntry>
<dataInfo>HCVDB at CNRS</dataInfo>
<dataInstitution>Institut de Biologie et Chimie des Protéines, CNRS, University of Lyon , Lyon-Gerland</dataInstitution>
<dataLocation>France</dataLocation>
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</resources>
<tags>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000208" pattern="^\w+$">
<name>Genatlas</name>
<definition>GenAtlas is a database containing information on human genes, markers and phenotypes.</definition>
<uris>
<uri type="URN">urn:miriam:genatlas</uri>
<uri type="URL">http://identifiers.org/genatlas/</uri>
</uris>
<namespace>genatlas</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:9835018</documentation>
</documentations>
<resources>
<resource id="MIR:00100267" state="up" reliability="99">
<dataResource>http://genatlas.medecine.univ-paris5.fr/</dataResource>
<dataEntityExample>HBB</dataEntityExample>
<dataEntry>http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$id</dataEntry>
<dataInfo>Genatlas at Paris Descartes University</dataInfo>
<dataInstitution>Paris Descartes University, Paris</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>disorder</tag>
<tag>gene</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000209" pattern="^\d+(\.\d+(\.\d+(\.\d+)?)?)?$">
<name>CATH superfamily</name>
<definition>The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification.</definition>
<uris>
<uri type="URN">urn:miriam:cath.superfamily</uri>
<uri type="URL">http://identifiers.org/cath.superfamily/</uri>
</uris>
<namespace>cath.superfamily</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:9309224</documentation>
</documentations>
<resources>
<resource id="MIR:00100268" state="down" reliability="95">
<dataResource>http://www.cathdb.info/</dataResource>
<dataEntityExample>1.10.10.200</dataEntityExample>
<dataEntry>http://www.cathdb.info/cathnode/$id</dataEntry>
<dataInfo>CATH superfamily at UCL</dataInfo>
<dataInstitution>Institute of Structural and Molecular Biology, University College London</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>protein</tag>
<tag>schema.org</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000210" pattern="^\w+$">
<name>CATH domain</name>
<definition>The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains.</definition>
<uris>
<uri type="URN">urn:miriam:cath.domain</uri>
<uri type="URL">http://identifiers.org/cath.domain/</uri>
</uris>
<namespace>cath.domain</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:9309224</documentation>
</documentations>
<resources>
<resource id="MIR:00100269" state="up" reliability="98">
<dataResource>http://www.cathdb.info/</dataResource>
<dataEntityExample>1cukA01</dataEntityExample>
<dataEntry>http://www.cathdb.info/domain/$id</dataEntry>
<dataInfo>CATH domain at UCL</dataInfo>
<dataInstitution>Institute of Structural and Molecular Biology, University College London</dataInstitution>
<dataLocation>UK</dataLocation>
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</resources>
<tags>
<tag>classification</tag>
<tag>protein</tag>
<tag>schema.org</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000211" pattern="^\d+$">
<name>GeneFarm</name>
<definition>GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.</definition>
<uris>
<uri type="URN">urn:miriam:genefarm</uri>
<uri type="URL">http://identifiers.org/genefarm/</uri>
</uris>
<namespace>genefarm</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608279</documentation>
</documentations>
<resources>
<resource id="MIR:00100270" state="down" reliability="56">
<dataResource>http://urgi.versailles.inra.fr/Genefarm/</dataResource>
<dataEntityExample>4892</dataEntityExample>
<dataEntry>https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$id</dataEntry>
<dataInfo>GeneFarm at Unité de Recherche en Génomique Végétale</dataInfo>
<dataInstitution>Unité de Recherche en Génomique Végétale, Evry</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>genome</tag>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000212" pattern="^\w+$">
<name>GPCRDB</name>
<synonyms>
<synonym>G protein-coupled receptor database</synonym>
</synonyms>
<definition>The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.</definition>
<uris>
<uri type="URN">urn:miriam:gpcrdb</uri>
<uri type="URL">http://identifiers.org/gpcrdb/</uri>
</uris>
<namespace>gpcrdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21045054</documentation>
</documentations>
<resources>
<resource id="MIR:00100271" state="up" reliability="88">
<dataResource>http://www.gpcrdb.org/</dataResource>
<dataEntityExample>RL3R1_HUMAN</dataEntityExample>
<dataEntry>http://www.gpcrdb.org/protein/$id/</dataEntry>
<dataInfo>GPCRDB at Radboud University</dataInfo>
<dataInstitution>Radboud University Nijmegen Medical Centre, Nijmegen,</dataInstitution>
<dataLocation>Holland</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000213" pattern="^\w+$">
<name>HOGENOM</name>
<definition>HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.</definition>
<uris>
<uri type="URN">urn:miriam:hogenom</uri>
<uri type="URL">http://identifiers.org/hogenom/</uri>
</uris>
<namespace>hogenom</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19534752</documentation>
</documentations>
<resources>
<resource id="MIR:00100272" state="up" reliability="96">
<dataResource>http://pbil.univ-lyon1.fr/databases/hogenom/</dataResource>
<dataEntityExample>HBG284870</dataEntityExample>
<dataEntry>http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$id</dataEntry>
<dataInfo>HOGENOM at CNRS</dataInfo>
<dataInstitution>Laboratoire de Biométrie et Biologie Evolutive, CNRS, Lyon</dataInstitution>
<dataLocation>France</dataLocation>
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</resources>
<tags>
<tag>classification</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000214" pattern="^ENSGT\d+$">
<name>GeneTree</name>
<synonyms>
<synonym>Ensembl GeneTree</synonym>
</synonyms>
<definition>Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl.</definition>
<uris>
<uri type="URN">urn:miriam:genetree</uri>
<uri type="URL">http://identifiers.org/genetree/</uri>
</uris>
<namespace>genetree</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381931</documentation>
</documentations>
<resources>
<resource id="MIR:00100273" state="probably up" reliability="99">
<dataResource>http://www.ensembl.org/</dataResource>
<dataEntityExample>ENSGT00550000074763</dataEntityExample>
<dataEntry>http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$id</dataEntry>
<dataInfo>GeneTree at Ensembl</dataInfo>
<dataInstitution>Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>gene</tag>
<tag>protein</tag>
<tag>schema.org</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000215" pattern="^\w{4}$">
<name>HSSP</name>
<synonyms>
<synonym>Homology-derived Structure of Proteins</synonym>
</synonyms>
<definition>HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.</definition>
<uris>
<uri type="URN">urn:miriam:hssp</uri>
<uri type="URL">http://identifiers.org/hssp/</uri>
</uris>
<namespace>hssp</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:7937066</documentation>
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<resources>
<resource id="MIR:00100274" state="down" reliability="82">
<dataResource>http://swift.cmbi.kun.nl/swift/hssp/</dataResource>
<dataEntityExample>102l</dataEntityExample>
<dataEntry>ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$id.hssp.bz2</dataEntry>
<dataInfo>HSSP at EMBL</dataInfo>
<dataInstitution>Protein Design Group, European Molecular Biology Laboratory, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
<resource id="MIR:00100458" state="unknown" reliability="93">
<dataResource>ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/</dataResource>
<dataEntityExample>102l</dataEntityExample>
<dataEntry>ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$id.hssp.bz2</dataEntry>
<dataInfo>HSSP at CMBI</dataInfo>
<dataInstitution>Nijmegen Centre for Molecular Life Sciences, CMBI, Nijmegen</dataInstitution>
<dataLocation>Holland</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>protein</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000216" pattern="^Rv\d{4}(A|B|c)?$">
<name>MycoBrowser tuberculosis</name>
<synonyms>
<synonym>TubercuList</synonym>
</synonyms>
<definition>Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.</definition>
<uris>
<uri type="URN">urn:miriam:myco.tuber</uri>
<uri type="URL">http://identifiers.org/myco.tuber/</uri>
</uris>
<namespace>myco.tuber</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20980200</documentation>
</documentations>
<resources>
<resource id="MIR:00100275" state="up" reliability="95">
<dataResource>http://tuberculist.epfl.ch/</dataResource>
<dataEntityExample>Rv1908c</dataEntityExample>
<dataEntry>http://tuberculist.epfl.ch/quicksearch.php?gene+name=$id</dataEntry>
<dataInfo>MycoBrowser tuberculosis at Global Health Institute</dataInfo>
<dataInstitution>Global Health Institute, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000217" pattern="^ML\w+$">
<name>MycoBrowser leprae</name>
<synonyms>
<synonym>Leproma</synonym>
</synonyms>
<definition>Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.</definition>
<uris>
<uri type="URN">urn:miriam:myco.lepra</uri>
<uri type="URL">http://identifiers.org/myco.lepra/</uri>
</uris>
<namespace>myco.lepra</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20980200</documentation>
</documentations>
<resources>
<resource id="MIR:00100276" state="down" reliability="93">
<dataResource>http://mycobrowser.epfl.ch/leprosy.html</dataResource>
<dataEntityExample>ML0224</dataEntityExample>
<dataEntry>http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$id</dataEntry>
<dataInfo>MycoBrowser leprae at Global Health Institute</dataInfo>
<dataInstitution>Global Health Institute, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000218" pattern="^MMAR\_\d+$">
<name>MycoBrowser marinum</name>
<synonyms>
<synonym>marinolist</synonym>
</synonyms>
<definition>Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.</definition>
<uris>
<uri type="URN">urn:miriam:myco.marinum</uri>
<uri type="URL">http://identifiers.org/myco.marinum/</uri>
</uris>
<namespace>myco.marinum</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20980200</documentation>
</documentations>
<resources>
<resource id="MIR:00100277" state="down" reliability="93">
<dataResource>http://mycobrowser.epfl.ch/marinolist.html</dataResource>
<dataEntityExample>MMAR_2462</dataEntityExample>
<dataEntry>http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$id</dataEntry>
<dataInfo>MycoBrowser marinum at Global Health Institute</dataInfo>
<dataInstitution>Global Health Institute, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000219" pattern="^MSMEG\w+$">
<name>MycoBrowser smegmatis</name>
<synonyms>
<synonym>smegmalist</synonym>
</synonyms>
<definition>Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.</definition>
<uris>
<uri type="URN">urn:miriam:myco.smeg</uri>
<uri type="URL">http://identifiers.org/myco.smeg/</uri>
</uris>
<namespace>myco.smeg</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20980200</documentation>
</documentations>
<resources>
<resource id="MIR:00100278" state="down" reliability="93">
<dataResource>http://mycobrowser.epfl.ch/smegmalist.html</dataResource>
<dataEntityExample>MSMEG_3769</dataEntityExample>
<dataEntry>http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$id</dataEntry>
<dataInfo>MycoBrowser smegmatis at Global Health Institute</dataInfo>
<dataInstitution>Global Health Institute, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000220" pattern="^\d+$">
<name>Orphanet</name>
<synonyms>
<synonym>Orpha</synonym>
</synonyms>
<definition>Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases.</definition>
<uris>
<uri type="URN">urn:miriam:orphanet</uri>
<uri type="URL">http://identifiers.org/orphanet/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/orphanet</uri>
</uris>
<namespace>orphanet</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19058507</documentation>
</documentations>
<resources>
<resource id="MIR:00100279" state="up" reliability="99" primary="true">
<dataResource>http://www.orpha.net/consor/</dataResource>
<dataEntityExample>85163</dataEntityExample>
<dataEntry>http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$id</dataEntry>
<dataInfo>Orphanet at Inserm</dataInfo>
<dataInstitution>Inserm, Hôpital Broussais, Paris</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
<resource id="MIR:00100701" state="down" reliability="74">
<dataResource>http://orphanet.bio2rdf.org/fct</dataResource>
<dataEntityExample>85163</dataEntityExample>
<dataEntry>http://orphanet.bio2rdf.org/describe/?url=http://bio2rdf.org/orphanet:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
<tag>drug</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000221" pattern="^\w+$">
<name>OrthoDB</name>
<definition>OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups</definition>
<uris>
<uri type="URN">urn:miriam:orthodb</uri>
<uri type="URL">http://identifiers.org/orthodb/</uri>
</uris>
<namespace>orthodb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20972218</documentation>
</documentations>
<resources>
<resource id="MIR:00100280" state="up" reliability="99">
<dataResource>http://cegg.unige.ch/orthodb4</dataResource>
<dataEntityExample>Q9P0K8</dataEntityExample>
<dataEntry>http://cegg.unige.ch/orthodb/results?searchtext=$id</dataEntry>
<dataInfo>OrthoDB at Swiss Institute of Bioinformatics</dataInfo>
<dataInstitution>Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, Geneva</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>protein</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000222" pattern="^\d+$">
<name>Peroxibase</name>
<definition>Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.</definition>
<uris>
<uri type="URN">urn:miriam:peroxibase</uri>
<uri type="URL">http://identifiers.org/peroxibase/</uri>
</uris>
<namespace>peroxibase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19112168</documentation>
</documentations>
<resources>
<resource id="MIR:00100281" state="up" reliability="98">
<dataResource>http://peroxibase.toulouse.inra.fr/</dataResource>
<dataEntityExample>5282</dataEntityExample>
<dataEntry>http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$id</dataEntry>
<dataInfo>Peroxibase at University of Geneva</dataInfo>
<dataInstitution>Department of Plant Biology, University of Geneva, Geneva</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>enzyme</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000223" pattern="^\w+$">
<name>PhylomeDB</name>
<definition>PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.</definition>
<uris>
<uri type="URN">urn:miriam:phylomedb</uri>
<uri type="URL">http://identifiers.org/phylomedb/</uri>
</uris>
<namespace>phylomedb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17962297</documentation>
</documentations>
<resources>
<resource id="MIR:00100282" state="probably up" reliability="97">
<dataResource>http://phylomedb.org/</dataResource>
<dataEntityExample>Phy000CLXM_RAT</dataEntityExample>
<dataEntry>http://phylomedb.org/?seqid=$id</dataEntry>
<dataInfo>PhylomeDB at Centro de Investigación Príncipe Felipe</dataInfo>
<dataInstitution>Bioinformatics Department,Centro de Investigación Príncipe Felipe, Valencia</dataInstitution>
<dataLocation>Spain</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>protein</tag>
<tag>taxonomy</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000224" pattern="^\d+$">
<name>SubstrateDB</name>
<synonyms>
<synonym>PMAP substrateDB</synonym>
</synonyms>
<definition>The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.</definition>
<uris>
<uri type="URN">urn:miriam:pmap.substratedb</uri>
<uri type="URL">http://identifiers.org/pmap.substratedb/</uri>
</uris>
<namespace>pmap.substratedb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18842634</documentation>
</documentations>
<resources>
<resource id="MIR:00100283" state="up" reliability="96">
<dataResource>http://substrate.burnham.org/</dataResource>
<dataEntityExample>1915</dataEntityExample>
<dataEntry>http://substrate.burnham.org/protein/annotation/$id/html</dataEntry>
<dataInfo>SubstrateDB at The Burnham Institute for Medical Research</dataInfo>
<dataInstitution>The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>protein</tag>
<tag>reaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000225" pattern="^\d+$">
<name>CutDB</name>
<synonyms>
<synonym>PMAP cutDB</synonym>
</synonyms>
<definition>The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).</definition>
<uris>
<uri type="URN">urn:miriam:pmap.cutdb</uri>
<uri type="URL">http://identifiers.org/pmap.cutdb/</uri>
</uris>
<namespace>pmap.cutdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17142225</documentation>
</documentations>
<resources>
<resource id="MIR:00100284" state="up" reliability="99">
<dataResource>http://cutdb.burnham.org</dataResource>
<dataEntityExample>25782</dataEntityExample>
<dataEntry>http://cutdb.burnham.org/relation/show/$id</dataEntry>
<dataInfo>CutDB at The Burnham Institute for Medical Research</dataInfo>
<dataInstitution>The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>protein</tag>
<tag>reaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000226" pattern="^\w+$">
<name>ProtClustDB</name>
<synonyms>
<synonym>Protein Clusters Database</synonym>
<synonym>Entrez ProtClustDB</synonym>
</synonyms>
<definition>ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.</definition>
<uris>
<uri type="URN">urn:miriam:protclustdb</uri>
<uri type="URL">http://identifiers.org/protclustdb/</uri>
</uris>
<namespace>protclustdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18940865</documentation>
</documentations>
<resources>
<resource id="MIR:00100285" state="down" reliability="88">
<dataResource>http://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters</dataResource>
<dataEntityExample>O80725</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$id</dataEntry>
<dataInfo>ProtClustDB at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000227" pattern="^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$">
<name>PMP</name>
<synonyms>
<synonym>Protein Model Portal</synonym>
</synonyms>
<definition>The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers.</definition>
<uris>
<uri type="URN">urn:miriam:pmp</uri>
<uri type="URL">http://identifiers.org/pmp/</uri>
</uris>
<namespace>pmp</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19037750</documentation>
</documentations>
<resources>
<resource id="MIR:00100286" state="down" reliability="90">
<dataResource>http://www.proteinmodelportal.org/</dataResource>
<dataEntityExample>Q0VCA6</dataEntityExample>
<dataEntry>http://www.proteinmodelportal.org/query/uniprot/$id</dataEntry>
<dataInfo>PMP at University of Basel</dataInfo>
<dataInstitution>Biozentrum, University of Basel, Basel</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000228" pattern="^\d+$">
<name>ProtoNet ProteinCard</name>
<definition>ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.</definition>
<uris>
<uri type="URN">urn:miriam:protonet.proteincard</uri>
<uri type="URL">http://identifiers.org/protonet.proteincard/</uri>
</uris>
<namespace>protonet.proteincard</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16672244</documentation>
</documentations>
<resources>
<resource id="MIR:00100287" state="up" reliability="99">
<dataResource>http://www.protonet.cs.huji.ac.il/</dataResource>
<dataEntityExample>16941567</dataEntityExample>
<dataEntry>http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$id</dataEntry>
<dataInfo>ProtoNet at Hebrew University</dataInfo>
<dataInstitution>Hebrew University, Jerusalem</dataInstitution>
<dataLocation>Israel</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000229" pattern="^\d+$">
<name>ProtoNet Cluster</name>
<definition>ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.</definition>
<uris>
<uri type="URN">urn:miriam:protonet.cluster</uri>
<uri type="URL">http://identifiers.org/protonet.cluster/</uri>
</uris>
<namespace>protonet.cluster</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16672244</documentation>
</documentations>
<resources>
<resource id="MIR:00100288" state="up" reliability="99">
<dataResource>http://www.protonet.cs.huji.ac.il/</dataResource>
<dataEntityExample>4349895</dataEntityExample>
<dataEntry>http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$id</dataEntry>
<dataInfo>ProtoNet at Hebrew University</dataInfo>
<dataInstitution>Hebrew University, Jerusalem</dataInstitution>
<dataLocation>Israel</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>clustering</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000230" pattern="^\d+$">
<name>REBASE</name>
<synonyms>
<synonym>Restriction Enzyme Database</synonym>
</synonyms>
<definition>REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.</definition>
<uris>
<uri type="URN">urn:miriam:rebase</uri>
<uri type="URL">http://identifiers.org/rebase/</uri>
</uris>
<namespace>rebase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19846593</documentation>
</documentations>
<resources>
<resource id="MIR:00100289" state="up" reliability="99">
<dataResource>http://rebase.neb.com/rebase/</dataResource>
<dataEntityExample>101</dataEntityExample>
<dataEntry>http://rebase.neb.com/rebase/enz/$id.html</dataEntry>
<dataInfo>REBASE at New England Biolabs</dataInfo>
<dataInstitution>New England Biolabs, Ipswich, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>enzyme</tag>
<tag>reaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000231" pattern="^\w+$" restricted="true">
<name>SWISS-MODEL</name>
<definition>The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for sequences registered is SWISS-PROT.</definition>
<uris>
<uri type="URN">urn:miriam:swiss-model</uri>
<uri type="URL">http://identifiers.org/swiss-model/</uri>
</uris>
<namespace>swiss-model</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18931379</documentation>
</documentations>
<resources>
<resource id="MIR:00100290" state="up" reliability="98">
<dataResource>http://swissmodel.expasy.org/</dataResource>
<dataEntityExample>P23298</dataEntityExample>
<dataEntry>http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id</dataEntry>
<dataInfo>SWISS-MODEL at SIB Swiss Institute of Bioinformatics</dataInfo>
<dataInstitution>Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="4" desc="Identifier instability">
<statement>Identifiers to individual models are not stable, since they can change between releases.</statement>
<link desc="FAQ">http://swissmodel.expasy.org/?pid=smd06</link>
</restriction>
</restrictions>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000232" pattern="^\D{4}\d{6}(\-\D{2})?$">
<name>VectorBase</name>
<definition>VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis.</definition>
<uris>
<uri type="URN">urn:miriam:vectorbase</uri>
<uri type="URL">http://identifiers.org/vectorbase/</uri>
</uris>
<namespace>vectorbase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19028744</documentation>
</documentations>
<resources>
<resource id="MIR:00100291" state="down" reliability="43" primary="true">
<dataResource>http://www.vectorbase.org/</dataResource>
<dataEntityExample>ISCW007415</dataEntityExample>
<dataEntry>https://www.vectorbase.org/search/site/$id?&site="Genome"</dataEntry>
<dataInfo>Vectorbase at EMBL-EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>genome</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000233" pattern="^DOID\:\d+$">
<name>Human Disease Ontology</name>
<synonyms>
<synonym>DO</synonym>
</synonyms>
<definition>The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.</definition>
<uris>
<uri type="URN">urn:miriam:doid</uri>
<uri type="URL">http://identifiers.org/doid/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.do</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.do/</uri>
</uris>
<namespace>doid</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkr972</documentation>
<documentation type="URL">http://www.disease-ontology.org/</documentation>
</documentations>
<resources>
<resource id="MIR:00100292" state="up" reliability="96">
<dataResource>http://bioportal.bioontology.org/ontologies/DOID</dataResource>
<dataEntityExample>DOID:11337</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/DOID/$id</dataEntry>
<dataInfo>Human Disease Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100293" state="up" reliability="98">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/doid</dataResource>
<dataEntityExample>DOID:11337</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=$id</dataEntry>
<dataInfo>Human Disease Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100297" state="up" reliability="99">
<dataResource>http://disease-ontology.org/</dataResource>
<dataEntityExample>DOID:11337</dataEntityExample>
<dataEntry>http://disease-ontology.org/term/$id</dataEntry>
<dataInfo>Human Disease Ontology at Northwestern University</dataInfo>
<dataInstitution>University of Maryland (Maryland) and Northwestern University (Illinois)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
<tag>human</tag>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000234" pattern="^CCO\:\w+$">
<name>Cell Cycle Ontology</name>
<definition>The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.</definition>
<uris>
<uri type="URN">urn:miriam:cco</uri>
<uri type="URL">http://identifiers.org/cco/</uri>
</uris>
<namespace>cco</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19480664</documentation>
</documentations>
<resources>
<resource id="MIR:00100294" state="down" reliability="73">
<dataResource>https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO</dataResource>
<dataEntityExample>CCO:P0000023</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>Cell Cycle Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100295" obsolete="true">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>CCO:P0000023</dataEntityExample>
<dataEntry>http://bioportal.bioontology.org/ontologies/1507?p=terms&conceptid=$id</dataEntry>
<dataInfo>Cell Cycle Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000235" pattern="MIMAT\d{7}">
<name>miRBase mature sequence</name>
<definition>The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.</definition>
<uris>
<uri type="URN">urn:miriam:mirbase.mature</uri>
<uri type="URL">http://identifiers.org/mirbase.mature/</uri>
</uris>
<namespace>mirbase.mature</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkq1027</documentation>
</documentations>
<resources>
<resource id="MIR:00100296" state="up" reliability="99">
<dataResource>http://www.mirbase.org/</dataResource>
<dataEntityExample>MIMAT0000001</dataEntityExample>
<dataEntry>http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id</dataEntry>
<dataInfo>miRBase</dataInfo>
<dataInstitution>Faculty of Life Sciences, University of Manchester</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
</datatype>
<datatype id="MIR:00000236" pattern="^NX_\w+">
<name>nextProt</name>
<definition>neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases.</definition>
<uris>
<uri type="URN">urn:miriam:nextprot</uri>
<uri type="URL">http://identifiers.org/nextprot/</uri>
</uris>
<namespace>nextprot</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22139911</documentation>
<documentation type="URL">http://www.nextprot.org/db/open/page/about-nextprot</documentation>
</documentations>
<resources>
<resource id="MIR:00100300" state="probably up" reliability="98">
<dataResource>http://www.nextprot.org/</dataResource>
<dataEntityExample>NX_O00165</dataEntityExample>
<dataEntry>http://www.nextprot.org/db/entry/$id</dataEntry>
<dataInfo>nextProt at Swiss Institute of Bioinformatics</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics, Geneva</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000237" pattern="^\d{1,7}\-\d{2}\-\d$" restricted="true">
<name>CAS</name>
<synonyms>
<synonym>Chemical Abstracts Service</synonym>
<synonym>CAS Registry Number</synonym>
<synonym>CAS Number</synonym>
<synonym>CASRN</synonym>
</synonyms>
<definition>CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.</definition>
<uris>
<uri type="URN">urn:miriam:cas</uri>
<uri type="URL">http://identifiers.org/cas/</uri>
</uris>
<namespace>cas</namespace>
<documentations>
<documentation type="URL">http://www.cas.org/index.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100301" state="up" reliability="99">
<dataResource>http://commonchemistry.org</dataResource>
<dataEntityExample>50-00-0</dataEntityExample>
<dataEntry>http://commonchemistry.org/ChemicalDetail.aspx?ref=$id</dataEntry>
<dataInfo>CAS through Common Chemistry</dataInfo>
<dataInstitution>American Chemistry Society, Washington, DC</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100302" obsolete="true">
<dataResource>http://www.ncbi.nlm.nih.gov/pccompound</dataResource>
<dataEntityExample>50-00-0</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=$id</dataEntry>
<dataInfo>CAS through PubChem Compound</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>CAS provides fee-based services.</statement>
<link desc="brief costing description">http://cas.org/aboutcas/faq.html#cost</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000238" pattern="^(T0\d+|\w{3,5})$">
<name>KEGG Genome</name>
<synonyms>
<synonym>KEGG Organism</synonym>
<!--<synonym>KEGG</synonym>-->
</synonyms>
<definition>KEGG Genome is a collection of organisms whose genomes have been completely sequenced.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.genome</uri>
<uri type="URL">http://identifiers.org/kegg.genome/</uri>
</uris>
<namespace>kegg.genome</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22080510</documentation>
</documentations>
<resources>
<resource id="MIR:00100303" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/catalog/org_list.html</dataResource>
<dataEntityExample>eco</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG Genome Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center, Kyoto</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000239" pattern="^T3\d+$">
<name>KEGG Metagenome</name>
<!--<synonyms>-->
<!--<synonym>KEGG</synonym>-->
<!--</synonyms>-->
<definition>The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.metagenome</uri>
<uri type="URL">http://identifiers.org/kegg.metagenome/</uri>
</uris>
<namespace>kegg.metagenome</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22080510</documentation>
</documentations>
<resources>
<resource id="MIR:00100304" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/catalog/org_list3.html</dataResource>
<dataEntityExample>T30002</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG Metagenome Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center, Kyoto</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000240" pattern="^oai\:cwi\.nl\:\d+$">
<name>NARCIS</name>
<synonyms>
<synonym>National Academic Research and Collaborations Information System</synonym>
</synonyms>
<definition>NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases.</definition>
<uris>
<uri type="URN">urn:miriam:narcis</uri>
<uri type="URL">http://identifiers.org/narcis/</uri>
</uris>
<namespace>narcis</namespace>
<documentations>
<documentation type="URL">http://www.narcis.nl/about/Language/en</documentation>
</documentations>
<resources>
<resource id="MIR:00100306" state="up" reliability="98">
<dataResource>http://www.narcis.nl/?Language=en</dataResource>
<dataEntityExample>oai:cwi.nl:4725</dataEntityExample>
<dataEntry>http://www.narcis.nl/publication/RecordID/$id</dataEntry>
<dataInfo>NARCIS at The Hague</dataInfo>
<dataInstitution>NARCIS, Royal Netherlands Academy of Science and Arts</dataInstitution>
<dataLocation>Holland</dataLocation>
</resource>
<resource id="MIR:00100305" obsolete="true">
<dataResource>http://persistent-identifier.nl/</dataResource>
<dataEntityExample>oai:cwi.nl:4725</dataEntityExample>
<dataEntry>http://oai.cwi.nl/oai?verb=GetRecord&metadataPrefix=nl_didl&identifier=oai:cwi.nl:$id</dataEntry>
<dataInfo>Dutch publication NBN through Persistent-identifier (redirection)</dataInfo>
<dataInstitution>Dans, The Hague</dataInstitution>
<dataLocation>Holland</dataLocation>
</resource>
</resources>
<tags>
<tag>bibliography</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000241" pattern="^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$">
<name>Japan Chemical Substance Dictionary</name>
<definition>The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).</definition>
<uris>
<uri type="URN">urn:miriam:jcsd</uri>
<uri type="URL">http://identifiers.org/jcsd/</uri>
</uris>
<namespace>jcsd</namespace>
<documentations>
<documentation type="URL">http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp</documentation>
</documentations>
<resources>
<resource id="MIR:00100307" state="down" reliability="66">
<dataResource>http://jglobal.jst.go.jp/en/</dataResource>
<dataEntityExample>J55.713G</dataEntityExample>
<dataEntry>http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$id</dataEntry>
<dataInfo>Japan Chemical Substance Dictionary</dataInfo>
<dataInstitution>Japan Science and Technology Agency</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000242" pattern="^PW:\d{7}$">
<name>Pathway Ontology</name>
<definition>The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.</definition>
<uris>
<uri type="URN">urn:miriam:pw</uri>
<uri type="URL">http://identifiers.org/pw/</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.pw/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.pw</uri>
</uris>
<namespace>pw</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21478484</documentation>
</documentations>
<resources>
<resource id="MIR:00100309" state="up" reliability="99">
<dataResource>http://rgd.mcw.edu/rgdweb/ontology/search.html</dataResource>
<dataEntityExample>PW:0000208</dataEntityExample>
<dataEntry>http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=$id</dataEntry>
<dataInfo>Pathway Ontology at Rat Genome Database</dataInfo>
<dataInstitution>Medical College of Wisconsin, Wisconsin</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100310" state="up" reliability="98">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/pw</dataResource>
<dataEntityExample>PW:0000208</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/pw/terms?obo_id=$id</dataEntry>
<dataInfo>Pathway Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100311" state="up" reliability="97">
<dataResource>http://bioportal.bioontology.org/ontologies/PW</dataResource>
<dataEntityExample>PW:0000208</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/PW/$id</dataEntry>
<dataInfo>Pathway Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>mammalian</tag>
<tag>ontology</tag>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000243" pattern="^[SED]R[APRSXZ]\d+$">
<name>Sequence Read Archive</name>
<definition>The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.</definition>
<uris>
<uri type="URN">urn:miriam:insdc.sra</uri>
<uri type="URL">http://identifiers.org/insdc.sra/</uri>
</uris>
<namespace>insdc.sra</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22009675</documentation>
</documentations>
<resources>
<resource id="MIR:00100312" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/sra</dataResource>
<dataEntityExample>SRX000007</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/sra/$id?&report=full</dataEntry>
<dataInfo>Sequence Read Archive at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100313" state="probably up" reliability="99">
<dataResource>http://www.ebi.ac.uk/ena</dataResource>
<dataEntityExample>SRX000007</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/$id</dataEntry>
<dataInfo>European Nucleotide Archive (ENA)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100314" state="up" reliability="96">
<dataResource>http://trace.ddbj.nig.ac.jp/dra/</dataResource>
<dataEntityExample>SRX000007</dataEntityExample>
<dataEntry>http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$id</dataEntry>
<dataInfo>DDBJ Sequence Read Archive (DRA)</dataInfo>
<dataInstitution>DNA Data Bank of Japan, Mishima, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000244" pattern="^\w+$">
<name>ScerTF</name>
<definition>ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.</definition>
<uris>
<uri type="URN">urn:miriam:scretf</uri>
<uri type="URL">http://identifiers.org/scretf/</uri>
</uris>
<namespace>scretf</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22140105</documentation>
</documentations>
<resources>
<resource id="MIR:00100315" state="up" reliability="99">
<dataResource>http://stormo.wustl.edu/ScerTF/</dataResource>
<dataEntityExample>RSC3</dataEntityExample>
<dataEntry>http://stormo.wustl.edu/ScerTF/details/$id/</dataEntry>
<dataInfo>ScerTF at Washington University</dataInfo>
<dataInstitution>Department of Genetics, Washington University Medical School, St Louis, Missouri</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000245" pattern="^PA\w+$" restricted="true">
<name>PharmGKB Gene</name>
<definition>The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.</definition>
<uris>
<uri type="URN">urn:miriam:pharmgkb.gene</uri>
<uri type="URL">http://identifiers.org/pharmgkb.gene/</uri>
</uris>
<namespace>pharmgkb.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22103613</documentation>
</documentations>
<resources>
<resource id="MIR:00100316" state="down" reliability="73">
<dataResource>http://www.pharmgkb.org/</dataResource>
<dataEntityExample>PA131</dataEntityExample>
<dataEntry>http://www.pharmgkb.org/gene/$id</dataEntry>
<dataInfo>PharmGKB Gene at Stanford</dataInfo>
<dataInstitution>Department of Genetics, School of Medicine, Stanford University, Stanford, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The data may be used for research purposes only.</statement>
<link desc="terms and conditions of data use">http://www.pharmgkb.org/home/policies/web-data.jsp</link>
</restriction>
</restrictions>
<tags>
<tag>gene</tag>
<tag>pharmacogenomics</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000246" pattern="^MNEST\d+$">
<name>miRNEST</name>
<definition>miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.</definition>
<uris>
<uri type="URN">urn:miriam:mirnest</uri>
<uri type="URL">http://identifiers.org/mirnest/</uri>
</uris>
<namespace>mirnest</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22135287</documentation>
</documentations>
<resources>
<resource id="MIR:00100317" state="up" reliability="92">
<dataResource>http://rhesus.amu.edu.pl/mirnest/copy/</dataResource>
<dataEntityExample>MNEST029358</dataEntityExample>
<dataEntry>http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$id</dataEntry>
<dataInfo>miRNEST at Adam Mickiewicz University</dataInfo>
<dataInstitution>Institute of Molecular Biology, Adam Mickiewicz University, Poznan</dataInstitution>
<dataLocation>Poland</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000247" pattern="^\d+$">
<name>NAPP</name>
<synonyms>
<synonym>Nucleic Acid Phylogenetic Profiling</synonym>
</synonyms>
<definition>NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters.</definition>
<uris>
<uri type="URN">urn:miriam:napp</uri>
<uri type="URL">http://identifiers.org/napp/</uri>
</uris>
<namespace>napp</namespace>
<resources>
<resource id="MIR:00100318" state="up" reliability="97">
<dataResource>http://napp.u-psud.fr/</dataResource>
<dataEntityExample>351</dataEntityExample>
<dataEntry>http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$id</dataEntry>
<dataInfo>NAPP at CNRS</dataInfo>
<dataInstitution>Institut de Génétique et Microbiologie, UMR 8621, CNRS, Université Paris Sud, Paris</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000248" pattern="^\d+$">
<name>NONCODE v3</name>
<definition>NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.</definition>
<uris>
<uri type="URN">urn:miriam:noncodev3</uri>
<uri type="URL">http://identifiers.org/noncodev3/</uri>
<uri type="URN" deprecated="true">urn:miriam:noncode</uri>
<uri type="URL" deprecated="true">http://identifiers.org/noncode/</uri>
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<namespace>noncodev3</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22135294</documentation>
</documentations>
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<resource id="MIR:00100319" state="down" reliability="56">
<dataResource>http://www.noncode.org/</dataResource>
<dataEntityExample>377550</dataEntityExample>
<dataEntry>http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$id</dataEntry>
<dataInfo>NONCODE at Chinese Academy of Sciences</dataInfo>
<dataInstitution>Bioinformatics Research Group, Chinese Academy of Sciences, Beijing</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000249" pattern="^virsi\d+$">
<name>VIRsiRNA</name>
<synonyms>
<synonym>Virus siRNA database</synonym>
<synonym>VIRsiRNAdb</synonym>
</synonyms>
<definition>The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.</definition>
<uris>
<uri type="URN">urn:miriam:virsirna</uri>
<uri type="URL">http://identifiers.org/virsirna/</uri>
</uris>
<namespace>virsirna</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22139916</documentation>
</documentations>
<resources>
<resource id="MIR:00100320" state="up" reliability="97">
<dataResource>http://crdd.osdd.net/servers/virsirnadb</dataResource>
<dataEntityExample>virsi1909</dataEntityExample>
<dataEntry>http://crdd.osdd.net/servers/virsirnadb/record.php?details=$id</dataEntry>
<dataInfo>VIRsiRNA at Institute of Microbial Technology</dataInfo>
<dataInstitution>Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India</dataInstitution>
<dataLocation>India</dataLocation>
</resource>
</resources>
<tags>
<tag>mammalian</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000250" pattern="^[A-Za-z_0-9]+$">
<name>ELM</name>
<synonyms>
<synonym>Eukaryotic Linear Motifs</synonym>
</synonyms>
<definition>Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances.</definition>
<uris>
<uri type="URN">urn:miriam:elm</uri>
<uri type="URL">http://identifiers.org/elm/</uri>
</uris>
<namespace>elm</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22110040</documentation>
</documentations>
<resources>
<resource id="MIR:00100321" state="up" reliability="99">
<dataResource>http://elm.eu.org/</dataResource>
<dataEntityExample>CLV_MEL_PAP_1</dataEntityExample>
<dataEntry>http://elm.eu.org/elms/elmPages/$id.html</dataEntry>
<dataInfo>ELM at EMBL (Germany)</dataInfo>
<dataInstitution>Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>eukaryotic</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000251" pattern="^\d+$">
<name>MimoDB</name>
<synonyms>
<synonym>Mimotope Database</synonym>
<synonym>BDB</synonym>
<synonym>Biopanning Data Bank</synonym>
</synonyms>
<definition>MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.</definition>
<uris>
<uri type="URN">urn:miriam:mimodb</uri>
<uri type="URL">http://identifiers.org/mimodb/</uri>
</uris>
<namespace>mimodb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22053087</documentation>
</documentations>
<resources>
<resource id="MIR:00100322" state="up" reliability="92">
<dataResource>http://immunet.cn/bdb/</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://immunet.cn/bdb/index.php/mimoset/$id</dataEntry>
<dataInfo>BDB at University of Electronic Science and Technology of China</dataInfo>
<dataInstitution>Key Laboratory for Neuroinformation of Ministry of Education, University of Electronic Science and Technology of China, Sichuan</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000252" pattern="^\d+$">
<name>SitEx</name>
<definition>SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.</definition>
<uris>
<uri type="URN">urn:miriam:sitex</uri>
<uri type="URL">http://identifiers.org/sitex/</uri>
</uris>
<namespace>sitex</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22139920</documentation>
</documentations>
<resources>
<resource id="MIR:00100323" state="down" reliability="72">
<dataResource>http://www-bionet.sscc.ru/sitex/</dataResource>
<dataEntityExample>1000</dataEntityExample>
<dataEntry>http://www-bionet.sscc.ru/sitex/index.php?siteid=$id</dataEntry>
<dataInfo>SitEx at Novosibirsk State University</dataInfo>
<dataInstitution>Novosibirsk State University, Novosibirsk</dataInstitution>
<dataLocation>Russia</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>eukaryotic</tag>
<tag>sequence</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000253" pattern="^[A-Z0-9]+$">
<name>BYKdb</name>
<synonyms>
<synonym>Bacterial protein tYrosine Kinase database</synonym>
</synonyms>
<definition>The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.</definition>
<uris>
<uri type="URN">urn:miriam:bykdb</uri>
<uri type="URL">http://identifiers.org/bykdb/</uri>
</uris>
<namespace>bykdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22080550</documentation>
</documentations>
<resources>
<resource id="MIR:00100324" state="up" reliability="72">
<dataResource>http://bykdb.ibcp.fr/BYKdb/</dataResource>
<dataEntityExample>A0A010GJI9</dataEntityExample>
<dataEntry>https://bykdb.ibcp.fr/data/html/annotated/$id.html</dataEntry>
<dataInfo>BYKdb at CNRS</dataInfo>
<dataInstitution>Unité Bases Moléculaires et Structurales des Systèmes Infectieux; CNRS - Université Claude Bernard, Lyon</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>microbial</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000254" pattern="^\d+$" restricted="true">
<name>Conoserver</name>
<definition>ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.</definition>
<uris>
<uri type="URN">urn:miriam:conoserver</uri>
<uri type="URL">http://identifiers.org/conoserver/</uri>
</uris>
<namespace>conoserver</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18065428</documentation>
<documentation type="PMID">urn:miriam:pubmed:22058133</documentation>
</documentations>
<resources>
<resource id="MIR:00100325" state="up" reliability="99">
<dataResource>http://www.conoserver.org/</dataResource>
<dataEntityExample>2639</dataEntityExample>
<dataEntry>http://www.conoserver.org/?page=card&table=protein&id=$id</dataEntry>
<dataInfo>ConoServer at University of Queensland</dataInfo>
<dataInstitution>Institute for Molecular Bioscience, The University of Queensland, Brisbane</dataInstitution>
<dataLocation>Australia</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Conoserver can only be used for academic research.</statement>
<link desc="the statement on each page">http://www.conoserver.org/</link>
</restriction>
</restrictions>
<tags>
<tag>drug</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000255" pattern="^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$">
<name>TopFind</name>
<definition>TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.</definition>
<uris>
<uri type="URN">urn:miriam:topfind</uri>
<uri type="URL">http://identifiers.org/topfind/</uri>
</uris>
<namespace>topfind</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22102574</documentation>
</documentations>
<resources>
<resource id="MIR:00100326" state="up" reliability="93">
<dataResource>http://clipserve.clip.ubc.ca/topfind</dataResource>
<dataEntityExample>Q9UKQ2</dataEntityExample>
<dataEntry>http://clipserve.clip.ubc.ca/topfind/proteins/$id</dataEntry>
<dataInfo>TopFind at University of British Columbia</dataInfo>
<dataInstitution>Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000256" pattern="^\w+$">
<name>MIPModDB</name>
<definition>MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.</definition>
<uris>
<uri type="URN">urn:miriam:mipmod</uri>
<uri type="URL">http://identifiers.org/mipmod/</uri>
</uris>
<namespace>mipmod</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22080560</documentation>
</documentations>
<resources>
<resource id="MIR:00100327" state="up" reliability="96">
<dataResource>http://bioinfo.iitk.ac.in/MIPModDB</dataResource>
<dataEntityExample>HOSAPI0399</dataEntityExample>
<dataEntry>http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$id</dataEntry>
<dataInfo>MIPModDB at Indian Institute of Technology Kanpur</dataInfo>
<dataInstitution>Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur</dataInstitution>
<dataLocation>India</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000257" pattern="^\d+$" restricted="true">
<name>Cell Image Library</name>
<synonyms>
<synonym>CIL</synonym>
<synonym>The Cell: An Image Library-CCDB</synonym>
<synonym>The Cell: An Image Library-Cell Centered Database</synonym>
</synonyms>
<definition>The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.</definition>
<uris>
<uri type="URN">urn:miriam:cellimage</uri>
<uri type="URL">http://identifiers.org/cellimage/</uri>
</uris>
<namespace>cellimage</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1017%2FS1551929511000034</documentation>
<documentation type="URL">http://cellimagelibrary.org/pages/about</documentation>
</documentations>
<resources>
<resource id="MIR:00100328" state="up" reliability="99">
<dataResource>http://cellimagelibrary.org/</dataResource>
<dataEntityExample>24801</dataEntityExample>
<dataEntry>http://cellimagelibrary.org/images/$id</dataEntry>
<dataInfo>Cell Image Library at American Society for Cell Biology</dataInfo>
<dataInstitution>American Society for Cell Biology, Bethesda, Maryland and The National Center for Microscopy and Imaging Research, San Diego, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Each image may be individually associated with its own copyright restriction, which should be consulted for appropriateness by users.</statement>
<link desc="General description of licenses.">http://cellimagelibrary.org/pages/license</link>
</restriction>
</restrictions>
<tags>
<tag>image library</tag>
</tags>
</datatype>
<datatype id="MIR:00000258" pattern="^\w+(\-|\.|\w)*$">
<name>COMBINE specifications</name>
<definition>The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.</definition>
<uris>
<uri type="URN">urn:miriam:combine.specifications</uri>
<uri type="URL">http://identifiers.org/combine.specifications/</uri>
</uris>
<namespace>combine.specifications</namespace>
<documentations>
<documentation type="URL">http://co.mbine.org/about</documentation>
</documentations>
<resources>
<resource id="MIR:00100329" state="up" reliability="99">
<dataResource>http://co.mbine.org/standards/</dataResource>
<dataEntityExample>sbgn.er.level-1.version-1.2</dataEntityExample>
<dataEntry>http://co.mbine.org/specifications/$id</dataEntry>
<dataInfo>COMBINE at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000259" pattern="^ZDB\-GEN0\-\d+\-\d+$">
<name>ZFIN Phenotype</name>
<definition>ZFIN serves as the zebrafish model organism database. This collection references the phenotypes observed for any given genotype.</definition>
<uris>
<uri type="URN">urn:miriam:zfin.phenotype</uri>
<uri type="URL">http://identifiers.org/zfin.phenotype/</uri>
</uris>
<namespace>zfin.phenotype</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17991680</documentation>
</documentations>
<resources>
<resource id="MIR:00100332" state="up" reliability="100">
<dataResource>http://zfin.org</dataResource>
<dataEntityExample>ZDB-GENO-980202-899</dataEntityExample>
<dataEntry>http://zfin.org/$id</dataEntry>
<dataInfo>ZFIN Phenotype at University of Oregon</dataInfo>
<dataInstitution>Zebrafish Information Network, University of Oregon, USA</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000260" pattern="^ZDB\-GEN0\-\d+\-\d+$">
<name>ZFIN Expression</name>
<definition>ZFIN serves as the zebrafish model organism database. This collection references the set of expressed genes for any given genotype.</definition>
<uris>
<uri type="URN">urn:miriam:zfin.expression</uri>
<uri type="URL">http://identifiers.org/zfin.expression/</uri>
</uris>
<namespace>zfin.expression</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17991680</documentation>
</documentations>
<resources>
<resource id="MIR:00100333" state="up" reliability="93">
<dataResource>http://zfin.org</dataResource>
<dataEntityExample>ZDB-GENO-980202-899</dataEntityExample>
<dataEntry>http://zfin.org/$id</dataEntry>
<dataInfo>ZFIN Expression at University of Oregon</dataInfo>
<dataInstitution>Zebrafish Information Network, University of Oregon, USA</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000261" pattern="^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$">
<name>CABRI</name>
<definition>CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it.</definition>
<uris>
<uri type="URN">urn:miriam:cabri</uri>
<uri type="URL">http://identifiers.org/cabri/</uri>
</uris>
<namespace>cabri</namespace>
<documentations>
<documentation type="URL">http://www.cabri.org/guidelines.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100334" state="up" reliability="95" primary="true">
<dataResource>http://www.cabri.org/</dataResource>
<dataEntityExample>dsmz_mutz-id:ACC 291</dataEntityExample>
<dataEntry>http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id]</dataEntry>
<dataInfo>CABRI Cell Lines catalogue in Genova (SRS)</dataInfo>
<dataInstitution>National Cancer Research Institute of Genova, Genova</dataInstitution>
<dataLocation>Italy</dataLocation>
</resource>
<resource id="MIR:00100335" state="up" reliability="95">
<dataResource>http://www.be.cabri.org/</dataResource>
<dataEntityExample>dsmz_mutz-id:ACC 291</dataEntityExample>
<dataEntry>http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id]</dataEntry>
<dataInfo>CABRI Cell Lines catalogue in Brussels (SRS)</dataInfo>
<dataInstitution>BCCM, Brussels</dataInstitution>
<dataLocation>Belgium</dataLocation>
</resource>
<resource id="MIR:00100336" obsolete="true">
<dataResource>http://www.fr.cabri.org/</dataResource>
<dataEntityExample>dsmz_mutz-id:ACC 291</dataEntityExample>
<dataEntry>http://www.fr.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id]</dataEntry>
<dataInfo>CABRI Cell Lines catalogue in Paris (SRS)</dataInfo>
<dataInstitution>nstitut Pasteur, Paris</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>catalogue</tag>
<tag>eukaryotic</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000262" pattern="^\w{2,3}\d{2,4}(\w)?$" restricted="true">
<name>CYGD</name>
<definition>The MIPS Comprehensive Yeast Genome Database (CYGD) provides information on the molecular structure and functional network of the entirely sequenced the budding yeast, Saccharomyces cerevisiae, as well as on related yeasts which are used for comparative analysis.</definition>
<uris>
<uri type="URN">urn:miriam:cygd</uri>
<uri type="URL">http://identifiers.org/cygd/</uri>
</uris>
<namespace>cygd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608217</documentation>
<documentation type="URL">http://mips.gsf.de/</documentation>
</documentations>
<resources>
<resource id="MIR:00100684" state="probably up" reliability="96">
<dataResource>http://pedant.helmholtz-muenchen.de/pedant3htmlview/pedant3view?Method=start_method&Db=p3_p13838_Sac_cerev</dataResource>
<dataEntityExample>YFL039c</dataEntityExample>
<dataEntry>http://pedant.helmholtz-muenchen.de/pedant3htmlview/pedant3view?Db=p3_p13838_Sac_cerev&Method=ReportGene&GeneticelemCode=$id</dataEntry>
<dataInfo>CYGD PEDANT Interface at Biomax Informatics</dataInfo>
<dataInstitution>Biomax Informatics AG, Planegg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
<resource id="MIR:00100337" obsolete="true">
<dataResource>http://mips.gsf.de/genre/proj/yeast/</dataResource>
<dataEntityExample>YFL039c</dataEntityExample>
<dataEntry>http://mips.gsf.de/genre/proj/yeast/singleGeneReport.html?entry=$id</dataEntry>
<dataInfo>CYGD at MIPS</dataInfo>
<dataInstitution>Institute for Bioinformatics (MIPS)</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
<resource id="MIR:00100338" obsolete="true">
<dataResource>http://mips.helmholtz-muenchen.de/genre/proj/yeast/</dataResource>
<dataEntityExample>YFL039c</dataEntityExample>
<dataEntry>http://mips.helmholtz-muenchen.de/genre/proj/yeast/singleGeneReport.html?entry=$id</dataEntry>
<dataInfo>CYGD at MIPS (GmbH)</dataInfo>
<dataInstitution>Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, GmbH, Neuherberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Accompanying disclaimer on each page states that data and services are for academic, non-commercial use only.</statement>
<link desc="disclaimer statement">http://mips.helmholtz-muenchen.de/genre/proj/yeast/About/index.html</link>
</restriction>
</restrictions>
<tags>
<tag>gene</tag>
<tag>genome</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000263" pattern="^KIAA\d{4}$" restricted="true">
<name>HUGE</name>
<definition>The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.</definition>
<uris>
<uri type="URN">urn:miriam:huge</uri>
<uri type="URL">http://identifiers.org/huge/</uri>
</uris>
<namespace>huge</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681467</documentation>
</documentations>
<resources>
<resource id="MIR:00100339" state="up" reliability="99">
<dataResource>http://www.kazusa.or.jp/huge/</dataResource>
<dataEntityExample>KIAA0001</dataEntityExample>
<dataEntry>http://www.kazusa.or.jp/huge/gfpage/$id/</dataEntry>
<dataInfo>HUGE at Kazusa DNA Research Institute</dataInfo>
<dataInstitution>Kazusa DNA Research Institute, Chiba</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The information provided is for research purposes only.</statement>
<link desc="Terms and conditions of data use.">http://www.kazusa.or.jp/disclaimers.html</link>
</restriction>
</restrictions>
<tags>
<tag>DNA</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000264" pattern="^\d+$">
<name>BindingDB</name>
<definition>BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.</definition>
<uris>
<uri type="URN">urn:miriam:bindingDB</uri>
<uri type="URL">http://identifiers.org/bindingDB/</uri>
</uris>
<namespace>bindingDB</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17145705</documentation>
</documentations>
<resources>
<resource id="MIR:00100340" state="up" reliability="99">
<dataResource>http://www.bindingdb.org/bind/index.jsp</dataResource>
<dataEntityExample>22360</dataEntityExample>
<dataEntry>http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=$id</dataEntry>
<dataInfo>BindingDB At Skaggs School of Pharmacy & Pharmaceutical Sciences</dataInfo>
<dataInstitution>Skaggs School of Pharmacy & Pharmaceutical Sciences, La Jolla, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>drug</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000265" pattern="^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$" restricted="true">
<name>STRING</name>
<synonyms>
<synonym>Search Tool for Retrieval of Interacting Genes/Proteins</synonym>
</synonyms>
<definition>STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.
