llbase.cellbase-core.4.6.2.source-code.configuration.json Maven / Gradle / Ivy
{
"version": "v4",
"apiVersion": "${cellbase.version}",
"wiki": "https://github.com/opencb/cellbase/wiki",
"maintenanceFlagFile": "/tmp/maintenance",
"maintainerContact": "[email protected]",
"databases": {
"mongodb": {
"host": "${CELLBASE.DB.MONGODB.HOST}",
"user": "${CELLBASE.DB.USER}",
"password": "${CELLBASE.DB.PASSWORD}",
"options": {
"authenticationDatabase": "${CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE}",
"readPreference": "${CELLBASE.DB.MONGODB.READPREFERENCE}",
"replicaSet": "${CELLBASE.DB.MONGODB.REPLICASET}",
"connectionsPerHost": 20
}
},
"neo4j": {
"hsapiens": {
"host": "${CELLBASE.DB.NEO4J.HOST}",
"user": "${CELLBASE.DB.USER}",
"password": "${CELLBASE.DB.PASSWORD}"
},
"mmusculus": {
"host": "${CELLBASE.DB.NEO4J.HOST}",
"user": "${CELLBASE.DB.USER}",
"password": "${CELLBASE.DB.PASSWORD}"
}
}
},
"defaultOutdir": "/tmp",
"download": {
"ensembl": {
"database": {
"host": "ensembldb.ensembl.org:3306",
"user": "anonymous",
"password": ""
},
"libs": "${CELLBASE.ENSEMBL.LIBS}",
"url": {
"host": "ftp://ftp.ensembl.org/pub"
}
},
"ensemblGenomes":{
"database":{
"host": "mysql-eg-publicsql.ebi.ac.uk:4157",
"user": "anonymous",
"password": ""
},
"libs": "${CELLBASE.ENSEMBL.LIBS}",
"url":{
"host":"ftp://ftp.ensemblgenomes.org/pub"
}
},
"geneUniprotXref": {
"host": "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/"
},
"geneExpressionAtlas": {
"host": "ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/gxa/allgenes_updown_in_organism_part_2.0.14.tab.gz"
},
"mirbase": {
"host": "ftp://mirbase.org/pub/mirbase/CURRENT/"
},
"mirbaseReadme": {
"host": "ftp://mirbase.org/pub/mirbase/CURRENT/README"
},
"targetScan": {
"host": "http://hgdownload.cse.ucsc.edu/goldenPath/"
},
"miRTarBase": {
"host": "http://mirtarbase.mbc.nctu.edu.tw/cache/download/4.5/"
},
"uniprot": {
"host": "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz"
},
"uniprotRelNotes": {
"host": "ftp://ftp.uniprot.org/pub/databases/uniprot/relnotes.txt"
},
"intact": {
"host": "ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.txt"
},
"interpro": {
"host": "ftp://ftp.ebi.ac.uk/pub/databases/interpro/current/protein2ipr.dat.gz"
},
"interproRelNotes": {
"host": "ftp://ftp.ebi.ac.uk/pub/databases/interpro/current/release_notes.txt"
},
"conservation": {
"host": "ftp://hgdownload.cse.ucsc.edu/goldenPath/"
},
"gerp": {
"host": "http://mendel.stanford.edu/SidowLab/downloads/gerp/hg19.GERP_scores.tar.gz"
},
"clinvar": {
"host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2018-10.xml.gz"
},
"clinvarSummary": {
"host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz"
},
"clinvarVariationAllele": {
"host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variation_allele.txt.gz"
},
"clinvarEfoTerms": {
"host": "ftp://ftp.ebi.ac.uk/pub/databases/eva/ClinVar/2015/ClinVar_Traits_EFO_Names_260615.csv"
},
"iarctp53": {
"host": "http://p53.iarc.fr/ajax/Zipper.ashx"
},
"docm": {
"host": "http://docm.genome.wustl.edu/api/"
},
"docmVersion": {
"host": "http://docm.genome.wustl.edu"
},
"dgv": {
"host": "http://dgv.tcag.ca/v106/docs"
},
