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BioPAX Semantic Rules and Best Practices validation
<?xml version="1.0" encoding="UTF-8"?>
<!--
-->
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:p="http://www.springframework.org/schema/p"
xmlns:context="http://www.springframework.org/schema/context"
xmlns:oxm="http://www.springframework.org/schema/oxm"
xmlns:aop="http://www.springframework.org/schema/aop"
xmlns:util="http://www.springframework.org/schema/util"
xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context.xsd
http://www.springframework.org/schema/oxm http://www.springframework.org/schema/oxm/spring-oxm.xsd
http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop.xsd
http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util.xsd">
<context:spring-configured/>
<context:annotation-config/>
<!-- XrefRule, XrefSynonymDbRule additional (optional) configuration
The following LISTS of DB (biodata source) synonyms and typos will
merge with overlapping groups from Miriam and PSI-MI ("database citation"
ontology branch) and then used to warn about non-standard but
somewhat close/known names and probably auto-fix all such cases. If
the first name in a list below is a STANDARD name (found in Miriam or MI),
then the corresponding PREFERRED name will be suggested as the replacement.
If the first name in a list below is a STANDARD Miriam datasource name, then
the rules will be able also to check identifiers using the ID pattern.
Otherwise (- not Miriam, no pattern), it won't validate identifiers.
-->
<util:set id="extraDbSynonyms">
<list>
<value>PDB</value>
<value>RCSB PDB</value>
</list>
<list>
<value>ENTREZ GENE</value>
<value>ENTREZ_GENE</value>
<value>LOCUS_LINK</value>
<value>LOCUSLINK</value>
<value>LOCUS-LINK</value>
<value>ENTREZGENE</value>
<value>ENTREZ GENE/LOCUSLINK</value>
</list>
<list>
<value>NCBI GI</value>
<value>ENTREZ GI</value>
<value>GI</value>
</list>
<list>
<value>PUBCHEM-SUBSTANCE</value>
<value>NCBI PUBCHEM</value>
<value>PUBCHEM SUBSTANCE</value>
<value>PUBCHEM</value>
</list>
<list>
<value>PUBMED</value>
<value>PMID</value>
<value>MEDLINE</value>
</list>
<list>
<value>UNIPROT</value>
<value>SWISS-PROT</value>
<value>SWISSPROT</value>
<value>SWISSTREMBL</value>
<value>SWP</value>
<value>SWISS-PROT/TREMBL</value>
<value>UNIPROTKB</value>
<value>REACTOME PROTEIN</value>
<value>UNIPROT KNOWLEDGE BASE</value>
<value>PIR</value>
<value>PIR-SSD</value>
</list>
<list>
<value>GO</value>
<value>GENE ONTOLOGY</value>
<value>GENE_ONTOLOGY</value>
</list>
<list>
<value>UM-BBD</value>
<value>UMBBD</value>
</list>
<list>
<value>PSI-MI</value>
<value>PSI MI</value>
<value>PSIMI</value>
<value>MI</value>
</list>
<list>
<value>REFSEQ PROTEIN</value>
<value>REFSEQ</value>
<value>REF_SEQ</value>
<value>REF-SEQ</value>
<value>REF_SEQ PROTEIN</value>
</list>
<list>
<value>HGNC SYMBOL</value>
<value>HGNC_SYMBOL</value>
<value>GENE SYMBOL</value>
<value>GENE_SYMBOL</value>
</list>
<list>
<value>TAXONOMY</value>
<value>NCBI TAXONOMY</value>
<value>NCBI_TAXONOMY</value>
<value>NCBI-TAXONOMY</value>
<value>TAXON</value>
<value>NCBITAXON</value>
<value>NCBI-TAXON</value>
<value>NCBI TAXON</value>
<value>NCBI_TAXON</value>
</list>
<list>
<value>NUCLEOTIDE SEQUENCE DATABASE</value>
<value>NCBI GENBANK</value>
<value>GENBANK</value>
<value>DDBJ</value>
<value>EMBL-BANK</value>
<value>EMBL</value>
</list>
<list>
<value>PROTEIN GENBANK IDENTIFIER</value>
<value>GENPEPT</value>
</list>
<list>
<value>KEGG COMPOUND</value>
<value>COMPOUND</value>
<value>KEGG LIGAND</value>
<value>LIGAND</value>
</list>
<list>
<value>KEGG GENOMES</value>
<value>KEGG GENOME</value>
</list>
<list>
<value>KEGG GENES</value>
<value>KEGG GENE</value>
</list>
<list>
<value>AFFYMETRIX</value>
</list>
<list>
<value>KEGG Glycan</value>
<value>GLYCAN</value>
</list>
<list>
<value>IOB</value>
</list>
<list>
<value>SGD</value>
</list>
<list>
<value>ENCODE</value>
</list>
<list>
<value>AMAZE</value>
</list>
<list>
<value>HUGE</value>
</list>
<list>
<value>HPRD</value>
</list>
<list>
<value>UNIPARC</value>
</list>
<list>
<value>SWISS-MODEL</value>
</list>
<list>
<value>CAS</value>
</list>
<list>
<value>UNIGENE</value>
</list>
<list>
<value>EVIDENCE CODE ONTOLOGY</value>
<value>ECO</value>
<value>EVIDENCE CODE</value>
</list>
<list>
<value>REACTOME</value>
<value>REACTOME STABLE ID</value>
</list>
<list>
<value>BIOCYC</value>
<value>HUMANCYC</value>
<value>MOUSECYC</value>
</list>
<list>
<value>CL</value>
<value>CELL TYPE ONTOLOGY</value>
<value>CELL ONTOLOGY</value>
</list>
</util:set>
<!-- end of the XrefRule config. -->
<bean id="validator" class="org.biopax.validator.impl.ValidatorImpl" />
<!-- BiopaxValidatorUtils configuration -->
<bean id="rulesMessageSource"
class="org.springframework.context.support.ResourceBundleMessageSource">
<property name="basenames">
<list>
<value>rules</value> <!-- classpath:rules.properties resource -->
<value>codes</value> <!-- classpath:codes.properties resource -->
<value>profiles</value> <!-- classpath:profiles.properties resource -->
</list>
</property>
</bean>
<bean id="utils" class="org.biopax.validator.api.ValidatorUtils">
<property name="messageSource" ref="rulesMessageSource" />
<property name="locale" value="en" />
<property name="maxErrors" value="10000" />
</bean>
<!-- end of BiopaxValidatorUtils config. -->
<bean id="ontologyManager" class="org.biopax.validator.utils.BiopaxOntologyManager" scope="singleton">
<constructor-arg index="0">
<util:properties local-override="false" location="classpath:obo.properties"/>
</constructor-arg>
</bean>
<!-- a helper and a proxy to access MIRIAM and MI database citation and regexps
to validate their corresponding IDs -->
<bean id="xrefHelper" class="org.biopax.validator.utils.XrefHelper" scope="singleton">
<constructor-arg ref="extraDbSynonyms"/>
<constructor-arg ref="ontologyManager" />
</bean>
<context:component-scan base-package="org.biopax.validator.rules"/>
</beans>