The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.</definition>
<uris>
<uri type="URN">urn:miriam:string</uri>
<uri type="URL">http://identifiers.org/string/</uri>
</uris>
<namespace>string</namespace>
<documentations>
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</documentations>
<resources>
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<dataResource>http://string.embl.de/</dataResource>
<dataEntityExample>P53350</dataEntityExample>
<dataEntry>http://string.embl.de/interactions/$id</dataEntry>
<dataInfo>STRING at Heidelberg</dataInfo>
<dataInstitution>European Molecular Biology Laboratory, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
<resource id="MIR:00100342" state="down" reliability="83">
<dataResource>http://string-db.org/</dataResource>
<dataEntityExample>P53350</dataEntityExample>
<dataEntry>http://string-db.org/interactions/$id</dataEntry>
<dataInfo>STRING Mirror at Heidelberg</dataInfo>
<dataInstitution>European Molecular Biology Laboratory, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="4" desc="Identifier instability">
<statement>Identifiers are regenerated each time a new STRING version is released, hence the specific information recorded between versions may differ.</statement>
</restriction>
</restrictions>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000266" pattern="^\w{14}$" restricted="true">
<name>STITCH</name>
<definition>STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.</definition>
<uris>
<uri type="URN">urn:miriam:stitch</uri>
<uri type="URL">http://identifiers.org/stitch/</uri>
</uris>
<namespace>stitch</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18084021</documentation>
</documentations>
<resources>
<resource id="MIR:00100343" state="up" reliability="97">
<dataResource>http://stitch.embl.de/</dataResource>
<dataEntityExample>BQJCRHHNABKAKU</dataEntityExample>
<dataEntry>http://stitch.embl.de/interactions/$id</dataEntry>
<dataInfo>STITCH</dataInfo>
<dataInstitution>European Molecular Biology Laboratory, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="4" desc="Identifier instability">
<statement>Identifiers are regenerated each time a new version is released. The best way to reference this information is to use the first segment (14 characters) of an InChi key.</statement>
<link desc="InChi key description">http://www.inchi.info/inchikey_overview_en.html</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000267" pattern="^Q[A-Z0-9]+$">
<name>Anatomical Therapeutic Chemical Vetinary</name>
<definition>The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.</definition>
<uris>
<uri type="URN">urn:miriam:atcvet</uri>
<uri type="URL">http://identifiers.org/atcvet/</uri>
</uris>
<namespace>atcvet</namespace>
<documentations>
<documentation type="URL">http://www.whocc.no/atcvet/atcvet_methodology/purpose_of_the_atcvet_system/</documentation>
</documentations>
<resources>
<resource id="MIR:00100344" state="down" reliability="76">
<dataResource>http://www.whocc.no/atcvet/atcvet_index/</dataResource>
<dataEntityExample>QJ51RV02</dataEntityExample>
<dataEntry>http://www.whocc.no/atcvet/atcvet_index/?code=$id</dataEntry>
<dataInfo>Anatomical Therapeutic Chemical Vet Index at WHO</dataInfo>
<dataInstitution>World Health Organisation</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>drug</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000268" pattern="^\d+$">
<name>Phenol-Explorer</name>
<definition>Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.</definition>
<uris>
<uri type="URN">urn:miriam:phenolexplorer</uri>
<uri type="URL">http://identifiers.org/phenolexplorer/</uri>
</uris>
<namespace>phenolexplorer</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fdatabase%2Fbap024</documentation>
</documentations>
<resources>
<resource id="MIR:00100345" state="up" reliability="97">
<dataResource>http://www.phenol-explorer.eu/foods/</dataResource>
<dataEntityExample>75</dataEntityExample>
<dataEntry>http://phenol-explorer.eu/foods/$id</dataEntry>
<dataInfo>Phenol-Explorer Database on Phenol content of foods</dataInfo>
<dataInstitution>INRA and University of Alberta</dataInstitution>
<dataLocation>France and Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
</tags>
</datatype>
<datatype id="MIR:00000269" pattern="^(\w+)?\d+$" restricted="true">
<name>SNOMED CT</name>
<definition>SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.</definition>
<uris>
<uri type="URN">urn:miriam:snomedct</uri>
<uri type="URL">http://identifiers.org/snomedct/</uri>
</uris>
<namespace>snomedct</namespace>
<documentations>
<documentation type="URL">http://www.connectingforhealth.nhs.uk/systemsandservices/data/snomed/</documentation>
</documentations>
<resources>
<resource id="MIR:00100405" state="down" reliability="83">
<dataResource>http://www.snomedbrowser.com/</dataResource>
<dataEntityExample>284196006</dataEntityExample>
<dataEntry>http://www.snomedbrowser.com/Codes/Details/$id</dataEntry>
<dataInfo>SNOMED-CT at The National Pathology Exchange</dataInfo>
<dataInstitution>The Health Informatics Service, NHS, West Yorkshire</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100346" obsolete="true">
<dataResource>http://vtsl.vetmed.vt.edu/</dataResource>
<dataEntityExample>284196006</dataEntityExample>
<dataEntry>http://vtsl.vetmed.vt.edu/TerminologyMgt/Browser/ISA.cfm?SCT_ConceptID=$id</dataEntry>
<dataInfo>SNOMED CT at Virginia</dataInfo>
<dataInstitution>Virginia Maryland Regional College of Veterinary Medicine, Virginia</dataInstitution>
<dataLocation>USA</dataLocation>
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<resource id="MIR:00100347" obsolete="true">
<dataResource>http://www.ihtsdo.org/snomed-ct/</dataResource>
<dataEntityExample>284196006</dataEntityExample>
<dataEntry>http://unknown/$id</dataEntry>
<dataInfo>SNOMED CT at The International Health Terminology Standards Development Organization.</dataInfo>
<dataInstitution>IHTSDO, Copenhagen</dataInstitution>
<dataLocation>Denmark</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Access to data may require a license, depending on whether or not it is used in a member country, and for a particular purpose.</statement>
<link desc="license information">http://www.ihtsdo.org/join-us/</link>
</restriction>
</restrictions>
<tags>
<tag>controlled vocabulary</tag>
</tags>
</datatype>
<datatype id="MIR:00000270" pattern="^[A-Za-z0-9]+$" restricted="true">
<name>MeSH 2012</name>
<synonyms>
<synonym>Medical Subject Headings 2012</synonym>
</synonyms>
<definition>MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012.</definition>
<uris>
<uri type="URN">urn:miriam:mesh.2012</uri>
<uri type="URL">http://identifiers.org/mesh.2012/</uri>
</uris>
<namespace>mesh.2012</namespace>
<documentations>
<documentation type="URL">http://www.nlm.nih.gov/pubs/factsheets/mesh.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100349" state="down" reliability="78">
<dataResource>http://www.nlm.nih.gov/mesh/</dataResource>
<dataEntityExample>17186</dataEntityExample>
<dataEntry>http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$id&view=expanded</dataEntry>
<dataInfo>MeSH at National Library of Medicine</dataInfo>
<dataInstitution>U.S. National Library of Medicine, National Institute of Health, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100348" obsolete="true">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>D018377</dataEntityExample>
<dataEntry>http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=$id</dataEntry>
<dataInfo>MeSH at BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Records accessed through MESH may include content that itself has some copyright restriction when reproduced.</statement>
<link desc="copyright and fair use information">http://www.nlm.nih.gov/copyright.html</link>
</restriction>
<restriction type="4" desc="Identifier instability">
<statement>Access to Mesh 2012 uses identifiers that could potentially change. We recommend the use of the stable MeSH collection (http://identifiers.org/mesh/). If you have issues accessing Mesh 2012, you may wish to try the ftp service.</statement>
<link desc="ftp access for MeSH 2012 records">ftp://nlmpubs.nlm.nih.gov/online/mesh/.asciimesh/c2012.bin</link>
</restriction>
</restrictions>
<tags>
<tag>controlled vocabulary</tag>
</tags>
</datatype>
<datatype id="MIR:00000271" pattern="^C\d{8}">
<name>KnapSack</name>
<definition>Knapsack provides information on metabolites and the taxonomic class with which they are associated.</definition>
<uris>
<uri type="URN">urn:miriam:knapsack</uri>
<uri type="URL">http://identifiers.org/knapsack/</uri>
</uris>
<namespace>knapsack</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22123792</documentation>
<documentation type="URL">http://kanaya.aist-nara.ac.jp/KNApSAcK/Manual/KNApSAcKManual.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100350" state="up" reliability="98">
<dataResource>http://kanaya.aist-nara.ac.jp/KNApSAcK/</dataResource>
<dataEntityExample>C00000001</dataEntityExample>
<dataEntry>http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=$id</dataEntry>
<dataInfo>KnapSack at Nara Institute</dataInfo>
<dataInstitution>Nara Institute of Science and Technology</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>metabolite</tag>
</tags>
</datatype>
<datatype id="MIR:00000272" pattern="^\d+$" restricted="true">
<name>Canadian Drug Product Database</name>
<synonyms>
<synonym>DPD</synonym>
</synonyms>
<definition>The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).</definition>
<uris>
<uri type="URN">urn:miriam:cdpd</uri>
<uri type="URL">http://identifiers.org/cdpd/</uri>
</uris>
<namespace>cdpd</namespace>
<documentations>
<documentation type="URL">http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/terminolog-eng.php</documentation>
</documentations>
<resources>
<resource id="MIR:00100351" state="restricted access" reliability="0">
<dataResource>http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp</dataResource>
<dataEntityExample>63250</dataEntityExample>
<dataEntry>http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$id</dataEntry>
<dataInfo>Canadian Drug Identification Number at Health Canada</dataInfo>
<dataInstitution>Health Canada, Ottawa, Ontario</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>Need an active session to access information (timeout set at 29 mins).</statement>
</restriction>
</restrictions>
<tags>
<tag>drug</tag>
<tag>registry</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000273" pattern="^[A-Z]{2}[A-Z0-9][0-9]{5}$" restricted="true">
<name>MassBank</name>
<definition>MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).</definition>
<uris>
<uri type="URN">urn:miriam:massbank</uri>
<uri type="URL">http://identifiers.org/massbank/</uri>
</uris>
<namespace>massbank</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20623627</documentation>
</documentations>
<resources>
<resource id="MIR:00100353" state="up" reliability="95" primary="true">
<dataResource>http://www.massbank.jp</dataResource>
<dataEntityExample>PB000166</dataEntityExample>
<dataEntry>http://www.massbank.jp/jsp/FwdRecord.jsp?id=$id</dataEntry>
<dataInfo>MassBank in Japan</dataInfo>
<dataInstitution>The MassBank Consortium</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
<resource id="MIR:00100666" state="down" reliability="79">
<dataResource>http://www.massbank.eu/</dataResource>
<dataEntityExample>PB000166</dataEntityExample>
<dataEntry>http://www.massbank.eu/MassBank/jsp/FwdRecord.jsp?id=$id</dataEntry>
<dataInfo>MassBank in Europe</dataInfo>
<dataInstitution>NORMAN Network and The MassBank Consortium</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
<resource id="MIR:00100352" obsolete="true">
<dataResource>http://msbi.ipb-halle.de/MassBank/</dataResource>
<dataEntityExample>PB000166</dataEntityExample>
<dataEntry>http://msbi.ipb-halle.de/MassBank/jsp/FwdRecord.jsp?id=$id</dataEntry>
<dataInfo>MassBank in Germany</dataInfo>
<dataInstitution>The MassBank Consortium</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Downloading, copying, saving, or printing out of materials for purposes other than academic research or education is prohibited.</statement>
<link desc="improper use description">http://www.massbank.jp/en/regulation.html</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
<tag>mass spectrometry</tag>
<tag>metabolite</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000274" pattern="^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" restricted="true">
<name>Golm Metabolome Database</name>
<synonyms>
<synonym>GMD</synonym>
</synonyms>
<definition>Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.</definition>
<uris>
<uri type="URN">urn:miriam:gmd</uri>
<uri type="URL">http://identifiers.org/gmd/</uri>
</uris>
<namespace>gmd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15613389</documentation>
<documentation type="PMID">urn:miriam:pubmed:20526350</documentation>
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<resources>
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<dataResource>http://gmd.mpimp-golm.mpg.de/</dataResource>
<dataEntityExample>68513255-fc44-4041-bc4b-4fd2fae7541d</dataEntityExample>
<dataEntry>http://gmd.mpimp-golm.mpg.de/Metabolites/$id.aspx</dataEntry>
<dataInfo>Golm Metabolome Database at Max Planck Institute of Molecular Plant Physiology</dataInfo>
<dataInstitution>Max Planck Institute of Molecular Plant Physiology, Potsdam</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Data in this collection is restricted for non-academic users.</statement>
<link desc="terms and conditions">http://gmd.mpimp-golm.mpg.de/termsconditions.aspx</link>
</restriction>
</restrictions>
<tags>
<tag>metabolite</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000275" pattern="^\d+$">
<name>HomoloGene</name>
<definition>HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.</definition>
<uris>
<uri type="URN">urn:miriam:homologene</uri>
<uri type="URL">http://identifiers.org/homologene/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/homologene</uri>
</uris>
<namespace>homologene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21097890</documentation>
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<resources>
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<dataResource>http://www.ncbi.nlm.nih.gov/homologene/</dataResource>
<dataEntityExample>1000</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/homologene/$id</dataEntry>
<dataInfo>Homologene at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100699" state="down" reliability="83">
<dataResource>http://homologene.bio2rdf.org/fct</dataResource>
<dataEntityExample>1000</dataEntityExample>
<dataEntry>http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>eukaryotic</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000276" pattern="^c\d+$">
<name>UM-BBD Compound</name>
<synonyms>
<synonym>University of Minnesota Biocatalysis/Biodegradation Database (Compound)</synonym>
</synonyms>
<definition>The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.</definition>
<uris>
<uri type="URN">urn:miriam:umbbd.compound</uri>
<uri type="URL">http://identifiers.org/umbbd.compound/</uri>
</uris>
<namespace>umbbd.compound</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19767608</documentation>
</documentations>
<resources>
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<dataResource>http://umbbd.ethz.ch/</dataResource>
<dataEntityExample>c0001</dataEntityExample>
<dataEntry>http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$id</dataEntry>
<dataInfo>Biocatalysis/Biodegradation Database Mirror (Compound) at ETH Zurich</dataInfo>
<dataInstitution>ETH, Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
<resource id="MIR:00100356" obsolete="true">
<dataResource>http://umbbd.msi.umn.edu/index.html</dataResource>
<dataEntityExample>c0001</dataEntityExample>
<dataEntry>http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=c&compID=$id</dataEntry>
<dataInfo>Biocatalysis/Biodegradation Database (Compound) at University of Minnesota</dataInfo>
<dataInstitution>Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>metabolite</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000277" pattern="^A\d+$">
<name>ABS</name>
<synonyms>
<synonym>Annotated regulatory Binding Sites database</synonym>
</synonyms>
<definition>The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography.</definition>
<uris>
<uri type="URN">urn:miriam:abs</uri>
<uri type="URL">http://identifiers.org/abs/</uri>
</uris>
<namespace>abs</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381947</documentation>
</documentations>
<resources>
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<dataResource>http://genome.crg.es/datasets/abs2005/</dataResource>
<dataEntityExample>A0014</dataEntityExample>
<dataEntry>http://genome.crg.es/datasets/abs2005/entries/$id.html</dataEntry>
<dataInfo>ABS at IMIM</dataInfo>
<dataInstitution>Institut Municipal d'Investigaci&oacute; M&egrave;dica, Barcelona</dataInstitution>
<dataLocation>Spain</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>interaction</tag>
</tags>
</datatype>
<datatype id="MIR:00000278" pattern="^\d{5}$">
<name>APD</name>
<synonyms>
<synonym>Antimicrobial Peptide Database</synonym>
</synonyms>
<definition>The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.</definition>
<uris>
<uri type="URN">urn:miriam:apd</uri>
<uri type="URL">http://identifiers.org/apd/</uri>
</uris>
<namespace>apd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681488</documentation>
</documentations>
<resources>
<resource id="MIR:00100359" state="up" reliability="99">
<dataResource>http://aps.unmc.edu/AP/</dataResource>
<dataEntityExample>01001</dataEntityExample>
<dataEntry>http://aps.unmc.edu/AP/database/query_output.php?ID=$id</dataEntry>
<dataInfo>APD at Nebraska</dataInfo>
<dataInstitution>Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>drug</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000279" pattern="^\d+$" restricted="true">
<name>ChemDB</name>
<definition>ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.</definition>
<uris>
<uri type="URN">urn:miriam:chemdb</uri>
<uri type="URL">http://identifiers.org/chemdb/</uri>
</uris>
<namespace>chemdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17599932</documentation>
</documentations>
<resources>
<resource id="MIR:00100360" state="up" reliability="96">
<dataResource>http://cdb.ics.uci.edu/</dataResource>
<dataEntityExample>3966782</dataEntityExample>
<dataEntry>http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$id</dataEntry>
<dataInfo>ChemDB at UC Irvine</dataInfo>
<dataInstitution>University of California, Irvine</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Commercial access may require acquisition of a license.</statement>
<link desc="license contact on main page">http://cdb.ics.uci.edu/index.htm</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000280" pattern="^\d+$" restricted="true">
<name>DPV</name>
<synonyms>
<synonym>Description of Plant Viruses</synonym>
<synonym>DPVweb</synonym>
</synonyms>
<definition>Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.</definition>
<uris>
<uri type="URN">urn:miriam:dpv</uri>
<uri type="URL">http://identifiers.org/dpv/</uri>
</uris>
<namespace>dpv</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381892</documentation>
</documentations>
<resources>
<resource id="MIR:00100361" state="up" reliability="99">
<dataResource>http://www.dpvweb.net/</dataResource>
<dataEntityExample>100</dataEntityExample>
<dataEntry>http://www.dpvweb.net/dpv/showdpv.php?dpvno=$id</dataEntry>
<dataInfo>DPV at Rothamsted</dataInfo>
<dataInstitution>Plant-Pathogen Interactions Division, Wheat Pathogenesis Programme, Rothamsted Research Harpenden, Hertfordshire</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Information on this site may be subject to copyright.</statement>
<link desc="copyright warning statement">http://www.dpvweb.net/index.php</link>
</restriction>
</restrictions>
<tags>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000281" pattern="^\d+$" restricted="true">
<name>IUPHAR receptor</name>
<synonyms>
<synonym>International Union of Basic and Clinical Pharmacology</synonym>
<synonym>IUPHAR-DB</synonym>
</synonyms>
<definition>The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.</definition>
<uris>
<uri type="URN">urn:miriam:iuphar.receptor</uri>
<uri type="URL">http://identifiers.org/iuphar.receptor/</uri>
</uris>
<namespace>iuphar.receptor</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23087376</documentation>
</documentations>
<resources>
<resource id="MIR:00100362" state="up" reliability="98" primary="true">
<dataResource>http://www.guidetopharmacology.org/targets.jsp</dataResource>
<dataEntityExample>101</dataEntityExample>
<dataEntry>http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id</dataEntry>
<dataInfo>IUPHAR Receptor at University of Edinburgh</dataInfo>
<dataInstitution>Centre for Cardiovascular Science, University of Edinburgh, Edinburgh</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Material from this site may be downloaded for personal, non-commercial use.</statement>
<link desc="copyright statement">http://www.iuphar-db.org/copyright.jsp</link>
</restriction>
</restrictions>
<tags>
<tag>mammalian</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000282" pattern="^[a-z0-9-]+$">
<name>Aceview Worm</name>
<synonyms>
<synonym>AceView WormGenes</synonym>
</synonyms>
<definition>AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.</definition>
<uris>
<uri type="URN">urn:miriam:aceview.worm</uri>
<uri type="URL">http://identifiers.org/aceview.worm/</uri>
</uris>
<namespace>aceview.worm</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16925834</documentation>
</documentations>
<resources>
<resource id="MIR:00100363" state="up" reliability="98">
<dataResource>http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm</dataResource>
<dataEntityExample>aap-1</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$id</dataEntry>
<dataInfo>AceView Worm at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000283" pattern="^[A-Za-z0-9-]+$" restricted="true">
<name>ASAP</name>
<definition>ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources.</definition>
<uris>
<uri type="URN">urn:miriam:asap</uri>
<uri type="URL">http://identifiers.org/asap/</uri>
</uris>
<namespace>asap</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12519969</documentation>
</documentations>
<resources>
<resource id="MIR:00100364" state="restricted access" reliability="100">
<dataResource>http://asap.ahabs.wisc.edu/asap/home.php</dataResource>
<dataEntityExample>ABE-0009634</dataEntityExample>
<dataEntry>http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$id</dataEntry>
<dataInfo>ASAP at University of Wisconsin</dataInfo>
<dataInstitution>Animal Health and Biomedical Sciences, University of Wisconsin, Madison</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>May require the acceptance of terms and conditions.</statement>
<link desc="Terms and conditions of data use.">http://asap.ahabs.wisc.edu/asap/ASAP-DataReleasePolicy.htm</link>
</restriction>
</restrictions>
<tags>
<tag>gene</tag>
<tag>genome</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000284" pattern="^\d+$">
<name>ATCC</name>
<synonyms>
<synonym>American Type Culture Collection</synonym>
</synonyms>
<definition>The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.</definition>
<uris>
<uri type="URN">urn:miriam:atcc</uri>
<uri type="URL">http://identifiers.org/atcc/</uri>
</uris>
<namespace>atcc</namespace>
<documentations>
<documentation type="URL">http://www.atcc.org/About/tabid/138/Default.aspx</documentation>
</documentations>
<resources>
<resource id="MIR:00100365" state="down" reliability="95">
<dataResource>http://www.atcc.org/</dataResource>
<dataEntityExample>11303</dataEntityExample>
<dataEntry>http://www.lgcstandards-atcc.org/Products/All/$id.aspx</dataEntry>
<dataInfo>ATCC in Virginia</dataInfo>
<dataInstitution>American Type Culture Collection, Manassas, Virginia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>catalogue</tag>
<tag>eukaryotic</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000285" pattern="^\w+(\.)?(\d+)?$" restricted="true">
<name>BDGP EST</name>
<synonyms>
<synonym>Berkeley Drosophila Genome Project EST</synonym>
</synonyms>
<definition>The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI).</definition>
<uris>
<uri type="URN">urn:miriam:bdgp.est</uri>
<uri type="URL">http://identifiers.org/bdgp.est/</uri>
</uris>
<namespace>bdgp.est</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12537569</documentation>
</documentations>
<resources>
<resource id="MIR:00100366" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/dbEST/index.html</dataResource>
<dataEntityExample>EY223054.1</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/nucest/$id</dataEntry>
<dataInfo>BDGP EST at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="6" desc="Collection subset">
<statement>Data is a subset of a larger collection.</statement>
<link desc="description of data collection">http://www.fruitfly.org/EST/EST.shtml#ck_est</link>
</restriction>
</restrictions>
<tags>
<tag>eukaryotic</tag>
<tag>expression</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000286" pattern="^DDB_G\d+$">
<name>Dictybase Gene</name>
<definition>The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information.</definition>
<uris>
<uri type="URN">urn:miriam:dictybase.gene</uri>
<uri type="URL">http://identifiers.org/dictybase.gene/</uri>
</uris>
<namespace>dictybase.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21087999</documentation>
</documentations>
<resources>
<resource id="MIR:00100367" state="up" reliability="99">
<dataResource>http://dictybase.org/</dataResource>
<dataEntityExample>DDB_G0267522</dataEntityExample>
<dataEntry>http://dictybase.org/gene/$id</dataEntry>
<dataInfo>Dictybase Gene at Northwestern University</dataInfo>
<dataInstitution>Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, Chicago, Illinois</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000287" pattern="^M\d+$" restricted="true">
<name>IMGT LIGM</name>
<synonyms>
<synonym>IMGT/LIGM-DB</synonym>
</synonyms>
<definition>IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.</definition>
<uris>
<uri type="URN">urn:miriam:imgt.ligm</uri>
<uri type="URL">http://identifiers.org/imgt.ligm/</uri>
</uris>
<namespace>imgt.ligm</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381979</documentation>
</documentations>
<resources>
<resource id="MIR:00100369" state="down" reliability="86">
<dataResource>http://genius.embnet.dkfz-heidelberg.de/</dataResource>
<dataEntityExample>M94112</dataEntityExample>
<dataEntry>http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$id']</dataEntry>
<dataInfo>IMGT LIGM through DKFZ (SRS)</dataInfo>
<dataInstitution>DKFZ TP3, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
<resource id="MIR:00100428" state="up" reliability="98" primary="true">
<dataResource>http://www.imgt.org/</dataResource>
<dataEntityExample>M94112</dataEntityExample>
<dataEntry>http://www.imgt.org/ligmdb/view?id=$id</dataEntry>
<dataInfo>IMGT LIGM at CNRS</dataInfo>
<dataInstitution>CNRS, Montpellier University, Montpellier</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
<resource id="MIR:00100368" obsolete="true">
<dataResource>http://www.ebi.ac.uk/imgt/</dataResource>
<dataEntityExample>M94112</dataEntityExample>
<dataEntry>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+1fmSL1g8Xvs+-e+[IMGTLIGM:'$id']</dataEntry>
<dataInfo>IMGT LIGM through EBI (SRS)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The data are provided as a service to the scientific community to be used only for research and educational purposes.</statement>
<link desc="disclaimer information">http://www.imgt.org/Warranty.html</link>
</restriction>
</restrictions>
<tags>
<tag>immunogenetics</tag>
<tag>mammalian</tag>
</tags>
</datatype>
<datatype id="MIR:00000288" pattern="^\w+(\.\d+)?">
<name>Worfdb</name>
<synonyms>
<synonym>Worm Orf DB</synonym>
</synonyms>
<definition>WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends).</definition>
<uris>
<uri type="URN">urn:miriam:worfdb</uri>
<uri type="URL">http://identifiers.org/worfdb/</uri>
</uris>
<namespace>worfdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15489327</documentation>
</documentations>
<resources>
<resource id="MIR:00100370" state="up" reliability="99">
<dataResource>http://worfdb.dfci.harvard.edu/</dataResource>
<dataEntityExample>T01B6.1</dataEntityExample>
<dataEntry>http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$id</dataEntry>
<dataInfo>Worm Orf DB at Harvard</dataInfo>
<dataInstitution>Center for Cancer Systems Biology, Harvard Medical School, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000289" pattern="^[A-Za-z0-9]+$" restricted="true">
<name>NEXTDB</name>
<synonyms>
<synonym>Nematode Expression Pattern Database</synonym>
</synonyms>
<definition>NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones.</definition>
<uris>
<uri type="URN">urn:miriam:nextdb</uri>
<uri type="URL">http://identifiers.org/nextdb/</uri>
</uris>
<namespace>nextdb</namespace>
<documentations>
<documentation type="URL">http://nematode.lab.nig.ac.jp/method/index.php</documentation>
</documentations>
<resources>
<resource id="MIR:00100371" state="up" reliability="97">
<dataResource>http://nematode.lab.nig.ac.jp/</dataResource>
<dataEntityExample>6b1</dataEntityExample>
<dataEntry>http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$id</dataEntry>
<dataInfo>NEXTDB at Shizuoka</dataInfo>
<dataInstitution>National Institute of Genetics, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="5" desc="Collection maintenance">
<statement>The information does not appear to have been updated in a number of years.</statement>
<link desc="copyright date">http://nematode.lab.nig.ac.jp/</link>
</restriction>
</restrictions>
<tags>
<tag>eukaryotic</tag>
<tag>expression</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000290" pattern="^\d+$" obsolete="true" replacement="MIR:00000185">
<comment>As of November 2013, this collection is no longer accessible.</comment>
<name>Plant Genome Network</name>
<definition>The Plant Genome Network (PGN) is a resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. All data are directly derived from chromatograms with original and intermediate data stored in the database.</definition>
<uris>
<uri type="URN">urn:miriam:pgn</uri>
<uri type="URL">http://identifiers.org/pgn/</uri>
</uris>
<namespace>pgn</namespace>
<documentations>
<documentation type="URL">http://pgn.cornell.edu/help/about.pl</documentation>
</documentations>
<resources>
<resource id="MIR:00100372" state="down" reliability="68">
<dataResource>http://pgn.cornell.edu/</dataResource>
<dataEntityExample>196828</dataEntityExample>
<dataEntry>http://pgn.cornell.edu/unigene/unigene_assembly_contigs.pl?unigene_id=$id</dataEntry>
<dataInfo>PGN at Cornell University</dataInfo>
<dataInstitution>Cornell University, Ithaca, New York</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000291" pattern="^\w+(\-)?\w+(\-)?\w+$">
<name>SoyBase</name>
<definition>SoyBase is a repository for curated genetics, genomics and related data resources for soybean.</definition>
<uris>
<uri type="URN">urn:miriam:soybase</uri>
<uri type="URL">http://identifiers.org/soybase/</uri>
</uris>
<namespace>soybase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20008513</documentation>
</documentations>
<resources>
<resource id="MIR:00100373" state="down" reliability="73">
<dataResource>http://soybase.org/</dataResource>
<dataEntityExample>BARC-013845-01256</dataEntityExample>
<dataEntry>http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$id</dataEntry>
<dataInfo>SoyBase at Iowa State University</dataInfo>
<dataInstitution>USDA-ARS-CICGRU, Iowa State University, Iowa</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000292" pattern="^MF_\d+$">
<name>HAMAP</name>
<synonyms>
<synonym>High-quality Automated and Manual Annotation of microbial Proteomes</synonym>
</synonyms>
<definition>HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.</definition>
<uris>
<uri type="URN">urn:miriam:hamap</uri>
<uri type="URL">http://identifiers.org/hamap/</uri>
</uris>
<namespace>hamap</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12798039</documentation>
</documentations>
<resources>
<resource id="MIR:00100374" state="down" reliability="95">
<dataResource>http://hamap.expasy.org/</dataResource>
<dataEntityExample>MF_01400</dataEntityExample>
<dataEntry>http://hamap.expasy.org/unirule/$id</dataEntry>
<dataInfo>HAPMAP at Swiss Institute of Bioinformatics</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics, Geneva</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>annotation</tag>
<tag>microbial</tag>
</tags>
</datatype>
<datatype id="MIR:00000293" pattern="^m\w+$" restricted="true">
<name>Rouge</name>
<synonyms>
<synonym>Rodent Unidentified Gene-Encoded Large Proteins</synonym>
</synonyms>
<definition>The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.</definition>
<uris>
<uri type="URN">urn:miriam:rouge</uri>
<uri type="URL">http://identifiers.org/rouge/</uri>
</uris>
<namespace>rouge</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15368895</documentation>
</documentations>
<resources>
<resource id="MIR:00100375" state="up" reliability="99">
<dataResource>http://www.kazusa.or.jp/rouge/</dataResource>
<dataEntityExample>mKIAA4200</dataEntityExample>
<dataEntry>http://www.kazusa.or.jp/rouge/gfpage/$id/</dataEntry>
<dataInfo>Rouge at Kazusa DNA Research Institute</dataInfo>
<dataInstitution>Kazusa DNA Research Institute, Chiba</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The information provided is for research purposes only.</statement>
<link desc="Terms and conditions of data use.">http://www.kazusa.or.jp/disclaimers.html</link>
</restriction>
</restrictions>
<tags>
<tag>gene</tag>
<tag>mammalian</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000294" pattern="^[AEP]-\w{4}-\d+$">
<name>ArrayExpress Platform</name>
<definition>ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results.</definition>
<uris>
<uri type="URN">urn:miriam:arrayexpress.platform</uri>
<uri type="URL">http://identifiers.org/arrayexpress.platform/</uri>
</uris>
<namespace>arrayexpress.platform</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12519949</documentation>
</documentations>
<resources>
<resource id="MIR:00100376" state="up" reliability="100">
<dataResource>http://www.ebi.ac.uk/arrayexpress/</dataResource>
<dataEntityExample>A-GEOD-50</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/arrayexpress/arrays/$id</dataEntry>
<dataInfo>ArrayExpress Platform at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>microarray</tag>
</tags>
</datatype>
<datatype id="MIR:00000295" pattern="^\d+$">
<name>CGSC Strain</name>
<synonyms>
<synonym>Coli Genetic Stock Center</synonym>
</synonyms>
<definition>The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.</definition>
<uris>
<uri type="URN">urn:miriam:cgsc</uri>
<uri type="URL">http://identifiers.org/cgsc/</uri>
</uris>
<namespace>cgsc</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:1475178</documentation>
</documentations>
<resources>
<resource id="MIR:00100377" state="up" reliability="99">
<dataResource>http://cgsc.biology.yale.edu/index.php</dataResource>
<dataEntityExample>11042</dataEntityExample>
<dataEntry>http://cgsc.biology.yale.edu/Strain.php?ID=$id</dataEntry>
<dataInfo>CGSC at Yale university</dataInfo>
<dataInstitution>Dept. of Molecular, Cellular, and Developmental Biology, Yale University, Conneticut</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>microbial</tag>
<tag>strain</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000296" pattern="^COG\d+$" obsolete="true" replacement="MIR:00000119">
<comment>As of September 2013, this collection is no longer maintained. Various archives are available at: ftp://ftp.ncbi.nih.gov/pub/COG/.</comment>
<name>COGs</name>
<synonyms>
<synonym>Clusters of Orthologous Groups</synonym>
</synonyms>
<definition>Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.</definition>
<uris>
<uri type="URN">urn:miriam:cogs</uri>
<uri type="URL">http://identifiers.org/cogs/</uri>
</uris>
<namespace>cogs</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12969510</documentation>
</documentations>
<resources>
<resource id="MIR:00100378" state="down" reliability="73">
<dataResource>http://www.ncbi.nlm.nih.gov/COG/</dataResource>
<dataEntityExample>COG0001</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?$id</dataEntry>
<dataInfo>COGs at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>genome</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000297" pattern="^\d\w+$">
<name>DragonDB DNA</name>
<definition>DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information.</definition>
<uris>
<uri type="URN">urn:miriam:dragondb.dna</uri>
<uri type="URL">http://identifiers.org/dragondb.dna/</uri>
</uris>
<namespace>dragondb.dna</namespace>
<resources>
<resource id="MIR:00100379" state="down" reliability="66">
<dataResource>http://www.antirrhinum.net/</dataResource>
<dataEntityExample>3hB06</dataEntityExample>
<dataEntry>http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id;class=DNA</dataEntry>
<dataInfo>DragonDB DNA at University of British Columbia</dataInfo>
<dataInstitution>University of British Columbia, Vancouver</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000298" pattern="^\w+$">
<name>DragonDB Protein</name>
<definition>DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.</definition>
<uris>
<uri type="URN">urn:miriam:dragondb.protein</uri>
<uri type="URL">http://identifiers.org/dragondb.protein/</uri>
</uris>
<namespace>dragondb.protein</namespace>
<resources>
<resource id="MIR:00100380" state="down" reliability="66">
<dataResource>http://www.antirrhinum.net/</dataResource>
<dataEntityExample>AMDEFA</dataEntityExample>
<dataEntry>http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id;class=Peptide</dataEntry>
<dataInfo>DragonDB Protein at University of British Columbia</dataInfo>
<dataInstitution>University of British Columbia, Vancouver</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>plant</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000299" pattern="^\w+$">
<name>DragonDB Locus</name>
<definition>DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.</definition>
<uris>
<uri type="URN">urn:miriam:dragondb.locus</uri>
<uri type="URL">http://identifiers.org/dragondb.locus/</uri>
</uris>
<namespace>dragondb.locus</namespace>
<resources>
<resource id="MIR:00100381" state="down" reliability="66">
<dataResource>http://www.antirrhinum.net/</dataResource>
<dataEntityExample>DEF</dataEntityExample>
<dataEntry>http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id&amp;class=Locus</dataEntry>
<dataInfo>DragonDB Locus at University of British Columbia</dataInfo>
<dataInstitution>University of British Columbia, Vancouver</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000300" pattern="^\w+$" restricted="true">
<name>DragonDB Allele</name>
<definition>DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information.</definition>
<uris>
<uri type="URN">urn:miriam:dragondb.allele</uri>
<uri type="URL">http://identifiers.org/dragondb.allele/</uri>
</uris>
<namespace>dragondb.allele</namespace>
<resources>
<resource id="MIR:00100382" state="down" reliability="66">
<dataResource>http://www.antirrhinum.net/</dataResource>
<dataEntityExample>cho</dataEntityExample>
<dataEntry>http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id&amp;class=Allele</dataEntry>
<dataInfo>DragonDB Allele at University of British Columbia</dataInfo>
<dataInstitution>University of British Columbia, Vancouver</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Images are subject to copyright.</statement>
<link desc="Statement on front page.">http://www.antirrhinum.net/</link>
</restriction>
</restrictions>
<tags>
<tag>gene</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000301" pattern="^\d{4}-\d{3}[\dX]$" restricted="true">
<name>ISSN</name>
<definition>The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books.</definition>
<uris>
<uri type="URN">urn:miriam:issn</uri>
<uri type="URL">http://identifiers.org/issn/</uri>
</uris>
<namespace>issn</namespace>
<documentations>
<documentation type="URL">http://catalog.loc.gov/help/number.htm</documentation>
</documentations>
<resources>
<resource id="MIR:00100383" state="restricted access" reliability="0">
<dataResource>http://catalog.loc.gov/webvoy.htm</dataResource>
<dataEntityExample>0745-4570</dataEntityExample>
<dataEntry>https://catalog.loc.gov/vwebv/search?searchCode=STNO&searchArg=$id&searchType=1&recCount=25</dataEntry>
<dataInfo>ISSN at Library of Congress</dataInfo>
<dataInstitution>Library of Congress Online Catalogue, Washington DC</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>Session time out prevents direct links.</statement>
<link desc="timeout info">http://catalog.loc.gov/help/timeout.htm</link>
</restriction>
</restrictions>
<tags>
<tag>bibliography</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000302" pattern="^[SCTAGMNU]\d+$">
<name>MEROPS Family</name>
<definition>The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.</definition>
<uris>
<uri type="URN">urn:miriam:merops.family</uri>
<uri type="URL">http://identifiers.org/merops.family/</uri>
</uris>
<namespace>merops.family</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17991683</documentation>
</documentations>
<resources>
<resource id="MIR:00100384" state="down" reliability="83">
<dataResource>http://merops.sanger.ac.uk/index.htm</dataResource>
<dataEntityExample>S1</dataEntityExample>
<dataEntry>http://merops.sanger.ac.uk/cgi-bin/famsum?family=$id</dataEntry>
<dataInfo>Merops Family at Sanger Institute</dataInfo>
<dataInstitution>Wellcome Trust Sanger Institute, Hinxton</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>enzyme</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000303" pattern="^\w+$">
<name>MGED Ontology</name>
<synonyms>
<synonym>MO</synonym>
</synonyms>
<definition>The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data.</definition>
<uris>
<uri type="URN">urn:miriam:mo</uri>
<uri type="URL">http://identifiers.org/mo/</uri>
</uris>
<namespace>mo</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16428806</documentation>
<documentation type="URL">http://mged.sourceforge.net/ontologies/index.php</documentation>
</documentations>
<resources>
<resource id="MIR:00100385" state="up" reliability="96">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>ArrayGroup</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/MO/$id</dataEntry>
<dataInfo>MGED Ontology at BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100568" state="up" reliability="99">
<dataResource>http://mged.sourceforge.net/ontologies/MGEDontology.php</dataResource>
<dataEntityExample>ArrayGroup</dataEntityExample>
<dataEntry>http://mged.sourceforge.net/ontologies/MGEDontology.php#$id</dataEntry>
<dataInfo>MGED Ontology at SourceForge</dataInfo>
<dataInstitution>(Ontology Working Group), European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000304" pattern="^(\w+)?\d+$">
<name>NASC code</name>
<synonyms>
<synonym>The Nottingham Arabidopsis Stock Centre</synonym>
</synonyms>
<definition>The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.</definition>
<uris>
<uri type="URN">urn:miriam:nasc</uri>
<uri type="URL">http://identifiers.org/nasc/</uri>
</uris>
<namespace>nasc</namespace>
<resources>
<resource id="MIR:00100386" state="up" reliability="98">
<dataResource>http://arabidopsis.info/</dataResource>
<dataEntityExample>N1899</dataEntityExample>
<dataEntry>http://arabidopsis.info/StockInfo?NASC_id=$id</dataEntry>
<dataInfo>NASC at University of Nottingham</dataInfo>
<dataInstitution>The Nottingham Arabidopsis Stock Centre, University of Nottingham</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>plant</tag>
<tag>strain</tag>
</tags>
</datatype>
<datatype id="MIR:00000305" pattern="^\w\d{4}\w\d{2}(\-[35])?$">
<name>NIAEST</name>
<definition>A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones.</definition>
<uris>
<uri type="URN">urn:miriam:niaest</uri>
<uri type="URL">http://identifiers.org/niaest/</uri>
</uris>
<namespace>niaest</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14744099</documentation>
<documentation type="URL">http://lgsun.grc.nia.nih.gov/cDNA/</documentation>
</documentations>
<resources>
<resource id="MIR:00100387" state="down" reliability="50">
<dataResource>http://lgsun.grc.nia.nih.gov/cDNA/</dataResource>
<dataEntityExample>J0705A10</dataEntityExample>
<dataEntry>http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$id</dataEntry>
<dataInfo>NIAEST at National Institute on Aging</dataInfo>
<dataInstitution>National Institute on Aging, NIH</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>gene</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000306" pattern="^TF\w+$">
<name>Pazar Transcription Factor</name>
<synonyms>
<synonym>Pazar Database</synonym>
</synonyms>
<definition>The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.</definition>
<uris>
<uri type="URN">urn:miriam:pazar</uri>
<uri type="URL">http://identifiers.org/pazar/</uri>
</uris>
<namespace>pazar</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18971253</documentation>
</documentations>
<resources>
<resource id="MIR:00100388" state="up" reliability="99">
<dataResource>http://www.pazar.info/</dataResource>
<dataEntityExample>TF0001053</dataEntityExample>
<dataEntry>http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$id</dataEntry>
<dataInfo>Pazar Transcription Factor at University of British Columbia</dataInfo>
<dataInstitution>Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000307" pattern="^PO:\d+$">
<name>Plant Ontology</name>
<synonyms>
<synonym>PO</synonym>
</synonyms>
<definition>The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.</definition>
<uris>
<uri type="URN">urn:miriam:po</uri>
<uri type="URL">http://identifiers.org/po/</uri>
<uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/PO</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.po</uri>
<uri type="URL" deprecated="true">http://identifiers.org/obo.po/</uri>
</uris>
<namespace>po</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18194960</documentation>
</documentations>
<resources>
<resource id="MIR:00100389" state="up" reliability="99">
<dataResource>http://www.plantontology.org/</dataResource>
<dataEntityExample>PO:0009089</dataEntityExample>
<dataEntry>http://www.plantontology.org/amigo/go.cgi?view=details&query=$id</dataEntry>
<dataInfo>Plant Ontology through Amigo</dataInfo>
<dataInstitution>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100390" state="up" reliability="96">
<dataResource>http://bioportal.bioontology.org/ontologies/PO</dataResource>
<dataEntityExample>PO:0009089</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/PO/$id</dataEntry>
<dataInfo>Plant Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100676" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/po</dataResource>
<dataEntityExample>PO:0009089</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/po/terms?obo_id=$id</dataEntry>
<dataInfo>Plant Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000308" pattern="^\d{3}$">
<name>RNA Modification Database</name>
<synonyms>
<synonym>RNAmods</synonym>
</synonyms>
<definition>The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.</definition>
<uris>
<uri type="URN">urn:miriam:rnamods</uri>
<uri type="URL">http://identifiers.org/rnamods/</uri>
</uris>
<namespace>rnamods</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:9399834</documentation>
<documentation type="URL">http://rna-mdb.cas.albany.edu/RNAmods/rnadesc.htm</documentation>
</documentations>
<resources>
<resource id="MIR:00100391" state="up" reliability="98">
<dataResource>http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm</dataResource>
<dataEntityExample>101</dataEntityExample>
<dataEntry>http://mods.rna.albany.edu/mods/modifications/view/$id</dataEntry>
<dataInfo>RNA Modification Database at University of Utah</dataInfo>
<dataInstitution>Department of Medicinal Chemistry and Department of Biochemistry, University of Utah, Salt Lake City, Utah</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>nucleotide</tag>
</tags>
</datatype>
<datatype id="MIR:00000309" pattern="^CMC_\d+$" restricted="true" obsolete="true" replacement="">
<comment>WARNING: this data collection has been deprecated!
As of June 2015, this data collection has been archived by the data provider. Archived data is available <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/sites/default/files/adv_page_assets/connections_map_data_20120208.zip'>here</a>. For further information, please see <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/about/help/cm'>this page</a>.
We recommend usage of the following data collection for pathway related annotation and referencing <a href='http://www.ebi.ac.uk/miriam/cura/collections/MIR:00000018' title='Reactome'>REACTOME</a>.</comment>
<name>Science Signaling Pathway-Independent Component</name>
<definition>The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway independent component information.</definition>
<uris>
<uri type="URN">urn:miriam:sciencesignaling.pic</uri>
<uri type="URL">http://identifiers.org/sciencesignaling.pic/</uri>
</uris>
<namespace>sciencesignaling.pic</namespace>
<documentations>
<documentation type="URL">http://www.sciencemag.org/site/help/librarians/sci_signal_faq.xhtml</documentation>
</documentations>
<resources>
<resource id="MIR:00100392" state="down" reliability="77">
<dataResource>http://stke.sciencemag.org/</dataResource>
<dataEntityExample>CMC_15493</dataEntityExample>
<dataEntry>http://stke.sciencemag.org/cgi/cm/stkecm;$id</dataEntry>
<dataInfo>Science Signaling: Pathway-Independent Component at Science Magazine</dataInfo>
<dataInstitution>Science Mag, Washington DC</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>material for personal and noncommercial use</statement>
<link desc="copyright statement">http://www.sciencemag.org/site/help/readers/copyright.xhtml</link>
</restriction>
</restrictions>
<tags>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000310" pattern="^CMN_\d+$" restricted="true" obsolete="true" replacement="">
<comment>WARNING: this data collection has been deprecated!
As of June 2015, this data collection has been archived by the data provider. Archived data is available <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/sites/default/files/adv_page_assets/connections_map_data_20120208.zip'>here</a>. For further information, please see <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/about/help/cm'>this page</a>.
We recommend usage of the following data collection for pathway related annotation and referencing <a href='http://www.ebi.ac.uk/miriam/cura/collections/MIR:00000018' title='Reactome'>REACTOME</a>.</comment>
<name>Science Signaling Pathway-Dependent Component</name>
<definition>The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway-dependent component information.</definition>
<uris>
<uri type="URN">urn:miriam:sciencesignaling.pdc</uri>
<uri type="URL">http://identifiers.org/sciencesignaling.pdc/</uri>
</uris>
<namespace>sciencesignaling.pdc</namespace>
<documentations>
<documentation type="URL">http://www.sciencemag.org/site/help/librarians/sci_signal_faq.xhtml</documentation>
</documentations>
<resources>
<resource id="MIR:00100393" state="down" reliability="77">
<dataResource>http://stke.sciencemag.org/</dataResource>
<dataEntityExample>CMN_15494</dataEntityExample>
<dataEntry>http://stke.sciencemag.org/cgi/cm/stkecm;$id</dataEntry>
<dataInfo>Science Signaling: Pathway-dependent Component at Science Magazine</dataInfo>
<dataInstitution>Science Mag, Washington DC</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>material for personal and noncommercial use</statement>
<link desc="copyright statement">http://www.sciencemag.org/site/help/readers/copyright.xhtml</link>
</restriction>
</restrictions>
<tags>
<tag>interaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000311" pattern="^CMP_\d+$" restricted="true" obsolete="true" replacement="">
<comment>WARNING: this data collection has been deprecated!
As of June 2015, this data collection has been archived by the data provider. Archived data is available <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/sites/default/files/adv_page_assets/connections_map_data_20120208.zip'>here</a>. For further information, please see <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/about/help/cm'>this page</a>.