"simpleRepeats": {
"host": "http://hgdownload.cse.ucsc.edu/goldenPath"
},
"windowMasker": {
"host": "http://hgdownload.cse.ucsc.edu/goldenPath"
},
"genomicSuperDups": {
"host": "http://hgdownload.cse.ucsc.edu/goldenPath"
},
"gwasCatalog": {
"host": "ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/2016/09/28/gwas-catalog-associations.tsv"
},
"hpo": {
"host": "http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt"
},
"disgenet": {
"host": "http://www.disgenet.org/ds/DisGeNET/results/all_gene_disease_associations.tsv.gz"
},
"disgenetReadme": {
"host": "http://www.disgenet.org/ds/DisGeNET/results/readme.txt"
},
"dgidb": {
"host": "http://dgidb.org/data/interactions.tsv"
},
"cadd": {
"host": "http://krishna.gs.washington.edu/download/CADD/v1.3/whole_genome_SNVs.tsv.gz"
},
"reactome": {
"host": "http://www.reactome.org/download/current/biopax.zip"
}
},
"species": {
"vertebrates": [
{
"id": "hsapiens",
"scientificName": "Homo sapiens",
"assemblies": [
{
"ensemblVersion":"82_37",
"name":"GRCh37"
},
{
"ensemblVersion":"89_38",
"name":"GRCh38"
}
],
"data":[
"genome",
"genome_info",
"gene",
"gene_disease_association",
"variation",
"variation_functional_score",
"regulation",
"protein",
"conservation",
"clinical_variants",
"clinical",
"svs",
"repeats"
]
},
{
"id":"mmusculus",
"scientificName":"Mus musculus",
"assemblies":[
{
"ensemblVersion":"82_38",
"name":"GRCm38"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation",
"regulation",
"protein",
"conservation"
]
},
{
"id":"drerio",
"scientificName":"Danio rerio",
"assemblies":[
{
"ensemblVersion":"82_10",
"name":"GRCz10"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation",
"protein"
]
},
{
"id":"rnorvegicus",
"scientificName":"Rattus norvegicus",
"assemblies":[
{
"ensemblVersion":"82_6",
"name":"Rnor_6.0"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation",
"protein"
]
},
{
"id":"ptroglodytes",
"scientificName":"Pan troglodytes",
"assemblies":[
{
"ensemblVersion":"82_214",
"name":"CHIMP2.1.4"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation"
]
},
{
"id":"ggorilla",
"scientificName":"Gorilla gorilla",
"assemblies":[
{
"ensemblVersion":"82_31",
"name":"gorGor3.1"
}
],
"data":[
"genome",
"genome_info",
"gene"
]
},
{
"id":"csabaeus",
"scientificName":"Chlorocebus sabaeus",
"assemblies":[
{
"ensemblVersion":"82_1",
"name":"ChlSab1.1"
}
],
"data":[
"genome",
"genome_info",
"gene"
]
},
{
"id":"sscrofa",
"scientificName":"Sus scrofa",
"assemblies":[
{
"ensemblVersion":"82_102",
"name":"Sscrofa10.2"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation",
"protein"
]
},
{
"id":"cfamiliaris",
"scientificName":"Canis familiaris",
"assemblies":[
{
"ensemblVersion":"82_31",
"name":"CanFam3.1"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation"
]
}
],
"metazoa":[
{
"id":"celegans",
"scientificName":"Caenorhabditis elegans",
"assemblies":[
{
"ensemblVersion":"29_82_245",
"name":"WBcel235"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation",
"protein"
]
},
{
"id":"dmelanogaster",
"scientificName":"Drosophila melanogaster",
"assemblies":[
{
"ensemblVersion":"29_82_6",
"name":"BDGP6"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation",