We recommend usage of the following data collection for pathway related annotation and referencing <a href='http://www.ebi.ac.uk/miriam/cura/collections/MIR:00000018' title='Reactome'>REACTOME</a>.</comment>
<name>Science Signaling Pathway</name>
<definition>The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway information.</definition>
<uris>
<uri type="URN">urn:miriam:sciencesignaling.path</uri>
<uri type="URL">http://identifiers.org/sciencesignaling.path/</uri>
</uris>
<namespace>sciencesignaling.path</namespace>
<documentations>
<documentation type="URL">http://www.sciencemag.org/site/help/librarians/sci_signal_faq.xhtml</documentation>
</documentations>
<resources>
<resource id="MIR:00100394" state="down" reliability="77">
<dataResource>http://stke.sciencemag.org/</dataResource>
<dataEntityExample>CMP_18019</dataEntityExample>
<dataEntry>http://stke.sciencemag.org/cgi/cm/stkecm;$id</dataEntry>
<dataInfo>Science Signaling: Pathway at Science Magazine</dataInfo>
<dataInstitution>Science Mag, Washington DC</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>material for personal and noncommercial use</statement>
<link desc="copyright ststement">http://www.sciencemag.org/site/help/readers/copyright.xhtml</link>
</restriction>
</restrictions>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000312" pattern="^TB[1,2]?:[A-Z][a-z]?\d+$">
<name>TreeBASE</name>
<definition>TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.</definition>
<uris>
<uri type="URN">urn:miriam:treebase</uri>
<uri type="URL">http://identifiers.org/treebase/</uri>
</uris>
<namespace>treebase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12801879</documentation>
</documentations>
<resources>
<resource id="MIR:00100395" state="down" reliability="59">
<dataResource>http://treebase.org/</dataResource>
<dataEntityExample>TB2:S1000</dataEntityExample>
<dataEntry>http://purl.org/phylo/treebase/phylows/study/$id?format=html</dataEntry>
<dataInfo>TreeBASE (hosted at National Evolutionary Synthesis Center)</dataInfo>
<dataInstitution>Phyloinformatics Research Foundation, Durham, North Carolina</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
</tags>
</datatype>
<datatype id="MIR:00000313" pattern="^TTHERM\_\d+$">
<name>Tetrahymena Genome Database</name>
<synonyms>
<synonym>TGD</synonym>
</synonyms>
<definition>The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature.</definition>
<uris>
<uri type="URN">urn:miriam:tgd</uri>
<uri type="URL">http://identifiers.org/tgd/</uri>
</uris>
<namespace>tgd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381920</documentation>
</documentations>
<resources>
<resource id="MIR:00100396" state="down" reliability="90">
<dataResource>http://ciliate.org/index.php/</dataResource>
<dataEntityExample>TTHERM_00648910</dataEntityExample>
<dataEntry>http://ciliate.org/index.php/feature/details/$id</dataEntry>
<dataInfo>TGD at Stanford University</dataInfo>
<dataInstitution>Department of Genetics, School of Medicine, Stanford University, Stanford, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000314" pattern="^\w+(\_)?\w+$" obsolete="true" replacement="MIR:00000202">
<comment>CMR is no longer supported by the JCVI and has been taken offline. More information at: http://www.jcvi.org/cms/research/past-projects/cmr/overview/</comment>
<name>CMR Gene</name>
<synonyms>
<synonym>Comprehensive Microbial Resource Gene Page</synonym>
</synonyms>
<definition>The Comprehensive Microbial Resource (CMR) contains annotation for all complete microbial genomes and allows for a wide variety of data retrievals. This collection refers to the Gene Page which provides information pertaining to a specific gene such as the Locus Name, Gene Symbol, Coordinates, DNA Molecule Name, and Gene Length.</definition>
<uris>
<uri type="URN">urn:miriam:cmr.gene</uri>
<uri type="URL">http://identifiers.org/cmr.gene/</uri>
</uris>
<namespace>cmr.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11125067</documentation>
</documentations>
<resources>
<resource id="MIR:00100397" state="down" reliability="95">
<dataResource>http://cmr.jcvi.org/cgi-bin/CMR/CmrHomePage.cgi</dataResource>
<dataEntityExample>NTL15EF2281</dataEntityExample>
<dataEntry>http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=$id</dataEntry>
<dataInfo>CMR at JCVI</dataInfo>
<dataInstitution>The Institute for Genomic Research, Rockville, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000315" pattern="^TIGR\d+$">
<name>TIGRFAMS</name>
<definition>TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins.</definition>
<uris>
<uri type="URN">urn:miriam:tigrfam</uri>
<uri type="URL">http://identifiers.org/tigrfam/</uri>
</uris>
<namespace>tigrfam</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11125067</documentation>
</documentations>
<resources>
<resource id="MIR:00100398" state="up" reliability="97">
<dataResource>http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi</dataResource>
<dataEntityExample>TIGR00010</dataEntityExample>
<dataEntry>http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$id</dataEntry>
<dataInfo>TIGRFAM at JCVI</dataInfo>
<dataInstitution>The Institute for Genomic Research, Rockville, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000316" pattern="^\w+$">
<name>Animal TFDB Family</name>
<synonyms>
<synonym>Animal Transcription Factor Database</synonym>
</synonyms>
<definition>The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.</definition>
<uris>
<uri type="URN">urn:miriam:atfdb.family</uri>
<uri type="URL">http://identifiers.org/atfdb.family/</uri>
</uris>
<namespace>atfdb.family</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22080564</documentation>
</documentations>
<resources>
<resource id="MIR:00100399" state="down" reliability="84">
<dataResource>http://www.bioguo.org/AnimalTFDB/family_index.php</dataResource>
<dataEntityExample>CUT</dataEntityExample>
<dataEntry>http://www.bioguo.org/AnimalTFDB/family.php?fam=$id</dataEntry>
<dataInfo>Animal TFDB at Hubei Bioinformatics & Molecular Imaging Key Laboratory</dataInfo>
<dataInstitution>Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000317" pattern="^\d+$" restricted="true">
<name>IUPHAR family</name>
<definition>The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.</definition>
<uris>
<uri type="URN">urn:miriam:iuphar.family</uri>
<uri type="URL">http://identifiers.org/iuphar.family/</uri>
</uris>
<namespace>iuphar.family</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23087376</documentation>
</documentations>
<resources>
<resource id="MIR:00100708" state="up" reliability="99">
<dataResource>http://www.guidetopharmacology.org/</dataResource>
<dataEntityExample>78</dataEntityExample>
<dataEntry>http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$id</dataEntry>
<dataInfo>The IUPHAR/BPS Guide to PHARMACOLOGY</dataInfo>
<dataInstitution>International Union of Pharmacology, Edinburgh</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100400" obsolete="true">
<dataResource>http://www.iuphar-db.org/</dataResource>
<dataEntityExample>78</dataEntityExample>
<dataEntry>http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=$id</dataEntry>
<dataInfo>IUPHAR family at University of Edinburgh</dataInfo>
<dataInstitution>Centre for Cardiovascular Science, University of Edinburgh, Edinburgh</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Material from this site may be downloaded for personal, non-commercial use.</statement>
<link desc="copyright statement">http://www.iuphar-db.org/copyright.jsp</link>
</restriction>
</restrictions>
<tags>
<tag>mammalian</tag>
<tag>schema.org</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000318" pattern="^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$" restricted="true">
<name>DBG2 Introns</name>
<synonyms>
<synonym>Database for Bacterial Group II Introns</synonym>
</synonyms>
<definition>The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.</definition>
<uris>
<uri type="URN">urn:miriam:dbg2introns</uri>
<uri type="URL">http://identifiers.org/dbg2introns/</uri>
</uris>
<namespace>dbg2introns</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22080509</documentation>
</documentations>
<resources>
<resource id="MIR:00100401" state="up" reliability="96">
<dataResource>http://webapps2.ucalgary.ca/~groupii/</dataResource>
<dataEntityExample>Cu.me.I1</dataEntityExample>
<dataEntry>http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$id</dataEntry>
<dataInfo>Bacterial Group II Introns at University of Calgary</dataInfo>
<dataInstitution>Department of Biological Sciences, University of Calgary, Calgary, Alberta</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="4" desc="Identifier instability">
<statement>Some introns from previous versions have been removed.</statement>
<link desc="news on front page">http://webapps2.ucalgary.ca/~groupii/</link>
</restriction>
</restrictions>
<tags>
<tag>DNA</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000319" pattern="\d+$" restricted="true">
<name>Spectral Database for Organic Compounds</name>
<synonyms>
<synonym>SDBS</synonym>
</synonyms>
<definition>The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra.</definition>
<uris>
<uri type="URN">urn:miriam:sdbs</uri>
<uri type="URL">http://identifiers.org/sdbs/</uri>
</uris>
<namespace>sdbs</namespace>
<documentations>
<documentation type="URL">http://riodb01.ibase.aist.go.jp/sdbs/LINKS/Introduction_eng.html</documentation>
<documentation type="URL">http://riodb01.ibase.aist.go.jp/sdbs/</documentation>
</documentations>
<resources>
<resource id="MIR:00100402" state="restricted access" reliability="0">
<dataResource>http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi</dataResource>
<dataEntityExample>4544</dataEntityExample>
<dataEntry>http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$id</dataEntry>
<dataInfo>SDBS at AIST</dataInfo>
<dataInstitution>National Institute of Advanced Industrial Science and Technology (AIST)</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Not for commercial use</statement>
<link desc="restriction statement provided in disclaimer">http://riodb01.ibase.aist.go.jp/sdbs/LINKS/disclaimer_eng.html</link>
</restriction>
<restriction type="3" desc="Access restriction">
<statement>Requires acceptance of terms and conditions</statement>
<link desc="pop-up when terms have not been accepted">http://riodb01.ibase.aist.go.jp/sdbs/LINKS/disclaimer_eng.html</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
<tag>mass spectrometry</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000320" pattern="^\w+$" restricted="true">
<name>Vbase2</name>
<definition>The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.</definition>
<uris>
<uri type="URN">urn:miriam:vbase2</uri>
<uri type="URL">http://identifiers.org/vbase2/</uri>
</uris>
<namespace>vbase2</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608286</documentation>
</documentations>
<resources>
<resource id="MIR:00100403" state="up" reliability="99">
<dataResource>http://www.vbase2.org/vbase2.php</dataResource>
<dataEntityExample>humIGHV025</dataEntityExample>
<dataEntry>http://www.vbase2.org/vgene.php?id=$id</dataEntry>
<dataInfo>Vbase2 at German Research Centre for Biotechnology</dataInfo>
<dataInstitution>Department of Experimental Immunology, German Research Centre for Biotechnology, Braunschweig</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Non-commercial use only</statement>
<link desc="vbase disclaimer">http://www.vbase2.org/vbdisclaimer.php</link>
</restriction>
<restriction type="5" desc="Collection maintenance">
<statement>The date given for last database update is 2006, hence information may be outdated.</statement>
<link desc="date listed">http://www.vbase2.org/vbase2.php</link>
</restriction>
</restrictions>
<tags>
<tag>human</tag>
<tag>immunogenetics</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000321" pattern="^spike\d{5}$">
<name>SPIKE Map</name>
<synonyms>
<synonym>Signaling Pathways Integrated Knowledge Engine</synonym>
</synonyms>
<definition>SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.</definition>
<uris>
<uri type="URN">urn:miriam:spike.map</uri>
<uri type="URL">http://identifiers.org/spike.map/</uri>
</uris>
<namespace>spike.map</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18289391</documentation>
<documentation type="PMID">urn:miriam:pubmed:21097778</documentation>
</documentations>
<resources>
<resource id="MIR:00100404" state="up" reliability="99">
<dataResource>http://www.cs.tau.ac.il/~spike/</dataResource>
<dataEntityExample>spike00001</dataEntityExample>
<dataEntry>http://www.cs.tau.ac.il/~spike/maps/$id.html</dataEntry>
<dataInfo>SPIKE database at Tel Aviv University</dataInfo>
<dataInstitution>School of Computer Sciences and School of Medicine, Tel Aviv University</dataInstitution>
<dataLocation>Israel</dataLocation>
</resource>
</resources>
<tags>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000322" pattern="^\d{4}$" restricted="true">
<name>METLIN</name>
<synonyms>
<synonym>Metabolite and Tandem Mass Spectrometry Database</synonym>
</synonyms>
<definition>The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.</definition>
<uris>
<uri type="URN">urn:miriam:metlin</uri>
<uri type="URL">http://identifiers.org/metlin/</uri>
</uris>
<namespace>metlin</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16404815</documentation>
</documentations>
<resources>
<resource id="MIR:00100406" state="down" reliability="52">
<dataResource>http://masspec.scripps.edu/</dataResource>
<dataEntityExample>1455</dataEntityExample>
<dataEntry>http://metlin.scripps.edu/metabo_info.php?molid=$id</dataEntry>
<dataInfo>METLIN at Scripps Center, Molecular Biology and Center for Mass Spectrometry, La Jolla</dataInfo>
<dataInstitution>Scripps Research Institute, San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>METLIN services may not be used in commercial applications.</statement>
<link desc="terms of use">http://metlin.scripps.edu/terms.php</link>
</restriction>
</restrictions>
<tags>
<tag>mass spectrometry</tag>
<tag>metabolite</tag>
</tags>
</datatype>
<datatype id="MIR:00000323" pattern="^\w+$" restricted="true">
<name>GeneCards</name>
<definition>The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene.</definition>
<uris>
<uri type="URN">urn:miriam:genecards</uri>
<uri type="URL">http://identifiers.org/genecards/</uri>
</uris>
<namespace>genecards</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20689021</documentation>
</documentations>
<resources>
<resource id="MIR:00100407" state="up" reliability="75" primary="true">
<dataResource>http://www.genecards.org/</dataResource>
<dataEntityExample>ABL1</dataEntityExample>
<dataEntry>http://www.genecards.org/cgi-bin/carddisp.pl?gene=$id</dataEntry>
<dataInfo>GeneCards at Weizmann Institute</dataInfo>
<dataInstitution>Department of Molecular Genetics, Weizmann Institute of Science, Rehovot</dataInstitution>
<dataLocation>Israel</dataLocation>
</resource>
<resource id="MIR:00100408" obsolete="true">
<dataResource>http://genecards.bii.a-star.edu.sg/</dataResource>
<dataEntityExample>ABL1</dataEntityExample>
<dataEntry>http://genecards.bii.a-star.edu.sg/cgi-bin/carddisp.pl?gene=$id</dataEntry>
<dataInfo>Genecards at A*STAR</dataInfo>
<dataInstitution>Bioinformatics Institute, A*STAR</dataInstitution>
<dataLocation>Singapore</dataLocation>
</resource>
<resource id="MIR:00100409" obsolete="true">
<dataResource>http://p570e70p1.ophid.utoronto.ca/genecards/index.php</dataResource>
<dataEntityExample>ABL1</dataEntityExample>
<dataEntry>http://p570e70p1.ophid.utoronto.ca/genecards/cgi-bin/carddisp.pl?gene=$id</dataEntry>
<dataInfo>Genecards at University of Toronto</dataInfo>
<dataInstitution>University Health Network, University of Toronoto, Toronto</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
<resource id="MIR:00100410" obsolete="true">
<dataResource>http://bioinformatics.mdanderson.org/genecards/</dataResource>
<dataEntityExample>ABL1</dataEntityExample>
<dataEntry>http://bioinformatics.mdanderson.org/genecards/cgi-bin/carddisp.pl?gene=$id</dataEntry>
<dataInfo>GeneCards at University of Texas</dataInfo>
<dataInstitution>Univ of Texas M.D. Anderson Cancer Center, Houston, Texas</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100411" obsolete="true">
<dataResource>http://www6.unito.it/cards/</dataResource>
<dataEntityExample>ABL1</dataEntityExample>
<dataEntry>http://www6.unito.it/cards/cgi-bin/carddisp.pl?gene=$id</dataEntry>
<dataInfo>GeneCards at University of Torino</dataInfo>
<dataInstitution>Dept. of Clinical and Biological Sciences , Univ of Torino</dataInstitution>
<dataLocation>Italy</dataLocation>
</resource>
<resource id="MIR:00100412" obsolete="true">
<dataResource>http://genecards.bioinformatics.nl/</dataResource>
<dataEntityExample>ABL1</dataEntityExample>
<dataEntry>http://genecards.bioinformatics.nl/cgi-bin/carddisp.pl?gene=$id</dataEntry>
<dataInfo>GeneCards at Wageningen</dataInfo>
<dataInstitution>Laboratory of Bioinformatics, Wageningen UR, Wageningen</dataInstitution>
<dataLocation>Holland</dataLocation>
</resource>
<resource id="MIR:00100413" obsolete="true">
<dataResource>http://genecards_v3.hgc.jp/</dataResource>
<dataEntityExample>ABL1</dataEntityExample>
<dataEntry>http://genecards_v3.hgc.jp/cgi-bin/carddisp.pl?gene=$id</dataEntry>
<dataInfo>GeneCards at University of Tokyo</dataInfo>
<dataInstitution>Human Genome Center, Institute of Medical Science, Univ of Tokyo</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Commercial use requires a license.</statement>
<link desc="terms of use">http://www.genecards.org/AcademicTermsOfUse.shtml?noHdrFtr</link>
</restriction>
</restrictions>
<tags>
<tag>gene</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000324" pattern="^\d+$" restricted="true">
<name>MMRRC</name>
<synonyms>
<synonym>Mutant Mouse Regional Resource Centers</synonym>
</synonyms>
<definition>The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.</definition>
<uris>
<uri type="URN">urn:miriam:mmrrc</uri>
<uri type="URL">http://identifiers.org/mmrrc/</uri>
</uris>
<namespace>mmrrc</namespace>
<documentations>
<documentation type="URL">http://www.mmrrc.org/about/generalInfo.php</documentation>
</documentations>
<resources>
<resource id="MIR:00100414" state="probably up" reliability="89">
<dataResource>http://www.mmrrc.org/</dataResource>
<dataEntityExample>70</dataEntityExample>
<dataEntry>http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$id</dataEntry>
<dataInfo>MMRRC at University of North Carolina</dataInfo>
<dataInstitution>University of North Carolina</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>restriction due to embedded MGI data</statement>
<link desc="data download restriction">http://www.mmrrc.org/about/data_download.php</link>
</restriction>
</restrictions>
<tags>
<tag>catalogue</tag>
<tag>mammalian</tag>
<tag>strain</tag>
</tags>
</datatype>
<datatype id="MIR:00000325" pattern="^r\d+$">
<name>UM-BBD Reaction</name>
<synonyms>
<synonym>University of Minnesota Biocatalysis/Biodegradation Database (Reaction)</synonym>
</synonyms>
<definition>The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information.</definition>
<uris>
<uri type="URN">urn:miriam:umbbd.reaction</uri>
<uri type="URL">http://identifiers.org/umbbd.reaction/</uri>
</uris>
<namespace>umbbd.reaction</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19767608</documentation>
</documentations>
<resources>
<resource id="MIR:00100416" state="up" reliability="99">
<dataResource>http://umbbd.ethz.ch/</dataResource>
<dataEntityExample>r0001</dataEntityExample>
<dataEntry>http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$id</dataEntry>
<dataInfo>Biocatalysis/Biodegradation Database Mirror (Reaction) at ETH Zurich</dataInfo>
<dataInstitution>ETH, Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
<resource id="MIR:00100415" obsolete="true">
<dataResource>http://umbbd.msi.umn.edu/index.html</dataResource>
<dataEntityExample>r0001</dataEntityExample>
<dataEntry>http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=$id</dataEntry>
<dataInfo>Biocatalysis/Biodegradation Database (Reaction) at University of Minnesota</dataInfo>
<dataInstitution>Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>microbial</tag>
<tag>reaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000326" pattern="^e\d+$">
<name>UM-BBD Enzyme</name>
<synonyms>
<synonym>University of Minnesota Biocatalysis/Biodegradation Database (Enzyme)</synonym>
</synonyms>
<definition>The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.</definition>
<uris>
<uri type="URN">urn:miriam:umbbd.enzyme</uri>
<uri type="URL">http://identifiers.org/umbbd.enzyme/</uri>
</uris>
<namespace>umbbd.enzyme</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19767608</documentation>
</documentations>
<resources>
<resource id="MIR:00100418" state="up" reliability="99">
<dataResource>http://umbbd.ethz.ch/</dataResource>
<dataEntityExample>e0333</dataEntityExample>
<dataEntry>http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$id</dataEntry>
<dataInfo>Biocatalysis/Biodegradation Database Mirror (Enzyme) at ETH Zurich</dataInfo>
<dataInstitution>ETH, Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
<resource id="MIR:00100417" obsolete="true">
<dataResource>http://umbbd.msi.umn.edu/index.html</dataResource>
<dataEntityExample>e0333</dataEntityExample>
<dataEntry>http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=$id</dataEntry>
<dataInfo>Biocatalysis/Biodegradation Database (Enzyme) at University of Minnesota</dataInfo>
<dataInstitution>Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>enzyme</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000327" pattern="^\w+$">
<name>UM-BBD Pathway</name>
<synonyms>
<synonym>University of Minnesota Biocatalysis/Biodegradation Database (Pathway)</synonym>
</synonyms>
<definition>The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information.</definition>
<uris>
<uri type="URN">urn:miriam:umbbd.pathway</uri>
<uri type="URL">http://identifiers.org/umbbd.pathway/</uri>
</uris>
<namespace>umbbd.pathway</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19767608</documentation>
</documentations>
<resources>
<resource id="MIR:00100420" state="up" reliability="99">
<dataResource>http://umbbd.ethz.ch/</dataResource>
<dataEntityExample>ala</dataEntityExample>
<dataEntry>http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$id</dataEntry>
<dataInfo>Biocatalysis/Biodegradation Database Mirror (Pathway) at ETH Zurich</dataInfo>
<dataInstitution>ETH, Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
<resource id="MIR:00100419" obsolete="true">
<dataResource>http://umbbd.msi.umn.edu/index.html</dataResource>
<dataEntityExample>ala</dataEntityExample>
<dataEntry>http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=p&pathway_abbr=$id</dataEntry>
<dataInfo>Biocatalysis/Biodegradation Database (Pathway) at University of Minnesota</dataInfo>
<dataInstitution>Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>microbial</tag>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000328" pattern="^bt\d+$">
<name>UM-BBD Biotransformation Rule</name>
<definition>The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.</definition>
<uris>
<uri type="URN">urn:miriam:umbbd.rule</uri>
<uri type="URL">http://identifiers.org/umbbd.rule/</uri>
</uris>
<namespace>umbbd.rule</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19767608</documentation>
<documentation type="URL">http://sivabio.50webs.com/pps.htm</documentation>
</documentations>
<resources>
<resource id="MIR:00100421" state="up" reliability="99">
<dataResource>http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules</dataResource>
<dataEntityExample>bt0001</dataEntityExample>
<dataEntry>http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$id</dataEntry>
<dataInfo>Biocatalysis/Biodegradation Database Mirror (Biotransformation Rule) at ETH Zurich</dataInfo>
<dataInstitution>ETH, Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
<resource id="MIR:00100422" obsolete="true">
<dataResource>http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allrules</dataResource>
<dataEntityExample>bt0001</dataEntityExample>
<dataEntry>http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=$id</dataEntry>
<dataInfo>Biocatalysis/Biodegradation Database Mirror (Biotransformation Rules) at University of Minnesota</dataInfo>
<dataInstitution>Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>microbial</tag>
<tag>reaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000329" pattern="^\d+(\w+)?$">
<name>mirEX</name>
<definition>mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.</definition>
<uris>
<uri type="URN">urn:miriam:mirex</uri>
<uri type="URL">http://identifiers.org/mirex/</uri>
</uris>
<namespace>mirex</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22013167</documentation>
</documentations>
<resources>
<resource id="MIR:00100423" state="down" reliability="74">
<dataResource>http://comgen.pl/mirex/?page=home</dataResource>
<dataEntityExample>165a</dataEntityExample>
<dataEntry>http://comgen.pl/mirex1/?page=results/record&name=$id&exref=pp2a&limit=yes</dataEntry>
<dataInfo>mirEX at Adam Mickiewicz University</dataInfo>
<dataInstitution>Institute of Molecular Biology, Adam Mickiewicz University, Poznan</dataInstitution>
<dataLocation>Poland</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>gene</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000330" pattern="^DDB\d+$">
<name>Dictybase EST</name>
<definition>The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information.</definition>
<uris>
<uri type="URN">urn:miriam:dictybase.est</uri>
<uri type="URL">http://identifiers.org/dictybase.est/</uri>
</uris>
<namespace>dictybase.est</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21087999</documentation>
</documentations>
<resources>
<resource id="MIR:00100424" state="up" reliability="99">
<dataResource>http://dictybase.org/</dataResource>
<dataEntityExample>DDB0016567</dataEntityExample>
<dataEntry>http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$id</dataEntry>
<dataInfo>Dictybase Gene at Northwestern University</dataInfo>
<dataInstitution>Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, Chicago, Illinois</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>plant</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000331" pattern="^[A-Z0-9*:]+$">
<name>IMGT HLA</name>
<synonyms>
<synonym>IPD IMGT/HLA</synonym>
</synonyms>
<definition>IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature.</definition>
<uris>
<uri type="URN">urn:miriam:imgt.hla</uri>
<uri type="URL">http://identifiers.org/imgt.hla/</uri>
</uris>
<namespace>imgt.hla</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381979</documentation>
</documentations>
<resources>
<resource id="MIR:00100425" state="up" reliability="99">
<dataResource>http://www.ebi.ac.uk/imgt/hla/allele.html</dataResource>
<dataEntityExample>A*01:01:01:01</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$id</dataEntry>
<dataInfo>IMGT HLA at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>immunogenetics</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000332" pattern="^\d+$">
<name>Flystock</name>
<synonyms>
<synonym>Bloomington Drosophila Stock Center at Indiana University</synonym>
</synonyms>
<definition>The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.</definition>
<uris>
<uri type="URN">urn:miriam:flystock</uri>
<uri type="URL">http://identifiers.org/flystock/</uri>
</uris>
<namespace>flystock</namespace>
<documentations>
<documentation type="URL">http://flystocks.bio.indiana.edu/Inst/history.htm</documentation>
</documentations>
<resources>
<resource id="MIR:00100426" state="down" reliability="94">
<dataResource>http://flystocks.bio.indiana.edu/bloomhome.htm</dataResource>
<dataEntityExample>33159</dataEntityExample>
<dataEntry>http://flystocks.bio.indiana.edu/Reports/$id.html</dataEntry>
<dataInfo>Flystock at Indiana University</dataInfo>
<dataInstitution>BDSC, Department of Biology, Indiana University, Bloomington</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>strain</tag>
</tags>
</datatype>
<datatype id="MIR:00000333" pattern="^[0-9][A-Za-z0-9]{3}$" restricted="true">
<name>OPM</name>
<synonyms>
<synonym>Orientations of Proteins in Membranes</synonym>
</synonyms>
<definition>The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.</definition>
<uris>
<uri type="URN">urn:miriam:opm</uri>
<uri type="URL">http://identifiers.org/opm/</uri>
</uris>
<namespace>opm</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21890895</documentation>
</documentations>
<resources>
<resource id="MIR:00100427" state="up" reliability="99">
<dataResource>http://opm.phar.umich.edu/</dataResource>
<dataEntityExample>1h68</dataEntityExample>
<dataEntry>http://opm.phar.umich.edu/protein.php?pdbid=$id</dataEntry>
<dataInfo>OPM at University of Michigan</dataInfo>
<dataInstitution>Department of Medicinal Chemistry, College of Pharmacy, University of Michigan</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="6" desc="Collection subset">
<statement>Based upon, and uses identifiers from, a subset of PDB entries.</statement>
<link desc="statistic table">http://opm.phar.umich.edu/</link>
</restriction>
</restrictions>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000334" pattern="^\d+$" restricted="true">
<name>Allergome</name>
<definition>Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.</definition>
<uris>
<uri type="URN">urn:miriam:allergome</uri>
<uri type="URL">http://identifiers.org/allergome/</uri>
</uris>
<namespace>allergome</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17434469</documentation>
</documentations>
<resources>
<resource id="MIR:00100429" state="probably up" reliability="93">
<dataResource>http://www.allergome.org/</dataResource>
<dataEntityExample>1948</dataEntityExample>
<dataEntry>http://www.allergome.org/script/dettaglio.php?id_molecule=$id</dataEntry>
<dataInfo>Allergome at Rome</dataInfo>
<dataInstitution>Center for Clinical and Experimental Allergology, Rome</dataInstitution>
<dataLocation>Italy</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Non-commercial license associated.</statement>
<link desc="license cited">http://creativecommons.org/licenses/by-nc-sa/2.5/deed.en</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000335" pattern="^S\w+(\.)?\w+(\.)?$">
<name>PomBase</name>
<definition>PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets.</definition>
<uris>
<uri type="URN">urn:miriam:pombase</uri>
<uri type="URL">http://identifiers.org/pombase/</uri>
</uris>
<namespace>pombase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22039153</documentation>
</documentations>
<resources>
<resource id="MIR:00100430" state="down" reliability="91">
<dataResource>http://www.pombase.org/</dataResource>
<dataEntityExample>SPCC13B11.01</dataEntityExample>
<dataEntry>http://www.pombase.org/spombe/result/$id</dataEntry>
<dataInfo>PomBase at University of Cambridge</dataInfo>
<dataInstitution>Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000336" pattern="^ENSG\d{11}$" restricted="true">
<name>HPA</name>
<synonyms>
<synonym>Human Protein Atlas</synonym>
</synonyms>
<definition>The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.</definition>
<uris>
<uri type="URN">urn:miriam:hpa</uri>
<uri type="URL">http://identifiers.org/hpa/</uri>
</uris>
<namespace>hpa</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18669619</documentation>
</documentations>
<resources>
<resource id="MIR:00100431" state="up" reliability="99">
<dataResource>http://www.proteinatlas.org/</dataResource>
<dataEntityExample>ENSG00000026508</dataEntityExample>
<dataEntry>http://www.proteinatlas.org/$id</dataEntry>
<dataInfo>Human Protein Atlas at AlbaNova University</dataInfo>
<dataInstitution>Department of Proteomics, School of Biotechnology, AlbaNova University Center, Stockholm</dataInstitution>
<dataLocation>Sweden</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>May not be suitable for commercial use.</statement>
<link desc="data usage">http://www.proteinatlas.org/about/datausage</link>
</restriction>
</restrictions>
<tags>
<tag>disease</tag>
<tag>image library</tag>
<tag>protein</tag>
<tag>schema.org</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000337" pattern="^\d+$" restricted="true">
<name>JAX Mice</name>
<definition>JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory.</definition>
<uris>
<uri type="URN">urn:miriam:jaxmice</uri>
<uri type="URL">http://identifiers.org/jaxmice/</uri>
</uris>
<namespace>jaxmice</namespace>
<documentations>
<documentation type="URL">http://www.jax.org/about/index.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100432" state="up" reliability="99">
<dataResource>http://jaxmice.jax.org/</dataResource>
<dataEntityExample>005012</dataEntityExample>
<dataEntry>http://jaxmice.jax.org/strain/$id.html</dataEntry>
<dataInfo>JAX Mice at Jackson Laboratory</dataInfo>
<dataInstitution>The Jackson Laboratory, Sacremento, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>free for non-commercial or personal use</statement>
<link desc="terms and conditions">http://www.jax.org/about/legal.html</link>
</restriction>
</restrictions>
<tags>
<tag>mammalian</tag>
<tag>schema.org</tag>
<tag>strain</tag>
</tags>
</datatype>
<datatype id="MIR:00000338" pattern="^\d+$">
<name>uBio NameBank</name>
<synonyms>
<synonym>Universal Biological Indexer and Organizer (NameBank)</synonym>
</synonyms>
<definition>NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.</definition>
<uris>
<uri type="URN">urn:miriam:ubio.namebank</uri>
<uri type="URL">http://identifiers.org/ubio.namebank/</uri>
</uris>
<namespace>ubio.namebank</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16861205</documentation>
</documentations>
<resources>
<resource id="MIR:00100433" state="up" reliability="83">
<dataResource>http://www.ubio.org</dataResource>
<dataEntityExample>2555646</dataEntityExample>
<dataEntry>http://www.ubio.org/browser/details.php?namebankID=$id</dataEntry>
<dataInfo>uBio NameBank at The Marine Biological Laboratory</dataInfo>
<dataInstitution>Marine Biological Laboratory, Woods Hole, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>controlled vocabulary</tag>
<tag>taxonomy</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000339" pattern="^\w+\_\d+(\.\d+)?$">
<name>YeTFasCo</name>
<synonyms>
<synonym>Yeast Transcription Factor Specificity Compendium</synonym>
</synonyms>
<definition>The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.</definition>
<uris>
<uri type="URN">urn:miriam:yetfasco</uri>
<uri type="URL">http://identifiers.org/yetfasco/</uri>
</uris>
<namespace>yetfasco</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22102575</documentation>
</documentations>
<resources>
<resource id="MIR:00100434" state="up" reliability="99">
<dataResource>http://yetfasco.ccbr.utoronto.ca/</dataResource>
<dataEntityExample>YOR172W_571.0</dataEntityExample>
<dataEntry>http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$id</dataEntry>
<dataInfo>YeTFasCo at University of Toronto</dataInfo>
<dataInstitution>Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>gene</tag>
<tag>interaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000340" pattern="^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)?">
<name>TarBase</name>
<definition>TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used.</definition>
<uris>
<uri type="URN">urn:miriam:tarbase</uri>
<uri type="URL">http://identifiers.org/tarbase/</uri>
</uris>
<namespace>tarbase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22135297</documentation>
</documentations>
<resources>
<resource id="MIR:00100713" state="up" reliability="99">
<dataResource>http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index</dataResource>
<dataEntityExample>hsa-let-7a-2-3p</dataEntityExample>
<dataEntry>http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$id</dataEntry>
<dataInfo>TarBase v7 at University of Thessaly</dataInfo>
<dataInstitution>DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly</dataInstitution>
<dataLocation>Greece</dataLocation>
</resource>
<resource id="MIR:00100435" obsolete="true">
<dataResource>http://diana.cslab.ece.ntua.gr/DianaToolsNew/index.php?r=tarbase</dataResource>
<dataEntityExample>hsa-let-7</dataEntityExample>
<dataEntry>http://diana.cslab.ece.ntua.gr/DianaToolsNew/index.php?r=tarbase/index&mirnas=$id</dataEntry>
<dataInfo>TarBase v6 at IMIS Institute</dataInfo>
<dataInstitution>IMIS Institute, Athena Research Center, Athens</dataInstitution>
<dataLocation>Greece</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>interaction</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000341" pattern="^CH_\d+$">
<name>CharProt</name>
<definition>CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.</definition>
<uris>
<uri type="URN">urn:miriam:charprot</uri>
<uri type="URL">http://identifiers.org/charprot/</uri>
</uris>
<namespace>charprot</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22140108</documentation>
</documentations>
<resources>
<resource id="MIR:00100436" state="down" reliability="80">
<dataResource>http://www.jcvi.org/charprotdb</dataResource>
<dataEntityExample>CH_001923</dataEntityExample>
<dataEntry>http://www.jcvi.org/charprotdb/index.cgi/view/$id</dataEntry>
<dataInfo>CharProt at JCVI</dataInfo>
<dataInstitution>J Craig Venter institute, Rockville, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>annotation</tag>
<tag>controlled vocabulary</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000342" pattern="^[A-Z0-9]{5}\d+$" restricted="true">
<name>OMA Protein</name>
<synonyms>
<synonym>Orthologous MAtrix</synonym>
</synonyms>
<definition>OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.</definition>
<uris>
<uri type="URN">urn:miriam:oma.protein</uri>
<uri type="URL">http://identifiers.org/oma.protein/</uri>
</uris>
<namespace>oma.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21113020</documentation>
</documentations>
<resources>
<resource id="MIR:00100437" state="down" reliability="74">
<dataResource>http://omabrowser.org/cgi-bin/gateway.pl</dataResource>
<dataEntityExample>HUMAN16963</dataEntityExample>
<dataEntry>http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$id</dataEntry>
<dataInfo>OMA Protein through OMA browser at ETH Zurich</dataInfo>
<dataInstitution>ETH Zurich, Computer Science, Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Terms of service under a noncommercial license.</statement>
<link desc="terms of service">http://omabrowser.org/about.html</link>
</restriction>
</restrictions>
<tags>
<tag>clustering</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000343" pattern="^[A-Z]+$" restricted="true">
<name>OMA Group</name>
<definition>OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.</definition>
<uris>
<uri type="URN">urn:miriam:oma.grp</uri>
<uri type="URL">http://identifiers.org/oma.grp/</uri>
</uris>
<namespace>oma.grp</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21113020</documentation>
</documentations>
<resources>
<resource id="MIR:00100438" state="down" reliability="89">
<dataResource>http://omabrowser.org/cgi-bin/gateway.pl</dataResource>
<dataEntityExample>LCSCCPN</dataEntityExample>
<dataEntry>http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$id</dataEntry>
<dataInfo>OMA Group through OMA browser at ETH Zurich</dataInfo>
<dataInstitution>ETH Zurich, Computer Science, Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Terms of service under a noncommercial license.</statement>
<link desc="terms of service">http://omabrowser.org/about.html</link>
</restriction>
</restrictions>
<tags>
<tag>clustering</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000344" pattern="^(\w+\d+(\.\d+)?)|(NP_\d+)$" restricted="true">
<name>NCBI Protein</name>
<definition>The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.</definition>
<uris>
<uri type="URN">urn:miriam:ncbiprotein</uri>
<uri type="URL">http://identifiers.org/ncbiprotein/</uri>
</uris>
<namespace>ncbiprotein</namespace>
<documentations>
<documentation type="URL">http://www.ncbi.nlm.nih.gov/protein</documentation>
</documentations>
<resources>
<resource id="MIR:00100439" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/protein</dataResource>
<dataEntityExample>CAA71118.1</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/protein/$id</dataEntry>
<dataInfo>NCBI Protein at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="2" desc="Data aggregation">
<statement>This collection is an aggregation of a variety of data sources.</statement>
<link desc="source list">http://www.ncbi.nlm.nih.gov/protein</link>
</restriction>
</restrictions>
<tags>
<tag>protein</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000345" pattern="^\w{3}\d{5}(\.\d+)?$" restricted="true">
<name>GenPept</name>
<synonyms>
<synonym>protein genbank identifier</synonym>
</synonyms>
<definition>The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.</definition>
<uris>
<uri type="URN">urn:miriam:genpept</uri>
<uri type="URL">http://identifiers.org/genpept/</uri>
</uris>
<namespace>genpept</namespace>
<documentations>
<documentation type="URL">http://www.ncbi.nlm.nih.gov/protein</documentation>
</documentations>
<resources>
<resource id="MIR:00100440" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/protein</dataResource>
<dataEntityExample>CAA71118.1</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/protein/$id?report=genpept</dataEntry>
<dataInfo>GenPept at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="6" desc="Collection subset">
<statement>This collection is a subset of the information found in the NCBI protein database.</statement>
<link desc="GenPept listed as source for 'Protein'">http://www.ncbi.nlm.nih.gov/guide/all/</link>
</restriction>
</restrictions>
<tags>
<tag>genome</tag>
<tag>protein</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000346" pattern="^\d+$" restricted="true">
<name>UniGene</name>
<definition>A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.</definition>
<uris>
<uri type="URN">urn:miriam:unigene</uri>
<uri type="URL">http://identifiers.org/unigene/</uri>
</uris>
<namespace>unigene</namespace>
<documentations>
<documentation type="URL">http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch21</documentation>
</documentations>
<resources>
<resource id="MIR:00100441" state="restricted access" reliability="0">
<dataResource>http://www.ncbi.nlm.nih.gov/unigene</dataResource>
<dataEntityExample>4900</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$id</dataEntry>
<dataInfo>UniGene at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology , Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>It is not possible to directly specify a cluster ID without providing an organism abbreviation.</statement>
<link desc="FAQ">http://www.ncbi.nlm.nih.gov/UniGene/help.cgi?item=FAQ#q12</link>
</restriction>
</restrictions>
</datatype>
<datatype id="MIR:00000347" pattern="^\d+$">
<name>BitterDB Receptor</name>
<definition>BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.</definition>
<uris>
<uri type="URN">urn:miriam:bitterdb.rec</uri>
<uri type="URL">http://identifiers.org/bitterdb.rec/</uri>
</uris>
<namespace>bitterdb.rec</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21940398</documentation>
</documentations>
<resources>
<resource id="MIR:00100442" state="up" reliability="89">
<dataResource>http://bitterdb.agri.huji.ac.il/dbbitter.php</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://bitterdb.agri.huji.ac.il/Receptor.php?id=$id</dataEntry>
<dataInfo>BitterDB Receptor at The Hebrew University of Jerusalem</dataInfo>
<dataInstitution>The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot</dataInstitution>
<dataLocation>Israel</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>human</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000348" pattern="^\d+$">
<name>BitterDB Compound</name>
<definition>BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.</definition>
<uris>
<uri type="URN">urn:miriam:bitterdb.cpd</uri>
<uri type="URL">http://identifiers.org/bitterdb.cpd/</uri>
</uris>
<namespace>bitterdb.cpd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21940398</documentation>
</documentations>
<resources>
<resource id="MIR:00100443" state="up" reliability="89">
<dataResource>http://bitterdb.agri.huji.ac.il/dbbitter.php</dataResource>
<dataEntityExample>46</dataEntityExample>
<dataEntry>http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$id</dataEntry>
<dataInfo>BitterDB Compound at The Hebrew University of Jerusalem</dataInfo>
<dataInstitution>The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot</dataInstitution>
<dataLocation>Israel</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000349" pattern="^PRJ[DEN][A-Z]\d+$">
<name>BioProject</name>
<definition>BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories.</definition>
<uris>
<uri type="URN">urn:miriam:bioproject</uri>
<uri type="URL">http://identifiers.org/bioproject/</uri>
</uris>
<namespace>bioproject</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22110025</documentation>
<documentation type="PMID">urn:miriam:pubmed:22139929</documentation>
</documentations>
<resources>
<resource id="MIR:00100444" state="up" reliability="96">
<dataResource>http://trace.ddbj.nig.ac.jp/bioproject/</dataResource>
<dataEntityExample>PRJDB3</dataEntityExample>
<dataEntry>http://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=$id</dataEntry>
<dataInfo>BioProject at DNA Data Bank of Japan</dataInfo>
<dataInstitution>DNA Data Bank of Japan, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
<resource id="MIR:00100445" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/bioproject</dataResource>
<dataEntityExample>PRJDB3</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/bioproject?term=$id</dataEntry>
<dataInfo>BioProject at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100446" state="probably up" reliability="99">
<dataResource>http://www.ebi.ac.uk/ena/</dataResource>
<dataEntityExample>PRJDB3</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/$id</dataEntry>
<dataInfo>BioProject at European Nucleotide Archive (ENA)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>annotation</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000350" pattern="^SAM[NED](\w)?\d+$">
<name>BioSample</name>
<synonyms>
<synonym>BioSDe</synonym>
<synonym>BioSdn</synonym>
</synonyms>
<definition>The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.</definition>
<uris>
<uri type="URN">urn:miriam:biosample</uri>
<uri type="URL">http://identifiers.org/biosample/</uri>
</uris>
<namespace>biosample</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22096232</documentation>
</documentations>
<resources>
<resource id="MIR:00100447" state="probably up" reliability="98" primary="true">
<dataResource>http://www.ebi.ac.uk/biosamples/</dataResource>
<dataEntityExample>SAMEA2397676</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/biosamples/sample/$id</dataEntry>
<dataInfo>BioSample Database at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100706" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/biosample</dataResource>
<dataEntityExample>SAMN00000002</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/biosample?term=$id</dataEntry>
<dataInfo>BioSample at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100707" state="up" reliability="95">
<dataResource>http://trace.ddbj.nig.ac.jp/biosample/</dataResource>
<dataEntityExample>SAMD00005257</dataEntityExample>
<dataEntry>http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$id</dataEntry>
<dataInfo>BioSample at DNA Data Bank of Japan</dataInfo>
<dataInstitution>Institution DNA Data Bank of Japan, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>annotation</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000351" pattern="^TA\d+$">
<name>PiroplasmaDB</name>
<definition>PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.</definition>
<uris>
<uri type="URN">urn:miriam:piroplasma</uri>
<uri type="URL">http://identifiers.org/piroplasma/</uri>
</uris>
<namespace>piroplasma</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19914931</documentation>
</documentations>
<resources>
<resource id="MIR:00100448" state="down" reliability="73">
<dataResource>http://piroplasmadb.org/</dataResource>
<dataEntityExample>TA14985</dataEntityExample>
<dataEntry>http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id</dataEntry>
<dataInfo>PiroplasmaBD at EuPathDB</dataInfo>
<dataInstitution>Center for Tropical &amp; Emerging Global Diseases, University of Georgia, Georgia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000352" pattern="^UDB\d{6}$">
<name>Unite</name>
<definition>UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa.</definition>
<uris>
<uri type="URN">urn:miriam:unite</uri>
<uri type="URL">http://identifiers.org/unite/</uri>
</uris>
<namespace>unite</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20409185</documentation>
</documentations>
<resources>
<resource id="MIR:00100449" state="up" reliability="93">
<dataResource>http://unite.ut.ee/</dataResource>
<dataEntityExample>UDB000691</dataEntityExample>
<dataEntry>http://unite.ut.ee/bl_forw.php?nimi=$id</dataEntry>
<dataInfo>Unite at University of Tartu</dataInfo>
<dataInstitution>Institute of Botany, University of Tartu, Tartu</dataInstitution>
<dataLocation>Estonia</dataLocation>
</resource>
</resources>
<tags>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000353" pattern="^C\d+$" restricted="true">
<name>NCIm</name>
<synonyms>
<synonym>National Cancer Institute Metathesaurus</synonym>
<synonym>NCI metathesaurus</synonym>
</synonyms>
<definition>NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical.</definition>
<uris>
<uri type="URN">urn:miriam:ncim</uri>
<uri type="URL">http://identifiers.org/ncim/</uri>
</uris>
<namespace>ncim</namespace>
<documentations>
<documentation type="URL">http://ncim.nci.nih.gov/ncimbrowser/pages/help.jsf</documentation>
</documentations>
<resources>
<resource id="MIR:00100450" state="down" reliability="51">
<dataResource>http://ncim.nci.nih.gov/</dataResource>
<dataEntityExample>C0026339</dataEntityExample>
<dataEntry>http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$id</dataEntry>
<dataInfo>NCIm at National Cancer Institue</dataInfo>
<dataInstitution>National Cancer Institute, Center for Bioinformatics, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Some proprietary terminologies are included, with permission, and have restrictions on their use.</statement>
<link desc="source terminologies">http://ncimeta.nci.nih.gov/ncimbrowser/pages/source_help_info.jsf</link>
</restriction>
</restrictions>
<tags>
<tag>controlled vocabulary</tag>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>compartment</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000354" pattern="^[A-Z]C\d{1,3}$">
<name>ProGlycProt</name>
<definition>ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information.</definition>
<uris>
<uri type="URN">urn:miriam:proglyc</uri>
<uri type="URL">http://identifiers.org/proglyc/</uri>
</uris>
<namespace>proglyc</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22039152</documentation>
</documentations>
<resources>
<resource id="MIR:00100451" state="up" reliability="87">
<dataResource>http://www.proglycprot.org/</dataResource>
<dataEntityExample>AC119</dataEntityExample>
<dataEntry>http://www.proglycprot.org/detail.aspx?ProId=$id</dataEntry>
<dataInfo>ProGlycProt at IMT</dataInfo>
<dataInstitution>Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh</dataInstitution>
<dataLocation>India</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000355" pattern="^[A-Za-z-0-9]+$">
<name>PolBase</name>
<definition>Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity.</definition>
<uris>
<uri type="URN">urn:miriam:polbase</uri>
<uri type="URL">http://identifiers.org/polbase/</uri>
</uris>
<namespace>polbase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21993301</documentation>
</documentations>
<resources>
<resource id="MIR:00100452" state="up" reliability="77">
<dataResource>http://polbase.neb.com/</dataResource>
<dataEntityExample>19-T4</dataEntityExample>
<dataEntry>https://polbase.neb.com/polymerases/$id#sequences</dataEntry>
<dataInfo>PolBase at New England BioLabs</dataInfo>
<dataInstitution>New England Biolabs, Ipswich, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>enzyme</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000356" pattern="^\w+\_\w+$">
<name>NucleaRDB</name>
<definition>NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.</definition>
<uris>
<uri type="URN">urn:miriam:nuclearbd</uri>
<uri type="URL">http://identifiers.org/nuclearbd/</uri>
</uris>
<namespace>nuclearbd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22064856</documentation>
</documentations>
<resources>
<resource id="MIR:00100453" state="down" reliability="60">
<dataResource>http://www.receptors.org/nucleardb/</dataResource>
<dataEntityExample>prgr_human</dataEntityExample>
<dataEntry>http://www.receptors.org/nucleardb/proteins/$id</dataEntry>
<dataInfo>NucleaRDB at Radboud University Nijmegen Medical Centre</dataInfo>
<dataInstitution>CMBI, Radboud University Nijmegen Medical Centre, Dreijenplein, Wageningen</dataInstitution>
<dataLocation>Holland</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000357" pattern="^\w+$">
<name>SUPFAM</name>
<synonyms>
<synonym>SUPERFAMILY</synonym>
</synonyms>
<definition>SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt.</definition>
<uris>
<uri type="URN">urn:miriam:supfam</uri>
<uri type="URL">http://identifiers.org/supfam/</uri>
</uris>
<namespace>supfam</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19036790</documentation>
</documentations>
<resources>
<resource id="MIR:00100454" state="up" reliability="98">
<dataResource>http://supfam.org/SUPERFAMILY/</dataResource>
<dataEntityExample>SSF57615</dataEntityExample>
<dataEntry>http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id</dataEntry>
<dataInfo>SUPFAM at MRC and University of Bristol</dataInfo>
<dataInstitution>MRC Laboratory of Molecular Biology, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000358" pattern="^LOC\_Os\d{1,2}g\d{5}$">
<name>Rice Genome Annotation Project</name>
<definition>The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.</definition>
<uris>
<uri type="URN">urn:miriam:ricegap</uri>
<uri type="URL">http://identifiers.org/ricegap/</uri>
</uris>
<namespace>ricegap</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17145706</documentation>
</documentations>
<resources>
<resource id="MIR:00100455" state="up" reliability="100">
<dataResource>http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml</dataResource>
<dataEntityExample>LOC_Os02g13300</dataEntityExample>
<dataEntry>http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$id</dataEntry>
<dataInfo>Rice Genome Annotation Project at TIGR</dataInfo>
<dataInstitution>The Institute for Genomic Research, Rockville, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000359" pattern="^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$" restricted="true">
<name>PINA</name>
<synonyms>
<synonym>Protein Interaction Network Analysis</synonym>
</synonyms>
<definition>Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.</definition>
<uris>
<uri type="URN">urn:miriam:pina</uri>
<uri type="URL">http://identifiers.org/pina/</uri>
</uris>
<namespace>pina</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19079255</documentation>
</documentations>
<resources>
<resource id="MIR:00100456" state="down" reliability="68">
<dataResource>http://cbg.garvan.unsw.edu.au/pina/</dataResource>
<dataEntityExample>Q13485</dataEntityExample>
<dataEntry>http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$id&showExtend=null</dataEntry>
<dataInfo>Protein Interaction Network Analysis (PINA) at Garvan Institute</dataInfo>
<dataInstitution>Garvan Institute of Medical Research, Sydney</dataInstitution>
<dataLocation>Australia</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="2" desc="Data aggregation">
<statement>Protein-protein interaction data from IntAct, MINT, BioGRID, DIP, HPRD, MIPS/MPact, and Protein annotations from UniProt, Ensembl, WormBase.</statement>
<link desc="data sources">http://cbg.garvan.unsw.edu.au/pina/interactome.stat.do</link>
</restriction>
</restrictions>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000360" pattern="^TS-\d{4}$">
<name>Tissue List</name>
<definition>The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified.</definition>
<uris>
<uri type="URN">urn:miriam:tissuelist</uri>
<uri type="URL">http://identifiers.org/tissuelist/</uri>
</uris>
<namespace>tissuelist</namespace>
<documentations>
<documentation type="URL">http://www.expasy.org/cgi-bin/lists?tisslist.txt</documentation>
</documentations>
<resources>
<resource id="MIR:00100457" state="up" reliability="99">
<dataResource>http://www.uniprot.org/docs/tisslist.txt</dataResource>
<dataEntityExample>TS-0285</dataEntityExample>
<dataEntry>http://www.uniprot.org/tissues/$id</dataEntry>
<dataInfo>Tissue List at Swiss Institute of Bioinformatics</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics (SIB), Geneva</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>controlled vocabulary</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000361" pattern="^\d+$">
<name>BacMap Biography</name>
<definition>BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.</definition>
<uris>
<uri type="URN">urn:miriam:bacmap.biog</uri>
<uri type="URL">http://identifiers.org/bacmap.biog/</uri>
</uris>
<namespace>bacmap.biog</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22135301</documentation>
</documentations>
<resources>
<resource id="MIR:00100459" state="up" reliability="97">
<dataResource>http://bacmap.wishartlab.com/</dataResource>
<dataEntityExample>1050</dataEntityExample>
<dataEntry>http://bacmap.wishartlab.com/organisms/$id</dataEntry>
<dataInfo>BacMap Biography at University of Alberta</dataInfo>
<dataInstitution>Department of Computing Science, Food and Nutritional Science, University of Alberta, Edmonton</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000362" pattern="^[A-Za-z-0-9_]+(\@)?$" restricted="true">
<name>HGNC Symbol</name>
<synonyms>
<synonym>HUGO Gene Nomenclature Committee Symbol</synonym>
</synonyms>
<definition>The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.</definition>
<uris>
<uri type="URN">urn:miriam:hgnc.symbol</uri>
<uri type="URL">http://identifiers.org/hgnc.symbol/</uri>
</uris>
<namespace>hgnc.symbol</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17984084</documentation>
<documentation type="PMID">urn:miriam:pubmed:20929869</documentation>
<documentation type="PMID">urn:miriam:pubmed:23161694</documentation>
</documentations>
<resources>
<resource id="MIR:00100460" state="up" reliability="97">
<dataResource>http://www.genenames.org/</dataResource>
<dataEntityExample>DAPK1</dataEntityExample>
<dataEntry>http://www.genenames.org/cgi-bin/gene_symbol_report?match=$id</dataEntry>
<dataInfo>HGNC Symbol at HUGO Genome Nomenclature Committee</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="4" desc="Identifier instability">
<statement>The main HGNC collection [MIR:00000080] should be used in preference as it has more robust identifiers.</statement>
<link desc="symbol status">http://www.genenames.org/guidelines.html/#symbolstatus</link>
</restriction>
</restrictions>
<tags>
<tag>gene</tag>
<tag>human</tag>
<tag>schema.org</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000363" pattern="^P\d{5}$">
<name>PANTHER Pathway</name>
<definition>The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components.</definition>
<uris>
<uri type="URN">urn:miriam:panther.pathway</uri>
<uri type="URL">http://identifiers.org/panther.pathway/</uri>
</uris>
<namespace>panther.pathway</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12952881</documentation>
</documentations>
<resources>
<resource id="MIR:00100461" state="probably up" reliability="98">
<dataResource>http://www.pantherdb.org/</dataResource>
<dataEntityExample>P00024</dataEntityExample>
<dataEntry>http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$id</dataEntry>
<dataInfo>PANTHER Pathway at USC (Los Angeles)</dataInfo>
<dataInstitution>Keck School of Medicine, University of Southern California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<annotation>
<format name="SBML">
<elements>
<element>reaction</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000364" pattern="^bsg-[dscp]\d{6}$">
<name>FAIRsharing</name>
<definition>The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.</definition>
<uris>
<uri type="URN">urn:miriam:fairsharing</uri>
<uri type="URL">http://identifiers.org/fairsharing/</uri>
<uri type="URN" deprecated="true">urn:miriam:biosharing</uri>
</uris>
<namespace>fairsharing</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21304729</documentation>
</documentations>
<resources>
<resource id="MIR:00100463" state="up" reliability="89" primary="true">
<dataResource>https://fairsharing.org/</dataResource>
<dataEntityExample>bsg-000052</dataEntityExample>
<dataEntry>https://fairsharing.org/$id</dataEntry>
<dataInfo>FAIRSharing at University of Oxford</dataInfo>
<dataInstitution>Oxford e-Research Centre, University of Oxford, Oxford</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>registry</tag>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000365" pattern="^[A-Za-z_0-9]+$" restricted="true">
<name>FungiDB</name>
<definition>FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.</definition>
<uris>
<uri type="URN">urn:miriam:fungidb</uri>
<uri type="URL">http://identifiers.org/fungidb/</uri>
</uris>
<namespace>fungidb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22064857</documentation>
</documentations>
<resources>
<resource id="MIR:00100464" state="down" reliability="72">
<dataResource>http://FungiDB.org</dataResource>
<dataEntityExample>CNBG_0001</dataEntityExample>
<dataEntry>http://fungidb.org/gene/$id</dataEntry>
<dataInfo>FungiDB at University of California</dataInfo>
<dataInstitution>Department of Plant Pathology & Microbiology, University of California, Riverside, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="2" desc="Data aggregation">
<statement>Provides access to information from multiple fungal species.</statement>
<link desc="fungal genomes">http://fungidb.org/fungidb.b2/showXmlDataContent.do?name=XmlQuestions.GenomeDataType</link>
</restriction>
</restrictions>
<tags>
<tag>gene</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000366" pattern="^\d+$">
<name>DARC</name>
<synonyms>
<synonym>Database of Aligned Ribosomal Complexes</synonym>
</synonyms>
<definition>DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.</definition>
<uris>
<uri type="URN">urn:miriam:darc</uri>
<uri type="URL">http://identifiers.org/darc/</uri>
</uris>
<namespace>darc</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22009674</documentation>
</documentations>
<resources>
<resource id="MIR:00100465" state="down" reliability="58">
<dataResource>http://darcsite.genzentrum.lmu.de/darc/index.php</dataResource>
<dataEntityExample>1250</dataEntityExample>
<dataEntry>http://darcsite.genzentrum.lmu.de/darc/view.php?id=$id</dataEntry>
<dataInfo>DARC at University of Munich</dataInfo>
<dataInstitution>Gene Center and Department for Biochemistry and Center for integrated Protein Science Munich, University of Munich, Munich</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000367" pattern="^DRSC\d+$">
<name>DRSC</name>
<synonyms>
<synonym>FlyRNAi</synonym>
<synonym>Drosophila RNAi Screening Cente</synonym>
</synonyms>
<definition>The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.</definition>
<uris>
<uri type="URN">urn:miriam:drsc</uri>
<uri type="URL">http://identifiers.org/drsc/</uri>
</uris>
<namespace>drsc</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22067456</documentation>
</documentations>
<resources>
<resource id="MIR:00100466" state="down" reliability="79">
<dataResource>http://flyrnai.org/</dataResource>
<dataEntityExample>DRSC05221</dataEntityExample>
<dataEntry>http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$id</dataEntry>
<dataInfo>DRSC at Harvard Medical School</dataInfo>
<dataInstitution>Department of Genetics, Harvard Medical School, Boston, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>expression</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000368" pattern="^\d+$">
<name>OriDB Schizosaccharomyces</name>
<definition>OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe.</definition>
<uris>
<uri type="URN">urn:miriam:oridb.schizo</uri>
<uri type="URL">http://identifiers.org/oridb.schizo/</uri>
</uris>
<namespace>oridb.schizo</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22121216</documentation>
</documentations>
<resources>
<resource id="MIR:00100467" state="up" reliability="99">
<dataResource>http://pombe.oridb.org/index.php</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://pombe.oridb.org/details.php?id=$id</dataEntry>
<dataInfo>OriDB Schizosaccharomyces at University of Nottingham</dataInfo>
<dataInstitution>Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000369" pattern="^\d+$">
<name>OriDB Saccharomyces</name>
<definition>OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.</definition>
<uris>
<uri type="URN">urn:miriam:oridb.sacch</uri>
<uri type="URL">http://identifiers.org/oridb.sacch/</uri>
</uris>
<namespace>oridb.sacch</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22121216</documentation>
</documentations>
<resources>
<resource id="MIR:00100468" state="up" reliability="99">
<dataResource>http://cerevisiae.oridb.org/index.php</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://cerevisiae.oridb.org/details.php?id=$id</dataEntry>
<dataInfo>OriDB Saccharomyces at University of Nottingham</dataInfo>
<dataInstitution>Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000370" pattern="^\d+$">
<name>PSCDB</name>
<synonyms>
<synonym>Protein Structural Change DataBase</synonym>
</synonyms>
<definition>The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.</definition>
<uris>
<uri type="URN">urn:miriam:pscdb</uri>
<uri type="URL">http://identifiers.org/pscdb/</uri>
</uris>
<namespace>pscdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22080505</documentation>
</documentations>
<resources>
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<dataResource>http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html</dataResource>
<dataEntityExample>051</dataEntityExample>
<dataEntry>http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$id.html</dataEntry>
<dataInfo>PSCDB at Nagoya University</dataInfo>
<dataInstitution>Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000371" pattern="^\d+$">
<name>SCOP</name>
<synonyms>
<synonym>Structural Classification of Proteins</synonym>
</synonyms>
<definition>The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes.</definition>
<uris>
<uri type="URN">urn:miriam:scop</uri>
<uri type="URL">http://identifiers.org/scop/</uri>
</uris>
<namespace>scop</namespace>
<resources>
<resource id="MIR:00100470" state="down" reliability="97">
<dataResource>http://scop.mrc-lmb.cam.ac.uk/scop/</dataResource>
<dataEntityExample>47419</dataEntityExample>
<dataEntry>http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$id</dataEntry>
<dataInfo>SCOP at MRC</dataInfo>
<dataInstitution>MRC Laboratory of Molecular Biology, Centre for Protein Engineering, Hills Road, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100471" state="up" reliability="99">
<dataResource>http://scop.berkeley.edu/</dataResource>
<dataEntityExample>47419</dataEntityExample>
<dataEntry>http://scop.berkeley.edu/sunid=$id</dataEntry>
<dataInfo>SCOP at Berkeley</dataInfo>
<dataInstitution>University of California, Berkeley</dataInstitution>
<dataLocation>USA</dataLocation>
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<resource id="MIR:00100472" obsolete="true">
<dataResource>http://scop.bic.nus.edu.sg/</dataResource>
<dataEntityExample>47419</dataEntityExample>
<dataEntry>http://scop.bic.nus.edu.sg/search.cgi?sunid=$id</dataEntry>
<dataInfo>SCOP at National University Singapore</dataInfo>
<dataInstitution>National University Singapore</dataInstitution>
<dataLocation>Singapore</dataLocation>
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<tags>
<tag>classification</tag>
<tag>protein</tag>
<tag>structure</tag>
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<annotation>
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<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000372" pattern="^[A-Z]+[0-9]+(\.\d+)?$">
<name>ENA</name>
<synonyms>
<synonym>European Nucleotide Archive</synonym>
<synonym>Embl-Bank</synonym>
</synonyms>
<definition>The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers.</definition>
<uris>
<uri type="URN">urn:miriam:ena.embl</uri>
<uri type="URL">http://identifiers.org/ena.embl/</uri>
</uris>
<namespace>ena.embl</namespace>
<documentations>
<documentation type="URL">http://www.ebi.ac.uk/ena/about/embl_bank_format</documentation>
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<resources>
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<dataResource>http://www.ebi.ac.uk/ena/</dataResource>
<dataEntityExample>BN000065</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/$id</dataEntry>
<dataInfo>ENA at European Bioinformatics Institute</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
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</resources>
<tags>
<tag>nucleotide</tag>
<tag>sequence</tag>
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<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000373" pattern="^[0-9][A-Za-z0-9]{3}$">
<name>DOMMINO</name>
<synonyms>
<synonym>Database of Macromolecular Interactions</synonym>
</synonyms>
<definition>DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.</definition>
<uris>
<uri type="URN">urn:miriam:dommino</uri>
<uri type="URL">http://identifiers.org/dommino/</uri>
</uris>
<namespace>dommino</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22135305</documentation>
</documentations>
<resources>
<resource id="MIR:00100474" state="up" reliability="99">
<dataResource>http://dommino.org/</dataResource>
<dataEntityExample>2GC4</dataEntityExample>
<dataEntry>http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$id</dataEntry>
<dataInfo>DOMMINO at University of Missouri</dataInfo>
<dataInstitution>Informatics Institute and Department of Computer Science and Bond Life Science Center, University of Missouri, Columbia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000374" pattern="^PTN\d{9}$">
<name>PANTHER Node</name>
<definition>The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes.</definition>
<uris>
<uri type="URN">urn:miriam:panther.node</uri>
<uri type="URL">http://identifiers.org/panther.node/</uri>
</uris>
<namespace>panther.node</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12952881</documentation>
</documentations>
<resources>
<resource id="MIR:00100475" state="probably up" reliability="93">
<dataResource>http://pantree.org/</dataResource>
<dataEntityExample>PTN000000026</dataEntityExample>
<dataEntry>http://www.pantree.org/node/annotationNode.jsp?id=$id</dataEntry>
<dataInfo>PANTHER Node at USC (Los Angeles)</dataInfo>
<dataInstitution>Keck School of Medicine, University of Southern California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000375" pattern="^CCDS\d+\.\d+$">
<name>Consensus CDS</name>
<synonyms>
<synonym>CCDS</synonym>
</synonyms>
<definition>The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.</definition>
<uris>
<uri type="URN">urn:miriam:ccds</uri>
<uri type="URL">http://identifiers.org/ccds/</uri>
</uris>
<namespace>ccds</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19498102</documentation>
</documentations>
<resources>
<resource id="MIR:00100477" state="up" reliability="93" primary="true">
<dataResource>http://www.ncbi.nlm.nih.gov/CCDS/</dataResource>
<dataEntityExample>CCDS13573.1</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$id</dataEntry>
<dataInfo>Consensus CDS at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>mammalian</tag>
<tag>protein</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000376" pattern="^LRG_\d+$">
<name>Locus Reference Genomic</name>
<synonyms>
<synonym>LRG</synonym>
</synonyms>
<definition>Locus Reference Genomic (LRG) provides identifiers to stable genomic DNA sequences for regions of the human genome, providing a recognized reference-sequence standard for reporting sequence variants. LRG is maintained by the NCBI and the European Bioinformatics Institute (EBI).</definition>
<uris>
<uri type="URN">urn:miriam:lrg</uri>
<uri type="URL">http://identifiers.org/lrg/</uri>
</uris>
<namespace>lrg</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20398331</documentation>
</documentations>
<resources>
<resource id="MIR:00100478" state="up" reliability="99">
<dataResource>http://www.lrg-sequence.org/</dataResource>
<dataEntityExample>LRG_1</dataEntityExample>
<dataEntry>ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$id.xml</dataEntry>
<dataInfo>Locus Reference Genomic at University of Leicester</dataInfo>
<dataInstitution>Department of Genetics, University of Leicester, Leicester</dataInstitution>
<dataLocation>UK</dataLocation>
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<resource id="MIR:00100627" state="up" reliability="93">
<dataResource>http://www.ensembl.org/</dataResource>
<dataEntityExample>LRG_1</dataEntityExample>
<dataEntry>http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id</dataEntry>
<dataInfo>Locus Reference Genomic through Ensembl</dataInfo>
<dataInstitution>EnSembl, Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100629" state="up" reliability="93">
<dataResource>http://asia.ensembl.org/</dataResource>
<dataEntityExample>LRG_1</dataEntityExample>
<dataEntry>http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id</dataEntry>
<dataInfo>Locus Reference Genomic through Ensembl mirror (asia)</dataInfo>
<dataInstitution></dataInstitution>
<dataLocation>Singapore</dataLocation>
</resource>
<resource id="MIR:00100630" state="down" reliability="93">
<dataResource>http://uswest.ensembl.org/</dataResource>
<dataEntityExample>LRG_1</dataEntityExample>
<dataEntry>http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id</dataEntry>
<dataInfo>Locus Reference Genomic through Ensembl mirror (US west)</dataInfo>
<dataInstitution></dataInstitution>
<dataLocation>USA</dataLocation>
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<resource id="MIR:00100631" state="up" reliability="93">
<dataResource>http://useast.ensembl.org/</dataResource>
<dataEntityExample>LRG_1</dataEntityExample>
<dataEntry>http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id</dataEntry>
<dataInfo>Locus Reference Genomic through Ensembl mirror (US east)</dataInfo>
<dataInstitution></dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>genome</tag>
<tag>human</tag>
<tag>schema.org</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000377" pattern="^\d+$" restricted="true">
<name>HPRD</name>
<synonyms>
<synonym>Human Protein Reference Database</synonym>
</synonyms>
<definition>The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.</definition>
<uris>
<uri type="URN">urn:miriam:hprd</uri>
<uri type="URL">http://identifiers.org/hprd/</uri>
</uris>
<namespace>hprd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18988627</documentation>
</documentations>
<resources>
<resource id="MIR:00100479" state="up" reliability="93">
<dataResource>http://www.hprd.org/</dataResource>
<dataEntityExample>00001</dataEntityExample>
<dataEntry>http://www.hprd.org/protein/$id</dataEntry>
<dataInfo>Human Protein Reference Database</dataInfo>
<dataInstitution>Institute of Bioinformatics, International Tech Park, Bangalore</dataInstitution>
<dataLocation>India</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>HPRD is free for non-commercial, where it may incur a license fee.</statement>
<link desc="license information">http://www.hprd.org/FAQ</link>
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<tags>
<tag>human</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000378" pattern="^\w+$">
<name>GXA Gene</name>
<synonyms>
<synonym>Gene Expression Atlas Gene</synonym>
</synonyms>
<definition>The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes.</definition>
<uris>
<uri type="URN">urn:miriam:gxa.gene</uri>
<uri type="URL">http://identifiers.org/gxa.gene/</uri>
</uris>
<namespace>gxa.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22064864</documentation>
</documentations>
<resources>
<resource id="MIR:00100482" state="up" reliability="79">
<dataResource>http://www.ebi.ac.uk/gxa/</dataResource>
<dataEntityExample>AT4G01080</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/gxa/genes/$id</dataEntry>
<dataInfo>GXA Gene at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
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</resources>
<tags>
<tag>expression</tag>
<tag>gene</tag>
<tag>microarray</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000379" pattern="^[AEP]-\w{4}-\d+$" restricted="true">
<name>GXA Expt</name>
<synonyms>
<synonym>Gene Expression Atlas Experiment</synonym>
</synonyms>
<definition>The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.</definition>
<uris>
<uri type="URN">urn:miriam:gxa.expt</uri>
<uri type="URL">http://identifiers.org/gxa.expt/</uri>
</uris>
<namespace>gxa.expt</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22064864</documentation>
</documentations>
<resources>
<resource id="MIR:00100483" state="up" reliability="77" primary="true">
<dataResource>http://www.ebi.ac.uk/gxa/</dataResource>
<dataEntityExample>E-MTAB-2037</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/gxa/experiments/$id</dataEntry>
<dataInfo>GXA Expt at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100857" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>E-MTAB-2037</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/atlas-experiments/$id</dataEntry>
<dataInfo>GXA Expt through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
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<restriction type="6" desc="Collection subset">
<statement>This collection is a curated subset of ArrayExpress [MIR:00000036].</statement>
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<tags>
<tag>expression</tag>
<tag>microarray</tag>
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<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
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<datatype id="MIR:00000380" pattern="^MTBLS\d+$">
<name>MetaboLights</name>
<definition>MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.</definition>
<uris>
<uri type="URN">urn:miriam:metabolights</uri>
<uri type="URL">http://identifiers.org/metabolights/</uri>
</uris>
<namespace>metabolights</namespace>
<documentations>
<documentation type="URL">http://www.ebi.ac.uk/metabolights/about</documentation>
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<dataEntityExample>MTBLS1</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/metabolights/$id</dataEntry>
<dataInfo>MetaboLights at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
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<resource id="MIR:00100853" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>MTBLS1</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/metabolights_dataset/$id</dataEntry>
<dataInfo>MataboLights through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
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<tag>metabolite</tag>
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<annotation>
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<elements>
<element>species</element>
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<datatype id="MIR:00000381" pattern="^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$">
<name>National Bibliography Number</name>
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<synonym>NBN</synonym>
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<definition>The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier.</definition>
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<uri type="URN">urn:miriam:nbn</uri>
<uri type="URL">http://identifiers.org/nbn/</uri>
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<namespace>nbn</namespace>
<documentations>
<documentation type="URL">http://tools.ietf.org/html/rfc3188</documentation>
<documentation type="URL">http://www.dnb.de/EN/Service/DigitaleDienste/URNService/urnservice_node.html</documentation>
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<dataInfo>NBN through URN Resolver at German National Library</dataInfo>
<dataInstitution>Deutsche Nationalbibliothek, Frankfurt</dataInstitution>
<dataLocation>Germany</dataLocation>
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<tag>bibliography</tag>
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<element>parameter</element>
<element>reaction</element>
<element>species</element>
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<datatype id="MIR:00000382" pattern="^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$">
<name>ORCID</name>
<synonyms>
<synonym>Open Researcher and Contributor ID</synonym>
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<definition>ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities.</definition>
<uris>
<uri type="URN">urn:miriam:orcid</uri>
<uri type="URL">http://identifiers.org/orcid/</uri>
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<namespace>orcid</namespace>
<documentations>
<documentation type="URL">https://about.orcid.org/about/what-is-orcid/our-principles</documentation>
<documentation type="URL">https://support.orcid.org/knowledgebase/articles/116780-structure-of-the-orcid-identifier</documentation>
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<dataResource>https://orcid.org</dataResource>
<dataEntityExample>0000-0002-6309-7327</dataEntityExample>
<dataEntry>https://orcid.org/$id</dataEntry>
<dataInfo>ORCID at Bethesda</dataInfo>
<dataInstitution>ORCID Inc, Bethesda, Mayrland</dataInstitution>
<dataLocation>USA</dataLocation>
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<tag>bibliography</tag>
</tags>
<annotation>
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<elements>
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</elements>
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<datatype id="MIR:00000383" pattern="^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$" restricted="true">
<name>InChI</name>
<synonyms>
<synonym>IUPAC International Chemical Identifier</synonym>
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<definition>The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.</definition>
<uris>
<uri type="URN">urn:miriam:inchi</uri>
<uri type="URL">http://identifiers.org/inchi/</uri>
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<namespace>inchi</namespace>
<documentations>
<documentation type="URL">http://www.iupac.org/inchi/</documentation>
<documentation type="URL">http://www.inchi-trust.org/</documentation>
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<resources>
<resource id="MIR:00100491" state="up" reliability="86">
<dataResource>http://rdf.openmolecules.net/</dataResource>
<dataEntityExample>InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</dataEntityExample>
<dataEntry>http://rdf.openmolecules.net/?$id</dataEntry>
<dataInfo>InChI through RDF Open Molecules</dataInfo>
<dataInstitution>BiGCaT, Department of Bioinformatics, Maastricht</dataInstitution>
<dataLocation>Netherlands</dataLocation>
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<resource id="MIR:00100492" state="up" reliability="99">
<dataResource>http://www.chemspider.com/</dataResource>
<dataEntityExample>InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</dataEntityExample>
<dataEntry>http://www.chemspider.com/$id</dataEntry>
<dataInfo>InChI through Chemspider</dataInfo>
<dataInstitution>Royal Society of Chemistry, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100493" state="down" reliability="97">
<dataResource>http://webbook.nist.gov/chemistry</dataResource>
<dataEntityExample>InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</dataEntityExample>
<dataEntry>http://webbook.nist.gov/cgi/cbook.cgi?$id</dataEntry>
<dataInfo>InChI through NIST</dataInfo>
<dataInstitution>National Institute of Standards and Technology, Gaithersburg, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100494" state="up" reliability="98">
<dataResource>http://www.ebi.ac.uk/chebi/</dataResource>
<dataEntityExample>InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$id</dataEntry>
<dataInfo>InChI through ChEBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="7" desc="Identifier non-conformity">
<statement>Identifiers are the structural representation of a substance.</statement>
<link desc="Main site for InChIs">http://www.iupac.org/home/publications/e-resources/inchi.html</link>
</restriction>
<restriction type="8" desc="Identifier independence">
<statement>Identifiers are not restricted to a specific data collection.</statement>
<link desc="Main site for InChIs">http://www.iupac.org/home/publications/e-resources/inchi.html</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000384" pattern="^[A-Za-z-0-9_]+$" restricted="true">
<name>Wikipedia (En)</name>
<definition>Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.</definition>
<uris>
<uri type="URN">urn:miriam:wikipedia.en</uri>
<uri type="URL">http://identifiers.org/wikipedia.en/</uri>
</uris>
<namespace>wikipedia.en</namespace>
<documentations>
<documentation type="URL">http://en.wikipedia.org/wiki/Wikipedia:About</documentation>
<documentation type="URL">http://wiki.dbpedia.org/Publications</documentation>
</documentations>
<resources>
<resource id="MIR:00100495" state="up" reliability="89">
<dataResource>http://en.wikipedia.org/wiki/Main_Page</dataResource>
<dataEntityExample>SM_UB-81</dataEntityExample>
<dataEntry>http://en.wikipedia.org/wiki/$id</dataEntry>
<dataInfo>Wikipedia (English)</dataInfo>
<dataInstitution>Wikimedia Foundation, San Francisco, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100496" state="up" reliability="94">
<dataResource>http://wiki.dbpedia.org/</dataResource>
<dataEntityExample>SM_UB-81</dataEntityExample>
<dataEntry>http://dbpedia.org/page/$id</dataEntry>
<dataInfo>Wikipedia structured content through DBpedia</dataInfo>
<dataInstitution>OpenLink Software, Burlington, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="7" desc="Identifier non-conformity">
<statement>Identifiers are formed of descriptive text, and may not be unique, in which case a disambiguation page is returned.</statement>
<link desc="documentation on disambiguation process">http://en.wikipedia.org/wiki/Wikipedia:Disambiguation</link>
</restriction>
</restrictions>
<tags>
<tag>encyclopedia</tag>
</tags>
</datatype>
<datatype id="MIR:00000385" pattern="^\w+$">
<name>PhosphoPoint Kinase</name>
<definition>PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.</definition>
<uris>
<uri type="URN">urn:miriam:phosphopoint.kinase</uri>
<uri type="URL">http://identifiers.org/phosphopoint.kinase/</uri>
</uris>
<namespace>phosphopoint.kinase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18689816</documentation>
</documentations>
<resources>
<resource id="MIR:00100499" state="down" reliability="32">
<dataResource>http://kinase.bioinformatics.tw/</dataResource>
<dataEntityExample>AURKA</dataEntityExample>
<dataEntry>http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$id&drawing=0&sorting=0&kinome=1</dataEntry>
<dataInfo>PhosphoPoint Kinase at National Taiwan University</dataInfo>
<dataInstitution>Department of Computer Science and Information Engineering, National Taiwan University</dataInstitution>
<dataLocation>Republic of China</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000386" pattern="^\w+$">
<name>PhosphoPoint Phosphoprotein</name>
<definition>PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information.</definition>
<uris>
<uri type="URN">urn:miriam:phosphopoint.protein</uri>
<uri type="URL">http://identifiers.org/phosphopoint.protein/</uri>
</uris>
<namespace>phosphopoint.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18689816</documentation>
</documentations>
<resources>
<resource id="MIR:00100500" state="down" reliability="32">
<dataResource>http://kinase.bioinformatics.tw/</dataResource>
<dataEntityExample>AURKA</dataEntityExample>
<dataEntry>http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$id&drawing=0&sorting=0&kinome=0</dataEntry>
<dataInfo>PhosphoPoint Phosphoprotein at National Taiwan University</dataInfo>
<dataInstitution>Department of Computer Science and Information Engineering, National Taiwan University</dataInstitution>
<dataLocation>Republic of China</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000387" pattern="^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])?" restricted="true">
<name>InChIKey</name>
<synonyms>
<synonym>hashed InChI</synonym>
</synonyms>
<definition>The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.</definition>
<uris>
<uri type="URN">urn:miriam:inchikey</uri>
<uri type="URL">http://identifiers.org/inchikey/</uri>
</uris>
<namespace>inchikey</namespace>
<documentations>
<documentation type="URL">http://en.wikipedia.org/wiki/International_Chemical_Identifier</documentation>
<documentation type="URL">http://www.inchi-trust.org/technical-faq/</documentation>
</documentations>
<resources>
<resource id="MIR:00100501" state="up" reliability="87">
<dataResource>http://www.chemspider.com/</dataResource>
<dataEntityExample>RYYVLZVUVIJVGH-UHFFFAOYSA-N</dataEntityExample>
<dataEntry>http://www.chemspider.com/inchikey=$id</dataEntry>
<dataInfo>InChIKey through ChemSpider</dataInfo>
<dataInstitution>Royal Society of Chemistry, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100505" state="up" reliability="98">
<dataResource>http://cactus.nci.nih.gov/chemical/structure</dataResource>
<dataEntityExample>RYYVLZVUVIJVGH-UHFFFAOYSA-N</dataEntityExample>
<dataEntry>http://cactus.nci.nih.gov/chemical/structure/$id/names</dataEntry>
<dataInfo>InChiKey resolver at NCI</dataInfo>
<dataInstitution>National Cancer Institute, Rockville, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="7" desc="Identifier non-conformity">
<statement>Identifiers are composed of non-standard characters and do not follow recommended practices.</statement>
<link desc="Registry FAQ">http://www.ebi.ac.uk/miriam/main/mdb?section=faq#RegistryRequirements</link>
</restriction>
<restriction type="8" desc="Identifier independence">
<statement>Identifiers are not restricted to a specific data collection, and are applicable universally.</statement>
<link desc="Main site for InChIs">http://www.iupac.org/home/publications/e-resources/inchi.html</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000388" pattern="^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$" restricted="true">
<name>UniProt Isoform</name>
<synonyms>
<synonym>UniProtKB Isoform</synonym>
</synonyms>
<definition>The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information.</definition>
<uris>
<uri type="URN">urn:miriam:uniprot.isoform</uri>
<uri type="URL">http://identifiers.org/uniprot.isoform/</uri>
</uris>
<namespace>uniprot.isoform</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381842</documentation>
<documentation type="URL">http://www.uniprot.org/faq/30</documentation>
</documentations>
<resources>
<resource id="MIR:00100502" state="up" reliability="99">
<dataResource>http://www.uniprot.org/</dataResource>
<dataEntityExample>Q5BJF6-3</dataEntityExample>
<dataEntry>http://www.uniprot.org/uniprot/$id</dataEntry>
<dataInfo>UniProt Isoform through Universal Protein Resource</dataInfo>
<dataInstitution>UniProt Consortium</dataInstitution>
<dataLocation>USA, UK and Switzerland</dataLocation>
</resource>
<resource id="MIR:00100503" state="up" reliability="99">
<dataResource>http://purl.uniprot.org/</dataResource>
<dataEntityExample>Q5BJF6-3</dataEntityExample>
<dataEntry>http://purl.uniprot.org/uniprot/$id</dataEntry>
<dataInfo>UniProt Isoform through Universal Protein Resource using Persistent URL system</dataInfo>
<dataInstitution>UniProt Consortium</dataInstitution>
<dataLocation>USA, UK and Switzerland</dataLocation>
</resource>
<resource id="MIR:00100504" state="up" reliability="99">
<dataResource>http://www.uniprot.org/uniparc/</dataResource>
<dataEntityExample>Q5BJF6-3</dataEntityExample>
<dataEntry>http://www.uniprot.org/uniparc/?query=$id</dataEntry>
<dataInfo>UniProt Isoform through UniParc</dataInfo>
<dataInstitution>UniProt Consortium</dataInstitution>
<dataLocation>USA, UK and Switzerland</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="6" desc="Collection subset">
<statement>UniProt Isoform is a subset of the information available from a standard UniProt record.</statement>
<link desc="Isoform description">http://www.uniprot.org/faq/30</link>
</restriction>
</restrictions>
<tags>
<tag>protein</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000389" pattern="^(ev\:)?E\d+$">
<name>KEGG Environ</name>
<synonyms>
<synonym>KEGG</synonym>
</synonyms>
<definition>KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.environ</uri>
<uri type="URL">http://identifiers.org/kegg.environ/</uri>
</uris>
<namespace>kegg.environ</namespace>
<documentations>
<documentation type="URL">http://www.genome.jp/kegg/drug/environ.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100506" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/drug/environ.html</dataResource>
<dataEntityExample>ev:E00032</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG ENVIRON Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>drug</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000390" pattern="^(cl|tum)\d+$">
<name>CLDB</name>
<synonyms>
<synonym>Cell Line Data Base</synonym>
</synonyms>
<definition>The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.</definition>
<uris>
<uri type="URN">urn:miriam:cldb</uri>
<uri type="URL">http://identifiers.org/cldb/</uri>
</uris>
<namespace>cldb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18927105</documentation>
</documentations>
<resources>
<resource id="MIR:00100508" state="up" reliability="86">
<dataResource>http://bioinformatics.hsanmartino.it/hypercldb/indexes.html</dataResource>
<dataEntityExample>cl3603</dataEntityExample>
<dataEntry>http://bioinformatics.hsanmartino.it/hypercldb/$id.html</dataEntry>
<dataInfo>CLDB at Genova</dataInfo>
<dataInstitution>Bioinformatics, Cell Bank, National Cancer Research Institute, Genova</dataInstitution>
<dataLocation>Italy</dataLocation>
</resource>
</resources>
<tags>
<tag>catalogue</tag>
<tag>mammalian</tag>
<tag>strain</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000391" pattern="^\d{7}$">
<name>Experimental Factor Ontology</name>
<synonyms>
<synonym>EFO</synonym>
</synonyms>
<definition>The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.</definition>
<uris>
<uri type="URN">urn:miriam:efo</uri>
<uri type="URL">http://identifiers.org/efo/</uri>
</uris>
<namespace>efo</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20200009</documentation>
</documentations>
<resources>
<resource id="MIR:00100509" state="up" reliability="96">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/efo</dataResource>
<dataEntityExample>0004859</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=EFO:$id</dataEntry>
<dataInfo>EFO through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100510" state="up" reliability="96">
<dataResource>http://bioportal.bioontology.org/ontologies/EFO</dataResource>
<dataEntityExample>0004859</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/EFO/efo:EFO_$id</dataEntry>
<dataInfo>EFO through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100511" state="up" reliability="98">
<dataResource>http://www.ebi.ac.uk/efo/</dataResource>
<dataEntityExample>0004859</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/efo/EFO_$id</dataEntry>
<dataInfo>EFO through Functional Genomics Group (EBI)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>parameter</element>
<element>species</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000392" pattern="^[A-Z_0-9]+$" restricted="true">
<name>HGMD</name>
<synonyms>
<synonym>Human Gene Mutation Database</synonym>
</synonyms>
<definition>The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.</definition>
<uris>
<uri type="URN">urn:miriam:hgmd</uri>
<uri type="URL">http://identifiers.org/hgmd/</uri>
</uris>
<namespace>hgmd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22948725</documentation>
</documentations>
<resources>
<resource id="MIR:00100512" state="restricted access" reliability="0">
<dataResource>http://www.hgmd.cf.ac.uk/ac/index.php</dataResource>
<dataEntityExample>CALM1</dataEntityExample>
<dataEntry>http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$id</dataEntry>
<dataInfo>HGMD at Cardiff University</dataInfo>
<dataInstitution>Cardiff University, Cardiff</dataInstitution>
<dataLocation>Wales</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>A copyright notice is in place.</statement>
<link desc="copyright notice">http://www.hgmd.cf.ac.uk/docs/copyright.html</link>
</restriction>
<restriction type="3" desc="Access restriction">
<statement>Requires registration to access data.</statement>
<link desc="registration link">http://www.hgmd.cf.ac.uk/docs/register.html</link>
</restriction>
</restrictions>
<tags>
<tag>disease</tag>
<tag>gene</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000393" pattern="^ACYPI\d{6}(-RA)?$" restricted="true">
<name>AphidBase Transcript</name>
<definition>AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.</definition>
<uris>
<uri type="URN">urn:miriam:aphidbase.transcript</uri>
<uri type="URL">http://identifiers.org/aphidbase.transcript/</uri>
</uris>
<namespace>aphidbase.transcript</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20482635</documentation>
</documentations>
<resources>
<resource id="MIR:00100513" state="up" reliability="97">
<dataResource>http://www.aphidbase.com/aphidbase</dataResource>
<dataEntityExample>ACYPI000159</dataEntityExample>
<dataEntry>http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$id</dataEntry>
<dataInfo>AphidBase at INRA</dataInfo>
<dataInstitution>INRA UMR, Le Rheu</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The use of information for commercial or publicity purposes is forbidden.</statement>
<link desc="legal notice">http://www.aphidbase.com/aphidbase/legal_mentions</link>
</restriction>
</restrictions>
<tags>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000394" pattern="\d{4,}((_[asx])?_at)?" restricted="true">
<name>Affymetrix Probeset</name>
<definition>An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.</definition>
<uris>
<uri type="URN">urn:miriam:affy.probeset</uri>
<uri type="URL">http://identifiers.org/affy.probeset/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/affymetrix</uri>
</uris>
<namespace>affy.probeset</namespace>
<documentations>
<documentation type="URL">http://www.affymetrix.com</documentation>
</documentations>
<resources>
<resource id="MIR:00100514" state="restricted access" reliability="0" primary="true">
<dataResource>http://www.affymetrix.com/</dataResource>
<dataEntityExample>243002_at</dataEntityExample>
<dataEntry>https://www.affymetrix.com/LinkServlet?probeset=$id</dataEntry>
<dataInfo>Affymetrix ProbeSet in Santa Clara</dataInfo>
<dataInstitution>Affymetrix, Santa Clara, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100672" state="restricted access" reliability="0">
<dataResource>http://cu.affymetrix.bio2rdf.org/fct/</dataResource>
<dataEntityExample>243002_at</dataEntityExample>
<dataEntry>http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Site is for personal non-commercial use</statement>
<link desc="terms of use">http://www.affymetrix.com/estore/browse/terms.jsp</link>
</restriction>
<restriction type="3" desc="Access restriction">
<statement>Requires registration and user log in.</statement>
<link desc="login">https://www.affymetrix.com/estore/user/login.jsp?toURL=/estore/</link>
</restriction>
</restrictions>
<tags>
<tag>genome</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000395" pattern="^\w{1,2}\d+$">
<name>TreeFam</name>
<definition>TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.</definition>
<uris>
<uri type="URN">urn:miriam:treefam</uri>
<uri type="URL">http://identifiers.org/treefam/</uri>
</uris>
<namespace>treefam</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381935</documentation>
</documentations>
<resources>
<resource id="MIR:00100515" state="up" reliability="98">
<dataResource>http://www.treefam.org/</dataResource>
<dataEntityExample>TF101014</dataEntityExample>
<dataEntry>http://www.treefam.org/family/$id</dataEntry>
<dataInfo>TreeFam database</dataInfo>
<dataInstitution>Beijing Genomics Institute, Beijing</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000396" pattern="^\d+$">
<name>CAPS-DB</name>
<definition>CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.</definition>
<uris>
<uri type="URN">urn:miriam:caps</uri>
<uri type="URL">http://identifiers.org/caps/</uri>
</uris>
<namespace>caps</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22021380</documentation>
</documentations>
<resources>
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<dataResource>http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home</dataResource>
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<dataInstitution>Leeds Institute of Molecular Medicine, Section of Experimental Therapeutics, University of Leeds, Leeds</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>protein</tag>
<tag>structure</tag>
</tags>
</datatype>
<datatype id="MIR:00000397" pattern="^[A-Za-z_0-9]+$" restricted="true">
<name>Cube db</name>
<definition>Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.</definition>
<uris>
<uri type="URN">urn:miriam:cubedb</uri>
<uri type="URL">http://identifiers.org/cubedb/</uri>
</uris>
<namespace>cubedb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22139934</documentation>
</documentations>
<resources>
<resource id="MIR:00100517" state="restricted access" reliability="0">
<dataResource>http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html</dataResource>
<dataEntityExample>AKR</dataEntityExample>
<dataEntry>http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$id/</dataEntry>
<dataInfo>Cube db at Bioinformatics Institute (Singapore)</dataInfo>
<dataInstitution>Bioinformatics Institute, Singapore</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>To identify specific results, it is necessary to also specify a 'cluster'.</statement>
</restriction>
</restrictions>
<tags>
<tag>domain</tag>
<tag>human</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000398" pattern="^IID\d+$">
<name>IDEAL</name>
<synonyms>
<synonym>Intrinsically Disordered proteins with Extensive Annotations and Literature</synonym>
</synonyms>
<definition>IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.</definition>
<uris>
<uri type="URN">urn:miriam:ideal</uri>
<uri type="URL">http://identifiers.org/ideal/</uri>
</uris>
<namespace>ideal</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22067451</documentation>
</documentations>
<resources>
<resource id="MIR:00100518" state="up" reliability="99">
<dataResource>http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/</dataResource>
<dataEntityExample>IID00001</dataEntityExample>
<dataEntry>http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/idealItem.php?id=$id</dataEntry>
<dataInfo>IDEAL at Maebashi Institute of Technology</dataInfo>
<dataInstitution>Faculty of Engineering, Maebashi Institute of Technology, Maebashi</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000399" pattern="^[0-9][A-Za-z0-9]{3}$">
<name>STAP</name>
<synonyms>
<synonym>Statistical Torsional Angles Potentials of NMR</synonym>
</synonyms>
<definition>STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB).</definition>
<uris>
<uri type="URN">urn:miriam:stap</uri>
<uri type="URL">http://identifiers.org/stap/</uri>
</uris>
<namespace>stap</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22102572</documentation>
</documentations>
<resources>
<resource id="MIR:00100519" state="up" reliability="91">
<dataResource>http://psb.kobic.re.kr/STAP/refinement/</dataResource>
<dataEntityExample>1a24</dataEntityExample>
<dataEntry>http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$id</dataEntry>
<dataInfo>STAP at Korean Bioinformation Center</dataInfo>
<dataInstitution>Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon</dataInstitution>
<dataLocation>South Korea</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000400" pattern="^[A-Za-z_0-9]+">
<name>Pocketome</name>
<definition>Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries.</definition>
<uris>
<uri type="URN">urn:miriam:pocketome</uri>
<uri type="URL">http://identifiers.org/pocketome/</uri>
</uris>
<namespace>pocketome</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22080553</documentation>
</documentations>
<resources>
<resource id="MIR:00100520" state="down" reliability="86">
<dataResource>http://www.pocketome.org/sfSearch.cgi?act=browseall</dataResource>
<dataEntityExample>1433C_TOBAC_1_252</dataEntityExample>
<dataEntry>http://www.pocketome.org/files/$id.html</dataEntry>
<dataInfo>Pocketome at UCSD Skaggs School</dataInfo>
<dataInstitution>UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000401" pattern="^[Gi|Gc]\d+$">
<name>GOLD genome</name>
<definition>The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.</definition>
<uris>
<uri type="URN">urn:miriam:gold.genome</uri>
<uri type="URL">http://identifiers.org/gold.genome/</uri>
</uris>
<namespace>gold.genome</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22135293</documentation>
</documentations>
<resources>
<resource id="MIR:00100521" state="up" reliability="76">
<dataResource>http://www.genomesonline.org/cgi-bin/GOLD/index.cgi</dataResource>
<dataEntityExample>Gi07796</dataEntityExample>
<dataEntry>http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$id</dataEntry>
<dataInfo>GOLD genome at Department of Energy Joint Genome Institute</dataInfo>
<dataInstitution>Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>registry</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000402" pattern="^Gm\d+$">
<name>GOLD metadata</name>
<definition>The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.</definition>
<uris>
<uri type="URN">urn:miriam:gold.meta</uri>
<uri type="URL">http://identifiers.org/gold.meta/</uri>
</uris>
<namespace>gold.meta</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22135293</documentation>
</documentations>
<resources>
<resource id="MIR:00100522" state="up" reliability="69">
<dataResource>http://www.genomesonline.org/cgi-bin/GOLD/index.cgi</dataResource>
<dataEntityExample>Gm00047</dataEntityExample>
<dataEntry>http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$id</dataEntry>
<dataInfo>GOLD metadata at Department of Energy Joint Genome Institute</dataInfo>
<dataInstitution>Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>annotation</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000403" pattern="^\d+$" restricted="true">
<name>BugBase Protocol</name>
<definition>BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols.</definition>
<uris>
<uri type="URN">urn:miriam:bugbase.protocol</uri>
<uri type="URL">http://identifiers.org/bugbase.protocol/</uri>
</uris>
<namespace>bugbase.protocol</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21948792</documentation>
</documentations>
<resources>
<resource id="MIR:00100523" state="restricted access" reliability="0">
<dataResource>http://bugs.sgul.ac.uk/E-BUGS</dataResource>
<dataEntityExample>67</dataEntityExample>
<dataEntry>http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$id&amp;action=view</dataEntry>
<dataInfo>BugBase Protocol at University of London</dataInfo>
<dataInstitution>Bacterial Microarray Group, St George's, University of London</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>Must accept terms and conditions to enter site, or register an account.</statement>
<link desc="main page">http://bugs.sgul.ac.uk/bugsbase/index.php</link>
</restriction>
</restrictions>
<tags>
<tag>expression</tag>
<tag>microarray</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000404" pattern="^\d+$" restricted="true">
<name>BugBase Expt</name>
<definition>BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments.</definition>
<uris>
<uri type="URN">urn:miriam:bugbase.expt</uri>
<uri type="URL">http://identifiers.org/bugbase.expt/</uri>
</uris>
<namespace>bugbase.expt</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21948792</documentation>
</documentations>
<resources>
<resource id="MIR:00100524" state="restricted access" reliability="0">
<dataResource>http://bugs.sgul.ac.uk/E-BUGS</dataResource>
<dataEntityExample>288</dataEntityExample>
<dataEntry>http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$id&action=view</dataEntry>
<dataInfo>BugBase Expt at University of London</dataInfo>
<dataInstitution>Bacterial Microarray Group, St George's, University of London</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>Must accept terms and conditions to enter site, or register an account.</statement>
<link desc="main page">http://bugs.sgul.ac.uk/bugsbase/index.php</link>
</restriction>
</restrictions>
<tags>
<tag>expression</tag>
<tag>microarray</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000405" pattern="^\d+$">
<name>Tree of Life</name>
<definition>The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny).
Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.</definition>
<uris>
<uri type="URN">urn:miriam:tol</uri>
<uri type="URL">http://identifiers.org/tol/</uri>
</uris>
<namespace>tol</namespace>
<documentations>
<documentation type="URL">http://tolweb.org</documentation>
</documentations>
<resources>
<resource id="MIR:00100525" state="up" reliability="97">
<dataResource>http://tolweb.org/tree/</dataResource>
<dataEntityExample>98034</dataEntityExample>
<dataEntry>http://tolweb.org/$id</dataEntry>
<dataInfo>Tree of Life Web</dataInfo>
<dataInstitution>University of Arizona</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000406" pattern="^VariO:\d+$">
<name>VariO</name>
<synonyms>
<synonym>Variation Ontology</synonym>
</synonyms>
<definition>The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.</definition>
<uris>
<uri type="URN">urn:miriam:vario</uri>
<uri type="URL">http://identifiers.org/vario/</uri>
</uris>
<namespace>vario</namespace>
<documentations>
<documentation type="URL">http://variationontology.org/</documentation>
</documentations>
<resources>
<resource id="MIR:00100526" state="up" reliability="97">
<dataResource>http://www.variationontology.org/</dataResource>
<dataEntityExample>VariO:0294</dataEntityExample>
<dataEntry>http://www.variationontology.org/cgi-bin/amivario/term-details.cgi?term=$id</dataEntry>
<dataInfo>VariO at Lund University</dataInfo>
<dataInstitution>Department of Experimental Medical Science, Lund University</dataInstitution>
<dataLocation>Sweden</dataLocation>
</resource>
<resource id="MIR:00100566" state="up" reliability="96">
<dataResource>http://bioportal.bioontology.org/ontologies/VARIO</dataResource>
<dataEntityExample>VariO:0294</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/VARIO/$id</dataEntry>
<dataInfo>VariO through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100677" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/vario</dataResource>
<dataEntityExample>VariO:0294</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/vario/terms?obo_id=$id</dataEntry>
<dataInfo>VariO through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>ontology</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000407" pattern="^[A-Za-z 0-9]+$">
<name>ViPR Strain</name>
<synonyms>
<synonym>Virus Pathogen Resource Strain</synonym>
</synonyms>
<definition>The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.</definition>
<uris>
<uri type="URN">urn:miriam:vipr</uri>
<uri type="URL">http://identifiers.org/vipr/</uri>
</uris>
<namespace>vipr</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23202522</documentation>
</documentations>
<resources>
<resource id="MIR:00100527" state="down" reliability="66">
<dataResource>http://www.viprbrc.org/brc/home.do?decorator=vipr</dataResource>
<dataEntityExample>BeAn 70563</dataEntityExample>
<dataEntry>http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$id&decorator=arena</dataEntry>
<dataInfo>ViPR Strain at J. Craig Venter Institute</dataInfo>
<dataInstitution>J. Craig Venter Institute, San Diego, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>strain</tag>
<tag>viral</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000408" pattern="^[A-Z-_0-9]+$">
<name>EPD</name>
<synonyms>
<synonym>Eukaryotic Promoter Database</synonym>
</synonyms>
<definition>The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.</definition>
<uris>
<uri type="URN">urn:miriam:epd</uri>
<uri type="URL">http://identifiers.org/epd/</uri>
</uris>
<namespace>epd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23193273</documentation>
</documentations>
<resources>
<resource id="MIR:00100528" state="down" reliability="89">
<dataResource>http://epd.vital-it.ch/</dataResource>
<dataEntityExample>TA_H3</dataEntityExample>
<dataEntry>http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$id</dataEntry>
<dataInfo>EPD at Swiss Institute of Bioinformatics</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics (SIB), Geneva</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
<resource id="MIR:00100529" obsolete="true">
<dataResource>http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-lib+EPD</dataResource>
<dataEntityExample>TA_H3</dataEntityExample>
<dataEntry>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+1fmSL1hlE31+-e+[EPD:'$id']</dataEntry>
<dataInfo>EPD through EBI (SRS)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>eukaryotic</tag>
<tag>expression</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000409" pattern="^RF\d{5}$">
<name>RFAM</name>
<synonyms>
<synonym>RNA Family Database</synonym>
</synonyms>
<definition>The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.</definition>
<uris>
<uri type="URN">urn:miriam:rfam</uri>
<uri type="URL">http://identifiers.org/rfam/</uri>
</uris>
<namespace>rfam</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23125362</documentation>
</documentations>
<resources>
<resource id="MIR:00100686" state="up" reliability="82" primary="true">
<dataResource>http://rfam.xfam.org/</dataResource>
<dataEntityExample>RF00230</dataEntityExample>
<dataEntry>http://rfam.xfam.org/family/$id</dataEntry>
<dataInfo>Rfam at EMBL-EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100530" obsolete="true">
<dataResource>http://rfam.sanger.ac.uk/</dataResource>
<dataEntityExample>RF00230</dataEntityExample>
<dataEntry>http://rfam.sanger.ac.uk/family/$id</dataEntry>
<dataInfo>RFAM at Sanger Institute</dataInfo>
<dataInstitution>Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100531" obsolete="true">
<dataResource>http://janelia.org/</dataResource>
<dataEntityExample>RF00230</dataEntityExample>
<dataEntry>http://rfam.janelia.org/family/$id</dataEntry>
<dataInfo>RFAM at Janelia Farm Research</dataInfo>
<dataInstitution>Janelia Farm Research Campus, Ashburn, Virginia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000410" pattern="^\d+$">
<name>Fungal Barcode</name>
<synonyms>
<synonym>International Fungal Working Group</synonym>
<synonym>FBOL</synonym>
<synonym>Fungal Barcode of Life</synonym>
</synonyms>
<definition>DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms.</definition>
<uris>
<uri type="URN">urn:miriam:fbol</uri>
<uri type="URL">http://identifiers.org/fbol/</uri>
</uris>
<namespace>fbol</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21564968</documentation>
</documentations>
<resources>
<resource id="MIR:00100532" state="up" reliability="99">
<dataResource>http://www.fungalbarcoding.org/</dataResource>
<dataEntityExample>2224</dataEntityExample>
<dataEntry>http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$id&Fields=All&ExactMatch=T</dataEntry>
<dataInfo>Fungal Barcode at Fungal Biodiversity Centre</dataInfo>
<dataInstitution>Fungal Biodiversity Centre, Utrecht</dataInstitution>
<dataLocation>Netherlands</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>eukaryotic</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000411" pattern="^\d+$" restricted="true">
<name>AFTOL</name>
<synonyms>
<synonym>Assembling the Fungal Tree of Life</synonym>
</synonyms>
<definition>The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.</definition>
<uris>
<uri type="URN">urn:miriam:aftol.taxonomy</uri>
<uri type="URL">http://identifiers.org/aftol.taxonomy/</uri>
</uris>
<namespace>aftol.taxonomy</namespace>
<resources>
<resource id="MIR:00100533" state="restricted access" reliability="0">
<dataResource>http://aftol.org/data.php</dataResource>
<dataEntityExample>959</dataEntityExample>
<dataEntry>http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$id</dataEntry>
<dataInfo>AFTOL at University of Minnesota</dataInfo>
<dataInstitution>Department of Plant Biology, University of Minnesota, Minnesota</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>Requires acceptance of terms and conditions.</statement>
<link desc="terns and conditions">http://wasabi.lutzonilab.net/pub/disclaimer</link>
</restriction>
</restrictions>
</datatype>
<datatype id="MIR:00000412" pattern="^[A-Za-z_0-9]+$">
<name>AspGD Locus</name>
<synonyms>
<synonym>Aspergillus Genome Database Locus</synonym>
</synonyms>
<definition>The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information.</definition>
<uris>
<uri type="URN">urn:miriam:aspgd.locus</uri>
<uri type="URL">http://identifiers.org/aspgd.locus/</uri>
</uris>
<namespace>aspgd.locus</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22080559</documentation>
</documentations>
<resources>
<resource id="MIR:00100534" state="up" reliability="99">
<dataResource>http://www.aspgd.org/</dataResource>
<dataEntityExample>ASPL0000349247</dataEntityExample>
<dataEntry>http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$id</dataEntry>
<dataInfo>AspGD at Stanford Medical School</dataInfo>
<dataInstitution>Department of Genetics, Stanford University Medical School, Stanford, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000413" pattern="^[A-Za-z_0-9]+$">
<name>AspGD Protein</name>
<definition>The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information.</definition>
<uris>
<uri type="URN">urn:miriam:aspgd.protein</uri>
<uri type="URL">http://identifiers.org/aspgd.protein/</uri>
</uris>
<namespace>aspgd.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22080559</documentation>
</documentations>
<resources>
<resource id="MIR:00100535" state="up" reliability="99">
<dataResource>http://www.aspgd.org/</dataResource>
<dataEntityExample>ASPL0000349247</dataEntityExample>
<dataEntry>http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$id</dataEntry>
<dataInfo>AspGD Protein at Stanford Medical School</dataInfo>
<dataInstitution>Department of Genetics, Stanford University Medical School, Stanford, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000414" pattern="^\d+$" obsolete="true" replacement="MIR:00000528">
<comment>Access to this legacy data is no longer supported.</comment>
<name>DrugBank Target v3</name>
<definition>The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 3 of the database.</definition>
<uris>
<uri type="URN">urn:miriam:drugbank.target</uri>
<uri type="URL">http://identifiers.org/drugbank.target/</uri>
</uris>
<namespace>drugbank.target</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381955</documentation>
</documentations>
<resources>
<resource id="MIR:00100537" state="down" reliability="74">
<dataResource>http://v3.drugbank.ca/</dataResource>
<dataEntityExample>54</dataEntityExample>
<dataEntry>http://v3.drugbank.ca/molecules/$id?as=target</dataEntry>
<dataInfo>DrugBank Target information version 3</dataInfo>
<dataInstitution>Departments of Computing Science, Biological Sciences, University of Alberta</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000415" pattern="^[A-Z]+[A-Z-0-9]{2,}$">
<name>AutDB</name>
<synonyms>
<synonym>Autism Database</synonym>
</synonyms>
<definition>AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.</definition>
<uris>
<uri type="URN">urn:miriam:autdb</uri>
<uri type="URL">http://identifiers.org/autdb/</uri>
</uris>
<namespace>autdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19015121</documentation>
</documentations>
<resources>
<resource id="MIR:00100538" state="up" reliability="81">
<dataResource>http://autism.mindspec.org/autdb/</dataResource>
<dataEntityExample>ADA</dataEntityExample>
<dataEntry>http://autism.mindspec.org/GeneDetail/$id</dataEntry>
<dataInfo>AutDB at MindSpec</dataInfo>
<dataInstitution>MindSpec Inc., Fairfax, Virginia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>disorder</tag>
<tag>gene</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000416" pattern="^\w+(\_)?\d+(\.\d+)?$">
<name>BacMap Map</name>
<definition>BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.</definition>
<uris>
<uri type="URN">urn:miriam:bacmap.map</uri>
<uri type="URL">http://identifiers.org/bacmap.map/</uri>
</uris>
<namespace>bacmap.map</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22135301</documentation>
</documentations>
<resources>
<resource id="MIR:00100539" state="up" reliability="99">
<dataResource>http://bacmap.wishartlab.com/</dataResource>
<dataEntityExample>AP011135</dataEntityExample>
<dataEntry>http://bacmap.wishartlab.com/maps/$id/index.html</dataEntry>
<dataInfo>BacMap Genome Map at University of Alberta</dataInfo>
<dataInstitution>Department of Computing Science, Food and Nutritional Science, University of Alberta, Edmonton</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000417" pattern="^(ENSFM|ENSGTV:)\d+$">
<name>Bgee family</name>
<definition>Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species.</definition>
<uris>
<uri type="URN">urn:miriam:bgee.family</uri>
<uri type="URL">http://identifiers.org/bgee.family/</uri>
</uris>
<namespace>bgee.family</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1007%2F978-3-540-69828-9_12</documentation>
</documentations>
<resources>
<resource id="MIR:00100540" state="down" reliability="90">
<dataResource>http://bgee.unil.ch/bgee/bgee</dataResource>
<dataEntityExample>ENSFM00500000270089</dataEntityExample>
<dataEntry>http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$id</dataEntry>
<dataInfo>Bgee at Lausanne</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>expression</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000418" pattern="^(ENS|FBgn)\w+$">
<name>Bgee gene</name>
<definition>Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression within anatomical structures within a species.</definition>
<uris>
<uri type="URN">urn:miriam:bgee.gene</uri>
<uri type="URL">http://identifiers.org/bgee.gene/</uri>
</uris>
<namespace>bgee.gene</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1007%2F978-3-540-69828-9_12</documentation>
</documentations>
<resources>
<resource id="MIR:00100541" state="down" reliability="90">
<dataResource>http://bgee.unil.ch/bgee/bgee</dataResource>
<dataEntityExample>ENSDARG00000013057</dataEntityExample>
<dataEntry>http://bgee.unil.ch/bgee/bgee?page=gene&action=summary&gene_id=$id</dataEntry>
<dataInfo>Bgee at Lausanne</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000419" pattern="^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$">
<name>Bgee stage</name>
<definition>Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.</definition>
<uris>
<uri type="URN">urn:miriam:bgee.stage</uri>
<uri type="URL">http://identifiers.org/bgee.stage/</uri>
</uris>
<namespace>bgee.stage</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1007%2F978-3-540-69828-9_12</documentation>
</documentations>
<resources>
<resource id="MIR:00100542" state="down" reliability="90">
<dataResource>http://bgee.unil.ch/bgee/bgee</dataResource>
<dataEntityExample>HsapDO:0000004</dataEntityExample>
<dataEntry>http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$id&stage_children=on</dataEntry>
<dataInfo>Bgee at Lausanne</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000420" pattern="^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$">
<name>Bgee organ</name>
<definition>Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.</definition>
<uris>
<uri type="URN">urn:miriam:bgee.organ</uri>
<uri type="URL">http://identifiers.org/bgee.organ/</uri>
</uris>
<namespace>bgee.organ</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1007%2F978-3-540-69828-9_12</documentation>
</documentations>
<resources>
<resource id="MIR:00100543" state="down" reliability="90">
<dataResource>http://bgee.unil.ch/bgee/bgee</dataResource>
<dataEntityExample>EHDAA:2185</dataEntityExample>
<dataEntry>http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$id&organ_children=on</dataEntry>
<dataInfo>Bgee at Lausanne</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>controlled vocabulary</tag>
<tag>expression</tag>
<tag>gene</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000421" pattern="^([hm]\_)?\w+Pathway$" restricted="true">
<name>BioCarta Pathway</name>
<definition>BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps.</definition>
<uris>
<uri type="URN">urn:miriam:biocarta.pathway</uri>
<uri type="URL">http://identifiers.org/biocarta.pathway/</uri>
</uris>
<namespace>biocarta.pathway</namespace>
<documentations>
<documentation type="URL">http://www.biocarta.com/about/index.asp</documentation>
</documentations>
<resources>
<resource id="MIR:00100544" state="up" reliability="93" primary="true">
<dataResource>http://www.biocarta.com/</dataResource>
<dataEntityExample>h_aktPathway</dataEntityExample>
<dataEntry>http://cgap.nci.nih.gov/Pathways/BioCarta/$id</dataEntry>
<dataInfo>BioCarta Pathway at NCI</dataInfo>
<dataInstitution>National Cancer Institute, Center for Bioinformatics, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Since Sept 2015, BioCarta is hosted by NCI, and no new pathways are being added.</statement>
<link desc="terms notice">http://www.genecarta.com/</link>
</restriction>
</restrictions>
<tags>
<tag>image library</tag>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000422" pattern="^G|P|U|C|S\d{5}$">
<name>PANTHER Pathway Component</name>
<definition>The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway
components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.</definition>
<uris>
<uri type="URN">urn:miriam:panther.pthcmp</uri>
<uri type="URL">http://identifiers.org/panther.pthcmp/</uri>
</uris>
<namespace>panther.pthcmp</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12952881</documentation>
</documentations>
<resources>
<resource id="MIR:00100545" state="probably up" reliability="98">
<dataResource>http://www.pantherdb.org/</dataResource>
<dataEntityExample>P00266</dataEntityExample>
<dataEntry>http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$id</dataEntry>
<dataInfo>PANTHER Pathway Component at USC (Los Angeles)</dataInfo>
<dataInstitution>Keck School of Medicine, University of Southern California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>pathway</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000423" pattern="^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" restricted="true">
<name>Golm Metabolome Database Profile</name>
<definition>Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.</definition>
<uris>
<uri type="URN">urn:miriam:gmd.profile</uri>
<uri type="URL">http://identifiers.org/gmd.profile/</uri>
</uris>
<namespace>gmd.profile</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15613389</documentation>
<documentation type="PMID">urn:miriam:pubmed:20526350</documentation>
</documentations>
<resources>
<resource id="MIR:00100546" state="up" reliability="99">
<dataResource>http://gmd.mpimp-golm.mpg.de/</dataResource>
<dataEntityExample>10b38aaf-b977-4950-85b8-f4775f66658d</dataEntityExample>
<dataEntry>http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$id</dataEntry>
<dataInfo>Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology</dataInfo>
<dataInstitution>Max Planck Institute of Molecular Plant Physiology, Potsdam</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Data in this collection is restricted for non-academic users.</statement>
<link desc="terms and conditions">http://gmd.mpimp-golm.mpg.de/termsconditions.aspx</link>
</restriction>
</restrictions>
<tags>
<tag>assay</tag>
<tag>metabolite</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000424" pattern="^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" restricted="true">
<name>Golm Metabolome Database GC-MS spectra</name>
<definition>Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.</definition>
<uris>
<uri type="URN">urn:miriam:gmd.gcms</uri>
<uri type="URL">http://identifiers.org/gmd.gcms/</uri>
</uris>
<namespace>gmd.gcms</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15613389</documentation>
<documentation type="PMID">urn:miriam:pubmed:20526350</documentation>
</documentations>
<resources>
<resource id="MIR:00100547" state="up" reliability="99">
<dataResource>http://gmd.mpimp-golm.mpg.de/</dataResource>
<dataEntityExample>53d583d8-40c6-40e1-9296-23f821cd77a5</dataEntityExample>
<dataEntry>http://gmd.mpimp-golm.mpg.de/Spectrums/$id</dataEntry>
<dataInfo>Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology</dataInfo>
<dataInstitution>Max Planck Institute of Molecular Plant Physiology, Potsdam</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Data in this collection is restricted for non-academic users.</statement>
<link desc="terms and conditions">http://gmd.mpimp-golm.mpg.de/termsconditions.aspx</link>
</restriction>
</restrictions>
<tags>
<tag>mass spectrometry</tag>
<tag>metabolite</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000425" pattern="^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" restricted="true">
<name>Golm Metabolome Database Reference Substance</name>
<definition>Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.</definition>
<uris>
<uri type="URN">urn:miriam:gmd.ref</uri>
<uri type="URL">http://identifiers.org/gmd.ref/</uri>
</uris>
<namespace>gmd.ref</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15613389</documentation>
<documentation type="PMID">urn:miriam:pubmed:20526350</documentation>
</documentations>
<resources>
<resource id="MIR:00100548" state="up" reliability="99">
<dataResource>http://gmd.mpimp-golm.mpg.de/</dataResource>
<dataEntityExample>8cf84adb-b4db-4807-ac98-0004247c35df</dataEntityExample>
<dataEntry>http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$id</dataEntry>
<dataInfo>Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology</dataInfo>
<dataInstitution>Max Planck Institute of Molecular Plant Physiology, Potsdam</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Data in this collection is restricted for non-academic users.</statement>
<link desc="terms and conditions">http://gmd.mpimp-golm.mpg.de/termsconditions.aspx</link>
</restriction>
</restrictions>
<tags>
<tag>catalogue</tag>
<tag>metabolite</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000426" pattern="^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" restricted="true">
<name>Golm Metabolome Database Analyte</name>
<definition>Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.</definition>
<uris>
<uri type="URN">urn:miriam:gmd.analyte</uri>
<uri type="URL">http://identifiers.org/gmd.analyte/</uri>
</uris>
<namespace>gmd.analyte</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15613389</documentation>
<documentation type="PMID">urn:miriam:pubmed:20526350</documentation>
</documentations>
<resources>
<resource id="MIR:00100549" state="up" reliability="99">
<dataResource>http://gmd.mpimp-golm.mpg.de/</dataResource>
<dataEntityExample>4f0fa9b6-514f-4ff4-98cc-0009bc08eb80</dataEntityExample>
<dataEntry>http://gmd.mpimp-golm.mpg.de/Analytes/$id</dataEntry>
<dataInfo>Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology</dataInfo>
<dataInstitution>Max Planck Institute of Molecular Plant Physiology, Potsdam</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Data in this collection is restricted for non-academic users.</statement>
<link desc="terms and conditions">http://gmd.mpimp-golm.mpg.de/termsconditions.aspx</link>
</restriction>
</restrictions>
<tags>
<tag>mass spectrometry</tag>
<tag>metabolite</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000427" pattern="^EBI\-[0-9]+$">
<name>IntAct Molecule</name>
<definition>IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.</definition>
<uris>
<uri type="URN">urn:miriam:intact.molecule</uri>
<uri type="URL">http://identifiers.org/intact.molecule/</uri>
</uris>
<namespace>intact.molecule</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681455</documentation>
<documentation type="PMID">urn:miriam:pubmed:17145710</documentation>
</documentations>
<resources>
<resource id="MIR:00100550" state="down" reliability="50">
<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
<dataEntityExample>EBI-366083</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/intact/molecule/$id</dataEntry>
<dataInfo>IntAct Molecule at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000428" pattern="^[A-Z0-9]+$">
<name>DEPOD</name>
<synonyms>
<synonym>human DEPhOsphorylation Database</synonym>
</synonyms>
<definition>The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.</definition>
<uris>
<uri type="URN">urn:miriam:depod</uri>
<uri type="URL">http://identifiers.org/depod/</uri>
</uris>
<namespace>depod</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:25332398</documentation>
<documentation type="DOI">urn:miriam:doi:10.1126%2Fscisignal.2003203</documentation>
</documentations>
<resources>
<resource id="MIR:00100551" state="down" reliability="44">
<dataResource>http://www.koehnlab.de/depod/</dataResource>
<dataEntityExample>PTPN1</dataEntityExample>
<dataEntry>http://www.koehnlab.de/depod/showp.php?gene=$id</dataEntry>
<dataInfo>DEPOD at EMBL</dataInfo>
<dataInstitution>European Molecular Biology Laboratory EMBL, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>interaction</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000429" pattern="^[A-Za-z0-9_-]+$">
<name>Cell Signaling Technology Pathways</name>
<definition>Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.</definition>
<uris>
<uri type="URN">urn:miriam:cst</uri>
<uri type="URL">http://identifiers.org/cst/</uri>
</uris>
<namespace>cst</namespace>
<documentations>
<documentation type="URL">http://www.cellsignal.com/about/index.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100552" state="up" reliability="98">
<dataResource>http://www.cellsignal.com/pathways/index.html</dataResource>
<dataEntityExample>Akt_PKB</dataEntityExample>
<dataEntry>http://www.cellsignal.com/reference/pathway/$id.html</dataEntry>
<dataInfo>CST Pathways at Cell Signaling Technology</dataInfo>
<dataInstitution>Cell Signaling Technology, Inc., Danvers, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>catalogue</tag>
<tag>immunogenetics</tag>
<tag>pathway</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000430" pattern="^\d+$">
<name>Cell Signaling Technology Antibody</name>
<definition>Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products.</definition>
<uris>
<uri type="URN">urn:miriam:cst.ab</uri>
<uri type="URL">http://identifiers.org/cst.ab/</uri>
</uris>
<namespace>cst.ab</namespace>
<documentations>
<documentation type="URL">http://www.cellsignal.com/about/index.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100553" state="up" reliability="98">
<dataResource>http://www.cellsignal.com/catalog/index.html</dataResource>
<dataEntityExample>3305</dataEntityExample>
<dataEntry>http://www.cellsignal.com/products/$id.html</dataEntry>
<dataInfo>CST Antibody at Cell Signaling Technology</dataInfo>
<dataInstitution>Cell Signaling Technology, Inc., Danvers, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>catalogue</tag>
<tag>immunogenetics</tag>
<tag>interaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000431" pattern="^\d+\-\d+\-\d+">
<name>National Drug Code</name>
<synonyms>
<synonym>NDC</synonym>
</synonyms>
<definition>The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily.</definition>
<uris>
<uri type="URN">urn:miriam:ndc</uri>
<uri type="URL">http://identifiers.org/ndc/</uri>
<uri type="URL" deprecated="true">http://bio2rdf.org/ndc</uri>
</uris>
<namespace>ndc</namespace>
<documentations>
<documentation type="URL">http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm</documentation>
</documentations>
<resources>
<resource id="MIR:00100554" state="up" reliability="95" primary="true">
<dataResource>http://www.accessdata.fda.gov/scripts/cder/ndc/</dataResource>
<dataEntityExample>0002-1975-61</dataEntityExample>
<dataEntry>http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$id</dataEntry>
<dataInfo>National Drug Code at Food and Drug Administration</dataInfo>
<dataInstitution>U.S. Food and Drug Administration, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100700" state="down" reliability="82">
<dataResource>http://ndc.bio2rdf.org/fct</dataResource>
<dataEntityExample>0002-1975-61</dataEntityExample>
<dataEntry>http://ndc.bio2rdf.org/describe/?url=http://bio2rdf.org/ndc:$id</dataEntry>
<dataInfo>Bio2RDF</dataInfo>
<dataInstitution>Bio2RDF.org</dataInstitution>
<dataLocation></dataLocation>
</resource>
<resource id="MIR:00100555" obsolete="true">
<dataResource>http://healthprovidersdata.com/</dataResource>
<dataEntityExample>0002-1975</dataEntityExample>
<dataEntry>http://healthprovidersdata.com/hipaa/codes/NDC_$id.aspx</dataEntry>
<dataInfo>National Drug Code at Health Providers Data</dataInfo>
<dataInstitution>Health Providers Data, Fargo, North Dakota</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>catalogue</tag>
<tag>drug</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000432" pattern="^[A-Za-z0-9]+$">
<name>Phytozome Locus</name>
<definition>Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.</definition>
<uris>
<uri type="URN">urn:miriam:phytozome.locus</uri>
<uri type="URL">http://identifiers.org/phytozome.locus/</uri>
</uris>
<namespace>phytozome.locus</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22110026</documentation>
</documentations>
<resources>
<resource id="MIR:00100556" state="down" reliability="42">
<dataResource>http://www.phytozome.net/</dataResource>
<dataEntityExample>Glyma0021s00410</dataEntityExample>
<dataEntry>http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$id</dataEntry>
<dataInfo>Phytozome Locus at Joint Genome Institute</dataInfo>
<dataInstitution>Joint Genome Institute, California, and the Center for Integrative Genomics, Lausanne</dataInstitution>
<dataLocation>USA and Switzerland</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000433" pattern="^BG\d+$">
<name>SubtiList</name>
<definition>SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.
SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.</definition>
<uris>
<uri type="URN">urn:miriam:subtilist</uri>
<uri type="URL">http://identifiers.org/subtilist/</uri>
</uris>
<namespace>subtilist</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11752255</documentation>
</documentations>
<resources>
<resource id="MIR:00100557" state="up" reliability="98">
<dataResource>http://genolist.pasteur.fr/SubtiList/</dataResource>
<dataEntityExample>BG11523</dataEntityExample>
<dataEntry>http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$id</dataEntry>
<dataInfo>SubtiList at Pasteur Institute</dataInfo>
<dataInstitution>Pasteur Institute, Paris</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000434" pattern="^[A-Za-z0-9-]+">
<name>DailyMed</name>
<definition>DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.</definition>
<uris>
<uri type="URN">urn:miriam:dailymed</uri>
<uri type="URL">http://identifiers.org/dailymed/</uri>
</uris>
<namespace>dailymed</namespace>
<documentations>
<documentation type="URL">http://dailymed.nlm.nih.gov/dailymed/help.cfm</documentation>
</documentations>
<resources>
<resource id="MIR:00100558" state="down" reliability="90">
<dataResource>http://dailymed.nlm.nih.gov/dailymed/</dataResource>
<dataEntityExample>8889bcd7-d0e9-434b-b09d-30132bd033b0</dataEntityExample>
<dataEntry>http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=$id</dataEntry>
<dataInfo>DailyMed at NLM</dataInfo>
<dataInstitution>U.S. National Library of Medicine, Bethesda, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>catalogue</tag>
<tag>drug</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000435" pattern="^\d+$" restricted="true">
<name>SIDER Drug</name>
<synonyms>
<synonym>Side Effect Resource</synonym>
</synonyms>
<definition>SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.</definition>
<uris>
<uri type="URN">urn:miriam:sider.drug</uri>
<uri type="URL">http://identifiers.org/sider.drug/</uri>
</uris>
<namespace>sider.drug</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20087340</documentation>
</documentations>
<resources>
<resource id="MIR:00100559" state="up" reliability="99">
<dataResource>http://sideeffects.embl.de/</dataResource>
<dataEntityExample>2244</dataEntityExample>
<dataEntry>http://sideeffects.embl.de/drugs/$id/</dataEntry>
<dataInfo>SIDER Drug v2 at EMBL (Heidelberg)</dataInfo>
<dataInstitution>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>This data is not free to commercial users.</statement>
<link desc="licence">http://creativecommons.org/licenses/by-nc-sa/3.0/</link>
</restriction>
</restrictions>
<tags>
<tag>drug</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000436" pattern="^C\d+$" restricted="true">
<name>SIDER Side Effect</name>
<definition>SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.</definition>
<uris>
<uri type="URN">urn:miriam:sider.effect</uri>
<uri type="URL">http://identifiers.org/sider.effect/</uri>
</uris>
<namespace>sider.effect</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20087340</documentation>
</documentations>
<resources>
<resource id="MIR:00100560" state="up" reliability="99">
<dataResource>http://sideeffects.embl.de/</dataResource>
<dataEntityExample>C0017565</dataEntityExample>
<dataEntry>http://sideeffects.embl.de/se/$id/</dataEntry>
<dataInfo>SIDER Side Effect v2 at EMBL (Heidelberg)</dataInfo>
<dataInstitution>Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>This data is not free to commercial users.</statement>
<link desc="licence">http://creativecommons.org/licenses/by-nc-sa/3.0/</link>
</restriction>
</restrictions>
<tags>
<tag>drug</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000437" pattern="^\d+$">
<name>WikiGenes</name>
<definition>WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.</definition>
<uris>
<uri type="URN">urn:miriam:wikigenes</uri>
<uri type="URL">http://identifiers.org/wikigenes/</uri>
</uris>
<namespace>wikigenes</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18728691</documentation>
</documentations>
<resources>
<resource id="MIR:00100567" state="up" reliability="96">
<dataResource>http://www.wikigenes.org/</dataResource>
<dataEntityExample>3771877</dataEntityExample>
<dataEntry>http://www.wikigenes.org/e/gene/e/$id.html</dataEntry>
<dataInfo>WikiGenes at Massachusetts Institute of Technology</dataInfo>
<dataInstitution>Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
<tag>gene</tag>
<tag>interaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000438" pattern="^S\d+$">
<name>Broad Fungal Genome Initiative</name>
<synonyms>
<synonym>Magnaporthe comparative genomics database</synonym>
</synonyms>
<definition>Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.</definition>
<uris>
<uri type="URN">urn:miriam:broad</uri>
<uri type="URL">http://identifiers.org/broad/</uri>
</uris>
<namespace>broad</namespace>
<documentations>
<documentation type="URL">http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/Info.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100569" state="down" reliability="64">
<dataResource>http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/</dataResource>
<dataEntityExample>S7000002168151102</dataEntityExample>
<dataEntry>http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$id</dataEntry>
<dataInfo>Broad Fungal Genome Initiative at Broad Institute</dataInfo>
<dataInstitution>Broad Institute of MIT and Harvard, Cambridge, Massachuchetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
<tag>fungal</tag>
<tag>genome</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000439" pattern="^[A-Z]{2}\d+$">
<name>Coriell Cell Repositories</name>
<definition>The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.</definition>
<uris>
<uri type="URN">urn:miriam:coriell</uri>
<uri type="URL">http://identifiers.org/coriell/</uri>
</uris>
<namespace>coriell</namespace>
<documentations>
<documentation type="URL">http://ccr.coriell.org/Default.aspx?public=true</documentation>
</documentations>
<resources>
<resource id="MIR:00100570" state="up" reliability="87">
<dataResource>http://ccr.coriell.org/</dataResource>
<dataEntityExample>GM17027</dataEntityExample>
<dataEntry>http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$id</dataEntry>
<dataInfo>Coriell Cell Repositories at Coriell Institute</dataInfo>
<dataInstitution>Coriell Institute for Medical Research, New Jersey</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>catalogue</tag>
<tag>human</tag>
<tag>mammalian</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000440" pattern="^\d+$" restricted="true">
<name>CORUM</name>
<definition>The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.</definition>
<uris>
<uri type="URN">urn:miriam:corum</uri>
<uri type="URL">http://identifiers.org/corum/</uri>
</uris>
<namespace>corum</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19884131</documentation>
</documentations>
<resources>
<resource id="MIR:00100571" state="down" reliability="66">
<dataResource>http://mips.helmholtz-muenchen.de/genre/proj/corum/</dataResource>
<dataEntityExample>100</dataEntityExample>
<dataEntry>http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=$id</dataEntry>
<dataInfo>CORUM at Institute for Bioinformatics and Systems Biology (Germany)</dataInfo>
<dataInstitution>Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum M&amp;uuml;nchen-German Research Center for Environmental Health, Neuherberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The associated data and services are for academic, non-commercial use only.</statement>
<link desc="statement on each page">http://mips.helmholtz-muenchen.de/genre/proj/corum/about/corum.html</link>
</restriction>
</restrictions>
<tags>
<tag>mammalian</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000441" pattern="^[A-Z]$" obsolete="true" replacement="MIR:00000119">
<comment>As of September 2013, this collection is no longer maintained. Various archives are available at: ftp://ftp.ncbi.nih.gov/pub/COG/. </comment>
<name>COGs Function</name>
<synonyms>
<synonym>Clusters of Orthologous Groups Function</synonym>
</synonyms>
<definition>Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. This collection references functional groups.</definition>
<uris>
<uri type="URN">urn:miriam:cogs.function</uri>
<uri type="URL">http://identifiers.org/cogs.function/</uri>
</uris>
<namespace>cogs.function</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12969510</documentation>
</documentations>
<resources>
<resource id="MIR:00100572" state="down" reliability="7">
<dataResource>http://www.ncbi.nlm.nih.gov/COG/</dataResource>
<dataEntityExample>A</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?fun=$id</dataEntry>
<dataInfo>COGs Function at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000442" pattern="^[A-Za-z0-9-]+$">
<name>EcoliWiki</name>
<definition>EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes.</definition>
<uris>
<uri type="URN">urn:miriam:ecoliwiki</uri>
<uri type="URL">http://identifiers.org/ecoliwiki/</uri>
</uris>
<namespace>ecoliwiki</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22064863</documentation>
</documentations>
<resources>
<resource id="MIR:00100573" state="up" reliability="97">
<dataResource>http://ecoliwiki.net/colipedia/</dataResource>
<dataEntityExample>aaeA</dataEntityExample>
<dataEntry>http://ecoliwiki.net/colipedia/index.php/$id:Gene</dataEntry>
<dataInfo>EcoliWiki at Texas Agrilife Research</dataInfo>
<dataInstitution>Texas Agrilife Research, Texas A&amp;M University College Station</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>microbial</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000443" pattern="^GenProp\d+$" obsolete="true" replacement="MIR:00000202">
<comment>Genome Properties (CMR) is no longer supported by the JCVI and has been taken offline. More information at: http://www.jcvi.org/cms/research/past-projects/cmr/overview/ </comment>
<name>Genome Properties</name>
<definition>The Genome Properties system captures key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties, expressed using controlled vocabulary, reflect gene content, phenotype, phylogeny and computational analyses. Additional properties are derived from curation, published reports and other forms of evidence.</definition>
<uris>
<uri type="URN">urn:miriam:genprop</uri>
<uri type="URL">http://identifiers.org/genprop/</uri>
</uris>
<namespace>genprop</namespace>
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<documentation type="PMID">urn:miriam:pubmed:15347579</documentation>
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<dataResource>http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenomePropertiesHomePage.cgi</dataResource>
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<dataInfo>Genome Properties at JCVI</dataInfo>
<dataInstitution>J Craig Venter institute, Rockville, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
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</resources>
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<tag>controlled vocabulary</tag>
<tag>microbial</tag>
</tags>
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<elements>
<element>model</element>
</elements>
</format>
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<datatype id="MIR:00000444" pattern="^\d+$">
<name>JSTOR</name>
<synonyms>
<synonym>Journal Storage</synonym>
</synonyms>
<definition>JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.</definition>
<uris>
<uri type="URN">urn:miriam:jstor</uri>
<uri type="URL">http://identifiers.org/jstor/</uri>
</uris>
<namespace>jstor</namespace>
<documentations>
<documentation type="URL">http://en.wikipedia.org/wiki/JSTOR</documentation>
<documentation type="URL">http://about.jstor.org/individuals-faq</documentation>
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<resource id="MIR:00100575" state="up" reliability="100">
<dataResource>http://www.jstor.org/</dataResource>
<dataEntityExample>3075966</dataEntityExample>
<dataEntry>http://www.jstor.org/stable/$id</dataEntry>
<dataInfo>JSTOR Online</dataInfo>
<dataInstitution>Ithaka Harbors, Inc., New York</dataInstitution>
<dataLocation>USA</dataLocation>
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</resources>
<tags>
<tag>bibliography</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
<element>parameter</element>
<element>reaction</element>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000445" pattern="^MA:\d+$">
<name>Mouse Adult Gross Anatomy</name>
<definition>A structured controlled vocabulary of the adult anatomy of the mouse (Mus)</definition>
<uris>
<uri type="URN">urn:miriam:ma</uri>
<uri type="URL">http://identifiers.org/ma/</uri>
</uris>
<namespace>ma</namespace>
<documentations>
<documentation type="URL">http://www.obofoundry.org/cgi-bin/detail.cgi?id=adult_mouse_anatomy</documentation>
<documentation type="URL">http://www.informatics.jax.org/searches/AMA_form.shtml</documentation>
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<dataResource>http://bioportal.bioontology.org/ontologies/MA</dataResource>
<dataEntityExample>MA:0002502</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/MA/$id</dataEntry>
<dataInfo>Mouse Adult Gross Anatomy through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
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<resource id="MIR:00100577" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/ma</dataResource>
<dataEntityExample>MA:0002502</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/ma/terms?obo_id=$id</dataEntry>
<dataInfo>Mouse Adult Gross Anatomy through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
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<resource id="MIR:00100578" state="up" reliability="100" primary="true">
<dataResource>http://www.informatics.jax.org/</dataResource>
<dataEntityExample>MA:0002502</dataEntityExample>
<dataEntry>http://www.informatics.jax.org/searches/AMA.cgi?id=$id</dataEntry>
<dataInfo>Mouse Adult Gross Anatomy at The Jackson Laboratory</dataInfo>
<dataInstitution>The Jackson Laboratory, Bar Harbor, Maine</dataInstitution>
<dataLocation>USA</dataLocation>
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<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>compartment</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000446" pattern="^UBERON\:\d+$">
<name>UBERON</name>
<synonyms>
<synonym>Uber Anatomy Ontology</synonym>
</synonyms>
<definition>Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.</definition>
<uris>
<uri type="URN">urn:miriam:uberon</uri>
<uri type="URL">http://identifiers.org/uberon/</uri>
<uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/UBERON</uri>
</uris>
<namespace>uberon</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22293552</documentation>
</documentations>
<resources>
<resource id="MIR:00100579" state="up" reliability="89">
<dataResource>http://bioportal.bioontology.org/ontologies/UBERON</dataResource>
<dataEntityExample>UBERON:0008203</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/UBERON/$id</dataEntry>
<dataInfo>UBERON through bioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
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<dataResource>https://www.ebi.ac.uk/ols/ontologies/uberon</dataResource>
<dataEntityExample>UBERON:0008203</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/uberon/terms?obo_id=$id</dataEntry>
<dataInfo>UBERON through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
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<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>compartment</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000447" pattern="^\d+$" restricted="true">
<name>Unimod</name>
<definition>Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).</definition>
<uris>
<uri type="URN">urn:miriam:unimod</uri>
<uri type="URL">http://identifiers.org/unimod/</uri>
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<namespace>unimod</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15174123</documentation>
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<dataResource>http://www.unimod.org/</dataResource>
<dataEntityExample>1200</dataEntityExample>
<dataEntry>http://www.unimod.org/modifications_view.php?editid1=$id</dataEntry>
<dataInfo>Unimod at Matrix Sciences Ltd.</dataInfo>
<dataInstitution>Matrix Science Ltd., London</dataInstitution>
<dataLocation>UK</dataLocation>
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<restriction type="3" desc="Access restriction">
<statement>This site requires a login, but can be accessed as guest.</statement>
<link desc="registration">http://www.unimod.org/register_disabled.html</link>
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<tags>
<tag>mass spectrometry</tag>
<tag>protein</tag>
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<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
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<name>VBRC</name>
<synonyms>
<synonym>Viral Bioinformatics Resource Center</synonym>
</synonyms>
<definition>The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.</definition>
<uris>
<uri type="URN">urn:miriam:vbrc</uri>
<uri type="URL">http://identifiers.org/vbrc/</uri>
</uris>
<namespace>vbrc</namespace>
<documentations>
<documentation type="URL">http://vbrc.org/about.asp</documentation>
</documentations>
<resources>
<resource id="MIR:00100582" state="down" reliability="38">
<dataResource>http://vbrc.org/</dataResource>
<dataEntityExample>35742</dataEntityExample>
<dataEntry>http://vbrc.org/gene_detail.asp?gene_id=$id</dataEntry>
<dataInfo>VBRC at University of Alabama</dataInfo>
<dataInstitution>University of Alabama, Birmingham and the University of Victoria, British Columbia</dataInstitution>
<dataLocation>USA and Canada</dataLocation>
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<tags>
<tag>genome</tag>
<tag>viral</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000449" pattern="^\d+$">
<name>ViralZone</name>
<definition>ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.</definition>
<uris>
<uri type="URN">urn:miriam:viralzone</uri>
<uri type="URL">http://identifiers.org/viralzone/</uri>
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<namespace>viralzone</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20947564</documentation>
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<dataResource>http://www.expasy.org/viralzone/</dataResource>
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<dataEntry>http://viralzone.expasy.org/all_by_protein/$id.html</dataEntry>
<dataInfo>ViralZone at SIB</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics, Centre Médical Universitaire, Geneva</dataInstitution>
<dataLocation>Switzerland</dataLocation>
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<tags>
<tag>image library</tag>
<tag>viral</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
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<datatype id="MIR:00000450" pattern="^GO_REF:\d{7}$">
<name>Gene Ontology Reference</name>
<synonyms>
<synonym>GO reference collection</synonym>
</synonyms>
<definition>The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made.</definition>
<uris>
<uri type="URN">urn:miriam:go.ref</uri>
<uri type="URL">http://identifiers.org/go.ref/</uri>
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<namespace>go.ref</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681407</documentation>
<documentation type="URL">http://www.geneontology.org/GO.consortiumlist.shtml</documentation>
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<dataResource>http://www.geneontology.org/cgi-bin/references.cgi</dataResource>
<dataEntityExample>GO_REF:0000041</dataEntityExample>
<dataEntry>http://www.geneontology.org/cgi-bin/references.cgi#$id</dataEntry>
<dataInfo>Gene Ontology Reference at The Gene Ontology Consortium</dataInfo>
<dataInstitution>The Gene Ontology Consortium</dataInstitution>
<dataLocation>USA</dataLocation>
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</resources>
<tags>
<tag>controlled vocabulary</tag>
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<datatype id="MIR:00000451" pattern="^\d+$">
<name>Rat Genome Database qTL</name>
<definition>Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes.</definition>
<uris>
<uri type="URN">urn:miriam:rgd.qtl</uri>
<uri type="URL">http://identifiers.org/rgd.qtl/</uri>
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<namespace>rgd.qtl</namespace>
<documentations>
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<dataResource>http://rgd.mcw.edu/</dataResource>
<dataEntityExample>1354581</dataEntityExample>
<dataEntry>http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$id</dataEntry>
<dataInfo>Rat Genome Database qTL at Medical College of Wisconsin</dataInfo>
<dataInstitution>Medical College of Wisconsin, Milwaukee, Wisconsin</dataInstitution>
<dataLocation>USA</dataLocation>
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<tags>
<tag>gene</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
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<datatype id="MIR:00000452" pattern="^\d+$">
<name>Rat Genome Database strain</name>
<definition>Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.</definition>
<uris>
<uri type="URN">urn:miriam:rgd.strain</uri>
<uri type="URL">http://identifiers.org/rgd.strain/</uri>
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<namespace>rgd.strain</namespace>
<documentations>
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<dataEntityExample>5688061</dataEntityExample>
<dataEntry>http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$id</dataEntry>
<dataInfo>Rat Genome Database strain at Medical College of Wisconsin</dataInfo>
<dataInstitution>Medical College of Wisconsin, Milwaukee, Wisconsin</dataInstitution>
<dataLocation>USA</dataLocation>
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<datatype id="MIR:00000453" pattern="^\d+$" restricted="true">
<name>DOOR</name>
<synonyms>
<synonym>Database for prOkaryotic OpeRons</synonym>
</synonyms>
<definition>DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes.</definition>
<uris>
<uri type="URN">urn:miriam:door</uri>
<uri type="URL">http://identifiers.org/door/</uri>
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<namespace>door</namespace>
<documentations>
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<dataResource>http://csbl1.bmb.uga.edu/OperonDB/DOOR.php</dataResource>
<dataEntityExample>60101</dataEntityExample>
<dataEntry>http://csbl1.bmb.uga.edu/OperonDB/genedetail.php?id=$id</dataEntry>
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<dataInstitution>Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia</dataInstitution>
<dataLocation>USA</dataLocation>
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<link desc="terms and conditions">http://csbl1.bmb.uga.edu/OperonDB/</link>
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<datatype id="MIR:00000454" pattern="^[AMCST][0-9x][0-9]$">
<name>Degradome Database</name>
<definition>The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced.</definition>
<uris>
<uri type="URN">urn:miriam:degradome</uri>
<uri type="URL">http://identifiers.org/degradome/</uri>
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<namespace>degradome</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18776217</documentation>
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<dataResource>http://degradome.uniovi.es/</dataResource>
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<dataEntry>http://degradome.uniovi.es/cgi-bin/protease/$id</dataEntry>
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<dataLocation>Spain</dataLocation>
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<datatype id="MIR:00000455" pattern="^\d+$">
<name>DBD</name>
<synonyms>
<synonym>Transcription Factor Database</synonym>
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<definition>The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins.</definition>
<uris>
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<uri type="URL">http://identifiers.org/dbd/</uri>
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<documentations>
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<dataEntry>http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$id+cat:DBD</dataEntry>
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<dataInstitution>MRC Laboratory of Molecular Biology, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
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<name>DATF</name>
<synonyms>
<synonym>Database of Arabidopsis transcription factors</synonym>
</synonyms>
<definition>DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.</definition>
<uris>
<uri type="URN">urn:miriam:datf</uri>
<uri type="URL">http://identifiers.org/datf/</uri>
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<namespace>datf</namespace>
<documentations>
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<dataResource>http://datf.cbi.pku.edu.cn/</dataResource>
<dataEntityExample>AT1G01030.1</dataEntityExample>
<dataEntry>http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$id</dataEntry>
<dataInfo>DATF through PlantTFDB</dataInfo>
<dataInstitution>Center for Bioinformatics, Peking</dataInstitution>
<dataLocation>Peoples Republic of China.</dataLocation>
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<datatype id="MIR:00000457" pattern="^\d+$">
<name>IUPHAR ligand</name>
<definition>The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.</definition>
<uris>
<uri type="URN">urn:miriam:iuphar.ligand</uri>
<uri type="URL">http://identifiers.org/iuphar.ligand/</uri>
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<namespace>iuphar.ligand</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23087376</documentation>
</documentations>
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<dataResource>http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all</dataResource>
<dataEntityExample>1755</dataEntityExample>
<dataEntry>http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id</dataEntry>
<dataInfo>IUPHAR ligand at University of Edinburgh</dataInfo>
<dataInstitution>Centre for Cardiovascular Science, University of Edinburgh, Edinburgh</dataInstitution>
<dataLocation>UK</dataLocation>
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<datatype id="MIR:00000458" pattern="^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$">
<name>Molbase</name>
<definition>Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier.</definition>
<uris>
<uri type="URN">urn:miriam:molbase</uri>
<uri type="URL">http://identifiers.org/molbase/</uri>
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<namespace>molbase</namespace>
<documentations>
<documentation type="URL">http://www.molbase.com/en/index.php?app=article&act=view&article_id=112</documentation>
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<dataResource>http://www.molbase.com/</dataResource>
<dataEntityExample>128796-39-4</dataEntityExample>
<dataEntry>http://www.molbase.com/en/index.php?app=search&search_keyword=$id</dataEntry>
<dataInfo>Molbase at Chinese Academy of Sciences</dataInfo>
<dataInstitution>Chinese Academy of Sciences, Xuhui District Shanghai</dataInstitution>
<dataLocation>China</dataLocation>
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<datatype id="MIR:00000459" pattern="^\d+$">
<name>YRC PDR</name>
<synonyms>
<synonym>Yeast Resource Center Public Data Repository</synonym>
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<definition>The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.</definition>
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<uri type="URN">urn:miriam:yrcpdr</uri>
<uri type="URL">http://identifiers.org/yrcpdr/</uri>
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<namespace>yrcpdr</namespace>
<documentations>
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<dataResource>http://www.yeastrc.org/pdr/</dataResource>
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<dataEntry>http://yeastrc.org/pdr/viewProtein.do?id=$id</dataEntry>
<dataInfo>YRC PDR at University of Washington</dataInfo>
<dataInstitution>Department of Biochemistry, University of Washington, Seattle</dataInstitution>
<dataLocation>USA</dataLocation>
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<datatype id="MIR:00000460" pattern="^[A-Z0-9]+$">
<name>Yeast Intron Database v3</name>
<definition>The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].</definition>
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<uri type="URN">urn:miriam:yid</uri>
<uri type="URL">http://identifiers.org/yid/</uri>
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<namespace>yid</namespace>
<documentations>
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<dataResource>http://compbio.soe.ucsc.edu/yeast_introns.html</dataResource>
<dataEntityExample>SNR17A</dataEntityExample>
<dataEntry>http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$id</dataEntry>
<dataInfo>Yeast Intron Database version 3 at Baskin School of Engineering</dataInfo>
<dataInstitution>Baskin School of Engineering, Center for Molecular Biology of RNA, University of California, Santa Cruz, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>eukaryotic</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000461" pattern="^\d+$">
<name>FuncBase Fly</name>
<definition>Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.</definition>
<uris>
<uri type="URN">urn:miriam:funcbase.fly</uri>
<uri type="URL">http://identifiers.org/funcbase.fly/</uri>
</uris>
<namespace>funcbase.fly</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20495000</documentation>
</documentations>
<resources>
<resource id="MIR:00100596" state="probably up" reliability="96">
<dataResource>http://func.mshri.on.ca/fly</dataResource>
<dataEntityExample>10194</dataEntityExample>
<dataEntry>http://func.mshri.on.ca/fly/genes/list_functional_scores/$id</dataEntry>
<dataInfo>FuncBase Fly at Harvard Medical School</dataInfo>
<dataInstitution>Harvard Medical School, Boston, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000462" pattern="^\d+$">
<name>FuncBase Human</name>
<definition>Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.</definition>
<uris>
<uri type="URN">urn:miriam:funcbase.human</uri>
<uri type="URL">http://identifiers.org/funcbase.human/</uri>
</uris>
<namespace>funcbase.human</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20495000</documentation>
</documentations>
<resources>
<resource id="MIR:00100597" state="probably up" reliability="96">
<dataResource>http://func.mshri.on.ca/human/</dataResource>
<dataEntityExample>119514</dataEntityExample>
<dataEntry>http://func.mshri.on.ca/human/genes/list_functional_scores/$id</dataEntry>
<dataInfo>FuncBase Human at Harvard Medical School</dataInfo>
<dataInstitution>Harvard Medical School, Boston, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000463" pattern="^\d+$">
<name>FuncBase Mouse</name>
<definition>Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.</definition>
<uris>
<uri type="URN">urn:miriam:funcbase.mouse</uri>
<uri type="URL">http://identifiers.org/funcbase.mouse/</uri>
</uris>
<namespace>funcbase.mouse</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20495000</documentation>
</documentations>
<resources>
<resource id="MIR:00100598" state="probably up" reliability="96">
<dataResource>http://func.mshri.on.ca/mouse/</dataResource>
<dataEntityExample>1351341</dataEntityExample>
<dataEntry>http://func.mshri.on.ca/mouse/genes/list_functional_scores/$id</dataEntry>
<dataInfo>FuncBase Mouse at Harvard Medical School</dataInfo>
<dataInstitution>Harvard Medical School, Boston, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000464" pattern="^\d+$">
<name>FuncBase Yeast</name>
<definition>Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.</definition>
<uris>
<uri type="URN">urn:miriam:funcbase.yeast</uri>
<uri type="URL">http://identifiers.org/funcbase.yeast/</uri>
</uris>
<namespace>funcbase.yeast</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20495000</documentation>
</documentations>
<resources>
<resource id="MIR:00100599" state="probably up" reliability="96">
<dataResource>http://func.mshri.on.ca/yeast</dataResource>
<dataEntityExample>2701</dataEntityExample>
<dataEntry>http://func.mshri.on.ca/yeast/genes/list_functional_scores/$id</dataEntry>
<dataInfo>FuncBase Yeast at Harvard Medical School</dataInfo>
<dataInstitution>Harvard Medical School, Boston, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000465" pattern="^Y[A-Z]{2}\d+[CW]$">
<name>YDPM</name>
<synonyms>
<synonym>Yeast Deletion Project and Proteomics of Mitochondria Database</synonym>
</synonyms>
<definition>The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.</definition>
<uris>
<uri type="URN">urn:miriam:ydpm</uri>
<uri type="URL">http://identifiers.org/ydpm/</uri>
</uris>
<namespace>ydpm</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12134146</documentation>
</documentations>
<resources>
<resource id="MIR:00100600" state="up" reliability="99">
<dataResource>http://www-deletion.stanford.edu/YDPM/</dataResource>
<dataEntityExample>YAL001C</dataEntityExample>
<dataEntry>http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$id</dataEntry>
<dataInfo>YDPM at Stanford University School of Medicine</dataInfo>
<dataInstitution>Stanford University School of Medicine, Stanford, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000466" pattern="^WBRNAi\d{8}$">
<name>WormBase RNAi</name>
<definition>WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.</definition>
<uris>
<uri type="URN">urn:miriam:wormbase.rnai</uri>
<uri type="URL">http://identifiers.org/wormbase.rnai/</uri>
</uris>
<namespace>wormbase.rnai</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:11125056</documentation>
<documentation type="PMID">urn:miriam:pubmed:17099234</documentation>
</documentations>
<resources>
<resource id="MIR:00100601" state="up" reliability="100">
<dataResource>http://www.wormbase.org/</dataResource>
<dataEntityExample>WBRNAi00086878</dataEntityExample>
<dataEntry>http://www.wormbase.org/species/c_elegans/rnai/$id</dataEntry>
<dataInfo>WormBase RNAi at Cold Spring Harbor Laboratory</dataInfo>
<dataInstitution>Cold Spring Harbor Laboratory, Cold Spring, Harbor New York</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000467" pattern="^\d{2}|\d{2}\.\d{2}|\d{2}\.\d{2}\.\d{2}|\d{2}\.\d{2}\.\d{2}\d{2}$">
<name>FunCat</name>
<synonyms>
<synonym>MIPS Functional Catalogue Database</synonym>
</synonyms>
<definition>The Functional Catalogue (FunCat) is a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism. It has been applied for the manual annotation of prokaryotes, fungi, plants and animals.</definition>
<uris>
<uri type="URN">urn:miriam:funcat</uri>
<uri type="URL">http://identifiers.org/funcat/</uri>
</uris>
<namespace>funcat</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15486203</documentation>
</documentations>
<resources>
<resource id="MIR:00100602" state="down" reliability="18">
<dataResource>http://mips.helmholtz-muenchen.de/funcatDB/</dataResource>
<dataEntityExample>32.01.01</dataEntityExample>
<dataEntry>http://mips.helmholtz-muenchen.de/funcatDB/cgi-bin/search_advanced.pl?action=2&wert=$id</dataEntry>
<dataInfo>FunCat at MIPS (Neuherberg)</dataInfo>
<dataInstitution>Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Neuherberg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000468" pattern="^\d+$">
<name>PASS2</name>
<synonyms>
<synonym>Protein Alignments organised as Structural Superfamilies</synonym>
</synonyms>
<definition>The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.</definition>
<uris>
<uri type="URN">urn:miriam:pass2</uri>
<uri type="URL">http://identifiers.org/pass2/</uri>
</uris>
<namespace>pass2</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22123743</documentation>
</documentations>
<resources>
<resource id="MIR:00100603" state="up" reliability="87">
<dataResource>http://caps.ncbs.res.in/pass2/</dataResource>
<dataEntityExample>46977</dataEntityExample>
<dataEntry>http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$id</dataEntry>
<dataInfo>PASS2 at National centre for Biological Sciences (India)</dataInfo>
<dataInstitution>National centre for Biological Sciences, TIFR, GKVK campus, Bangalore, Karnataka</dataInstitution>
<dataLocation>India</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000469" pattern="^\d+$">
<name>ICEberg element</name>
<definition>ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.</definition>
<uris>
<uri type="URN">urn:miriam:iceberg.element</uri>
<uri type="URL">http://identifiers.org/iceberg.element/</uri>
</uris>
<namespace>iceberg.element</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22009673</documentation>
</documentations>
<resources>
<resource id="MIR:00100604" state="probably up" reliability="97">
<dataResource>http://db-mml.sjtu.edu.cn/ICEberg/</dataResource>
<dataEntityExample>100</dataEntityExample>
<dataEntry>http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$id</dataEntry>
<dataInfo>ICEberg element at Shanghai Jiaotong University</dataInfo>
<dataInstitution>State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp;amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000470" pattern="^\d+$">
<name>ICEberg family</name>
<definition>ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.</definition>
<uris>
<uri type="URN">urn:miriam:iceberg.family</uri>
<uri type="URL">http://identifiers.org/iceberg.family/</uri>
</uris>
<namespace>iceberg.family</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22009673</documentation>
</documentations>
<resources>
<resource id="MIR:00100605" state="probably up" reliability="97">
<dataResource>http://db-mml.sjtu.edu.cn/ICEberg/</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$id</dataEntry>
<dataInfo>ICEberg family at Shanghai Jiaotong University</dataInfo>
<dataInstitution>State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000471" pattern="^\w+$">
<name>VFDB Genus</name>
<synonyms>
<synonym>Virulence Factor Database genus</synonym>
</synonyms>
<definition>VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.</definition>
<uris>
<uri type="URN">urn:miriam:vfdb.genus</uri>
<uri type="URL">http://identifiers.org/vfdb.genus/</uri>
</uris>
<namespace>vfdb.genus</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22067448</documentation>
</documentations>
<resources>
<resource id="MIR:00100606" state="up" reliability="99">
<dataResource>http://www.mgc.ac.cn/VFs/</dataResource>
<dataEntityExample>Chlamydia</dataEntityExample>
<dataEntry>http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$id</dataEntry>
<dataInfo>VFDB Genus at Institute of Pathogen Biology</dataInfo>
<dataInstitution>State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000472" pattern="^\w+$">
<name>VFDB Gene</name>
<definition>VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.</definition>
<uris>
<uri type="URN">urn:miriam:vfdb.gene</uri>
<uri type="URL">http://identifiers.org/vfdb.gene/</uri>
</uris>
<namespace>vfdb.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22067448</documentation>
</documentations>
<resources>
<resource id="MIR:00100607" state="up" reliability="99">
<dataResource>http://www.mgc.ac.cn/VFs/</dataResource>
<dataEntityExample>VFG2154</dataEntityExample>
<dataEntry>http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$id</dataEntry>
<dataInfo>VFDB Gene at Institute of Pathogen Biology</dataInfo>
<dataInstitution>State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000473" pattern="^[A-Za-z0-9]+$" restricted="true">
<name>MeSH 2013</name>
<definition>MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.</definition>
<uris>
<uri type="URN">urn:miriam:mesh.2013</uri>
<uri type="URL">http://identifiers.org/mesh.2013/</uri>
</uris>
<namespace>mesh.2013</namespace>
<documentations>
<documentation type="URL">http://www.nlm.nih.gov/pubs/factsheets/mesh.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100608" state="down" reliability="73">
<dataResource>http://www.nlm.nih.gov/mesh/</dataResource>
<dataEntityExample>17165</dataEntityExample>
<dataEntry>http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$id&view=expanded</dataEntry>
<dataInfo>MeSH 2013 at National Library of Medicine</dataInfo>
<dataInstitution>U.S. National Library of Medicine, National Institute of Health, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>Records accessed through MESH may include content that itself has some copyright restriction when reproduced.</statement>
<link desc="copyright and fair use information">http://www.nlm.nih.gov/copyright.html</link>
</restriction>
<restriction type="4" desc="Identifier instability">
<statement>Access to Mesh 2013 uses identifiers that could potentially change. We recommend the use of the stable MeSH collection (http://identifiers.org/mesh/). If you have issues accessing Mesh 2013, you may wish to try the ftp service.</statement>
<link desc="ftp://nlmpubs.nlm.nih.gov/online/mesh/.asciimesh/c2013.bin">ftp access for MeSH 2013 records</link>
</restriction>
</restrictions>
</datatype>
<datatype id="MIR:00000474" pattern="^([a-z]{3,5}_)?M\d{5}$">
<name>KEGG Module</name>
<!--<synonyms>-->
<!--<synonym>KEGG</synonym>-->
<!--</synonyms>-->
<definition>KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.module</uri>
<uri type="URL">http://identifiers.org/kegg.module/</uri>
</uris>
<namespace>kegg.module</namespace>
<documentations>
<documentation type="URL">http://www.kegg.jp/kegg/module.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100609" state="up" reliability="99" primary="true">
<dataResource>http://www.kegg.jp/kegg/module.html</dataResource>
<dataEntityExample>M00002</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG Module at Kyoto University Bioinformatics Center</dataInfo>
<dataInstitution>Department of Computational Biology, University of Tokyo, Tokyo</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>clustering</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000475" pattern="^H\d+$">
<name>KEGG Disease</name>
<!--<synonyms>-->
<!--<synonym>KEGG</synonym>-->
<!--</synonyms>-->
<definition>The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.disease</uri>
<uri type="URL">http://identifiers.org/kegg.disease/</uri>
</uris>
<namespace>kegg.disease</namespace>
<documentations>
<documentation type="URL">http://www.genome.jp/kegg/disease/</documentation>
</documentations>
<resources>
<resource id="MIR:00100610" state="up" reliability="99" primary="true">
<dataResource>http://www.genome.jp/kegg/disease/</dataResource>
<dataEntityExample>H00076</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG Disease at Kyoto University Bioinformatics Center</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center, Kyoto</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000476" pattern="^\d+$">
<name>MedlinePlus</name>
<definition>MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language.</definition>
<uris>
<uri type="URN">urn:miriam:medlineplus</uri>
<uri type="URL">http://identifiers.org/medlineplus/</uri>
</uris>
<namespace>medlineplus</namespace>
<documentations>
<documentation type="URL">http://www.nlm.nih.gov/medlineplus/aboutmedlineplus.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100611" state="up" reliability="99">
<dataResource>http://www.nlm.nih.gov/medlineplus/</dataResource>
<dataEntityExample>002804</dataEntityExample>
<dataEntry>http://www.nlm.nih.gov/medlineplus/ency/article/$id.htm</dataEntry>
<dataInfo>MedlinePlus at NCBI</dataInfo>
<dataInstitution>NCBI, NIH, Bethesda, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>encyclopedia</tag>
<tag>human</tag>
<tag>schema.org</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000477" pattern="^D\d{5}">
<name>LigandBox</name>
<definition>LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.</definition>
<uris>
<uri type="URN">urn:miriam:ligandbox</uri>
<uri type="URL">http://identifiers.org/ligandbox/</uri>
</uris>
<namespace>ligandbox</namespace>
<documentations>
<documentation type="URL">https://www.jstage.jst.go.jp/article/biophysics/9/0/9_113/_article</documentation>
</documentations>
<resources>
<resource id="MIR:00100612" state="up" reliability="98">
<dataResource>http://ligandbox.protein.osaka-u.ac.jp/ligandbox//cgi-bin/index.cgi?LANG=en</dataResource>
<dataEntityExample>D00001</dataEntityExample>
<dataEntry>http://ligandbox.protein.osaka-u.ac.jp/ligandbox/cgi-bin/liginf.cgi?id=$id</dataEntry>
<dataInfo>LigandBox at</dataInfo>
<dataInstitution>nstitute for Protein Research, Osaka University and Fujitsu Kyushu R&amp;D Center, Life Science Systems Dept., Fujitsu</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000478" pattern="^EP\d{4}$">
<name>GlycoEpitope</name>
<definition>GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.</definition>
<uris>
<uri type="URN">urn:miriam:glycoepitope</uri>
<uri type="URL">http://identifiers.org/glycoepitope/</uri>
</uris>
<namespace>glycoepitope</namespace>
<documentations>
<documentation type="URL">http://www.glycoepitope.jp/GlycoEpitope_guide_E.pdf</documentation>
</documentations>
<resources>
<resource id="MIR:00100613" state="up" reliability="97">
<dataResource>http://www.glycoepitope.jp/epitopes/</dataResource>
<dataEntityExample>EP0311</dataEntityExample>
<dataEntry>http://www.glycoepitope.jp/epitopes/$id</dataEntry>
<dataInfo>GlycoEpitope at Ritsumeikan University</dataInfo>
<dataInstitution>Kawasaki laboratory, Research Center for Glycobiotechnology, Ritsumeikan University</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>immunogenetics</tag>
<tag>interaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000479" pattern="^JCGG-STR\d{6}$">
<name>JCGGDB</name>
<synonyms>
<synonym>Japan Consortium for Glycobiology and Glycotechnology DataBase</synonym>
</synonyms>
<definition>JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.</definition>
<uris>
<uri type="URN">urn:miriam:jcggdb</uri>
<uri type="URL">http://identifiers.org/jcggdb/</uri>
</uris>
<namespace>jcggdb</namespace>
<documentations>
<documentation type="URL">http://jcggdb.jp/seturitu_en.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100614" state="up" reliability="88">
<dataResource>http://jcggdb.jp/index_en.html</dataResource>
<dataEntityExample>JCGG-STR008690</dataEntityExample>
<dataEntry>http://jcggdb.jp/idb/jcggdb/$id</dataEntry>
<dataInfo>JCGGDB at Advanced Science Institute (Japan)</dataInfo>
<dataInstitution>Advanced Science Institute(ASI), Chemical Biology Department Systems Glycobiology research Group, Saitama</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>lipid</tag>
<tag>polysaccharide</tag>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000480" pattern="^NONHSAG\d{5}$">
<name>NONCODE v4 Gene</name>
<definition>NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.</definition>
<uris>
<uri type="URN">urn:miriam:noncodev4.gene</uri>
<uri type="URL">http://identifiers.org/noncodev4.gene/</uri>
</uris>
<namespace>noncodev4.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22135294</documentation>
</documentations>
<resources>
<resource id="MIR:00100616" state="down" reliability="71">
<dataResource>http://www.bioinfo.org/NONCODEv4/</dataResource>
<dataEntityExample>NONHSAG00001</dataEntityExample>
<dataEntry>http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$id</dataEntry>
<dataInfo>NONCODE v4 Gene at Chinese Academy of Sciences</dataInfo>
<dataInstitution>Bioinformatics Research Group, Chinese Academy of Sciences, Beijing</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>gene</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000481" pattern="^NONHSAT\d{6}$">
<name>NONCODE v4 Transcript</name>
<definition>NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.</definition>
<uris>
<uri type="URN">urn:miriam:noncodev4.rna</uri>
<uri type="URL">http://identifiers.org/noncodev4.rna/</uri>
</uris>
<namespace>noncodev4.rna</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22135294</documentation>
</documentations>
<resources>
<resource id="MIR:00100617" state="down" reliability="71">
<dataResource>http://www.bioinfo.org/NONCODEv4/</dataResource>
<dataEntityExample>NONHSAT000001</dataEntityExample>
<dataEntry>http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$id</dataEntry>
<dataInfo>NONCODE v4 Transcript at Chinese Academy of Sciences</dataInfo>
<dataInstitution>Bioinformatics Research Group, Chinese Academy of Sciences, Beijing</dataInstitution>
<dataLocation>China</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000482" pattern="^\d+$">
<name>Oryzabase Gene</name>
<definition>Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.</definition>
<uris>
<uri type="URN">urn:miriam:oryzabase.gene</uri>
<uri type="URL">http://identifiers.org/oryzabase.gene/</uri>
</uris>
<namespace>oryzabase.gene</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16403737</documentation>
</documentations>
<resources>
<resource id="MIR:00100618" state="up" reliability="99">
<dataResource>http://www.shigen.nig.ac.jp/rice/oryzabaseV4/</dataResource>
<dataEntityExample>117</dataEntityExample>
<dataEntry>http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$id</dataEntry>
<dataInfo>Oryzabase v4 Gene at National Institute of Genetics (Japan)</dataInfo>
<dataInstitution>Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000483" pattern="^\d+$">
<name>Oryzabase Mutant</name>
<definition>Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.</definition>
<uris>
<uri type="URN">urn:miriam:oryzabase.mutant</uri>
<uri type="URL">http://identifiers.org/oryzabase.mutant/</uri>
</uris>
<namespace>oryzabase.mutant</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16403737</documentation>
</documentations>
<resources>
<resource id="MIR:00100619" state="up" reliability="98">
<dataResource>http://www.shigen.nig.ac.jp/rice/oryzabaseV4/</dataResource>
<dataEntityExample>21393</dataEntityExample>
<dataEntry>http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$id</dataEntry>
<dataInfo>Oryzabase v4 Mutant at National Institute of Genetics (Japan)</dataInfo>
<dataInstitution>Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>phenotype</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000484" pattern="^\d+$">