"protein"
]
},
{
"id":"agambiae",
"scientificName":"Anopheles gambiae",
"assemblies":[
{
"ensemblVersion":"29_82_4",
"name":"AgamP4"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation",
"protein"
]
}
],
"fungi":[
{
"id":"scerevisiae",
"scientificName":"Saccharomyces cerevisiae",
"assemblies":[
{
"ensemblVersion":"29_82_4",
"name":"R64-1-1"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation",
"protein"
]
},
{
"id":"afumigatus",
"scientificName":"Aspergillus fumigatus",
"assemblies":[
{
"ensemblVersion":"29_82_2",
"name":"CADRE"
}
],
"data":[
"genome",
"genome_info",
"gene"
]
},
{
"id":"anidulans",
"scientificName":"Aspergillus nidulans",
"assemblies":[
{
"ensemblVersion":"29_82_6",
"name":"ASM1142v1"
}
],
"data":[
"genome",
"genome_info",
"gene"
]
}
],
"protist":[
{
"id":"pfalciparum",
"scientificName":"Plasmodium falciparum",
"assemblies":[
{
"ensemblVersion":"29_82_3",
"name":"ASM276v1"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation",
"protein"
]
},
{
"id":"lmajor",
"scientificName":"Leishmania major",
"assemblies":[
{
"ensemblVersion":"29_82_2",
"name":"ASM272v2"
}
],
"data":[
"genome",
"genome_info",
"gene"
]
}
],
"plants":[
{
"id":"athaliana",
"scientificName":"Arabidopsis thaliana",
"assemblies":[
{
"ensemblVersion":"29_82_10",
"name":"TAIR10"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation",
"protein"
]
},
{
"id":"osativa",
"scientificName":"Oryza sativa",
"assemblies":[
{
"ensemblVersion":"29_82_7",
"name":"IRGSP-1.0"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation"
]
},
{
"id":"gmax",
"scientificName":"Glycine max",
"assemblies":[
{
"ensemblVersion":"29_82_1",
"name":"V1.0"
}
],
"data":[
"genome",
"genome_info",
"gene"
]
},
{
"id":"vvinifera",
"scientificName":"Vitis vinifera",
"assemblies":[
{
"ensemblVersion":"29_82_3",
"name":"IGGP_12x"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation"
]
},
{
"id":"zmays",
"scientificName":"Zea mays",
"assemblies":[
{
"ensemblVersion":"29_82_6",
"name":"AGPv3"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation"
]
},
{
"id":"sbicolor",
"scientificName":"Sorghum bicolor",
"assemblies":[
{
"ensemblVersion":"29_82_14",
"name":"Sorbi1"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation"
]
},
{
"id":"slycopersicum",
"scientificName":"Solanum lycopersicum",
"assemblies":[
{
"ensemblVersion":"29_82_250",
"name":"GCA_000188115.2"
}
],
"data":[
"genome",
"genome_info",
"gene",
"variation"
]
}
],
"virus" : [
{
"id":"evirus",
"scientificName":"Ebola virus",
"assemblies":[
{
"name":"KM034562v1"
}
],
"data":[
"genome",
"gene"
]
}
],
"bacteria": [
{
"id": "mpneumoniae",
"scientificName": "Mycoplasma pneumoniae M129",
"assemblies": [
{
"ensemblVersion":"29_82_1",
"ensemblCollection":"bacteria_0_collection",
"name":"ASM2734v1"
}
],
"data":[
"genome",
"genome_info",
"gene",
"protein"
]
},
{
"id": "ecoli",
"scientificName": "Escherichia coli",
"assemblies": [
{
"ensemblVersion":"29_82_1",
"ensemblCollection":"bacteria_91_collection",
"name":"HUSEC2011CHR1"
}
],
"data":[
"genome",
"genome_info",
"gene",
"protein"
]
}
]
}
}
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