<name>Oryzabase Strain</name>
<definition>Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.</definition>
<uris>
<uri type="URN">urn:miriam:oryzabase.strain</uri>
<uri type="URL">http://identifiers.org/oryzabase.strain/</uri>
</uris>
<namespace>oryzabase.strain</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16403737</documentation>
</documentations>
<resources>
<resource id="MIR:00100620" state="up" reliability="98">
<dataResource>http://www.shigen.nig.ac.jp/rice/oryzabaseV4/</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$id</dataEntry>
<dataInfo>Oryzabase v4 Strain at National Institute of Genetics (Japan)</dataInfo>
<dataInstitution>Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>plant</tag>
<tag>strain</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000485" pattern="^\d+$">
<name>Oryzabase Stage</name>
<definition>Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.</definition>
<uris>
<uri type="URN">urn:miriam:oryzabase.stage</uri>
<uri type="URL">http://identifiers.org/oryzabase.stage/</uri>
</uris>
<namespace>oryzabase.stage</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16403737</documentation>
</documentations>
<resources>
<resource id="MIR:00100621" state="up" reliability="98">
<dataResource>http://www.shigen.nig.ac.jp/rice/oryzabaseV4/</dataResource>
<dataEntityExample>34</dataEntityExample>
<dataEntry>http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$id</dataEntry>
<dataInfo>Oryzabase v4 Stage at National Institute of Genetics (Japan)</dataInfo>
<dataInstitution>Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>phenotype</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000486" pattern="^A[A-Z]+\d+$">
<name>Oryza Tag Line</name>
<synonyms>
<synonym>OTL</synonym>
</synonyms>
<definition>Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.</definition>
<uris>
<uri type="URN">urn:miriam:otl</uri>
<uri type="URL">http://identifiers.org/otl/</uri>
</uris>
<namespace>otl</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17947330</documentation>
</documentations>
<resources>
<resource id="MIR:00100622" state="up" reliability="94">
<dataResource>http://oryzatagline.cirad.fr/</dataResource>
<dataEntityExample>AADB12</dataEntityExample>
<dataEntry>http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$id</dataEntry>
<dataInfo>Oryza Tag Line at CIRAD-INRA-SUPAGRO-UMI</dataInfo>
<dataInstitution>CIRAD-INRA-SUPAGRO-UMII, Biological Systems Department, Montpellier</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>phenotype</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000487" pattern="^\d+$" restricted="true">
<name>Gene Wiki</name>
<definition>The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI.</definition>
<uris>
<uri type="URN">urn:miriam:genewiki</uri>
<uri type="URL">http://identifiers.org/genewiki/</uri>
</uris>
<namespace>genewiki</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18613750</documentation>
</documentations>
<resources>
<resource id="MIR:00100623" state="up" reliability="87">
<dataResource>http://en.wikipedia.org/wiki/Gene_Wiki</dataResource>
<dataEntityExample>1017</dataEntityExample>
<dataEntry>http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id</dataEntry>
<dataInfo>Gene Wiki through BioGPS</dataInfo>
<dataInstitution>Wikimedia Foundation, San Francisco, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="6" desc="Collection subset">
<statement>This collection is a subset of NCBI gene (MIR:00000069), accessed through BioGPS.</statement>
<link desc="BioGPS">http://biogps.org/</link>
</restriction>
</restrictions>
<tags>
<tag>encyclopedia</tag>
<tag>gene</tag>
<tag>human</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000488" pattern="^\d+$">
<name>PaxDb Organism</name>
<definition>PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.</definition>
<uris>
<uri type="URN">urn:miriam:paxdb.organism</uri>
<uri type="URL">http://identifiers.org/paxdb.organism/</uri>
</uris>
<namespace>paxdb.organism</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22535208</documentation>
</documentations>
<resources>
<resource id="MIR:00100624" state="probably up" reliability="98">
<dataResource>http://pax-db.org/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://pax-db.org/#!species/$id</dataEntry>
<dataInfo>PaxDb v3 at University of Zurich</dataInfo>
<dataInstitution>Institute of Molecular Life Sciences, University of Zurich, Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>genome</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000489" pattern="^\d+$">
<name>PaxDb Protein</name>
<definition>PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.</definition>
<uris>
<uri type="URN">urn:miriam:paxdb.protein</uri>
<uri type="URL">http://identifiers.org/paxdb.protein/</uri>
</uris>
<namespace>paxdb.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22535208</documentation>
</documentations>
<resources>
<resource id="MIR:00100625" state="probably up" reliability="98">
<dataResource>http://pax-db.org/</dataResource>
<dataEntityExample>977869</dataEntityExample>
<dataEntry>http://pax-db.org/#!protein/$id</dataEntry>
<dataInfo>PaxDb v3 at University of Zurich</dataInfo>
<dataInstitution>Institute of Molecular Life Sciences, University of Zurich, Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000490" pattern="^[A-Za-z0-9]+$">
<name>Protein Data Bank Ligand</name>
<definition>The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands.</definition>
<uris>
<uri type="URN">urn:miriam:pdb.ligand</uri>
<uri type="URL">http://identifiers.org/pdb.ligand/</uri>
</uris>
<namespace>pdb.ligand</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17142228</documentation>
<documentation type="PMID">urn:miriam:pubmed:10592235</documentation>
</documentations>
<resources>
<resource id="MIR:00100626" state="down" reliability="66">
<dataResource>http://www.pdb.org/</dataResource>
<dataEntityExample>TRQ</dataEntityExample>
<dataEntry>http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$id</dataEntry>
<dataInfo>PDB Ligand at RCSB</dataInfo>
<dataInstitution>Rutgers, The State University of New Jersey</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100650" state="up" reliability="99">
<dataResource>http://www.pdbe.org/</dataResource>
<dataEntityExample>TRQ</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id</dataEntry>
<dataInfo>PDB Ligand at Protein Databank in Europe (PDBe)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000491" pattern="^I\d{2}\.\d{3}$">
<name>MEROPS Inhibitor</name>
<definition>The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors.</definition>
<uris>
<uri type="URN">urn:miriam:merops.inhibitor</uri>
<uri type="URL">http://identifiers.org/merops.inhibitor/</uri>
</uris>
<namespace>merops.inhibitor</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17991683</documentation>
</documentations>
<resources>
<resource id="MIR:00100632" state="down" reliability="79">
<dataResource>http://merops.sanger.ac.uk/index.htm</dataResource>
<dataEntityExample>I31.952</dataEntityExample>
<dataEntry>http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$id</dataEntry>
<dataInfo>MEROPS Inhibitor at Sanger Institute</dataInfo>
<dataInstitution>Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>enzyme</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000492" pattern="^[A-Z_a-z]+$">
<name>Animal Diversity Web</name>
<definition>Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.</definition>
<uris>
<uri type="URN">urn:miriam:adw</uri>
<uri type="URL">http://identifiers.org/adw/</uri>
</uris>
<namespace>adw</namespace>
<documentations>
<documentation type="URL">http://www.lsa.umich.edu/ummz/default.asp</documentation>
</documentations>
<resources>
<resource id="MIR:00100633" state="up" reliability="99">
<dataResource>http://animaldiversity.ummz.umich.edu/</dataResource>
<dataEntityExample>Lycalopex_vetulus</dataEntityExample>
<dataEntry>http://animaldiversity.ummz.umich.edu/accounts/$id/</dataEntry>
<dataInfo>Animal Diversity Web at University of Michigan</dataInfo>
<dataInstitution>University of Michigan Museum of Zoology, Ann Arbor, Michigan</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000493" pattern="^[A-Z-_0-9]+$">
<name>GLIDA GPCR</name>
<synonyms>
<synonym>GPCR-LIgand DAtabase GPCR</synonym>
</synonyms>
<definition>The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors.</definition>
<uris>
<uri type="URN">urn:miriam:glida.gpcr</uri>
<uri type="URL">http://identifiers.org/glida.gpcr/</uri>
</uris>
<namespace>glida.gpcr</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381956</documentation>
<documentation type="PMID">urn:miriam:pubmed:17986454</documentation>
</documentations>
<resources>
<resource id="MIR:00100634" state="up" reliability="91">
<dataResource>http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/</dataResource>
<dataEntityExample>ACM1_HUMAN</dataEntityExample>
<dataEntry>http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$id</dataEntry>
<dataInfo>GLIDA GPCR at Kyoto University</dataInfo>
<dataInstitution>Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>interaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000494" pattern="^L\d+$">
<name>GLIDA Ligand</name>
<synonyms>
<synonym>GPCR-LIgand DAtabase Ligand</synonym>
</synonyms>
<definition>The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands.</definition>
<uris>
<uri type="URN">urn:miriam:glida.ligand</uri>
<uri type="URL">http://identifiers.org/glida.ligand/</uri>
</uris>
<namespace>glida.ligand</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381956</documentation>
<documentation type="PMID">urn:miriam:pubmed:17986454</documentation>
</documentations>
<resources>
<resource id="MIR:00100635" state="up" reliability="91">
<dataResource>http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/</dataResource>
<dataEntityExample>L000001</dataEntityExample>
<dataEntry>http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$id</dataEntry>
<dataInfo>GLIDA Ligand at Kyoto University</dataInfo>
<dataInstitution>Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>interaction</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000495" pattern="^\d+$">
<name>GRSDB</name>
<synonyms>
<synonym>G-Rich Sequences DataBase</synonym>
</synonyms>
<definition>GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.</definition>
<uris>
<uri type="URN">urn:miriam:grsdb</uri>
<uri type="URL">http://identifiers.org/grsdb/</uri>
</uris>
<namespace>grsdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381828</documentation>
</documentations>
<resources>
<resource id="MIR:00100636" state="up" reliability="93">
<dataResource>http://bioinformatics.ramapo.edu/GRSDB2/</dataResource>
<dataEntityExample>10142</dataEntityExample>
<dataEntry>http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$id</dataEntry>
<dataInfo>GRSDB v2 at Ramapo College of New Jersey</dataInfo>
<dataInstitution>Bioinformatics Group, School of Theoretical and Applied Science, Ramapo College of New Jersey, Mahwah</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>eukaryotic</tag>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000496" pattern="^rs\d+$">
<name>F-SNP</name>
<synonyms>
<synonym>Functional Single Nucleotide Polymorphism</synonym>
</synonyms>
<definition>The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.</definition>
<uris>
<uri type="URN">urn:miriam:fsnp</uri>
<uri type="URL">http://identifiers.org/fsnp/</uri>
</uris>
<namespace>fsnp</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17986460</documentation>
</documentations>
<resources>
<resource id="MIR:00100637" state="down" reliability="82">
<dataResource>http://compbio.cs.queensu.ca/F-SNP/</dataResource>
<dataEntityExample>rs17852708</dataEntityExample>
<dataEntry>http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&amp;id_type=snp_id&amp;id_val=$id</dataEntry>
<dataInfo>F-SNP at Queen's University (Canada)</dataInfo>
<dataInstitution>Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, Ontario</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>nucleotide</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000497" pattern="^\d+$">
<name>Homeodomain Research</name>
<definition>The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.</definition>
<uris>
<uri type="URN">urn:miriam:hdr</uri>
<uri type="URL">http://identifiers.org/hdr/</uri>
</uris>
<namespace>hdr</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20157477</documentation>
</documentations>
<resources>
<resource id="MIR:00100638" state="up" reliability="82">
<dataResource>http://research.nhgri.nih.gov/apps/homeodomain/web/</dataResource>
<dataEntityExample>63</dataEntityExample>
<dataEntry>http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&amp;view=proteins&amp;id=$id</dataEntry>
<dataInfo>Homeodomain Research at National Human Genome Research Institute (NIH)</dataInfo>
<dataInstitution>Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000498" pattern="^NOR\d+$">
<name>NORINE</name>
<definition>Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.</definition>
<uris>
<uri type="URN">urn:miriam:norine</uri>
<uri type="URL">http://identifiers.org/norine/</uri>
</uris>
<namespace>norine</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17913739</documentation>
</documentations>
<resources>
<resource id="MIR:00100639" state="up" reliability="96">
<dataResource>http://bioinfo.lifl.fr/norine/</dataResource>
<dataEntityExample>NOR00681</dataEntityExample>
<dataEntry>http://bioinfo.lifl.fr/norine/result.jsp?ID=$id</dataEntry>
<dataInfo>NORINE at Computer Science Laboratory of Lille</dataInfo>
<dataInstitution>Computer Science Laboratory of Lille, INRIA and ProBioGEM, University of Sciences and Technologies of Lille, Lille</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>fungal</tag>
<tag>microbial</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000499" pattern="^\d+$">
<name>Olfactory Receptor Database</name>
<synonyms>
<synonym>OrDB</synonym>
</synonyms>
<definition>The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs).</definition>
<uris>
<uri type="URN">urn:miriam:ordb</uri>
<uri type="URL">http://identifiers.org/ordb/</uri>
</uris>
<namespace>ordb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23585030</documentation>
</documentations>
<resources>
<resource id="MIR:00100640" state="up" reliability="89">
<dataResource>http://senselab.med.yale.edu/OrDB/</dataResource>
<dataEntityExample>8497</dataEntityExample>
<dataEntry>http://senselab.med.yale.edu/ORDB/Data/$id</dataEntry>
<dataInfo>Olfactory Receptor Database at Yale University School of Medicine</dataInfo>
<dataInstitution>Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000500" pattern="^\d+$">
<name>Odor Molecules DataBase</name>
<synonyms>
<synonym>OdorDB</synonym>
</synonyms>
<definition>OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors</definition>
<uris>
<uri type="URN">urn:miriam:odor</uri>
<uri type="URL">http://identifiers.org/odor/</uri>
</uris>
<namespace>odor</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23585030</documentation>
</documentations>
<resources>
<resource id="MIR:00100641" state="up" reliability="85">
<dataResource>http://senselab.med.yale.edu/OdorDB</dataResource>
<dataEntityExample>74</dataEntityExample>
<dataEntry>http://senselab.med.yale.edu/OdorDB/Data/$id/?db=5</dataEntry>
<dataInfo>Odor Molecules DataBase at Yale University School of Medicine</dataInfo>
<dataInstitution>Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000501" pattern="^\d+$">
<name>P3DB Protein</name>
<definition>Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.</definition>
<uris>
<uri type="URN">urn:miriam:p3db.protein</uri>
<uri type="URL">http://identifiers.org/p3db.protein/</uri>
</uris>
<namespace>p3db.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22973285</documentation>
</documentations>
<resources>
<resource id="MIR:00100642" state="up" reliability="98">
<dataResource>http://www.p3db.org/</dataResource>
<dataEntityExample>70</dataEntityExample>
<dataEntry>http://www.p3db.org/protein.php?id=$id&amp;ref=0</dataEntry>
<dataInfo>P3DB Protein at University of Missouri</dataInfo>
<dataInstitution>Department of Computer Science, University of Missouri, Columbia, Missouri</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>plant</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000502" pattern="^\d+$">
<name>P3DB Site</name>
<definition>Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.</definition>
<uris>
<uri type="URN">urn:miriam:p3db.site</uri>
<uri type="URL">http://identifiers.org/p3db.site/</uri>
</uris>
<namespace>p3db.site</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22973285</documentation>
</documentations>
<resources>
<resource id="MIR:00100643" state="up" reliability="98">
<dataResource>http://www.p3db.org/</dataResource>
<dataEntityExample>65</dataEntityExample>
<dataEntry>http://www.p3db.org/phosphosite.php?id=$id&ref=0</dataEntry>
<dataInfo>P3DB Site at University of Missouri</dataInfo>
<dataInstitution>Department of Computer Science, University of Missouri, Columbia, Missouri</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>plant</tag>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000503" pattern="^[A-Z0-9]+$">
<name>TOPDB</name>
<definition>The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.</definition>
<uris>
<uri type="URN">urn:miriam:topdb</uri>
<uri type="URL">http://identifiers.org/topdb/</uri>
</uris>
<namespace>topdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17921502</documentation>
</documentations>
<resources>
<resource id="MIR:00100644" state="up" reliability="99">
<dataResource>http://topdb.enzim.hu/</dataResource>
<dataEntityExample>AP00378</dataEntityExample>
<dataEntry>http://topdb.enzim.hu/?m=show&id=$id</dataEntry>
<dataInfo>TOPDB at Hungarian Academy of Sciences</dataInfo>
<dataInstitution>Institute of Enzymology, Hungarian Academy of Sciences, Budapest</dataInstitution>
<dataLocation>Hungary</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000504" pattern="^\d+$">
<name>Animal Genome Cattle QTL</name>
<definition>The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs.</definition>
<uris>
<uri type="URN">urn:miriam:cattleqtldb</uri>
<uri type="URL">http://identifiers.org/cattleqtldb/</uri>
</uris>
<namespace>cattleqtldb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23180796</documentation>
</documentations>
<resources>
<resource id="MIR:00100645" state="up" reliability="99">
<dataResource>http://www.animalgenome.org/cgi-bin/QTLdb/BT/index</dataResource>
<dataEntityExample>4685</dataEntityExample>
<dataEntry>http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$id</dataEntry>
<dataInfo>Animal QTL Cattle at Iowa State University</dataInfo>
<dataInstitution>Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000505" pattern="^\d+$">
<name>Animal Genome Chicken QTL</name>
<definition>The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs.</definition>
<uris>
<uri type="URN">urn:miriam:chickenqtldb</uri>
<uri type="URL">http://identifiers.org/chickenqtldb/</uri>
</uris>
<namespace>chickenqtldb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23180796</documentation>
</documentations>
<resources>
<resource id="MIR:00100646" state="up" reliability="99">
<dataResource>http://www.animalgenome.org/cgi-bin/QTLdb/GG/index</dataResource>
<dataEntityExample>14362</dataEntityExample>
<dataEntry>http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$id</dataEntry>
<dataInfo>Animal QTL Chicken at Iowa State University</dataInfo>
<dataInstitution>Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000506" pattern="^\d+$">
<name>Animal Genome Pig QTL</name>
<definition>The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.</definition>
<uris>
<uri type="URN">urn:miriam:pigqtldb</uri>
<uri type="URL">http://identifiers.org/pigqtldb/</uri>
</uris>
<namespace>pigqtldb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23180796</documentation>
</documentations>
<resources>
<resource id="MIR:00100647" state="up" reliability="99">
<dataResource>http://www.animalgenome.org/cgi-bin/QTLdb/SS/index</dataResource>
<dataEntityExample>14</dataEntityExample>
<dataEntry>http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$id</dataEntry>
<dataInfo>Animal QTL Pig at Iowa State University</dataInfo>
<dataInstitution>Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000507" pattern="^\d+$">
<name>Animal Genome Sheep QTL</name>
<definition>The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs.</definition>
<uris>
<uri type="URN">urn:miriam:sheepqtldb</uri>
<uri type="URL">http://identifiers.org/sheepqtldb/</uri>
</uris>
<namespace>sheepqtldb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23180796</documentation>
</documentations>
<resources>
<resource id="MIR:00100648" state="up" reliability="99">
<dataResource>http://www.animalgenome.org/cgi-bin/QTLdb/OA/index</dataResource>
<dataEntityExample>19803</dataEntityExample>
<dataEntry>http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$id</dataEntry>
<dataInfo>Animal QTL Sheep at Iowa State University</dataInfo>
<dataInstitution>Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>phenotype</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000508" pattern="^GRO\:\d+$">
<name>Gramene Growth Stage Ontology</name>
<definition>Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.</definition>
<uris>
<uri type="URN">urn:miriam:gramene.growthstage</uri>
<uri type="URL">http://identifiers.org/gramene.growthstage/</uri>
</uris>
<namespace>gramene.growthstage</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:21076153</documentation>
</documentations>
<resources>
<resource id="MIR:00100649" state="up" reliability="99">
<dataResource>http://www.gramene.org/</dataResource>
<dataEntityExample>GRO:0007133</dataEntityExample>
<dataEntry>http://www.gramene.org/db/ontology/search?id=$id</dataEntry>
<dataInfo>Gramene Growth Stage Ontology at Cold Spring Harbor</dataInfo>
<dataInstitution>Cold Spring Harbor Laboratory, New York</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>compartment</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000509" pattern="^(GI|gi)\:\d+$" restricted="true">
<name>NCBI GI</name>
<definition>The NCBI GI (or "gi") identifier is the original form of identifier for sequence records processed by the NCBI. This 'GenInfo' identifier system was used to access GenBank and related databases, and was assigned to both protein and nucleotide sequences.</definition>
<uris>
<uri type="URN">urn:miriam:ncbigi</uri>
<uri type="URL">http://identifiers.org/ncbigi/</uri>
</uris>
<namespace>ncbigi</namespace>
<documentations>
<documentation type="URL">http://www.ncbi.nlm.nih.gov/protein</documentation>
</documentations>
<resources>
<resource id="MIR:00100652" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/protein/</dataResource>
<dataEntityExample>GI:9082283</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/protein/$id</dataEntry>
<dataInfo>NCBI GI at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="6" desc="Collection subset">
<statement>Historical subset of NCBI gene and protein (MIR:00000069, MIR:00000344), which continue to be the recommended manner in which to reference nucelotide and protein sequence information.</statement>
<link desc="restriction guidelines">http://www.ebi.ac.uk/miriam/main/mdb?section=faq#CollectionsRestrictions</link>
</restriction>
<restriction type="7" desc="Identifier non-conformity">
<statement>It is not possible to discriminate protein or nucleotide entities based on the identifier.</statement>
<link desc="gi information">http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html</link>
</restriction>
</restrictions>
</datatype>
<datatype id="MIR:00000510" pattern="^[A-Z]+[0-9]+$">
<name>EBI Metagenomics Sample</name>
<definition>The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.</definition>
<uris>
<uri type="URN">urn:miriam:ebimetagenomics.samp</uri>
<uri type="URL">http://identifiers.org/ebimetagenomics.samp/</uri>
<uri type="URL" deprecated="true">http://identifiers.org/ebimetagenomics/</uri>
<uri type="URN" deprecated="true">urn:miriam:ebimetagenomics</uri>
</uris>
<namespace>ebimetagenomics.samp</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkt961</documentation>
</documentations>
<resources>
<resource id="MIR:00100656" state="up" reliability="93">
<dataResource>http://www.ebi.ac.uk/metagenomics</dataResource>
<dataEntityExample>SRS086444</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/metagenomics/samples/$id</dataEntry>
<dataInfo>EBI Metagenomics at European Bioinformatics Institute</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
</tags>
</datatype>
<datatype id="MIR:00000511" pattern="^EGAS\d{11}$">
<name>European Genome-phenome Archive Study</name>
<synonyms>
<synonym>EGA Study</synonym>
</synonyms>
<definition>The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.</definition>
<uris>
<uri type="URN">urn:miriam:ega.study</uri>
<uri type="URL">http://identifiers.org/ega.study/</uri>
</uris>
<namespace>ega.study</namespace>
<documentations>
<documentation type="URL">https://www.ebi.ac.uk/ega/about/introduction</documentation>
</documentations>
<resources>
<resource id="MIR:00100657" state="up" reliability="99" primary="true">
<dataResource>https://www.ebi.ac.uk/ega/studies</dataResource>
<dataEntityExample>EGAS00000000001</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ega/studies/$id</dataEntry>
<dataInfo>EGA Study at European Bioinformatics Institute</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100851" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>EGAS00000000001</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/ega/$id</dataEntry>
<dataInfo>EGA Study through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000512" pattern="^EGAD\d{11}$">
<name>European Genome-phenome Archive Dataset</name>
<synonyms>
<synonym>EGA Dataset</synonym>
</synonyms>
<definition>The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.</definition>
<uris>
<uri type="URN">urn:miriam:ega.dataset</uri>
<uri type="URL">http://identifiers.org/ega.dataset/</uri>
</uris>
<namespace>ega.dataset</namespace>
<documentations>
<documentation type="URL">https://www.ebi.ac.uk/ega/about/introduction</documentation>
</documentations>
<resources>
<resource id="MIR:00100658" state="up" reliability="99" primary="true">
<dataResource>https://www.ebi.ac.uk/ega/dataset</dataResource>
<dataEntityExample>EGAD00000000001</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ega/datasets/$id</dataEntry>
<dataInfo>EGA Dataset at European Bioinformatics Institute</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100852" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>EGAD00000000001</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/ega/$id</dataEntry>
<dataInfo>EGA Dataset through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000513" pattern="^(R)?PXD\d+{6}$">
<name>ProteomeXchange</name>
<definition>The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.</definition>
<uris>
<uri type="URN">urn:miriam:px</uri>
<uri type="URL">http://identifiers.org/px/</uri>
<uri type="URN" deprecated="true">urn:miriam:proteomexchange</uri>
</uris>
<namespace>px</namespace>
<documentations>
<documentation type="URL">http://www.proteomexchange.org/faq</documentation>
</documentations>
<resources>
<resource id="MIR:00100660" state="up" reliability="99">
<dataResource>http://www.proteomexchange.org/</dataResource>
<dataEntityExample>PXD000500</dataEntityExample>
<dataEntry>http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$id</dataEntry>
<dataInfo>ProteomeXchange at Seattle</dataInfo>
<dataInstitution>Institute for Systems Biology, Seattle, WA, USA</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>mass spectrometry</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000514" pattern="^[A-Za-z]+$">
<name>SBML RDF Vocabulary</name>
<definition>Vocabulary used in the RDF representation of SBML models.</definition>
<uris>
<uri type="URN">urn:miriam:biomodels.vocabulary</uri>
<uri type="URL">http://identifiers.org/biomodels.vocabulary/</uri>
</uris>
<namespace>biomodels.vocabulary</namespace>
<documentations>
<documentation type="URL">https://github.com/sarala/ricordo-rdfconverter/wiki</documentation>
</documentations>
<resources>
<resource id="MIR:00100661" state="up" reliability="99">
<dataResource>http://biomodels.net/rdf/vocabulary.rdf</dataResource>
<dataEntityExample>rateRule</dataEntityExample>
<dataEntry>http://biomodels.net/rdf/vocabulary.rdf#$id</dataEntry>
<dataInfo>Vocabulary via BioModels.net</dataInfo>
<dataInstitution>BioModels.net</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000515" pattern="^P(X|R)D\d+{6}$">
<name>PRIDE Project</name>
<definition>The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects.</definition>
<uris>
<uri type="URN">urn:miriam:pride.project</uri>
<uri type="URL">http://identifiers.org/pride.project/</uri>
</uris>
<namespace>pride.project</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381953</documentation>
<documentation type="PMID">urn:miriam:pubmed:16041671</documentation>
<documentation type="PMID">urn:miriam:pubmed:18033805</documentation>
<documentation type="PMID">urn:miriam:pubmed:18428683</documentation>
</documentations>
<resources>
<resource id="MIR:00100662" state="up" reliability="98" primary="true">
<dataResource>http://www.ebi.ac.uk/pride/</dataResource>
<dataEntityExample>PXD000440</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/pride/archive/projects/$id</dataEntry>
<dataInfo>PRIDE Project at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100858" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>PXD000440</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/pride/$id</dataEntry>
<dataInfo>PRIDE Project through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000516" pattern="^\d+{6}$">
<name>Antibody Registry</name>
<definition>The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.</definition>
<uris>
<uri type="URN">urn:miriam:antibodyregistry</uri>
<uri type="URL">http://identifiers.org/antibodyregistry/</uri>
</uris>
<namespace>antibodyregistry</namespace>
<documentations>
<documentation type="URL">http://antibodyregistry.org/</documentation>
</documentations>
<resources>
<resource id="MIR:00100664" state="up" reliability="98">
<dataResource>http://antibodyregistry.org/</dataResource>
<dataEntityExample>493771</dataEntityExample>
<dataEntry>http://antibodyregistry.org/AB_$id</dataEntry>
<dataInfo>Antibody Registry at University of California</dataInfo>
<dataInstitution>Neuroscience Information Framework, University of California, San Diego, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>immunogenetics</tag>
<tag>registry</tag>
</tags>
</datatype>
<datatype id="MIR:00000517" pattern="^MAMO_\d{7}$">
<name>Mathematical Modelling Ontology</name>
<synonyms>
<synonym>MAMO</synonym>
</synonyms>
<definition>The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.</definition>
<uris>
<uri type="URN">urn:miriam:mamo</uri>
<uri type="URL">http://identifiers.org/mamo/</uri>
</uris>
<namespace>mamo</namespace>
<documentations>
<documentation type="URL">http://sourceforge.net/projects/mamo-ontology/</documentation>
</documentations>
<resources>
<resource id="MIR:00100665" state="probably up" reliability="96">
<dataResource>http://bioportal.bioontology.org/ontologies/MAMO</dataResource>
<dataEntityExample>MAMO_0000026</dataEntityExample>
<dataEntry>http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$id</dataEntry>
<dataInfo>MAMO through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100758" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/mamo</dataResource>
<dataEntityExample>MAMO_0000026</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/mamo/terms?short_form=$id</dataEntry>
<dataInfo>MaMO through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000518" pattern="^(P)?EO\:\d{7}$">
<name>Plant Environment Ontology</name>
<synonyms>
<synonym>Plant Environment Conditions</synonym>
</synonyms>
<definition>The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.</definition>
<uris>
<uri type="URN">urn:miriam:eo</uri>
<uri type="URL">http://identifiers.org/eo/</uri>
<uri type="URN" deprecated="true">urn:miriam:peo</uri>
</uris>
<namespace>eo</namespace>
<documentations>
<documentation type="URL">http://wiki.plantontology.org/index.php/Plant_Environment_Ontology_Wiki</documentation>
</documentations>
<resources>
<resource id="MIR:00100667" state="up" reliability="98">
<dataResource>http://archive.gramene.org/db/ontology/search_term?id=EO:0007359</dataResource>
<dataEntityExample>EO:0007404</dataEntityExample>
<dataEntry>http://archive.gramene.org/db/ontology/search?query=$id</dataEntry>
<dataInfo>Plant Environment Ontology through Gramene</dataInfo>
<dataInstitution>Cold Spring Harbor Laboratory, New York</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100668" state="down" reliability="86">
<dataResource>http://bioportal.bioontology.org/ontologies/PECO</dataResource>
<dataEntityExample>EO:0007404</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/PECO/$id</dataEntry>
<dataInfo>Plant Environment Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100669" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/eo</dataResource>
<dataEntityExample>EO:0007404</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/eo/terms?obo_id=$id</dataEntry>
<dataInfo>Plant Environment Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>controlled vocabulary</tag>
<tag>plant</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000519" pattern="^[A-Za-z]+$">
<name>Identifiers.org Terms</name>
<synonyms>
<synonym>IdoT</synonym>
</synonyms>
<definition>Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.</definition>
<uris>
<uri type="URN">urn:miriam:idot</uri>
<uri type="URL">http://identifiers.org/idot/</uri>
</uris>
<namespace>idot</namespace>
<documentations>
<documentation type="URL">http://biomodels.net/vocab/idot.rdf</documentation>
</documentations>
<resources>
<resource id="MIR:00100670" state="up" reliability="99">
<dataResource>http://identifiers.org/</dataResource>
<dataEntityExample>identifierPattern</dataEntityExample>
<dataEntry>http://biomodels.net/vocab/idot.rdf#$id</dataEntry>
<dataInfo>IdoT via biomodels.net</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000520" pattern="^[A-Z0-9-]+(#[A-Z0-9-]+)?$" restricted="true">
<name>HGNC Family</name>
<definition>The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides symbols for both structural and functional gene families. This collection refers to records using the HGNC family symbol.</definition>
<uris>
<uri type="URN">urn:miriam:hgnc.family</uri>
<uri type="URL">http://identifiers.org/hgnc.family/</uri>
</uris>
<namespace>hgnc.family</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17984084</documentation>
<documentation type="PMID">urn:miriam:pubmed:20929869</documentation>
<documentation type="PMID">urn:miriam:pubmed:23161694</documentation>
</documentations>
<resources>
<resource id="MIR:00100671" state="up" reliability="99">
<dataResource>http://www.genenames.org/</dataResource>
<dataEntityExample>PADI</dataEntityExample>
<dataEntry>http://www.genenames.org/genefamilies/$id</dataEntry>
<dataInfo>HGNC Family at HUGO Genome Nomenclature Committee</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="5" desc="Collection maintenance">
<statement>HGNC Family has been reimplemented using numerical identifiers, and is not directly related to this version. We suggest the use of the new version: http://identifiers.org/hgnc.genefamily/</statement>
<link desc="HGNC notice for new gene family information">http://www.genenames.org/newer-gene-family-resource-available</link>
</restriction>
</restrictions>
<tags>
<tag>classification</tag>
<tag>gene</tag>
<tag>human</tag>
<tag>schema.org</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000521" pattern="^[A-Z0-9]+$">
<name>Yeast Intron Database v4.3</name>
<definition>The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].</definition>
<uris>
<uri type="URN">urn:miriam:yeastintron</uri>
<uri type="URL">http://identifiers.org/yeastintron/</uri>
</uris>
<namespace>yeastintron</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:12073325</documentation>
</documentations>
<resources>
<resource id="MIR:00100673" state="up" reliability="99">
<dataResource>http://intron.ucsc.edu/yeast4.3/</dataResource>
<dataEntityExample>SNR17A</dataEntityExample>
<dataEntry>http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&amp;orfName=$id</dataEntry>
<dataInfo>Yeast Intron Database version 4.3 at Baskin School of Engineering</dataInfo>
<dataInstitution>Baskin School of Engineering, Center for Molecular Biology of RNA, University of California, Santa Cruz, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>eukaryotic</tag>
<tag>sequence</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000522" pattern="^[A-Z_]{3}[0-9]{4,}$">
<name>Antibiotic Resistance Genes Database</name>
<synonyms>
<synonym>ARDB</synonym>
</synonyms>
<definition>The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.</definition>
<uris>
<uri type="URN">urn:miriam:ardb</uri>
<uri type="URL">http://identifiers.org/ardb/</uri>
</uris>
<namespace>ardb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18832362</documentation>
</documentations>
<resources>
<resource id="MIR:00100678" state="up" reliability="98">
<dataResource>http://ardb.cbcb.umd.edu/</dataResource>
<dataEntityExample>CAE46076</dataEntityExample>
<dataEntry>http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&amp;field=ni&amp;term=$id</dataEntry>
<dataInfo>ARDB at University of Maryland</dataInfo>
<dataInstitution>Center for Bioinformatics and Computational Biology, University of Maryland, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>drug</tag>
<tag>gene</tag>
</tags>
</datatype>
<datatype id="MIR:00000523" pattern="^.+$" obsolete="true" replacement="">
<comment>Pathema is no longer supported and has been taken offline. See more at: http://www.jcvi.org/cms/research/past-projects/pathema/overview/</comment>
<name>Pathema</name>
<definition>The over-arching goal of Pathema is to provide a core resource that will accelerated scientific progress towards understanding, detection, diagnosis and treatment of diseases caused by six clades of Category A-C pathogens — Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica — involved in new and re-emerging infectious diseases. Pathema provides comprehensive curated datasets for the targeted pathogen clades, along with advanced bioinformatics capabilities geared specifically towards biodefense requirements, and the identification of potential targets for vaccine development, therapeutics and diagnostics.</definition>
<uris>
<uri type="URN">urn:miriam:pathema</uri>
<uri type="URL">http://identifiers.org/pathema/</uri>
</uris>
<namespace>pathema</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19843611</documentation>
</documentations>
<resources>
<resource id="MIR:00100679" obsolete="true">
<dataResource>http://pathema.jcvi.org/</dataResource>
<dataEntry>http://pathema.jcvi.org/$id</dataEntry>
<dataInfo></dataInfo>
<dataInstitution></dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000524" pattern="^\d+$">
<name>ProteomicsDB Protein</name>
<definition>ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.</definition>
<uris>
<uri type="URN">urn:miriam:proteomicsdb.protein</uri>
<uri type="URL">http://identifiers.org/proteomicsdb.protein/</uri>
</uris>
<namespace>proteomicsdb.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24870543</documentation>
</documentations>
<resources>
<resource id="MIR:00100680" state="probably up" reliability="97">
<dataResource>https://www.proteomicsdb.org/#human</dataResource>
<dataEntityExample>53504</dataEntityExample>
<dataEntry>https://www.proteomicsdb.org/#human/proteinDetails/$id/summary</dataEntry>
<dataInfo>Proteomics DB Protein at Center for Integrated Protein Science</dataInfo>
<dataInstitution>Center for Integrated Protein Science, Munich,</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000525" pattern="^\d+$">
<name>ProteomicsDB Peptide</name>
<definition>ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.</definition>
<uris>
<uri type="URN">urn:miriam:proteomicsdb.peptide</uri>
<uri type="URL">http://identifiers.org/proteomicsdb.peptide/</uri>
</uris>
<namespace>proteomicsdb.peptide</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24870543</documentation>
</documentations>
<resources>
<resource id="MIR:00100681" state="probably up" reliability="97">
<dataResource>https://www.proteomicsdb.org/#peptideSearch</dataResource>
<dataEntityExample>53504</dataEntityExample>
<dataEntry>https://www.proteomicsdb.org/#human/proteinDetails/$id/peptides/</dataEntry>
<dataInfo>Proteomics DB Peptide at Center for Integrated Protein Science</dataInfo>
<dataInstitution>Center for Integrated Protein Science, Munich</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000526" pattern="^\d+$">
<name>Human Proteome Map Protein</name>
<synonyms>
<synonym>HPM</synonym>
</synonyms>
<definition>The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.</definition>
<uris>
<uri type="URN">urn:miriam:hpm.protein</uri>
<uri type="URL">http://identifiers.org/hpm.protein/</uri>
</uris>
<namespace>hpm.protein</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24870542</documentation>
</documentations>
<resources>
<resource id="MIR:00100682" state="up" reliability="95">
<dataResource>http://www.humanproteomemap.org/index.php</dataResource>
<dataEntityExample>1968</dataEntityExample>
<dataEntry>http://www.humanproteomemap.org/protein.php?hpm_id=$id</dataEntry>
<dataInfo>Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)</dataInfo>
<dataInstitution>Institute of Bioinformatics, International Tech Park, Bangalore</dataInstitution>
<dataLocation>India</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000527" pattern="^\d+$">
<name>Human Proteome Map Peptide</name>
<definition>The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.</definition>
<uris>
<uri type="URN">urn:miriam:hpm.peptide</uri>
<uri type="URL">http://identifiers.org/hpm.peptide/</uri>
</uris>
<namespace>hpm.peptide</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24870542</documentation>
</documentations>
<resources>
<resource id="MIR:00100683" state="up" reliability="97">
<dataResource>http://www.humanproteomemap.org/index.php</dataResource>
<dataEntityExample>9606117</dataEntityExample>
<dataEntry>http://www.humanproteomemap.org/spectrum.php?pep_id=$id</dataEntry>
<dataInfo>Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore)</dataInfo>
<dataInstitution>Institute of Bioinformatics, International Tech Park, Bangalore</dataInstitution>
<dataLocation>India</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000528" pattern="^BE\d{7}$">
<name>DrugBank Target v4</name>
<definition>The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.</definition>
<uris>
<uri type="URN">urn:miriam:drugbankv4.target</uri>
<uri type="URL">http://identifiers.org/drugbankv4.target/</uri>
</uris>
<namespace>drugbankv4.target</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24203711</documentation>
</documentations>
<resources>
<resource id="MIR:00100687" state="up" reliability="99">
<dataResource>http://www.drugbank.ca/targets</dataResource>
<dataEntityExample>BE0000048</dataEntityExample>
<dataEntry>http://www.drugbank.ca/biodb/bio_entities/$id</dataEntry>
<dataInfo>DrugBank Target information version 4</dataInfo>
<dataInstitution>Departments of Computing Science, Biological Sciences, University of Alberta</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000529" pattern="^(ZINC)?\d+$">
<name>ZINC</name>
<definition>ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.</definition>
<uris>
<uri type="URN">urn:miriam:zinc</uri>
<uri type="URL">http://identifiers.org/zinc/</uri>
</uris>
<namespace>zinc</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22587354</documentation>
<documentation type="URL">http://wiki.bkslab.org/index.php/ZINC_Database</documentation>
</documentations>
<resources>
<resource id="MIR:00100688" state="up" reliability="99" primary="true">
<dataResource>http://zinc15.docking.org/</dataResource>
<dataEntityExample>ZINC1084</dataEntityExample>
<dataEntry>http://zinc15.docking.org/substances/$id</dataEntry>
<dataInfo>ZINC at University of California (San Francisco)</dataInfo>
<dataInstitution>Shoichet Laboratory, Department of Pharmaceutical Chemistry, University of California, San Francisco</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000530" pattern="^FDB\d+$">
<name>FooDB Compound</name>
<definition>FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.</definition>
<uris>
<uri type="URN">urn:miriam:foodb.compound</uri>
<uri type="URL">http://identifiers.org/foodb.compound/</uri>
</uris>
<namespace>foodb.compound</namespace>
<documentations>
<documentation type="URL">http://foodb.ca/about</documentation>
</documentations>
<resources>
<resource id="MIR:00100689" state="up" reliability="95">
<dataResource>http://foodb.ca/foods</dataResource>
<dataEntityExample>FDB002100</dataEntityExample>
<dataEntry>http://foodb.ca/compounds/$id</dataEntry>
<dataInfo>FooDB database of food additives at University of Alberta</dataInfo>
<dataInstitution>University of Alberta, Edmonton, AB</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>structure</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000531" pattern="^[A-Z0-9]+$">
<name>UNII</name>
<synonyms>
<synonym>Substance Registration System</synonym>
<synonym>Unique ingredient identifier</synonym>
</synonyms>
<definition>The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.</definition>
<uris>
<uri type="URN">urn:miriam:unii</uri>
<uri type="URL">http://identifiers.org/unii/</uri>
</uris>
<namespace>unii</namespace>
<documentations>
<documentation type="URL">http://www.fda.gov/ForIndustry/DataStandards/SubstanceRegistrationSystem-UniqueIngredientIdentifierUNII/default.htm</documentation>
</documentations>
<resources>
<resource id="MIR:00100690" state="probably up" reliability="91">
<dataResource>http://fdasis.nlm.nih.gov/srs/</dataResource>
<dataEntityExample>3G6A5W338E</dataEntityExample>
<dataEntry>http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$id</dataEntry>
<dataInfo>UNII at U.S. Food and Drug Administration</dataInfo>
<dataInstitution>U.S. Food and Drug Administration, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>drug</tag>
</tags>
<annotation>
<format name="SBML">
<elements>
<element>species</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000532" pattern="^Orphanet(_|:)C?\d+$">
<name>Orphanet Rare Disease Ontology</name>
<synonyms>
<synonym>ORDO</synonym>
</synonyms>
<definition>The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.
It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).</definition>
<uris>
<uri type="URN">urn:miriam:orphanet.ordo</uri>
<uri type="URL">http://identifiers.org/orphanet.ordo/</uri>
<uri type="URL" deprecated="true">http://www.orpha.net/ORDO/</uri>
</uris>
<namespace>orphanet.ordo</namespace>
<documentations>
<documentation type="URL">http://www.orphadata.org/cgi-bin/inc/ordo_orphanet.inc.php</documentation>
</documentations>
<resources>
<resource id="MIR:00100705" state="up" reliability="99" primary="true">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/ordo</dataResource>
<dataEntityExample>Orphanet_C023</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form=$id</dataEntry>
<dataInfo>ORDO via OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
<tag>ontology</tag>
</tags>
</datatype>
<datatype id="MIR:00000533" pattern="^PAR:\d+$">
<name>Protein Affinity Reagents</name>
<synonyms>
<synonym>PSI-PAR</synonym>
</synonyms>
<definition>Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.</definition>
<uris>
<uri type="URN">urn:miriam:psipar</uri>
<uri type="URL">http://identifiers.org/psipar/</uri>
</uris>
<namespace>psipar</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:19674966</documentation>
</documentations>
<resources>
<resource id="MIR:00100709" state="down" reliability="50">
<dataResource>https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR</dataResource>
<dataEntityExample>PAR:0116</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>Protein Affinity Reagents through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000534" pattern="^RCV\d+(\.\d+)?$">
<name>ClinVar Record</name>
<definition>ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.</definition>
<uris>
<uri type="URN">urn:miriam:clinvar.record</uri>
<uri type="URL">http://identifiers.org/clinvar.record/</uri>
</uris>
<namespace>clinvar.record</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkt1113</documentation>
</documentations>
<resources>
<resource id="MIR:00100710" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/clinvar/</dataResource>
<dataEntityExample>RCV000033555.3</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/clinvar/$id/</dataEntry>
<dataInfo>ClinVar Record at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI), NIH, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000535" pattern="^[A-Z]+[0-9]+$">
<name>EBI Metagenomics Project</name>
<definition>The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references projects.</definition>
<uris>
<uri type="URN">urn:miriam:ebimetagenomics.proj</uri>
<uri type="URL">http://identifiers.org/ebimetagenomics.proj/</uri>
</uris>
<namespace>ebimetagenomics.proj</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkt961</documentation>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkt961</documentation>
</documentations>
<resources>
<resource id="MIR:00100711" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/metagenomics</dataResource>
<dataEntityExample>ERP004492</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/metagenomics/projects/$id</dataEntry>
<dataInfo>EBI metagenomics projects at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
</tags>
</datatype>
<datatype id="MIR:00000536" pattern="^\d{4}\-\d{6}\-\d{2}$">
<name>EU Clinical Trials</name>
<synonyms>
<synonym>EU Clinical Trials Register</synonym>
</synonyms>
<definition>The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.
It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.</definition>
<uris>
<uri type="URN">urn:miriam:euclinicaltrials</uri>
<uri type="URL">http://identifiers.org/euclinicaltrials/</uri>
</uris>
<namespace>euclinicaltrials</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkt961</documentation>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkt961</documentation>
<documentation type="URL">https://www.clinicaltrialsregister.eu/about.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100712" state="up" reliability="99">
<dataResource>https://www.clinicaltrialsregister.eu/</dataResource>
<dataEntityExample>2008-005144-16</dataEntityExample>
<dataEntry>https://www.clinicaltrialsregister.eu/ctr-search/search?query=$id</dataEntry>
<dataInfo>EU Clinical Trials at European Medicines Agency</dataInfo>
<dataInstitution>European Medicines Agency, London</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
<tag>disorder</tag>
<tag>human</tag>
<tag>pharmacogenomics</tag>
</tags>
</datatype>
<datatype id="MIR:00000537" pattern="^[A-Z]{2}\d+([A-Z])?$">
<name>Google Patents</name>
<definition>Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.</definition>
<uris>
<uri type="URN">urn:miriam:google.patent</uri>
<uri type="URL">http://identifiers.org/google.patent/</uri>
</uris>
<namespace>google.patent</namespace>
<documentations>
<documentation type="URL">https://support.google.com/faqs/answer/2539193?hl=en</documentation>
</documentations>
<resources>
<resource id="MIR:00100714" state="up" reliability="100">
<dataResource>https://www.google.com/patents/</dataResource>
<dataEntityExample>US4145692</dataEntityExample>
<dataEntry>https://www.google.com/patents/$id</dataEntry>
<dataInfo>Google Patents at Google</dataInfo>
<dataInstitution>Google Incorporated</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<tags>
<tag>registry</tag>
</tags>
</datatype>
<datatype id="MIR:00000538" pattern="^(D|PP|R|T|H|X|AI)?\d+$">
<name>USPTO</name>
<synonyms>
<synonym>United States Patent and Trademark Office</synonym>
</synonyms>
<definition>The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.</definition>
<uris>
<uri type="URN">urn:miriam:uspto</uri>
<uri type="URL">http://identifiers.org/uspto/</uri>
</uris>
<namespace>uspto</namespace>
<documentations>
<documentation type="URL">http://patft.uspto.gov/netahtml/PTO/help/helpfaq.htm</documentation>
</documentations>
<resources>
<resource id="MIR:00100715" state="up" reliability="99">
<dataResource>http://patft.uspto.gov/netahtml/PTO/index.html</dataResource>
<dataEntityExample>4145692</dataEntityExample>
<dataEntry>http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$id</dataEntry>
<dataInfo>USPTO patents at USPTO</dataInfo>
<dataInstitution>United States Patent and Trademark Office</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>registry</tag>
</tags>
</datatype>
<datatype id="MIR:00000539" pattern="^([A-H,Y]|[A-H, Y]\d+{2}|[A-H, Y]\d+{2}[A-Z]|[A-H, Y]\d+{2}[A-Z]\d+{1,3}|[A-H, Y]\d+{2}[A-Z]\d+{1,3}(\/)?\d+{2,})$">
<name>Cooperative Patent Classification</name>
<synonyms>
<synonym>CPC</synonym>
</synonyms>
<definition>The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.</definition>
<uris>
<uri type="URN">urn:miriam:cpc</uri>
<uri type="URL">http://identifiers.org/cpc/</uri>
</uris>
<namespace>cpc</namespace>
<documentations>
<documentation type="URL">http://worldwide.espacenet.com/help?quickHelpPage=classificationsearchCPC.1&amp;locale=en_EP&amp;method=handleQuickHelp</documentation>
</documentations>
<resources>
<resource id="MIR:00100716" state="probably up" reliability="99">
<dataResource>http://worldwide.espacenet.com/classification</dataResource>
<dataEntityExample>A01M1/026</dataEntityExample>
<dataEntry>http://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$id</dataEntry>
<dataInfo>Cooperative Patent Classification at Espace</dataInfo>
<dataInstitution>Espace, European Patent Office</dataInstitution>
<dataLocation></dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
</tags>
</datatype>
<datatype id="MIR:00000540" pattern="^HGVST\d+$">
<name>GWAS Central Study</name>
<definition>GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.</definition>
<uris>
<uri type="URN">urn:miriam:gwascentral.study</uri>
<uri type="URL">http://identifiers.org/gwascentral.study/</uri>
</uris>
<namespace>gwascentral.study</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24301061</documentation>
</documentations>
<resources>
<resource id="MIR:00100717" state="down" reliability="95">
<dataResource>http://www.gwascentral.org/studies</dataResource>
<dataEntityExample>HGVST1828</dataEntityExample>
<dataEntry>http://www.gwascentral.org/study/$id</dataEntry>
<dataInfo>GWAS Central Study at University of Leicester</dataInfo>
<dataInstitution>Department of Genetics, University of Leicester, Leicester</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000541" pattern="^\d{1,2}\-\d+\-[GATC]\-[GATC]$">
<name>ExAC Variant</name>
<definition>The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.</definition>
<uris>
<uri type="URN">urn:miriam:exac.variant</uri>
<uri type="URL">http://identifiers.org/exac.variant/</uri>
</uris>
<namespace>exac.variant</namespace>
<documentations>
<documentation type="URL">http://exac.broadinstitute.org/faq</documentation>
</documentations>
<resources>
<resource id="MIR:00100718" state="up" reliability="99">
<dataResource>http://exac.broadinstitute.org/</dataResource>
<dataEntityExample>22-46615880-T-C</dataEntityExample>
<dataEntry>http://exac.broadinstitute.org/variant/$id</dataEntry>
<dataInfo>ExAC Variant at Exome Aggregation Consortium</dataInfo>
<dataInstitution>Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000542" pattern="^HGVM\d+$">
<name>GWAS Central Marker</name>
<definition>GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.</definition>
<uris>
<uri type="URN">urn:miriam:gwascentral.marker</uri>
<uri type="URL">http://identifiers.org/gwascentral.marker/</uri>
</uris>
<namespace>gwascentral.marker</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24301061</documentation>
</documentations>
<resources>
<resource id="MIR:00100719" state="down" reliability="95">
<dataResource>http://www.gwascentral.org/markers/</dataResource>
<dataEntityExample>HGVM15354</dataEntityExample>
<dataEntry>http://www.gwascentral.org/marker/$id</dataEntry>
<dataInfo>GWAS Central Marker at University of Leicester</dataInfo>
<dataInstitution>Department of Genetics, University of Leicester, Leicester</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000543" pattern="^HGVP\d+$">
<name>GWAS Central Phenotype</name>
<definition>GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype.</definition>
<uris>
<uri type="URN">urn:miriam:gwascentral.phenotype</uri>
<uri type="URL">http://identifiers.org/gwascentral.phenotype/</uri>
</uris>
<namespace>gwascentral.phenotype</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24301061</documentation>
</documentations>
<resources>
<resource id="MIR:00100720" state="down" reliability="95">
<dataResource>http://www.gwascentral.org/phenotypes</dataResource>
<dataEntityExample>HGVPM623</dataEntityExample>
<dataEntry>http://www.gwascentral.org/phenotype/$id</dataEntry>
<dataInfo>GWAS Central Phenotype at University of Leicester</dataInfo>
<dataInstitution>Department of Genetics, University of Leicester, Leicester</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000544" pattern="(^LCL-\d+{4}$)|(^LDC-\d+{4}$)|(^ES-\d+{4}$)|(^LSC-\d+{4}$)|(^LPC-\d+{4}$)">
<name>LINCS Cell</name>
<definition>The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.</definition>
<uris>
<uri type="URN">urn:miriam:lincs.cell</uri>
<uri type="URL">http://identifiers.org/lincs.cell/</uri>
</uris>
<namespace>lincs.cell</namespace>
<documentations>
<documentation type="URL">http://www.lincsproject.org/LINCS/data/standards</documentation>
<documentation type="URL">http://bd2k-lincs.org/#/</documentation>
<documentation type="URL">https://biosharing.org/bsg-s000651</documentation>
</documentations>
<resources>
<resource id="MIR:00100721" state="probably up" reliability="99">
<dataResource>http://lincsportal.ccs.miami.edu/cells/</dataResource>
<dataEntityExample>LCL-2085</dataEntityExample>
<dataEntry>http://lincsportal.ccs.miami.edu/cells/#/view/$id</dataEntry>
<dataInfo>LINCS Portal</dataInfo>
<dataInstitution>University of Miami, BD2K-LINCS DCIC</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
</tags>
</datatype>
<datatype id="MIR:00000545" pattern="^\d+$">
<name>LINCS Protein</name>
<definition>The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.</definition>
<uris>
<uri type="URN">urn:miriam:lincs.protein</uri>
<uri type="URL">http://identifiers.org/lincs.protein/</uri>
</uris>
<namespace>lincs.protein</namespace>
<documentations>
<documentation type="URL">http://lincs.hms.harvard.edu/resources/tutorials-presentations/</documentation>
</documentations>
<resources>
<resource id="MIR:00100722" state="up" reliability="100">
<dataResource>http://lincs.hms.harvard.edu/db/proteins/</dataResource>
<dataEntityExample>200282</dataEntityExample>
<dataEntry>http://lincs.hms.harvard.edu/db/proteins/$id/</dataEntry>
<dataInfo>LINCS Protein at Harvard Medical School</dataInfo>
<dataInstitution>Harvard Medical School, Boston, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
</tags>
</datatype>
<datatype id="MIR:00000546" pattern="^LSM-\d+{4}$">
<name>LINCS Small Molecule</name>
<definition>The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).</definition>
<uris>
<uri type="URN">urn:miriam:lincs.smallmolecule</uri>
<uri type="URL">http://identifiers.org/lincs.smallmolecule/</uri>
<uri type="URN" deprecated="true">urn:miriam:lincs.molecule</uri>
</uris>
<namespace>lincs.smallmolecule</namespace>
<documentations>
<documentation type="URL">http://www.lincsproject.org/LINCS/data/standards</documentation>
<documentation type="URL">http://bd2k-lincs.org/#/</documentation>
<documentation type="URL">https://biosharing.org/bsg-s000655</documentation>
</documentations>
<resources>
<resource id="MIR:00100723" state="probably up" reliability="99">
<dataResource>http://lincsportal.ccs.miami.edu/SmallMolecules/</dataResource>
<dataEntityExample>LSM-6306</dataEntityExample>
<dataEntry>http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$id</dataEntry>
<dataInfo>LINCS Portal</dataInfo>
<dataInstitution>University of Miami, BD2K-LINCS DCIC, USA</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
</tags>
</datatype>
<datatype id="MIR:00000547" pattern="^ENST\d{11}$">
<name>ExAC Transcript</name>
<definition>The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.</definition>
<uris>
<uri type="URN">urn:miriam:exac.transcript</uri>
<uri type="URL">http://identifiers.org/exac.transcript/</uri>
</uris>
<namespace>exac.transcript</namespace>
<documentations>
<documentation type="URL">http://exac.broadinstitute.org/faq</documentation>
</documentations>
<resources>
<resource id="MIR:00100724" state="up" reliability="99">
<dataResource>http://exac.broadinstitute.org/</dataResource>
<dataEntityExample>ENST00000407236</dataEntityExample>
<dataEntry>http://exac.broadinstitute.org/transcript/$id</dataEntry>
<dataInfo>ExAC Transcript at Exome Aggregation Consortium</dataInfo>
<dataInstitution>Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000548" pattern="^ENSG\d{11}$">
<name>ExAC Gene</name>
<definition>The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.</definition>
<uris>
<uri type="URN">urn:miriam:exac.gene</uri>
<uri type="URL">http://identifiers.org/exac.gene/</uri>
</uris>
<namespace>exac.gene</namespace>
<documentations>
<documentation type="URL">http://exac.broadinstitute.org/faq</documentation>
</documentations>
<resources>
<resource id="MIR:00100725" state="up" reliability="99">
<dataResource>http://exac.broadinstitute.org/</dataResource>
<dataEntityExample>ENSG00000169174</dataEntityExample>
<dataEntry>http://exac.broadinstitute.org/gene/$id</dataEntry>
<dataInfo>ExAC Gene at Exome Aggregation Consortium</dataInfo>
<dataInstitution>Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000549" pattern="^Q\d+$">
<name>Wikidata</name>
<definition>Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.</definition>
<uris>
<uri type="URN">urn:miriam:wikidata</uri>
<uri type="URL">http://identifiers.org/wikidata/</uri>
</uris>
<namespace>wikidata</namespace>
<documentations>
<documentation type="URL">https://www.wikidata.org/wiki/Help:Contents</documentation>
</documentations>
<resources>
<resource id="MIR:00100726" state="up" reliability="81">
<dataResource>https://www.wikidata.org/</dataResource>
<dataEntityExample>Q2207226</dataEntityExample>
<dataEntry>https://www.wikidata.org/wiki/$id</dataEntry>
<dataInfo>Wikidata at Wikimedia Foundation</dataInfo>
<dataInstitution>Wikimedia Foundation, San Francisco, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>encyclopedia</tag>
</tags>
</datatype>
<datatype id="MIR:00000550" pattern="^SLM:\d+$">
<name>SwissLipids</name>
<definition>SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.</definition>
<uris>
<uri type="URN">urn:miriam:swisslipid</uri>
<uri type="URL">http://identifiers.org/swisslipid/</uri>
</uris>
<namespace>swisslipid</namespace>
<documentations>
<documentation type="URL">http://www.swisslipids.org/#/about</documentation>
</documentations>
<resources>
<resource id="MIR:00100727" state="probably up" reliability="100">
<dataResource>http://www.swisslipids.org/#/</dataResource>
<dataEntityExample>SLM:000048885</dataEntityExample>
<dataEntry>http://www.swisslipids.org/#/entity/$id/</dataEntry>
<dataInfo>SwissLipids at Swiss Institute of Bioinformatics</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics, Basel</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>lipid</tag>
<tag>metabolite</tag>
</tags>
</datatype>
<datatype id="MIR:00000551" pattern="^UPC\d{5}$" restricted="true">
<name>UniPathway Compound</name>
<definition>UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds.</definition>
<uris>
<uri type="URN">urn:miriam:unipathway.compound</uri>
<uri type="URL">http://identifiers.org/unipathway.compound/</uri>
</uris>
<namespace>unipathway.compound</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22102589</documentation>
</documentations>
<resources>
<resource id="MIR:00100728" state="down" reliability="30">
<dataResource>http://www.grenoble.prabi.fr/obiwarehouse/unipathway</dataResource>
<dataEntityExample>UPC04349</dataEntityExample>
<dataEntry>http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$id</dataEntry>
<dataInfo>UniPathway Compound at Swiss Institute of Bioinformatics (SIB)</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics (SIB) and French National Institute for Research in Computer Science and Control</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="6" desc="Collection subset">
<statement>This collection re-uses a modified version of the identifiers associated with KEGG Compound.</statement>
<link desc="Associated data collection">http://identifiers.org/kegg.compound/</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
<tag>metabolite</tag>
<tag>structure</tag>
</tags>
</datatype>
<datatype id="MIR:00000552" pattern="^\w+$">
<name>SEED Subsystem</name>
<definition>This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.</definition>
<uris>
<uri type="URN">urn:miriam:seed</uri>
<uri type="URL">http://identifiers.org/seed/</uri>
</uris>
<namespace>seed</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16214803</documentation>
</documentations>
<resources>
<resource id="MIR:00100729" state="down" reliability="33">
<dataResource>http://seed-viewer.theseed.org/seedviewer.cgi</dataResource>
<dataEntityExample>Biotin_biosynthesis</dataEntityExample>
<dataEntry>http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$id</dataEntry>
<dataInfo>SEED Subsystem at Argonne National Laboratory</dataInfo>
<dataInstitution>Argonne National Laboratory, University of Chicago, Argonne, Illinois</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>pathway</tag>
</tags>
</datatype>
<datatype id="MIR:00000553" pattern="^cpd\d+$">
<name>SEED Compound</name>
<definition>This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.</definition>
<uris>
<uri type="URN">urn:miriam:seed.compound</uri>
<uri type="URL">http://identifiers.org/seed.compound/</uri>
</uris>
<namespace>seed.compound</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16214803</documentation>
</documentations>
<resources>
<resource id="MIR:00100730" state="probably up" reliability="72">
<dataResource>http://modelseed.org/</dataResource>
<dataEntityExample>cpd15380</dataEntityExample>
<dataEntry>http://modelseed.org/biochem/compounds/$id</dataEntry>
<dataInfo>SEED Compound at Argonne National Laboratory</dataInfo>
<dataInstitution>Argonne National Laboratory, University of Chicago, Argonne, Illinois</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>metabolite</tag>
<tag>structure</tag>
</tags>
</datatype>
<datatype id="MIR:00000554" pattern="^[a-z_A-Z0-9]+$" restricted="true">
<name>BiGG Model</name>
<definition>BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.</definition>
<uris>
<uri type="URN">urn:miriam:bigg.model</uri>
<uri type="URL">http://identifiers.org/bigg.model/</uri>
</uris>
<namespace>bigg.model</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20426874</documentation>
</documentations>
<resources>
<resource id="MIR:00100731" state="up" reliability="99">
<dataResource>http://bigg.ucsd.edu/models</dataResource>
<dataEntityExample>iECABU_c1320</dataEntityExample>
<dataEntry>http://bigg.ucsd.edu/models/$id</dataEntry>
<dataInfo>BiGG Model at University of California</dataInfo>
<dataInstitution>Systems Biology Research Group at the University of California, San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The data may be used freely for research purposes only.</statement>
<link desc="license statement">http://bigg.ucsd.edu/#</link>
</restriction>
</restrictions>
<tags>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000555" pattern="^[a-z_A-Z]+$" restricted="true">
<name>BiGG Compartment</name>
<definition>BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments.</definition>
<uris>
<uri type="URN">urn:miriam:bigg.compartment</uri>
<uri type="URL">http://identifiers.org/bigg.compartment/</uri>
</uris>
<namespace>bigg.compartment</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20426874</documentation>
</documentations>
<resources>
<resource id="MIR:00100732" state="up" reliability="99">
<dataResource>http://bigg.ucsd.edu/compartments/</dataResource>
<dataEntityExample>c</dataEntityExample>
<dataEntry>http://bigg.ucsd.edu/compartments/$id</dataEntry>
<dataInfo>BiGG Compartment at University of California</dataInfo>
<dataInstitution>Systems Biology Research Group at the University of California, San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The data may be used freely for research purposes only.</statement>
<link desc="license statement">http://bigg.ucsd.edu/#</link>
</restriction>
</restrictions>
<tags>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000556" pattern="^[a-z_A-Z0-9]+$" restricted="true">
<name>BiGG Metabolite</name>
<definition>BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes.</definition>
<uris>
<uri type="URN">urn:miriam:bigg.metabolite</uri>
<uri type="URL">http://identifiers.org/bigg.metabolite/</uri>
</uris>
<namespace>bigg.metabolite</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20426874</documentation>
</documentations>
<resources>
<resource id="MIR:00100733" state="up" reliability="99">
<dataResource>http://bigg.ucsd.edu/universal/metabolites</dataResource>
<dataEntityExample>12dgr161</dataEntityExample>
<dataEntry>http://bigg.ucsd.edu/models/universal/metabolites/$id</dataEntry>
<dataInfo>BiGG Metabolite at University of Cakifornia</dataInfo>
<dataInstitution>Systems Biology Research Group at the University of California, San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The data may be used freely for research purposes only.</statement>
<link desc="license statement">http://bigg.ucsd.edu/#</link>
</restriction>
</restrictions>
<tags>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000557" pattern="^[a-z_A-Z0-9]+$" restricted="true">
<name>BiGG Reaction</name>
<definition>BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.</definition>
<uris>
<uri type="URN">urn:miriam:bigg.reaction</uri>
<uri type="URL">http://identifiers.org/bigg.reaction/</uri>
</uris>
<namespace>bigg.reaction</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20426874</documentation>
</documentations>
<resources>
<resource id="MIR:00100734" state="up" reliability="91">
<dataResource>http://bigg.ucsd.edu/universal/reactions</dataResource>
<dataEntityExample>13GS</dataEntityExample>
<dataEntry>http://bigg.ucsd.edu/models/universal/reactions/$id</dataEntry>
<dataInfo>BiGG Reaction at University of California</dataInfo>
<dataInstitution>Systems Biology Research Group at the University of California, San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="1" desc="License restriction">
<statement>The data may be used freely for research purposes only.</statement>
<link desc="license statement">http://bigg.ucsd.edu/#</link>
</restriction>
</restrictions>
<tags>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000558" pattern="^RRID:[A-Z_a-z-0-9]+$">
<name>RRID</name>
<synonyms>
<synonym>Research Resource IDentifier</synonym>
</synonyms>
<definition>The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.
The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.</definition>
<uris>
<uri type="URN">urn:miriam:rrid</uri>
<uri type="URL">http://identifiers.org/rrid/</uri>
</uris>
<namespace>rrid</namespace>
<documentations>
<documentation type="URL">https://scicrunch.org/page/scicrunch</documentation>
</documentations>
<resources>
<resource id="MIR:00100735" state="up" reliability="74">
<dataResource>https://scicrunch.org/resolver</dataResource>
<dataEntityExample>RRID:AB_262044</dataEntityExample>
<dataEntry>https://scicrunch.org/resolver/$id</dataEntry>
<dataInfo>RRID at SciCrunch</dataInfo>
<dataInstitution>University of California, San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>registry</tag>
</tags>
</datatype>
<datatype id="MIR:00000559" pattern="^C\d+$" restricted="true">
<name>UMLS</name>
<synonyms>
<synonym>Unified Medical Language System</synonym>
</synonyms>
<definition>The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.</definition>
<uris>
<uri type="URN">urn:miriam:umls</uri>
<uri type="URL">http://identifiers.org/umls/</uri>
</uris>
<namespace>umls</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681409</documentation>
<documentation type="URL">http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=nlmumls</documentation>
</documentations>
<resources>
<resource id="MIR:00100736" state="restricted access" reliability="0" primary="true">
<dataResource>http://linkedlifedata.com/</dataResource>
<dataEntityExample>C0021390</dataEntityExample>
<dataEntry>http://linkedlifedata.com/resource/umls/id/$id</dataEntry>
<dataInfo>Unified Medical Language System at LinkedLifeData</dataInfo>
<dataInstitution>Linkedlifedata, Ontotext, Sofia</dataInstitution>
<dataLocation>Bulgaria</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="3" desc="Access restriction">
<statement>While data is free to use in many circumstances under terms and conditions presented, these must be agreed to in the process of account creation.</statement>
<link desc="account creation">http://www.nlm.nih.gov/databases/umls.html</link>
</restriction>
</restrictions>
<tags>
<tag>controlled vocabulary</tag>
</tags>
</datatype>
<datatype id="MIR:00000560" pattern="^(C|D)\d{6}$">
<name>MeSH</name>
<synonyms>
<synonym>Medical Subject Headings</synonym>
</synonyms>
<definition>MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.</definition>
<uris>
<uri type="URN">urn:miriam:mesh</uri>
<uri type="URL">http://identifiers.org/mesh/</uri>
</uris>
<namespace>mesh</namespace>
<documentations>
<documentation type="URL">http://www.nlm.nih.gov/pubs/factsheets/mesh.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100737" state="probably up" reliability="91">
<dataResource>http://id.nlm.nih.gov/mesh/</dataResource>
<dataEntityExample>C000100</dataEntityExample>
<dataEntry>http://id.nlm.nih.gov/mesh/$id</dataEntry>
<dataInfo>MeSH Linked Data at National Library of Medicine</dataInfo>
<dataInstitution>U.S. National Library of Medicine, National Institute of Health, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000561" pattern="^EMD-\d{4}$">
<name>Electron Microscopy Data Bank</name>
<synonyms>
<synonym>EMDB</synonym>
</synonyms>
<definition>The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community.</definition>
<uris>
<uri type="URN">urn:miriam:emdb</uri>
<uri type="URL">http://identifiers.org/emdb/</uri>
</uris>
<namespace>emdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20935055</documentation>
</documentations>
<resources>
<resource id="MIR:00100738" state="up" reliability="98">
<dataResource>http://www.ebi.ac.uk/pdbe/emdb/</dataResource>
<dataEntityExample>EMD-1001</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/pdbe/entry/emdb/$id</dataEntry>
<dataInfo>EMDB at Protein Data Bank in Europe</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>mass spectrometry</tag>
</tags>
</datatype>
<datatype id="MIR:00000562" pattern="^MIRT\d{6}$">
<name>miRTarBase</name>
<definition>miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.</definition>
<uris>
<uri type="URN">urn:miriam:mirtarbase</uri>
<uri type="URL">http://identifiers.org/mirtarbase/</uri>
</uris>
<namespace>mirtarbase</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:26590260</documentation>
</documentations>
<resources>
<resource id="MIR:00100739" state="up" reliability="99">
<dataResource>http://mirtarbase.mbc.nctu.edu.tw/</dataResource>
<dataEntityExample>MIRT000002</dataEntityExample>
<dataEntry>http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$id</dataEntry>
<dataInfo>miRTarBase at National Chiao Tung University</dataInfo>
<dataInstitution>Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu</dataInstitution>
<dataLocation>Taiwan</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>nucleotide</tag>
</tags>
</datatype>
<datatype id="MIR:00000563" pattern="^\d+$">
<name>MedDRA</name>
<synonyms>
<synonym>Medical Dictionary for Regulatory Activities</synonym>
</synonyms>
<definition>The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).</definition>
<uris>
<uri type="URN">urn:miriam:meddra</uri>
<uri type="URL">http://identifiers.org/meddra/</uri>
</uris>
<namespace>meddra</namespace>
<documentations>
<documentation type="URL">http://www.meddra.org/basics</documentation>
</documentations>
<resources>
<resource id="MIR:00100740" state="up" reliability="97">
<dataResource>http://bioportal.bioontology.org/ontologies/MEDDRA</dataResource>
<dataEntityExample>10015919</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/MEDDRA/$id</dataEntry>
<dataInfo>MedDRA through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>controlled vocabulary</tag>
<tag>ontology</tag>
</tags>
</datatype>
<datatype id="MIR:00000564" pattern="^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$">
<name>DASHR</name>
<synonyms>
<synonym>Database of small human noncoding RNAs</synonym>
</synonyms>
<definition>DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.</definition>
<uris>
<uri type="URN">urn:miriam:dashr</uri>
<uri type="URL">http://identifiers.org/dashr/</uri>
</uris>
<namespace>dashr</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:26553799</documentation>
</documentations>
<resources>
<resource id="MIR:00100741" state="up" reliability="99">
<dataResource>http://lisanwanglab.org/DASHR/</dataResource>
<dataEntityExample>hsa-mir-200a</dataEntityExample>
<dataEntry>http://lisanwanglab.org/DASHR/entry/$id</dataEntry>
<dataInfo>DASHR at University of Pennsylvania</dataInfo>
<dataInstitution>Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
</datatype>
<datatype id="MIR:00000565" pattern="^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$">
<name>DASHR expression</name>
<definition>DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.</definition>
<uris>
<uri type="URN">urn:miriam:dashr.expression</uri>
<uri type="URL">http://identifiers.org/dashr.expression/</uri>
</uris>
<namespace>dashr.expression</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:26553799</documentation>
</documentations>
<resources>
<resource id="MIR:00100742" state="up" reliability="99">
<dataResource>http://lisanwanglab.org/DASHR/show-expression-table.php?start=0</dataResource>
<dataEntityExample>hsa-mir-200a</dataEntityExample>
<dataEntry>http://lisanwanglab.org/DASHR/entry/$id#exprPerTissueTable</dataEntry>
<dataInfo>DASHR expression at University of Pennsylvania</dataInfo>
<dataInstitution>Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>expression</tag>
<tag>human</tag>
<tag>nucleotide</tag>
<tag>sequence</tag>
</tags>
</datatype>
<datatype id="MIR:00000566" pattern="^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$">
<name>SPLASH</name>
<definition>The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.</definition>
<uris>
<uri type="URN">urn:miriam:splash</uri>
<uri type="URL">http://identifiers.org/splash/</uri>
</uris>
<namespace>splash</namespace>
<documentations>
<documentation type="URL">http://splash.fiehnlab.ucdavis.edu/</documentation>
</documentations>
<resources>
<resource id="MIR:00100746" state="probably up" reliability="83">
<dataResource>http://mona.fiehnlab.ucdavis.edu/</dataResource>
<dataEntityExample>splash10-0zq2000000-77302b0326a418630a84</dataEntityExample>
<dataEntry>http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$id</dataEntry>
<dataInfo>Mass Bank of North America (MoNA)</dataInfo>
<dataInstitution>University of Californai, Davis, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>mass spectrometry</tag>
<tag>metabolite</tag>
</tags>
</datatype>
<datatype id="MIR:00000567" pattern="^(MNXM\d+|BIOMASS)$">
<name>MetaNetX chemical</name>
<definition>MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.</definition>
<uris>
<uri type="URN">urn:miriam:metanetx.chemical</uri>
<uri type="URL">http://identifiers.org/metanetx.chemical/</uri>
</uris>
<namespace>metanetx.chemical</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:26527720</documentation>
<documentation type="PMID">urn:miriam:pubmed:23172809</documentation>
</documentations>
<resources>
<resource id="MIR:00100748" state="down" reliability="66">
<dataResource>http://www.metanetx.org/</dataResource>
<dataEntityExample>MNXM1723</dataEntityExample>
<dataEntry>http://www.metanetx.org/chem_info/$id</dataEntry>
<dataInfo>MetaNetX chemical at SIB Swiss Institute of Bioinformatics</dataInfo>
<dataInstitution>Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>chemical</tag>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000568" pattern="^MNXR\d+$">
<name>MetaNetX reaction</name>
<definition>MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.</definition>
<uris>
<uri type="URN">urn:miriam:metanetx.reaction</uri>
<uri type="URL">http://identifiers.org/metanetx.reaction/</uri>
</uris>
<namespace>metanetx.reaction</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:26527720</documentation>
<documentation type="PMID">urn:miriam:pubmed:23172809</documentation>
</documentations>
<resources>
<resource id="MIR:00100749" state="down" reliability="73">
<dataResource>http://www.metanetx.org/</dataResource>
<dataEntityExample>MNXR101574</dataEntityExample>
<dataEntry>http://www.metanetx.org/equa_info/$id</dataEntry>
<dataInfo>MetaNetX reaction at SIB Swiss Institute of Bioinformatics</dataInfo>
<dataInstitution>Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>model</tag>
<tag>reaction</tag>
</tags>
</datatype>
<datatype id="MIR:00000569" pattern="^(MNX[CD]\d+|BOUNDARY)$">
<name>MetaNetX compartment</name>
<definition>MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.</definition>
<uris>
<uri type="URN">urn:miriam:metanetx.compartment</uri>
<uri type="URL">http://identifiers.org/metanetx.compartment/</uri>
</uris>
<namespace>metanetx.compartment</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:26527720</documentation>
<documentation type="PMID">urn:miriam:pubmed:23172809</documentation>
</documentations>
<resources>
<resource id="MIR:00100750" state="down" reliability="73">
<dataResource>http://www.metanetx.org/</dataResource>
<dataEntityExample>MNXC15</dataEntityExample>
<dataEntry>http://www.metanetx.org/comp_info/$id</dataEntry>
<dataInfo>MetaNetX compartment at SIB Swiss Institute of Bioinformatics</dataInfo>
<dataInstitution>Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000570" pattern="^UCR\d{5}$" restricted="true">
<name>UniPathway Reaction</name>
<definition>UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions.</definition>
<uris>
<uri type="URN">urn:miriam:unipathway.reaction</uri>
<uri type="URL">http://identifiers.org/unipathway.reaction/</uri>
</uris>
<namespace>unipathway.reaction</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22102589</documentation>
</documentations>
<resources>
<resource id="MIR:00100752" state="down" reliability="27">
<dataResource>http://www.grenoble.prabi.fr/obiwarehouse/unipathway</dataResource>
<dataEntityExample>UCR00226</dataEntityExample>
<dataEntry>http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$id</dataEntry>
<dataInfo>UniPathway Reaction at Swiss Institute of Bioinformatics (SIB)</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics (SIB) and French National Institute for Research in Computer Science and Control</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="6" desc="Collection subset">
<statement>This collection re-uses a modified version of the identifiers associated with KEGG Reaction.</statement>
<link desc="Associated data collection">http://identifiers.org/kegg.reaction/</link>
</restriction>
</restrictions>
<tags>
<tag>reaction</tag>
</tags>
</datatype>
<datatype id="MIR:00000571" pattern="^HP:\d{7}$">
<name>Human Phenotype Ontology</name>
<synonyms>
<synonym>HPO</synonym>
</synonyms>
<definition>The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.</definition>
<uris>
<uri type="URN">urn:miriam:hp</uri>
<uri type="URL">http://identifiers.org/hp/</uri>
<uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/HP</uri>
<uri type="URN" deprecated="true">urn:miriam:hpo</uri>
</uris>
<namespace>hp</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24217912</documentation>
</documentations>
<resources>
<resource id="MIR:00100753" state="probably up" reliability="94" primary="true">
<dataResource>http://human-phenotype-ontology.github.io/</dataResource>
<dataEntityExample>HP:0000118</dataEntityExample>
<dataEntry>http://compbio.charite.de/hpoweb/showterm?id=$id</dataEntry>
<dataInfo>Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics</dataInfo>
<dataInstitution>Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin, Berlin</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
<resource id="MIR:00100754" state="up" reliability="98">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/hp</dataResource>
<dataEntityExample>HP:0000118</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/hp/terms?obo_id=$id</dataEntry>
<dataInfo>Human Phenotype Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>ontology</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000572" pattern="^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$">
<name>SASBDB</name>
<synonyms>
<synonym>Small Angle Scattering Biological Data Bank</synonym>
</synonyms>
<definition>Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.</definition>
<uris>
<uri type="URN">urn:miriam:sasbdb</uri>
<uri type="URL">http://identifiers.org/sasbdb/</uri>
</uris>
<namespace>sasbdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:25352555</documentation>
</documentations>
<resources>
<resource id="MIR:00100763" state="up" reliability="99">
<dataResource>http://www.sasbdb.org/</dataResource>
<dataEntityExample>SASDAX8</dataEntityExample>
<dataEntry>http://www.sasbdb.org/data/$id</dataEntry>
<dataInfo>SASBDB at European Molecular Biology Laboratory</dataInfo>
<dataInstitution>Biological Small Angle Scattering Group, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>domain</tag>
<tag>structure</tag>
</tags>
</datatype>
<datatype id="MIR:00000573" pattern="^\d+$">
<name>HGNC gene family</name>
<definition>The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.</definition>
<uris>
<uri type="URN">urn:miriam:hgnc.genefamily</uri>
<uri type="URL">http://identifiers.org/hgnc.genefamily/</uri>
</uris>
<namespace>hgnc.genefamily</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:26842383</documentation>
<documentation type="PMID">urn:miriam:pubmed:25361968</documentation>
</documentations>
<resources>
<resource id="MIR:00100765" state="up" reliability="100">
<dataResource>http://www.genenames.org/</dataResource>
<dataEntityExample>141</dataEntityExample>
<dataEntry>http://www.genenames.org/cgi-bin/genefamilies/set/$id</dataEntry>
<dataInfo>HGNC gene family at HUGO Genome Nomenclature Committee</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000574" pattern="^\d+$">
<name>MDM</name>
<synonyms>
<synonym>Medical Data Models</synonym>
</synonyms>
<definition>The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.</definition>
<uris>
<uri type="URN">urn:miriam:mdm</uri>
<uri type="URL">http://identifiers.org/mdm/</uri>
</uris>
<namespace>mdm</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:26868052</documentation>
</documentations>
<resources>
<resource id="MIR:00100766" state="up" reliability="23">
<dataResource>https://medical-data-models.org/</dataResource>
<dataEntityExample>4776</dataEntityExample>
<dataEntry>https://medical-data-models.org/forms/$id</dataEntry>
<dataInfo>MDM at University of Muenster</dataInfo>
<dataInstitution>Institute of Medical Informatics, University of Muenster</dataInstitution>
<dataLocation>Germany</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>registry</tag>
</tags>
</datatype>
<datatype id="MIR:00000575" pattern="^PROB_c\d+$">
<name>ProbOnto</name>
<synonyms>
<synonym>Probability Distribution Ontology</synonym>
</synonyms>
<definition>ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities.</definition>
<uris>
<uri type="URN">urn:miriam:probonto</uri>
<uri type="URL">http://identifiers.org/probonto/</uri>
</uris>
<namespace>probonto</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:27153608</documentation>
</documentations>
<resources>
<resource id="MIR:00100768" state="up" reliability="93">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/probonto</dataResource>
<dataEntityExample>PROB_c0000005</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$id</dataEntry>
<dataInfo>ProbOnto through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000576" pattern="^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$">
<name>APID Interactomes</name>
<synonyms>
<synonym>Agile Protein Interactomes DataServer</synonym>
</synonyms>
<definition>APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.</definition>
<uris>
<uri type="URN">urn:miriam:apid.interactions</uri>
<uri type="URL">http://identifiers.org/apid.interactions/</uri>
</uris>
<namespace>apid.interactions</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:27131791</documentation>
</documentations>
<resources>
<resource id="MIR:00100769" state="up" reliability="97">
<dataResource>http://cicblade.dep.usal.es:8080/APID/</dataResource>
<dataEntityExample>P01116</dataEntityExample>
<dataEntry>http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$id</dataEntry>
<dataInfo>APID at Salamanca</dataInfo>
<dataInstitution>Cancer Research Center (CiC-IBMCC), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Salamanca</dataInstitution>
<dataLocation>Spain</dataLocation>
</resource>
</resources>
<tags>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000577" pattern="^STOREDB:(STUDY|FILE|DATASET)\d+$">
<name>STOREDB</name>
<definition>STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.</definition>
<uris>
<uri type="URN">urn:miriam:storedb</uri>
<uri type="URL">http://identifiers.org/storedb/</uri>
</uris>
<namespace>storedb</namespace>
<documentations>
<documentation type="URL">https://www.storedb.org/store_v3/help.jsp</documentation>
</documentations>
<resources>
<resource id="MIR:00100771" state="up" reliability="88">
<dataResource>https://www.storedb.org/</dataResource>
<dataEntityExample>STOREDB:STUDY1040</dataEntityExample>
<dataEntry>https://www.storedb.org/?$id</dataEntry>
<dataInfo>STOREDB at University of Cambridge</dataInfo>
<dataInstitution>University of Cambridge, Department of Physiology, Downing Street, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000578" pattern="^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$" restricted="true">
<name>Kyoto Encyclopedia of Genes and Genomes</name>
<synonyms>
<synonym>KEGG</synonym>
</synonyms>
<definition>Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.</definition>
<uris>
<uri type="URN">urn:miriam:kegg</uri>
<uri type="URL">http://identifiers.org/kegg/</uri>
</uris>
<namespace>kegg</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:22700311</documentation>
</documentations>
<resources>
<resource id="MIR:00100773" state="up" reliability="100">
<dataResource>http://www.kegg.jp/</dataResource>
<dataEntityExample>hsa00190</dataEntityExample>
<dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG at Kyoto University Bioinformatics Center</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<restrictions>
<restriction type="2" desc="Data aggregation">
<statement>KEGG provides a variety of 'Data-oriented entry points', which are also represented separately in this Registry. For instance, kegg disease (http://identifiers.org/kegg.disease), kegg pathway (http://identifiers.org/kegg.pathway/), etc.</statement>
<link desc="multiple data-oriented collections">http://www.kegg.jp/</link>
</restriction>
</restrictions>
<tags>
<tag>chemical</tag>
<tag>genome</tag>
<tag>pathway</tag>
</tags>
</datatype>
<datatype id="MIR:00000579" pattern="^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$">
<name>Plant Transcription Factor Database</name>
<synonyms>
<synonym>PlantTFDB</synonym>
</synonyms>
<definition>The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.</definition>
<uris>
<uri type="URN">urn:miriam:planttfdb</uri>
<uri type="URL">http://identifiers.org/planttfdb/</uri>
</uris>
<namespace>planttfdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:24174544</documentation>
</documentations>
<resources>
<resource id="MIR:00100772" state="up" reliability="93">
<dataResource>http://planttfdb.cbi.pku.edu.cn</dataResource>
<dataEntityExample>Ath_AT1G01030.1</dataEntityExample>
<dataEntry>http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$id</dataEntry>
<dataInfo>PlantTFDB at Peking University</dataInfo>
<dataInstitution>Center for Bioinformatics, Peking University, Beijing</dataInstitution>
<dataLocation>Peoples Republic of China</dataLocation>
</resource>
</resources>
<tags>
<tag>DNA</tag>
<tag>interaction</tag>
<tag>protein</tag>
</tags>
</datatype>
<datatype id="MIR:00000580" pattern="^MP:\d{7}$">
<name>Mammalian Phenotype Ontology</name>
<definition>The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.</definition>
<uris>
<uri type="URN">urn:miriam:mp</uri>
<uri type="URL">http://identifiers.org/mp/</uri>
</uris>
<namespace>mp</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:20052305</documentation>
<documentation type="PMID">urn:miriam:pubmed:20052305</documentation>
</documentations>
<resources>
<resource id="MIR:00100774" state="down" reliability="35">
<dataResource>http://www.informatics.jax.org/</dataResource>
<dataEntityExample>MP:0005452</dataEntityExample>
<dataEntry>http://www.informatics.jax.org/searches/Phat.cgi?id=$id</dataEntry>
<dataInfo>Mammalian Phenotype Ontology at The Jackson Lab</dataInfo>
<dataInstitution>The Jackson Laboratory, Bar Harbor, Maine</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100775" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/mp/</dataResource>
<dataEntityExample>MP:0005452</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/mp/terms?obo_id=$id</dataEntry>
<dataInfo>Mammalian Phenotype Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100776" state="up" reliability="97">
<dataResource>https://bioportal.bioontology.org/ontologies/MP</dataResource>
<dataEntityExample>MP:0005452</dataEntityExample>
<dataEntry>https://bioportal.bioontology.org/ontologies/MP/$id</dataEntry>
<dataInfo>Mammalian Phenotype Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>mammalian</tag>
<tag>ontology</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000581" pattern="^\d+$">
<name>World Register of Marine Species</name>
<synonyms>
<synonym>WoRMS</synonym>
</synonyms>
<definition>The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts.</definition>
<uris>
<uri type="URN">urn:miriam:worms</uri>
<uri type="URL">http://identifiers.org/worms/</uri>
<uri type="URN" deprecated="true">urn:lsid:marinespecies.org:taxname:146421</uri>
</uris>
<namespace>worms</namespace>
<documentations>
<documentation type="URL">http://www.marinespecies.org/aphia.php?p=manual</documentation>
</documentations>
<resources>
<resource id="MIR:00100778" state="up" reliability="100">
<dataResource>http://www.marinespecies.org/</dataResource>
<dataEntityExample>146421</dataEntityExample>
<dataEntry>http://www.marinespecies.org/aphia.php?p=taxdetails&id=$id</dataEntry>
<dataInfo>World Register of Marine Species</dataInfo>
<dataInstitution>Flanders Marine Institute, Ostend</dataInstitution>
<dataLocation>Belgium</dataLocation>
</resource>
</resources>
<tags>
<tag>classification</tag>
<tag>taxonomy</tag>
</tags>
</datatype>
<datatype id="MIR:00000582" pattern="^MCDS_C_[a-zA-Z0-9]{1,10}$">
<name>MultiCellDS collection</name>
<definition>MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).</definition>
<uris>
<uri type="URN">urn:miriam:multicellds.collection</uri>
<uri type="URL">http://identifiers.org/multicellds.collection/</uri>
</uris>
<namespace>multicellds.collection</namespace>
<documentations>
<documentation type="URL">http://multicellds.org/</documentation>
<documentation type="URL">http://multicellds.org/</documentation>
<documentation type="URL">http://multicellds.org/</documentation>
</documentations>
<resources>
<resource id="MIR:00100779" state="up" reliability="99">
<dataResource>http://multicellds.org/MultiCellDB.php</dataResource>
<dataEntityExample>MCDS_C_0000000001</dataEntityExample>
<dataEntry>http://multicellds.org/MultiCellDB/$id</dataEntry>
<dataInfo>MultiCellDScollection at Keck School of Medicine</dataInfo>
<dataInstitution>Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000583" pattern="^MCDS_S_[a-zA-Z0-9]{1,10}$">
<name>MultiCellDS Digital snapshot</name>
<definition>MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.</definition>
<uris>
<uri type="URN">urn:miriam:multicellds.snapshot</uri>
<uri type="URL">http://identifiers.org/multicellds.snapshot/</uri>
</uris>
<namespace>multicellds.snapshot</namespace>
<resources>
<resource id="MIR:00100780" state="down" reliability="0">
<dataResource>http://multicellds.org/MultiCellDB.php</dataResource>
<dataEntityExample>MCDS_S_0000000001</dataEntityExample>
<dataEntry>http://multicellds.org/MultiCellDB/$id</dataEntry>
<dataInfo>MultiCellDS snapshot at Keck School of Medicine</dataInfo>
<dataInstitution>Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000584" pattern="^MCDS_L_[a-zA-Z0-9]{1,10}$">
<name>MultiCellDS Digital Cell Line</name>
<definition>MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.</definition>
<uris>
<uri type="URN">urn:miriam:multicellds.cell_line</uri>
<uri type="URL">http://identifiers.org/multicellds.cell_line/</uri>
</uris>
<namespace>multicellds.cell_line</namespace>
<resources>
<resource id="MIR:00100781" state="up" reliability="99">
<dataResource>http://multicellds.org/MultiCellDB.php</dataResource>
<dataEntityExample>MCDS_L_0000000001</dataEntityExample>
<dataEntry>http://multicellds.org/MultiCellDB/$id</dataEntry>
<dataInfo> MultiCellDS Digital Cell Line at Keck School of Medicine</dataInfo>
<dataInstitution>Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000585" pattern="^\d+$">
<name>E-cyanobacterium entity</name>
<definition>E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.</definition>
<uris>
<uri type="URN">urn:miriam:ecyano.entity</uri>
<uri type="URL">http://identifiers.org/ecyano.entity/</uri>
</uris>
<namespace>ecyano.entity</namespace>
<documentations>
<documentation type="URL">http://e-cyanobacterium.org/support/</documentation>
<documentation type="URL">https://sybila.fi.muni.cz/_media/wiki/cmsb2016.pdf</documentation>
</documentations>
<resources>
<resource id="MIR:00100782" state="down" reliability="24">
<dataResource>http://www.e-cyanobacterium.org/bcs/entity/</dataResource>
<dataEntityExample>23</dataEntityExample>
<dataEntry>http://e-cyanobacterium.org/bcs/entity/$id/</dataEntry>
<dataInfo>e-cyanobacterium entity at Masaryk University Brno</dataInfo>
<dataInstitution>Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno</dataInstitution>
<dataLocation>Czech Republic</dataLocation>
</resource>
</resources>
<tags>
<tag>metabolite</tag>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000586" pattern="^\d+$">
<name>E-cyanobacterium model</name>
<definition>E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.</definition>
<uris>
<uri type="URN">urn:miriam:ecyano.model</uri>
<uri type="URL">http://identifiers.org/ecyano.model/</uri>
</uris>
<namespace>ecyano.model</namespace>
<documentations>
<documentation type="URL">http://e-cyanobacterium.org/support/</documentation>
<documentation type="URL">https://sybila.fi.muni.cz/_media/wiki/cmsb2016.pdf</documentation>
</documentations>
<resources>
<resource id="MIR:00100783" state="down" reliability="24">
<dataResource>http://e-cyanobacterium.org/models/</dataResource>
<dataEntityExample>26</dataEntityExample>
<dataEntry>http://e-cyanobacterium.org/models/model/$id/</dataEntry>
<dataInfo>e-cyanobacterium entity at Masaryk University Brno</dataInfo>
<dataInstitution>Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno</dataInstitution>
<dataLocation>Czech Republic</dataLocation>
</resource>
</resources>
<tags>
<tag>microbial</tag>
<tag>model</tag>
</tags>
</datatype>
<datatype id="MIR:00000587" pattern="^\d+$">
<name>E-cyanobacterium rule</name>
<definition>E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.</definition>
<uris>
<uri type="URN">urn:miriam:ecyano.rule</uri>
<uri type="URL">http://identifiers.org/ecyano.rule/</uri>
</uris>
<namespace>ecyano.rule</namespace>
<documentations>
<documentation type="URL">http://e-cyanobacterium.org/support/</documentation>
<documentation type="URL">https://sybila.fi.muni.cz/_media/wiki/cmsb2016.pdf</documentation>
</documentations>
<resources>
<resource id="MIR:00100784" state="down" reliability="24">
<dataResource>http://www.e-cyanobacterium.org/bcs/rule/</dataResource>
<dataEntityExample>56</dataEntityExample>
<dataEntry>http://e-cyanobacterium.org/bcs/rule/$id/</dataEntry>
<dataInfo>e-cyanobacterium entity at Masaryk University Brno</dataInfo>
<dataInstitution>Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno</dataInstitution>
<dataLocation>Czech Republic</dataLocation>
</resource>
</resources>
<tags>
<tag>model</tag>
<tag>reaction</tag>
</tags>
</datatype>
<datatype id="MIR:00000588" pattern="^LD[SG]-\d+$">
<name>LINCS Data</name>
<definition>The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).</definition>
<uris>
<uri type="URN">urn:miriam:lincs.data</uri>
<uri type="URL">http://identifiers.org/lincs.data/</uri>
</uris>
<namespace>lincs.data</namespace>
<documentations>
<documentation type="URL">http://www.lincsproject.org/</documentation>
</documentations>
<resources>
<resource id="MIR:00100785" state="probably up" reliability="92" primary="true">
<dataResource>http://lincsportal.ccs.miami.edu/datasets/</dataResource>
<dataEntityExample>LDS-1110</dataEntityExample>
<dataEntry>http://lincsportal.ccs.miami.edu/datasets/#/view/$id</dataEntry>
<dataInfo>LINCS Data at University of Miami</dataInfo>
<dataInstitution>University of Miami, BD2K-LINCS DCIC</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100856" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>LDS-1110</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/lincs/$id</dataEntry>
<dataInfo>Lincs through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
</tags>
</datatype>
<datatype id="MIR:00000589" pattern="^\d+$">
<name>AGRICOLA</name>
<synonyms>
<synonym>Agricultural Online Access</synonym>
</synonyms>
<definition>AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.</definition>
<uris>
<uri type="URN">urn:miriam:agricola</uri>
<uri type="URL">http://identifiers.org/agricola/</uri>
<uri type="URN" deprecated="true">urn:miriam:argicola</uri>
</uris>
<namespace>agricola</namespace>
<documentations>
<documentation type="URL">http://www.nal.usda.gov/help/</documentation>
</documentations>
<resources>
<resource id="MIR:00100789" state="down" reliability="69">
<dataResource>http://agricola.nal.usda.gov/</dataResource>
<dataEntityExample>50018</dataEntityExample>
<dataEntry>http://ddr.nal.usda.gov/dspace/handle/10113/$id</dataEntry>
<dataInfo>AGRICOLA at National Agricultural Library</dataInfo>
<dataInstitution>National Agricultural Library, United States Department of Agriculture</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000590" pattern="^MS:\d{7}$">
<name>Mass Spectrometry Controlled Vocabulary</name>
<definition>The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.</definition>
<uris>
<uri type="URN">urn:miriam:ms</uri>
<uri type="URL">http://identifiers.org/ms/</uri>
</uris>
<namespace>ms</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23482073</documentation>
</documentations>
<resources>
<resource id="MIR:00100786" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/ms</dataResource>
<dataEntityExample>MS:1000001</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=$id</dataEntry>
<dataInfo>Mass Spectrometry Controlled Vocabulary through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100787" state="unknown" reliability="0">
<dataResource>https://bioportal.bioontology.org/ontologies/MS</dataResource>
<dataEntityExample>MS:1000001</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/MS/$id</dataEntry>
<dataInfo>Mass Spectrometry Controlled Vocabulary through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>controlled vocabulary</tag>
<tag>mass spectrometry</tag>
</tags>
</datatype>
<datatype id="MIR:00000591" pattern="^ENVO:\d{8}$">
<name>Environment Ontology</name>
<synonyms>
<synonym>ENVO</synonym>
</synonyms>
<definition>The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations.</definition>
<uris>
<uri type="URN">urn:miriam:envo</uri>
<uri type="URL">http://identifiers.org/envo/</uri>
</uris>
<namespace>envo</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:27664130</documentation>
</documentations>
<resources>
<resource id="MIR:00100790" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/envo</dataResource>
<dataEntityExample>ENVO:09200010</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=$id</dataEntry>
<dataInfo>The Environment Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100791" state="up" reliability="98">
<dataResource>http://purl.bioontology.org/ontology/ENVO/</dataResource>
<dataEntityExample>ENVO:09200010</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/ENVO/$id</dataEntry>
<dataInfo>The Environment Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>ontology</tag>
</tags>
</datatype>
<datatype id="MIR:00000592" pattern="^(ark\:)/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$">
<name>ARK</name>
<synonyms>
<synonym>Archival Resource Key</synonym>
</synonyms>
<definition>An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type.</definition>
<uris>
<uri type="URN">urn:miriam:ark</uri>
<uri type="URL">http://identifiers.org/ark/</uri>
</uris>
<namespace>ark</namespace>
<documentations>
<documentation type="URL">https://en.wikipedia.org/wiki/Archival_Resource_Key</documentation>
</documentations>
<resources>
<resource id="MIR:00100792" state="up" reliability="100">
<dataResource>http://n2t.net/</dataResource>
<dataEntityExample>ark:/12345/fk1234</dataEntityExample>
<dataEntry>http://n2t.net/$id</dataEntry>
<dataInfo>ARK via the Name-to-Thing resolver.</dataInfo>
<dataInstitution>California Digital Library, University of California Office of the President</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000593" pattern="^grid\.[0-9]+\.[a-f0-9]{1,2}$">
<name>GRID</name>
<synonyms>
<synonym>Global Research Identifier Database</synonym>
</synonyms>
<definition>International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.</definition>
<uris>
<uri type="URN">urn:miriam:grid</uri>
<uri type="URL">http://identifiers.org/grid/</uri>
</uris>
<namespace>grid</namespace>
<documentations>
<documentation type="URL">https://gridac.freshdesk.com/support/solutions</documentation>
</documentations>
<resources>
<resource id="MIR:00100793" state="up" reliability="100">
<dataResource>https://www.grid.ac/</dataResource>
<dataEntityExample>grid.225360.0</dataEntityExample>
<dataEntry>https://www.grid.ac/institutes/$id</dataEntry>
<dataInfo>GRID at Digital Science & Research Ltd.</dataInfo>
<dataInstitution>Digital Science &amp;amp; Research Ltd, London</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000594" pattern="^[CN]*\d{4,7}$">
<name>MedGen</name>
<definition>MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder.</definition>
<uris>
<uri type="URN">urn:miriam:medgen</uri>
<uri type="URL">http://identifiers.org/medgen/</uri>
</uris>
<namespace>medgen</namespace>
<documentations>
<documentation type="URL">https://www.ncbi.nlm.nih.gov/medgen/docs/help/#start</documentation>
</documentations>
<resources>
<resource id="MIR:00100794" state="up" reliability="100">
<dataResource>https://www.ncbi.nlm.nih.gov/medgen/</dataResource>
<dataEntityExample>760050</dataEntityExample>
<dataEntry>https://www.ncbi.nlm.nih.gov/medgen/$id</dataEntry>
<dataInfo>MedGen at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI), NIH, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
<tags>
<tag>gene</tag>
<tag>human</tag>
<tag>phenotype</tag>
</tags>
</datatype>
<datatype id="MIR:00000595" pattern="^SCV\d+(\.\d+)?$">
<name>ClinVar Submission</name>
<definition>ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.</definition>
<uris>
<uri type="URN">urn:miriam:clinvar.submission</uri>
<uri type="URL">http://identifiers.org/clinvar.submission/</uri>
<uri type="URN" deprecated="true">urn:miriam:clinvar.sub</uri>
</uris>
<namespace>clinvar.submission</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkt1113</documentation>
</documentations>
<resources>
<resource id="MIR:00100795" state="up" reliability="100">
<dataResource>http://www.ncbi.nlm.nih.gov/clinvar/</dataResource>
<dataEntityExample>SCV000151292</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/clinvar?term=$id</dataEntry>
<dataInfo>ClinVar Submission at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI), NIH, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000596" pattern="^\d+$">
<name>ClinVar Variant</name>
<definition>ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.</definition>
<uris>
<uri type="URN">urn:miriam:clinvar</uri>
<uri type="URL">http://identifiers.org/clinvar/</uri>
</uris>
<namespace>clinvar</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkt1113</documentation>
</documentations>
<resources>
<resource id="MIR:00100796" state="up" reliability="100">
<dataResource>http://www.ncbi.nlm.nih.gov/clinvar/</dataResource>
<dataEntityExample>12345</dataEntityExample>
<dataEntry>https://www.ncbi.nlm.nih.gov/clinvar/variation/$id</dataEntry>
<dataInfo>ClinVar Variant at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI), NIH, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000597" pattern="^\d{7}$">
<name>BioAssay Ontology</name>
<definition>The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.</definition>
<uris>
<uri type="URN">urn:miriam:bao</uri>
<uri type="URL">http://identifiers.org/bao/</uri>
</uris>
<namespace>bao</namespace>
<resources>
<resource id="MIR:00100797" state="up" reliability="98">
<dataResource>http://bioportal.bioontology.org/ontologies/BAO/</dataResource>
<dataEntityExample>0002989</dataEntityExample>
<dataEntry>http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$id</dataEntry>
<dataInfo>BioAssay Ontology through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100798" state="up" reliability="99">
<dataResource>https://bioportal.bioontology.org/ontologies/BAO/</dataResource>
<dataEntityExample>0002989</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/bao/terms?obo_id=BAO:$id</dataEntry>
<dataInfo>BioAssay Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<annotation>
<format name="SBML">
<elements>
<element>model</element>
</elements>
</format>
</annotation>
</datatype>
<datatype id="MIR:00000598" pattern="CVCL_[A-Z0-9]{4}">
<name>Cellosaurus</name>
<definition>The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.</definition>
<uris>
<uri type="URN">urn:miriam:cellosaurus</uri>
<uri type="URL">http://identifiers.org/cellosaurus/</uri>
</uris>
<namespace>cellosaurus</namespace>
<documentations>
<documentation type="URL">http://web.expasy.org/cellosaurus/description.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100799" state="down" reliability="74">
<dataResource>http://web.expasy.org/cellosaurus/</dataResource>
<dataEntityExample>CVCL_0030</dataEntityExample>
<dataEntry>http://web.expasy.org/cellosaurus/$id</dataEntry>
<dataInfo>Cellosaurus through SIB</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics</dataInstitution>
<dataLocation>Swizerland</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000599" pattern="^MIR:\d{8}$">
<name>Identifiers.org Registry</name>
<definition>The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources.</definition>
<uris>
<uri type="URN">urn:miriam:mir</uri>
<uri type="URL">http://identifiers.org/mir/</uri>
</uris>
<namespace>mir</namespace>
<documentations>
<documentation type="URL">http://biorxiv.org/content/early/2017/01/18/101279</documentation>
</documentations>
<resources>
<resource id="MIR:00100800" state="up" reliability="100">
<dataResource>http://identifiers.org/registry</dataResource>
<dataEntityExample>MIR:00100037</dataEntityExample>
<dataEntry>http://identifiers.org/registry?query="$id"</dataEntry>
<dataInfo>Identifiers.org Registry through EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000600" pattern="^[\w\-:,]{3,64}$">
<name>Progenetix</name>
<synonyms>
<synonym>Cancer Genome Knowledge Resource</synonym>
</synonyms>
<definition>The Progenetix database provides an overview of copy number abnormalities in human cancer from currently 32317 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1026 articles and represents 364 different cancer types, according to the International classification of Diseases in Oncology (ICD-O).</definition>
<uris>
<uri type="URN">urn:miriam:pgx</uri>
<uri type="URL">http://identifiers.org/pgx/</uri>
</uris>
<namespace>pgx</namespace>
<documentations>
<documentation type="URL">http://europepmc.org/abstract/MED/24225322</documentation>
<documentation type="URL">http://europepmc.org/abstract/MED/11751233</documentation>
</documentations>
<resources>
<resource id="MIR:00100801" state="up" reliability="96">
<dataResource>http://progenetix.org/</dataResource>
<dataEntityExample>icdom:8500_3</dataEntityExample>
<dataEntry>http://progenetix.org/pgx:$id</dataEntry>
<dataInfo>Progenetix</dataInfo>
<dataInstitution>University of Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000601" pattern="^[A-Z0-9]+$">
<name>COSMIC Gene</name>
<synonyms>
<synonym>Catalogue of Somatic Mutations in Cancer Gene</synonym>
</synonyms>
<definition>COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes.</definition>
<uris>
<uri type="URN">urn:miriam:cosmic</uri>
<uri type="URL">http://identifiers.org/cosmic/</uri>
</uris>
<namespace>cosmic</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:18428421</documentation>
</documentations>
<resources>
<resource id="MIR:00100802" state="down" reliability="95">
<dataResource>http://cancer.sanger.ac.uk/cosmic/</dataResource>
<dataEntityExample>BRAF</dataEntityExample>
<dataEntry>http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$id</dataEntry>
<dataInfo>COSMIC Gene at Sanger</dataInfo>
<dataInstitution>Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000602" pattern="^phs[0-9]{6}.v\d+.p\d+$">
<name>dbGaP</name>
<synonyms>
<synonym>Database of Genotypes and Phenotypes</synonym>
</synonyms>
<definition>The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.</definition>
<uris>
<uri type="URN">urn:miriam:dbgap</uri>
<uri type="URL">http://identifiers.org/dbgap/</uri>
</uris>
<namespace>dbgap</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1038%2Fng1007-1181</documentation>
</documentations>
<resources>
<resource id="MIR:00100803" state="up" reliability="99" primary="true">
<dataResource>https://www.ncbi.nlm.nih.gov/projects/gap</dataResource>
<dataEntityExample>phs000768.v2.p1</dataEntityExample>
<dataEntry>https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$id</dataEntry>
<dataInfo>dbGaP through NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000603" pattern="^\d{7}$">
<name>Information Artifact Ontology</name>
<definition>An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch.</definition>
<uris>
<uri type="URN">urn:miriam:iao</uri>
<uri type="URL">http://identifiers.org/iao/</uri>
</uris>
<namespace>iao</namespace>
<documentations>
<documentation type="URL">https://github.com/information-artifact-ontology/IAO</documentation>
</documentations>
<resources>
<resource id="MIR:00100804" state="up" reliability="95">
<dataResource>http://www.ontobee.org/ontology/IAO</dataResource>
<dataEntityExample>0000030</dataEntityExample>
<dataEntry>http://purl.obolibrary.org/obo/IAO_$id</dataEntry>
<dataInfo>IAO through Ontobee</dataInfo>
<dataInstitution>University of Pennsylvania</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000604" pattern="^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$">
<name>Genomic Data Commons Data Portal</name>
<definition>The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.</definition>
<uris>
<uri type="URN">urn:miriam:gdc</uri>
<uri type="URL">http://identifiers.org/gdc/</uri>
</uris>
<namespace>gdc</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1056%2FNEJMp1607591</documentation>
</documentations>
<resources>
<resource id="MIR:00100805" state="unknown" reliability="0">
<dataResource>https://gdc.cancer.gov</dataResource>
<dataEntityExample>ae8c77fe-e6c8-44d5-8265-4a38c637bbef</dataEntityExample>
<dataEntry>https://portal.gdc.cancer.gov/cases/$id</dataEntry>
<dataInfo>Genomic Data Commons</dataInfo>
<dataInstitution>National Cancer Institute Genomic Data Commons, NIH
</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000605" pattern="^\d{7}$">
<name>OMIT</name>
<synonyms>
<synonym>Ontology for miRNA Target</synonym>
</synonyms>
<definition>The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).</definition>
<uris>
<uri type="URN">urn:miriam:omit</uri>
<uri type="URL">http://identifiers.org/omit/</uri>
</uris>
<namespace>omit</namespace>
<resources>
<resource id="MIR:00100806" state="up" reliability="99">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/omit/</dataResource>
<dataEntityExample>0005506</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$id</dataEntry>
<dataInfo>Ontology for miRNA Target (OMIT) through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge
</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000606" pattern="^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$">
<name>INSDC CDS</name>
<definition>The coding sequence or protein identifiers as maintained in INSDC.</definition>
<uris>
<uri type="URN">urn:miriam:insdc.cds</uri>
<uri type="URL">http://identifiers.org/insdc.cds/</uri>
</uris>
<namespace>insdc.cds</namespace>
<resources>
<resource id="MIR:00100807" state="probably up" reliability="100">
<dataResource>http://www.ebi.ac.uk/ena</dataResource>
<dataEntityExample>AAA35559</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/$id</dataEntry>
<dataInfo>INSDC CDS through ENA</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100808" state="up" reliability="100">
<dataResource>https://www.ncbi.nlm.nih.gov/protein/</dataResource>
<dataEntityExample>AAA35559</dataEntityExample>
<dataEntry>https://www.ncbi.nlm.nih.gov/protein/$id</dataEntry>
<dataInfo>INSDC CDS through NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100809" state="up" reliability="96">
<dataResource>http://getentry.ddbj.nig.ac.jp</dataResource>
<dataEntityExample>AAA35559</dataEntityExample>
<dataEntry>http://getentry.ddbj.nig.ac.jp/getentry/dad/$id</dataEntry>
<dataInfo>INSDC CDS through DDBJ</dataInfo>
<dataInstitution>DNA Data Bank of Japan, Mishima, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000607" pattern="^GCA_[0-9]{9}\.[0-9]$">
<name>Genome assembly database</name>
<definition>The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.</definition>
<uris>
<uri type="URN">urn:miriam:insdc.gca</uri>
<uri type="URL">http://identifiers.org/insdc.gca/</uri>
</uris>
<namespace>insdc.gca</namespace>
<resources>
<resource id="MIR:00100810" state="probably up" reliability="100">
<dataResource>http://www.ebi.ac.uk/ena/browse/genome-assembly-database</dataResource>
<dataEntityExample>GCA_000155495.1</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/$id</dataEntry>
<dataInfo>Genome assembly database through ENA</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100811" state="up" reliability="100">
<dataResource>https://www.ncbi.nlm.nih.gov/assembly/</dataResource>
<dataEntityExample>GCA_000155495.1</dataEntityExample>
<dataEntry>https://www.ncbi.nlm.nih.gov/assembly/$id</dataEntry>
<dataInfo>Genome assembly database NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000608" pattern="^G[0-9]{5}[A-Z]{2}$">
<name>GlyTouCan</name>
<definition>GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.</definition>
<uris>
<uri type="URN">urn:miriam:glytoucan</uri>
<uri type="URL">http://identifiers.org/glytoucan/</uri>
</uris>
<namespace>glytoucan</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fglycob%2Fcwx066</documentation>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkv1041</documentation>
</documentations>
<resources>
<resource id="MIR:00100812" state="up" reliability="96">
<dataResource>https://glytoucan.org</dataResource>
<dataEntityExample>G00054MO</dataEntityExample>
<dataEntry>https://glytoucan.org/Structures/Glycans/$id</dataEntry>
<dataInfo>The Glycan Repository</dataInfo>
<dataInstitution>Soka University, Hachioji, Tokyo</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
</resources>
<tags>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000609" pattern="^CPD-\d{5}$">
<name>MetaCyc Compound</name>
<synonyms>
<synonym>MetaCyc Metabolic Pathway Database</synonym>
</synonyms>
<definition>MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.</definition>
<uris>
<uri type="URN">urn:miriam:metacyc.compound</uri>
<uri type="URL">http://identifiers.org/metacyc.compound/</uri>
</uris>
<namespace>metacyc.compound</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkv1164</documentation>
</documentations>
<resources>
<resource id="MIR:00100813" state="probably up" reliability="100">
<dataResource>https://metacyc.org</dataResource>
<dataEntityExample>CPD-10330</dataEntityExample>
<dataEntry>https://metacyc.org/compound?orgid=META&id=$id</dataEntry>
<dataInfo>MetaCyc Metabolic Pathway Database</dataInfo>
<dataInstitution>Bioinformatics Research Group at SRI International, CA</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000610" pattern="^RXN-\d{5}$">
<name>MetaCyc Reaction</name>
<definition>MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.</definition>
<uris>
<uri type="URN">urn:miriam:metacyc.reaction</uri>
<uri type="URL">http://identifiers.org/metacyc.reaction/</uri>
</uris>
<namespace>metacyc.reaction</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkv1164</documentation>
</documentations>
<resources>
<resource id="MIR:00100814" state="up" reliability="98">
<dataResource>https://metacyc.org</dataResource>
<dataEntityExample>RXN-14904</dataEntityExample>
<dataEntry>https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$id</dataEntry>
<dataInfo>MetaCyc Metabolic Pathway Database - Reaction</dataInfo>
<dataInstitution>Bioinformatics Research Group at SRI International, CA</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000611" pattern="\S+">
<name>DataONE</name>
<definition>DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.</definition>
<uris>
<uri type="URN">urn:miriam:d1id</uri>
<uri type="URL">http://identifiers.org/d1id/</uri>
</uris>
<namespace>d1id</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.5060%2FD2251G48</documentation>
</documentations>
<resources>
<resource id="MIR:00100815" state="up" reliability="100">
<dataResource>https://www.dataone.org</dataResource>
<dataEntityExample>00030692-0FE1-4A1B-955E-A2E55D659267</dataEntityExample>
<dataEntry>https://cn.dataone.org/cn/v2/resolve/{$id}</dataEntry>
<dataInfo>DataONE</dataInfo>
<dataInstitution>DataONE, Albuquerque, NM</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000612" pattern="^[1-4]\.[0-9]+\.[0-9]+\.[0-9]+$">
<name>CATH Protein Structural Domain Superfamily</name>
<definition>CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence.</definition>
<uris>
<uri type="URN">urn:miriam:cath</uri>
<uri type="URL">http://identifiers.org/cath/</uri>
<uri type="URN" deprecated="true">urn:miriam:cath.node</uri>
</uris>
<namespace>cath</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:27899584</documentation>
</documentations>
<resources>
<resource id="MIR:00100816" state="up" reliability="100">
<dataResource>http://www.cathdb.info</dataResource>
<dataEntityExample>1.10.8.10</dataEntityExample>
<dataEntry>http://www.cathdb.info/cathnode/$id</dataEntry>
<dataInfo>CATH Node through UCL</dataInfo>
<dataInstitution>University College London</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000613" pattern="^MMP\d+.\d+$">
<name>MarRef</name>
<synonyms>
<synonym>Marine Metagenomics Portal</synonym>
</synonyms>
<definition>MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.</definition>
<uris>
<uri type="URN">urn:miriam:mmp.ref</uri>
<uri type="URL">http://identifiers.org/mmp.ref/</uri>
</uris>
<namespace>mmp.ref</namespace>
<resources>
<resource id="MIR:00100817" state="unknown" reliability="0">
<dataResource>https://mmp.sfb.uit.no/databases/marref/</dataResource>
<dataEntityExample>MMP3312982.2</dataEntityExample>
<dataEntry>https://mmp.sfb.uit.no/databases/marref/#/records/$id</dataEntry>
<dataInfo>MarRef through SfB</dataInfo>
<dataInstitution>Center for Bioinformatics (SfB), UiT The Arctic university of Norway</dataInstitution>
<dataLocation>Norway</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000614" pattern="^MMP\d+.\d+$">
<name>MarDB</name>
<synonyms>
<synonym>Marine Metagenomics Portal</synonym>
</synonyms>
<definition>MarDB includes all sequenced marine microbial genomes regardless of level of completeness.</definition>
<uris>
<uri type="URN">urn:miriam:mmp.db</uri>
<uri type="URL">http://identifiers.org/mmp.db/</uri>
</uris>
<namespace>mmp.db</namespace>
<resources>
<resource id="MIR:00100818" state="unknown" reliability="0">
<dataResource>https://mmp.sfb.uit.no/databases/mardb/</dataResource>
<dataEntityExample>MMP02954345.1</dataEntityExample>
<dataEntry>https://mmp.sfb.uit.no/databases/mardb/#/records/$id</dataEntry>
<dataInfo>MarDB through SfB</dataInfo>
<dataInstitution>Center for Bioinformatics (SfB), UiT The Arctic university of Norway</dataInstitution>
<dataLocation>Norway</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000615" pattern="^MMP\d+.\d+$">
<name>MarCat</name>
<synonyms>
<synonym>Marine Metagenomics Portal</synonym>
</synonyms>
<definition>MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.</definition>
<uris>
<uri type="URN">urn:miriam:mmp.cat</uri>
<uri type="URL">http://identifiers.org/mmp.cat/</uri>
</uris>
<namespace>mmp.cat</namespace>
<resources>
<resource id="MIR:00100819" state="unknown" reliability="0">
<dataResource>https://mmp.sfb.uit.no/databases/marcat/</dataResource>
<dataEntityExample>MMP743597.11</dataEntityExample>
<dataEntry>https://mmp.sfb.uit.no/databases/marcat/#/records/$id</dataEntry>
<dataInfo>MarCat through SfB</dataInfo>
<dataInstitution>Center for Bioinformatics (SfB), UiT The Arctic university of Norway</dataInstitution>
<dataLocation>Norway</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000616" pattern="^[A-Za-z0-9\_]*$">
<name>BioTools</name>
<definition>Tool and data services registry.</definition>
<uris>
<uri type="URN">urn:miriam:biotools</uri>
<uri type="URL">http://identifiers.org/biotools/</uri>
</uris>
<namespace>biotools</namespace>
<resources>
<resource id="MIR:00100820" state="unknown" reliability="0">
<dataResource>https://bio.tools/</dataResource>
<dataEntityExample>uniprotkb</dataEntityExample>
<dataEntry>https://bio.tools/$id</dataEntry>
<dataInfo>BioTools</dataInfo>
<dataInstitution>Elixir-DK</dataInstitution>
<dataLocation>Denmark</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000617" pattern="^\d+$">
<name>AOPWiki</name>
<definition>International repository of Adverse Outcome Pathways.</definition>
<uris>
<uri type="URN">urn:miriam:aop</uri>
<uri type="URL">http://identifiers.org/aop/</uri>
</uris>
<namespace>aop</namespace>
<resources>
<resource id="MIR:00100821" state="unknown" reliability="0">
<dataResource>https://aopwiki.org/</dataResource>
<dataEntityExample>98</dataEntityExample>
<dataEntry>https://aopwiki.org/aops/$id</dataEntry>
<dataInfo>AOPWiki</dataInfo>
<dataInstitution>European Commision - DG Joint Research Centre and U.S Environmental Protection Agency</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000618" pattern="^GLDS-\d+$">
<name>NASA GeneLab</name>
<definition>NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.</definition>
<uris>
<uri type="URN">urn:miriam:ngl</uri>
<uri type="URL">http://identifiers.org/ngl/</uri>
</uris>
<namespace>ngl</namespace>
<resources>
<resource id="MIR:00100822" state="unknown" reliability="0">
<dataResource>https://genelab-data.ndc.nasa.gov/genelab/</dataResource>
<dataEntityExample>GLDS-141</dataEntityExample>
<dataEntry>https://genelab-data.ndc.nasa.gov/genelab/accession/$id</dataEntry>
<dataInfo>NASA GeneLab</dataInfo>
<dataInstitution>NASA's Ames Research Center</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000619" pattern="^[A-Za-z0-9\-\_]+$">
<name>Human Endogenous Retrovirus Database</name>
<definition>Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features.</definition>
<uris>
<uri type="URN">urn:miriam:erv</uri>
<uri type="URL">http://identifiers.org/erv/</uri>
</uris>
<namespace>erv</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681356</documentation>
</documentations>
<resources>
<resource id="MIR:00100823" state="up" reliability="100">
<dataResource>https://herv.img.cas.cz/</dataResource>
<dataEntityExample>THE1B</dataEntityExample>
<dataEntry>https://herv.img.cas.cz/s/$id</dataEntry>
<dataInfo>Human Endogenous Retrovirus Database</dataInfo>
<dataInstitution>Institute of Molecular Genetics, Academy of Sciences of the Czech Republic</dataInstitution>
<dataLocation>Czech Republic</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>human</tag>
</tags>
</datatype>
<datatype id="MIR:00000620" pattern="^[0-9]+$">
<name>Natural Product-Drug Interaction Research Data Repository</name>
<definition>The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs).</definition>
<uris>
<uri type="URN">urn:miriam:napdi</uri>
<uri type="URL">http://identifiers.org/napdi/</uri>
</uris>
<namespace>napdi</namespace>
<documentations>
<documentation type="URL">https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/extending-dideo-ontology-5.pdf</documentation>
</documentations>
<resources>
<resource id="MIR:00100824" state="unknown" reliability="0">
<dataResource>https://repo.napdi.org/</dataResource>
<dataEntityExample>28</dataEntityExample>
<dataEntry>https://repo.napdi.org/study/$id</dataEntry>
<dataInfo>Natural Product-Drug Interaction Research Data Repository</dataInfo>
<dataInstitution>National Center for Complementary and Integrative Health, National Institutes of Health, Washington D.C.</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000621" pattern="^[\w\-:,]{3,64}$">
<name>ArrayMap</name>
<definition>arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome.</definition>
<uris>
<uri type="URN">urn:miriam:arraymap</uri>
<uri type="URL">http://identifiers.org/arraymap/</uri>
</uris>
<namespace>arraymap</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:25428357</documentation>
</documentations>
<resources>
<resource id="MIR:00100825" state="unknown" reliability="0">
<dataResource>https://www.arraymap.org</dataResource>
<dataEntityExample>icdom:8500_3</dataEntityExample>
<dataEntry>https://www.arraymap.org/pgx:$id</dataEntry>
<dataInfo>ArrayMap</dataInfo>
<dataInstitution>Institute of Molecular Life Sciences, University of Zurich, Zurich</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>human</tag>
</tags>
</datatype>
<datatype id="MIR:00000622" pattern="^[0-9]+$">
<name>Benchmark Energy & Geometry Database</name>
<synonyms>
<synonym>BEGDB</synonym>
</synonyms>
<definition>The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.</definition>
<uris>
<uri type="URN">urn:miriam:begdb</uri>
<uri type="URL">http://identifiers.org/begdb/</uri>
</uris>
<namespace>begdb</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1135%2Fcccc20081261</documentation>
<documentation type="URL">http://cccc.uochb.cas.cz/73/10/1261/pdf/</documentation>
</documentations>
<resources>
<resource id="MIR:00100826" state="unknown" reliability="0">
<dataResource>http://www.begdb.com</dataResource>
<dataEntityExample>4214</dataEntityExample>
<dataEntry>http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$id</dataEntry>
<dataInfo>Benchmark Energy & Geometry Database</dataInfo>
<dataInstitution>Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague</dataInstitution>
<dataLocation>Czech Republic</dataLocation>
</resource>
</resources>
<tags>
<tag>structure</tag>
</tags>
</datatype>
<datatype id="MIR:00000623" pattern="^[0-9\-_]+$">
<name>CAMEO</name>
<synonyms>
<synonym>Continuous Automated Model EvaluatiOn</synonym>
</synonyms>
<definition>The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB.</definition>
<uris>
<uri type="URN">urn:miriam:cameo</uri>
<uri type="URL">http://identifiers.org/cameo/</uri>
</uris>
<namespace>cameo</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23624946</documentation>
</documentations>
<resources>
<resource id="MIR:00100827" state="unknown" reliability="0">
<dataResource>https://cameo3d.org</dataResource>
<dataEntityExample>2018-03-24_00000030_1</dataEntityExample>
<dataEntry>https://www.cameo3d.org/sp/targets/target/$id</dataEntry>
<dataInfo>CAMEO</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics, Biozentrum, University of Basel</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>structure</tag>
</tags>
</datatype>
<datatype id="MIR:00000624" pattern="^[0-9]+:[0-9]+$">
<name>SISu</name>
<synonyms>
<synonym>Sequence Initiative Suomi</synonym>
</synonyms>
<definition>The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.</definition>
<uris>
<uri type="URN">urn:miriam:sisu</uri>
<uri type="URL">http://identifiers.org/sisu/</uri>
</uris>
<namespace>sisu</namespace>
<documentations>
<documentation type="URL">http://www.sisuproject.fi/faq</documentation>
</documentations>
<resources>
<resource id="MIR:00100828" state="unknown" reliability="0">
<dataResource>http://www.sisuproject.fi/</dataResource>
<dataEntityExample>17:41223048</dataEntityExample>
<dataEntry>http://search.sisuproject.fi/#/variant/$id</dataEntry>
<dataInfo>SISu</dataInfo>
<dataInstitution>Sequencing Initiative Suomi project (SISu), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki</dataInstitution>
<dataLocation>Finland</dataLocation>
</resource>
</resources>
<tags>
<tag>human</tag>
<tag>sequence</tag>
</tags>
</datatype>
<datatype id="MIR:00000625" pattern="^mzspec:.+$">
<name>Universal Spectrum Identifier</name>
<definition>The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it.</definition>
<uris>
<uri type="URN">urn:miriam:mzspec</uri>
<uri type="URL">http://identifiers.org/mzspec/</uri>
</uris>
<namespace>mzspec</namespace>
<documentations>
<documentation type="URL">https://github.com/HUPO-PSI/UniversalSpectrumIdentifier</documentation>
</documentations>
<resources>
<resource id="MIR:00100829" state="unknown" reliability="0">
<dataResource>https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum</dataResource>
<dataEntityExample>mzspec:PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2</dataEntityExample>
<dataEntry>https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=$id</dataEntry>
<dataInfo>Universal Spectrum Identifier through Peptide Atlas</dataInfo>
<dataInstitution>Institute for Systems Biology</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000626" pattern="^[0-9]+$">
<name>CRISPRdb</name>
<definition>Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data.</definition>
<uris>
<uri type="URN">urn:miriam:crisprdb</uri>
<uri type="URL">http://identifiers.org/crisprdb/</uri>
</uris>
<namespace>crisprdb</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:17521438</documentation>
</documentations>
<resources>
<resource id="MIR:00100830" state="unknown" reliability="0">
<dataResource>http://crispr.i2bc.paris-saclay.fr/</dataResource>
<dataEntityExample>551115</dataEntityExample>
<dataEntry>http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$id</dataEntry>
<dataInfo>CRISPRdb</dataInfo>
<dataInstitution>Université Paris-Sud, Institut de Génétique et Microbiologie, Orsay,</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>microbial</tag>
<tag>sequence</tag>
</tags>
</datatype>
<datatype id="MIR:00000627" pattern="^[A-Za-z0-9]+$">
<name>GnpIS</name>
<definition>GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.</definition>
<uris>
<uri type="URN">urn:miriam:gnpis</uri>
<uri type="URL">http://identifiers.org/gnpis/</uri>
</uris>
<namespace>gnpis</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:23959375</documentation>
</documentations>
<resources>
<resource id="MIR:00100831" state="unknown" reliability="0">
<dataResource>https://urgi.versailles.inra.fr/gnpis/</dataResource>
<dataEntityExample>AY109603</dataEntityExample>
<dataEntry>https://urgi.versailles.inra.fr/gnpis/#result/term=$id</dataEntry>
<dataInfo>GnpIS</dataInfo>
<dataInstitution>URGI (Research Unit in Genomics-Info), INRA de Versailles, Route de Saint-Cyr, Versailles</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>fungal</tag>
<tag>genome</tag>
<tag>plant</tag>
</tags>
</datatype>
<datatype id="MIR:00000628" pattern="^[A-Za-z0-9\-\/]+$">
<name>LiceBase</name>
<definition>Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.</definition>
<uris>
<uri type="URN">urn:miriam:licebase</uri>
<uri type="URL">http://identifiers.org/licebase/</uri>
</uris>
<namespace>licebase</namespace>
<documentations>
<documentation type="URL">https://licebase.org/?q=node/760957</documentation>
</documentations>
<resources>
<resource id="MIR:00100832" state="unknown" reliability="0">
<dataResource>https://licebase.org</dataResource>
<dataEntityExample>EMLSAT00000003403</dataEntityExample>
<dataEntry>https://licebase.org/?q=$id</dataEntry>
<dataInfo>LiceBase</dataInfo>
<dataInstitution>Sea Lice Research Centre (SLRC), University of Bergen</dataInstitution>
<dataLocation>Norway</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>sequence</tag>
</tags>
</datatype>
<datatype id="MIR:00000629" pattern="^[A-Za-z]+\/[0-9]+$">
<name>SugarBind</name>
<definition>The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands.</definition>
<uris>
<uri type="URN">urn:miriam:sugarbind</uri>
<uri type="URL">http://identifiers.org/sugarbind/</uri>
</uris>
<namespace>sugarbind</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:26578555</documentation>
</documentations>
<resources>
<resource id="MIR:00100833" state="unknown" reliability="0">
<dataResource>http://sugarbind.expasy.org/</dataResource>
<dataEntityExample>lectins/172</dataEntityExample>
<dataEntry>http://sugarbind.expasy.org/$id</dataEntry>
<dataInfo>SugarBind</dataInfo>
<dataInstitution>Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
<tags>
<tag>disease</tag>
<tag>human</tag>
<tag>interaction</tag>
</tags>
</datatype>
<datatype id="MIR:00000630" pattern="^URS[0-9A-F]{10}(\_\d+)?$">
<name>RNAcentral</name>
<definition>RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.</definition>
<uris>
<uri type="URN">urn:miriam:rnacentral</uri>
<uri type="URL">http://identifiers.org/rnacentral/</uri>
</uris>
<namespace>rnacentral</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:27794554</documentation>
</documentations>
<resources>
<resource id="MIR:00100834" state="unknown" reliability="0">
<dataResource>http://rnacentral.org/</dataResource>
<dataEntityExample>URS0000759CF4</dataEntityExample>
<dataEntry>http://rnacentral.org/rna/$id</dataEntry>
<dataInfo>RNAcentral through EMBL-EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
<tags>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000631" pattern="^\d+$">
<name>MicroScope</name>
<synonyms>
<synonym>Microbial Genome Annotation & Analysis Platform</synonym>
</synonyms>
<definition>MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.</definition>
<uris>
<uri type="URN">urn:miriam:microscope</uri>
<uri type="URL">http://identifiers.org/microscope/</uri>
</uris>
<namespace>microscope</namespace>
<resources>
<resource id="MIR:00100836" state="down" reliability="0">
<dataResource>http://www.genoscope.cns.fr/agc/microscope</dataResource>
<dataEntityExample>5601141</dataEntityExample>
<dataEntry>http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$id</dataEntry>
<dataInfo>MicroScope</dataInfo>
<dataInstitution>Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Evry</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
<tags>
<tag>genome</tag>
<tag>microbial</tag>
</tags>
</datatype>
<datatype id="MIR:00000632" pattern="^[A-Za-z0-9]+$">
<name>SwissRegulon</name>
<definition>A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form.</definition>
<uris>
<uri type="URN">urn:miriam:swissregulon</uri>
<uri type="URL">http://identifiers.org/swissregulon/</uri>
</uris>
<namespace>swissregulon</namespace>
<resources>
<resource id="MIR:00100837" state="unknown" reliability="0">
<dataResource>http://swissregulon.unibas.ch</dataResource>
<dataEntityExample>AHR</dataEntityExample>
<dataEntry>http://swissregulon.unibas.ch/query/$id</dataEntry>
<dataInfo>SwissRegulon</dataInfo>
<dataInstitution>Swiss Institute of Bioinformatics</dataInstitution>
<dataLocation>Switzerland</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000633" pattern="^[A-Za-z0-9\/]+$">
<name>ValidatorDB</name>
<definition>Database of validation results for ligands and non-standard residues in the Protein Data Bank.</definition>
<uris>
<uri type="URN">urn:miriam:validatordb</uri>
<uri type="URL">http://identifiers.org/validatordb/</uri>
</uris>
<namespace>validatordb</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgku1118</documentation>
</documentations>
<resources>
<resource id="MIR:00100838" state="unknown" reliability="0">
<dataResource>https://webchem.ncbr.muni.cz/Platform/ValidatorDb/</dataResource>
<dataEntityExample>ByStructure/2h6o</dataEntityExample>
<dataEntry>https://webchem.ncbr.muni.cz/Platform/ValidatorDb/$id</dataEntry>
<dataInfo>ValidatorDB</dataInfo>
<dataInstitution>Central European Institute of Technology</dataInstitution>
<dataLocation>Czech Republic</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000634" pattern="^[a-z0-9\-]+$">
<name>Bio-MINDER Tissue Database</name>
<definition>Database of the dielectric properties of biological tissues.</definition>
<uris>
<uri type="URN">urn:miriam:biominder</uri>
<uri type="URL">http://identifiers.org/biominder/</uri>
</uris>
<namespace>biominder</namespace>
<resources>
<resource id="MIR:00100839" state="unknown" reliability="0">
<dataResource>https://datalab.rwth-aachen.de/MINDER</dataResource>
<dataEntityExample>aef4c195-9cf9-46db-a12a-7cfd1ff3eec3</dataEntityExample>
<dataEntry>https://datalab.rwth-aachen.de/MINDER/resource/$id</dataEntry>
<dataInfo>Bio-MINDER Tissue Database</dataInfo>
<dataInstitution>RWTH Aachen University / NUIG Galway</dataInstitution>
<dataLocation>Ireland</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000635" pattern="^[1-9][0-9]*$">
<name>NeuroVault Collection</name>
<definition>Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images.</definition>
<uris>
<uri type="URN">urn:miriam:neurovault.collection</uri>
<uri type="URL">http://identifiers.org/neurovault.collection/</uri>
<uri type="URN" deprecated="true">urn:miriam:neurovault</uri>
</uris>
<namespace>neurovault.collection</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.3389%2Ffninf.2015.00008</documentation>
</documentations>
<resources>
<resource id="MIR:00100840" state="unknown" reliability="0">
<dataResource>http://neurovault.org</dataResource>
<dataEntityExample>3304</dataEntityExample>
<dataEntry>https://neurovault.org/collections/$id</dataEntry>
<dataInfo>NeuroVault Collection</dataInfo>
<dataInstitution>Stanford University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000636" pattern="[a-zA-Z0-9_\(\_\)\[\]]+">
<name>VMH metabolite</name>
<definition>The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.</definition>
<uris>
<uri type="URN">urn:miriam:vmhmetabolite</uri>
<uri type="URL">http://identifiers.org/vmhmetabolite/</uri>
</uris>
<namespace>vmhmetabolite</namespace>
<resources>
<resource id="MIR:00100841" state="unknown" reliability="0">
<dataResource>http://vmh.uni.lu</dataResource>
<dataEntityExample>h2o</dataEntityExample>
<dataEntry>http://vmh.uni.lu/#metabolite/$id</dataEntry>
<dataInfo>VMH metabolite</dataInfo>
<dataInstitution>Luxembourg Centre for Systems Biomedicine, University of Luxembourg</dataInstitution>
<dataLocation>Luxembourg</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000637" pattern="^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$">
<name>MobiDB</name>
<definition>MobiDB is a database of protein disorder and mobility annotations.</definition>
<uris>
<uri type="URN">urn:miriam:mobidb</uri>
<uri type="URL">http://identifiers.org/mobidb/</uri>
</uris>
<namespace>mobidb</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkx1071</documentation>
</documentations>
<resources>
<resource id="MIR:00100842" state="unknown" reliability="0">
<dataResource>http://mobidb.bio.unipd.it</dataResource>
<dataEntityExample>P10636</dataEntityExample>
<dataEntry>http://mobidb.bio.unipd.it/$id</dataEntry>
<dataInfo>MobiDB</dataInfo>
<dataInstitution>University of Padua</dataInstitution>
<dataLocation>Italy</dataLocation>
</resource>
</resources>
<tags>
<tag>schema.org</tag>
</tags>
</datatype>
<datatype id="MIR:00000638" pattern="^[1-9][0-9]*$">
<name>NeuroVault Image</name>
<definition>Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images.</definition>
<uris>
<uri type="URN">urn:miriam:neurovault.image</uri>
<uri type="URL">http://identifiers.org/neurovault.image/</uri>
</uris>
<namespace>neurovault.image</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.3389%2Ffninf.2015.00008</documentation>
</documentations>
<resources>
<resource id="MIR:00100843" state="unknown" reliability="0">
<dataResource>http://neurovault.org</dataResource>
<dataEntityExample>58788</dataEntityExample>
<dataEntry>https://neurovault.org/images/$id</dataEntry>
<dataInfo>NeuroVault</dataInfo>
<dataInstitution>Stanford University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000639" pattern="^NMR:\d+$">
<name>Nuclear Magnetic Resonance Controlled Vocabulary</name>
<synonyms>
<synonym>nmrCV</synonym>
</synonyms>
<definition>nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi.</definition>
<uris>
<uri type="URN">urn:miriam:nmr</uri>
<uri type="URL">http://identifiers.org/nmr/</uri>
</uris>
<namespace>nmr</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1021%2Facs.analchem.7b02795</documentation>
</documentations>
<resources>
<resource id="MIR:00100844" state="unknown" reliability="0">
<dataResource>https://www.ebi.ac.uk/ols/ontologies/nmrcv</dataResource>
<dataEntityExample>NMR:1000003</dataEntityExample>
<dataEntry>https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=$id</dataEntry>
<dataInfo>NMR through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000640" pattern="[a-zA-Z0-9_\(\_\)\[\]]+">
<name>VMH reaction</name>
<definition>The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.</definition>
<uris>
<uri type="URN">urn:miriam:vmhreaction</uri>
<uri type="URL">http://identifiers.org/vmhreaction/</uri>
</uris>
<namespace>vmhreaction</namespace>
<resources>
<resource id="MIR:00100845" state="unknown" reliability="0">
<dataResource>https://vmh.uni.lu</dataResource>
<dataEntityExample>HEX1</dataEntityExample>
<dataEntry>https://vmh.uni.lu/#reaction/$id</dataEntry>
<dataInfo>VMH reaction</dataInfo>
<dataInstitution>Luxembourg Centre for Systems Biomedicine, University of Luxembourg</dataInstitution>
<dataLocation>Luxembourg</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000641" pattern="^[0-9\.]+$">
<name>Astrophysics Source Code Library</name>
<definition>The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).</definition>
<uris>
<uri type="URN">urn:miriam:ascl</uri>
<uri type="URL">http://identifiers.org/ascl/</uri>
</uris>
<namespace>ascl</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.5334%2Fjors.bv</documentation>
<documentation type="URL">https://arxiv.org/abs/1611.06219</documentation>
</documentations>
<resources>
<resource id="MIR:00100846" state="up" reliability="100">
<dataResource>http://ascl.net/</dataResource>
<dataEntityExample>1801.012</dataEntityExample>
<dataEntry>http://ascl.net/$id</dataEntry>
<dataInfo>Astrophysics Source Code Library</dataInfo>
<dataInstitution>Astrophysics Source Code Library, Houghton, MI</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000642" pattern="^FB\d{8}$">
<name>FaceBase Data Repository</name>
<definition>FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.</definition>
<uris>
<uri type="URN">urn:miriam:fb</uri>
<uri type="URL">http://identifiers.org/fb/</uri>
</uris>
<namespace>fb</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1242%2Fdev.135434</documentation>
</documentations>
<resources>
<resource id="MIR:00100847" state="unknown" reliability="0">
<dataResource>https://www.facebase.org</dataResource>
<dataEntityExample>FB00000917</dataEntityExample>
<dataEntry>https://www.facebase.org/data/record/#1/isa:dataset/accession=$id</dataEntry>
<dataInfo>FaceBase Data Repository</dataInfo>
<dataInstitution>University of Southern California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000643" pattern="^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$">
<name>GUDMAP</name>
<definition>The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.</definition>
<uris>
<uri type="URN">urn:miriam:gudmap</uri>
<uri type="URL">http://identifiers.org/gudmap/</uri>
</uris>
<namespace>gudmap</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1242%2Fdev.063594</documentation>
</documentations>
<resources>
<resource id="MIR:00100848" state="down" reliability="66">
<dataResource>http://www.gudmap.org/</dataResource>
<dataEntityExample>Q-2958</dataEntityExample>
<dataEntry>https://gudmap.org/id/$id</dataEntry>
<dataInfo>GUDMAP</dataInfo>
<dataInstitution>GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Consortium</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000644" pattern="^[a-z0-9\-_]+$">
<name>JRC Data Catalogue</name>
<definition>The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.</definition>
<uris>
<uri type="URN">urn:miriam:eu89h</uri>
<uri type="URL">http://identifiers.org/eu89h/</uri>
</uris>
<namespace>eu89h</namespace>
<resources>
<resource id="MIR:00100849" state="up" reliability="100">
<dataResource>http://data.jrc.ec.europa.eu/</dataResource>
<dataEntityExample>jrc-eurl-ecvam-chemagora</dataEntityExample>
<dataEntry>http://data.europa.eu/89h/$id</dataEntry>
<dataInfo>JRC Data Catalogue</dataInfo>
<dataInstitution>European Commission, Joint Research Centre (JRC)</dataInstitution>
<dataLocation>EU</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000645" pattern="^[A-Za-z0-9]+$">
<name>Minimal Identifiers for Transient Data</name>
<definition>Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.</definition>
<uris>
<uri type="URN">urn:miriam:minid</uri>
<uri type="URL">http://identifiers.org/minid/</uri>
</uris>
<namespace>minid</namespace>
<documentations>
<documentation type="DOI">urn:miriam:doi:10.1109%2FBigData.2016.7840618</documentation>
</documentations>
<resources>
<resource id="MIR:00100850" state="up" reliability="100">
<dataResource>http://minid.bd2k.org</dataResource>
<dataEntityExample>b97957</dataEntityExample>
<dataEntry>http://n2t.net/ark:/57799/$id</dataEntry>
<dataInfo>Minimal Identifiers for Transient Data</dataInfo>
<dataInstitution>Big Data for Discovery Science Consortium</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000646" pattern="^ST[0-9]{6}$">
<name>Metabolomics Workbench Study</name>
<definition>Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).</definition>
<uris>
<uri type="URN">urn:miriam:mw.study</uri>
<uri type="URL">http://identifiers.org/mw.study/</uri>
</uris>
<namespace>mw.study</namespace>
<resources>
<resource id="MIR:00100859" state="unknown" reliability="0" primary="true">
<dataResource>http://www.metabolomicsworkbench.org/</dataResource>
<dataEntityExample>ST000900</dataEntityExample>
<dataEntry>http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$id</dataEntry>
<dataInfo>Metabolomics Workbench Study</dataInfo>
<dataInstitution>University of California San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100860" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>ST000900</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/metabolomics_workbench/$id</dataEntry>
<dataInfo>Metabolomics Workbench Study through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000647" pattern="^PR[0-9]{6}$">
<name>Metabolomics Workbench Project</name>
<definition>Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).</definition>
<uris>
<uri type="URN">urn:miriam:mw.project</uri>
<uri type="URL">http://identifiers.org/mw.project/</uri>
</uris>
<namespace>mw.project</namespace>
<resources>
<resource id="MIR:00100861" state="unknown" reliability="0" primary="true">
<dataResource>http://www.metabolomicsworkbench.org/</dataResource>
<dataEntityExample>PR000001</dataEntityExample>
<dataEntry>http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$id</dataEntry>
<dataInfo>Metabolomics Workbench Project</dataInfo>
<dataInstitution>University of California San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000648" pattern="^\d+$">
<name>Metabolome Express</name>
<definition>A public place to process, interpret and share GC/MS metabolomics datasets.</definition>
<uris>
<uri type="URN">urn:miriam:mex</uri>
<uri type="URL">http://identifiers.org/mex/</uri>
</uris>
<namespace>mex</namespace>
<resources>
<resource id="MIR:00100862" state="unknown" reliability="0" primary="true">
<dataResource>https://www.metabolome-express.org/</dataResource>
<dataEntityExample>36</dataEntityExample>
<dataEntry>https://www.metabolome-express.org/datasetview.php?datasetid=$id</dataEntry>
<dataInfo>Metabolome Express</dataInfo>
<dataInstitution>Australian Research Council Centre of Excellence in Plant Energy Biology</dataInstitution>
<dataLocation>Australia</dataLocation>
</resource>
<resource id="MIR:00100863" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>36</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/metabolome_express/MEX$id</dataEntry>
<dataInfo>Metabolome Express through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000649" pattern="^GPM\d+$">
<name>GPMDB</name>
<definition>The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.</definition>
<uris>
<uri type="URN">urn:miriam:gpmdb</uri>
<uri type="URL">http://identifiers.org/gpmdb/</uri>
</uris>
<namespace>gpmdb</namespace>
<resources>
<resource id="MIR:00100864" state="unknown" reliability="0" primary="true">
<dataResource>http://gpmdb.thegpm.org/</dataResource>
<dataEntityExample>GPM32310002988</dataEntityExample>
<dataEntry>http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$id</dataEntry>
<dataInfo>GPMDB</dataInfo>
<dataInstitution>The Global Proteome Machine Organization</dataInstitution>
<dataLocation>Canada</dataLocation>
</resource>
<resource id="MIR:00100865" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>GPM32310002988</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/gpmdb/$id</dataEntry>
<dataInfo>GPMDB through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000650" pattern="^MSV\d+$">
<name>MassIVE</name>
<definition>MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data.</definition>
<uris>
<uri type="URN">urn:miriam:massive</uri>
<uri type="URL">http://identifiers.org/massive/</uri>
</uris>
<namespace>massive</namespace>
<resources>
<resource id="MIR:00100866" state="unknown" reliability="0">
<dataResource>https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp</dataResource>
<dataEntityExample>MSV000082131</dataEntityExample>
<dataEntry>https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$id</dataEntry>
<dataInfo>MassIVE</dataInfo>
<dataInstitution>University of California, San Diego</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100867" state="unknown" reliability="0">
<dataResource>https://www.omicsdi.org/</dataResource>
<dataEntityExample>MSV000082131</dataEntityExample>
<dataEntry>https://www.omicsdi.org/dataset/massive/$id</dataEntry>
<dataInfo>MassIVE through OmicsDI</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000651" pattern="^[a-zA-Z0-9][A-Za-z0-9_]+$">
<name>FamPlex</name>
<definition>FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.</definition>
<uris>
<uri type="URN">urn:miriam:fplx</uri>
<uri type="URL">http://identifiers.org/fplx/</uri>
</uris>
<namespace>fplx</namespace>
<documentations>
<documentation type="URL">https://www.biorxiv.org/content/early/2018/03/26/225698</documentation>
</documentations>
<resources>
<resource id="MIR:00100869" state="unknown" reliability="0">
<dataResource>http://bioportal.bioontology.org/ontologies/FPLX/</dataResource>
<dataEntityExample>RAS</dataEntityExample>
<dataEntry>http://bioportal.bioontology.org/ontologies/FPLX/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFPLX%23_$id</dataEntry>
<dataInfo>FPLX through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000652" pattern="^\d+$">
<name>AOPWiki (Key Event)</name>
<definition>International repository of Adverse Outcome Pathways.</definition>
<uris>
<uri type="URN">urn:miriam:aop.events</uri>
<uri type="URL">http://identifiers.org/aop.events/</uri>
</uris>
<namespace>aop.events</namespace>
<resources>
<resource id="MIR:00100870" state="unknown" reliability="0">
<dataResource>https://aopwiki.org/</dataResource>
<dataEntityExample>3</dataEntityExample>
<dataEntry>https://aopwiki.org/events/$id</dataEntry>
<dataInfo>AOPWiki (Key Event)</dataInfo>
<dataInstitution>European Commision - DG Joint Research Centre and U.S Environmental Protection Agency</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000653" pattern="^\d+$">
<name>AOPWiki (Key Event Relationship)</name>
<definition>International repository of Adverse Outcome Pathways.</definition>
<uris>
<uri type="URN">urn:miriam:aop.relationships</uri>
<uri type="URL">http://identifiers.org/aop.relationships/</uri>
</uris>
<namespace>aop.relationships</namespace>
<resources>
<resource id="MIR:00100871" state="unknown" reliability="0">
<dataResource>https://aopwiki.org/</dataResource>
<dataEntityExample>5</dataEntityExample>
<dataEntry>https://aopwiki.org/relationships/$id</dataEntry>
<dataInfo>AOPWiki (Key Event Relationship)</dataInfo>
<dataInstitution>European Commision - DG Joint Research Centre and U.S Environmental Protection Agency</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000654" pattern="^\d+$">
<name>AOPWiki (Stressor)</name>
<definition>International repository of Adverse Outcome Pathways.</definition>
<uris>
<uri type="URN">urn:miriam:aop.stressor</uri>
<uri type="URL">http://identifiers.org/aop.stressor/</uri>
</uris>
<namespace>aop.stressor</namespace>
<resources>
<resource id="MIR:00100872" state="unknown" reliability="0">
<dataResource>https://aopwiki.org/</dataResource>
<dataEntityExample>9</dataEntityExample>
<dataEntry>https://aopwiki.org/stressors/$id</dataEntry>
<dataInfo>AOPWiki (Stressor)</dataInfo>
<dataInstitution>European Commision - DG Joint Research Centre and U.S Environmental Protection Agency</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000655" pattern="^swh:[1-9]:[a-z][a-z][a-z]:[a-f0-9]+$">
<name>Software Heritage</name>
<definition>Software Heritage is the universal archive of software source code.</definition>
<uris>
<uri type="URN">urn:miriam:swh</uri>
<uri type="URL">http://identifiers.org/swh/</uri>
</uris>
<namespace>swh</namespace>
<documentations>
<documentation type="URL">https://hal.archives-ouvertes.fr/hal-01590958</documentation>
</documentations>
<resources>
<resource id="MIR:00100873" state="unknown" reliability="0">
<dataResource>https://archive.softwareheritage.org</dataResource>
<dataEntityExample>swh:1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d</dataEntityExample>
<dataEntry>https://archive.softwareheritage.org/browse/$id</dataEntry>
<dataInfo>Software Heritage</dataInfo>
<dataInstitution>INRIA</dataInstitution>
<dataLocation>France</dataLocation>
</resource>
</resources>
</datatype>
<datatype id="MIR:00000656" pattern="^[a-zA-Z0-9\-:#\.]+$">
<name>Data Object Service</name>
<definition>Assists in resolving data across cloud resources.</definition>
<uris>
<uri type="URN">urn:miriam:dev.ga4ghdos</uri>
<uri type="URL">http://identifiers.org/dev.ga4ghdos/</uri>
</uris>
<namespace>dev.ga4ghdos</namespace>
<resources>
<resource id="MIR:00100874" state="unknown" reliability="0">
<dataResource>http://github.com/ga4gh/data-object-service-schemas</dataResource>
<dataEntityExample>23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00</dataEntityExample>
<dataEntry>https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$id</dataEntry>
<dataInfo>Data Object Service</dataInfo>
<dataInstitution>University of California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
</datatype>
<listOfTags>
<tagDefinition>
<name>annotation</name>
<definition>Descriptive text, usually added by an author or curator, that provides extra information that may be missing or not immediately evident.</definition>
</tagDefinition>
<tagDefinition>
<name>assay</name>
<definition>A collection that specifies direct assay conditions and/or provides experimental results.</definition>
</tagDefinition>
<tagDefinition>
<name>bibliography</name>
<definition>A citation list which supports the information provided. This may include books, publications in journal, or URL links.</definition>
</tagDefinition>
<tagDefinition>
<name>catalogue</name>
<definition>A data collection providing information on commercially available products.</definition>
</tagDefinition>
<tagDefinition>
<name>chemical</name>
<definition>Data collections with this tag reference data pertaining to chemical compounds and substances.</definition>
</tagDefinition>
<tagDefinition>
<name>classification</name>
<definition>A classification scheme which does not necessarily depict a relationship between different groups, but only between individuals within a group. </definition>
</tagDefinition>
<tagDefinition>
<name>clustering</name>
<definition>Data collections with this tag contain data which has been processed in such a way as to generate subsets (clusters) within which some trait should be shared.</definition>
</tagDefinition>
<tagDefinition>
<name>controlled vocabulary</name>
<definition>Controlled vocabularies provide predefined and authorised terms for shared use by a community, providing a means to organise knowledge for subsequent processing.</definition>
</tagDefinition>
<tagDefinition>
<name>disease</name>
<definition>A disease is an abnormal condition of an organism that impairs bodily functions and can be deadly. It is also defined as a way of the body harming itself in an abnormal way, associated with specific symptoms and signs. [wikipedia]</definition>
</tagDefinition>
<tagDefinition>
<name>disorder</name>
<definition>The term "disorder" is often considered more value-neutral than the term "disease" [wikipedia]. Hence it may have no attributable signs or symptoms.</definition>
</tagDefinition>
<tagDefinition>
<name>DNA</name>
<definition>Data collections with this tag reference data pertaining to deoxyribonucleic acid.</definition>
</tagDefinition>
<tagDefinition>
<name>domain</name>
<definition>A domain is a protein subsequence that forms a three-dimensional structure, and can provide specific catalytic or binding sites as found in enzymes or regulatory proteins. A specific domain may appear in a variety of evolutionarily related proteins.</definition>
</tagDefinition>
<tagDefinition>
<name>drug</name>
<definition>A drug, broadly speaking, is any chemical substance that, when absorbed into the body of a living organism, alters normal bodily function [wikipedia].Toxins are included in this category.</definition>
</tagDefinition>
<tagDefinition>
<name>encyclopedia</name>
<definition>A generic knowledge repository not restricted to a particular domain, and which is primarily used for reference purposes.</definition>
</tagDefinition>
<tagDefinition>
<name>enzyme</name>
<definition>An enzyme is a biological catalyst of a chemical reaction. Most enzymes are proteins.</definition>
</tagDefinition>
<tagDefinition>
<name>eukaryotic</name>
<definition>Data collection pertaining to eukaryotic cells, which are differentiated from prokaryotic cells by the presence of a nucleus. This group includes human, plant, and fungal cells.</definition>
</tagDefinition>
<tagDefinition>
<name>expression</name>
<definition>Data collections associated with this tag pertain to the measurement of gene expression, often through the use of microarray techniques, and usually in quantitative fashion.</definition>
</tagDefinition>
<tagDefinition>
<name>fungal</name>
<definition>Data collection pertaining to species of fungi.</definition>
</tagDefinition>
<tagDefinition>
<name>gene</name>
<definition>Genes are discrete subsequences of genomic DNA and correspond to a unit of inheritance [based on wikipedia]. A data collection tagged 'gene' should include gene information in addition to purely sequence-oriented data.</definition>
</tagDefinition>
<tagDefinition>
<name>genome</name>
<definition>A genome is the full compliment of hereditary information (usually DNA) for a given organism, and includes coding and non-coding sequences where applicable. 'Genome' tagged data collections are those whose information is derived from genome level sequencing projects.</definition>
</tagDefinition>
<tagDefinition>
<name>human</name>
<definition>Data collections labelled 'human' should contain human centric data.</definition>
</tagDefinition>
<tagDefinition>
<name>image library</name>
<definition>A repository of static images or animations.</definition>
</tagDefinition>
<tagDefinition>
<name>immunogenetics</name>
<definition>A branch of research focused upon the relationship between one's genetics and immune response.</definition>
</tagDefinition>
<tagDefinition>
<name>interaction</name>
<definition>Data collections tagged 'interaction' should contain information relating to molecular interaction data, often protein-protein.</definition>
</tagDefinition>
<tagDefinition>
<name>kinetics</name>
<definition>Kinetics is the study of rates of reactions or chemical processes. Data collections tagged 'kinetics' should provide information such as rate laws and rate constants.</definition>
</tagDefinition>
<tagDefinition>
<name>lipid</name>
<definition>Data collection pertaining to lipids, which are lipophilic, naturally-occurring molecules.</definition>
</tagDefinition>
<tagDefinition>
<name>mammalian</name>
<definition>Data collections labelled 'mammalian' should contain mammal centric data.</definition>
</tagDefinition>
<tagDefinition>
<name>mass spectrometry</name>
<definition>Mass spectrometry is an analytical technique that identifies the chemical composition of a compound or sample on the basis of the mass-to-charge ratio of charged particles. [Wikipedia]</definition>
</tagDefinition>
<tagDefinition>
<name>metabolite</name>
<definition>Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules. A primary metabolite is directly involved in normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has an important ecological function. Examples include antibiotics and pigments.</definition>
</tagDefinition>
<tagDefinition>
<name>microarray</name>
<definition>Microarray is a high-throughput technology often used to measure gene expression.</definition>
</tagDefinition>
<tagDefinition>
<name>microbial</name>
<definition>Datatype relating to bacterial species</definition>
</tagDefinition>
<tagDefinition>
<name>model</name>
<definition>Data collection pertaining to mathematical models, encoded in a form that allows their use in simulation software.</definition>
</tagDefinition>
<tagDefinition>
<name>neuroscience</name>
<definition>Scientific study of the nervous system.</definition>
</tagDefinition>
<tagDefinition>
<name>nucleotide</name>
<definition>Data collections tagged with 'nucleotide' refer to DNA and RNA molecules.</definition>
</tagDefinition>
<tagDefinition>
<name>ontology</name>
<definition>Data collections tagged with 'ontology' reference those ontologies that are used in the life sciences.</definition>
</tagDefinition>
<tagDefinition>
<name>pathway</name>
<definition>Series of sequential chemical reactions that are referred to collectively.</definition>
</tagDefinition>
<tagDefinition>
<name>pharmacogenomics</name>
<definition>Pharmacogenomics is the branch of pharmacology which deals with the influence of genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms with a drug's efficacy or toxicity. [wiki] </definition>
</tagDefinition>
<tagDefinition>
<name>phenotype</name>
<definition>A phenotype is any observable characteristic of an organism, such as its morphology, development, biochemical or physiological properties, or behaviour [wikipedia].</definition>
</tagDefinition>
<tagDefinition>
<name>plant</name>
<definition>Dataype type should be focused on plant species</definition>
</tagDefinition>
<tagDefinition>
<name>polysaccharide</name>
<definition>Polysaccharides are polymeric carbohydrate structures, formed of repeating units (either mono- or di-saccharides) joined together by glycosidic bonds. These structures are often linear, but may contain various degrees of branching. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit.
[http://en.wikipedia.org/wiki/Polysaccharide]</definition>
</tagDefinition>
<tagDefinition>
<name>protein</name>
<definition>Data collections with this tag reference data pertaining to proteins.</definition>
</tagDefinition>
<tagDefinition>
<name>reaction</name>
<definition>A single chemical reaction which yields products which are, generally, different from the reactants. Data collections tagged 'reaction' focus on individual chemical reactions.</definition>
</tagDefinition>
<tagDefinition>
<name>registry</name>
<definition>A data collection within which information is registered or collated, effectively providing a catalogue for (community) reference purposes.</definition>
</tagDefinition>
<tagDefinition>
<name>schema.org</name>
<definition>Data collection containing Schema.org metadata.</definition>
</tagDefinition>
<tagDefinition>
<name>sequence</name>
<definition>Data collections tagged 'sequence' reference sequence data, such as DNA, RNA or protein.</definition>
</tagDefinition>
<tagDefinition>
<name>strain</name>
<definition>A genetic variant of a particular organism.</definition>
</tagDefinition>
<tagDefinition>
<name>structure</name>
<definition>Data collections with the 'structure' tag should reference chemical or 3-dimensional structure.</definition>
</tagDefinition>
<tagDefinition>
<name>taxonomy</name>
<definition>A classification scheme, arranged in a hierarchical structure, that depicts parent-child relationships between its members.</definition>
</tagDefinition>
<tagDefinition>
<name>viral</name>
<definition>Data collection pertaining to virus information.</definition>
</tagDefinition>
</listOfTags>
</miriam>
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