llbase.cellbase-core.3.1.1.source-code.configuration.json Maven / Gradle / Ivy
{
"version": "v3",
"apiVersion": "v3.1",
"wiki": "https://github.com/opencb/cellbase/wiki",
"database": {
"host": "${CELLBASE.DB.HOST}",
"port": "${CELLBASE.DB.PORT}",
"user": "${CELLBASE.DB.USER}",
"password": "${CELLBASE.DB.PASSWORD}",
"options": {
"authenticationDatabase": "${CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE}",
"readPreference": "${CELLBASE.DB.MONGODB.READPREFERENCE}"
}
},
"defaultOutdir": "/tmp",
"download": {
"ensembl": {
"database": {
"host": "ensembldb.ensembl.org",
"port": 3306,
"user": "anonymous",
"password": ""
},
"libs": "${CELLBASE.ENSEMBL.LIBS}",
"url": {
"host": "ftp://ftp.ensembl.org/pub"
}
},
"ensemblGenomes":{
"database":{
"host": "mysql-eg-publicsql.ebi.ac.uk",
"port": 4157,
"user": "anonymous",
"password": ""
},
"libs": "${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/"
},
"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"
},
"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"
},
"conservation": {
"host": "ftp://hgdownload.cse.ucsc.edu/goldenPath/"
},
"clinvar": {
"host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2015-03.xml.gz"
},
"gwasCatalog": {
"host": "http://www.ebi.ac.uk/gwas/api/search/downloads/full"
}
},
"species":{
"vertebrates":[
{
"id":"hsapiens",
"scientificName":"Homo sapiens",
"assemblies":[
{
"ensemblVersion":"75_37",
"name":"GRCh37"
},
{
"ensemblVersion":"79_38",
"name":"GRCh38"
}
],
"data":[
"genome",
"gene",
"variation",
"regulation",
"protein",
"conservation",
"clinical"
]
},
{
"id":"mmusculus",
"scientificName":"Mus musculus",
"assemblies":[
{
"ensemblVersion":"79_38",
"name":"GRCm38"
}
],
"data":[
"genome",
"gene",
"variation",
"regulation",
"protein",
"conservation"
]
},
{
"id":"drerio",
"scientificName":"Danio rerio",
"assemblies":[
{
"ensemblVersion":"79_9",
"name":"Zv9"
}
],
"data":[
"genome",
"gene",
"variation",
"protein"
]
},
{
"id":"rnorvegicus",
"scientificName":"Rattus norvegicus",
"assemblies":[
{
"ensemblVersion":"79_5",
"name":"Rnor_5.0"
}
],
"data":[
"genome",
"gene",
"variation",
"protein"
]
},
{
"id":"ptroglodytes",
"scientificName":"Pan troglodytes",
"assemblies":[
{
"ensemblVersion":"79_214",
"name":"CHIMP2.1.4"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"ggorilla",
"scientificName":"Gorilla gorilla",
"assemblies":[
{
"ensemblVersion":"79_31",
"name":"gorGor3.1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"pabelii",
"scientificName":"Pongo abelii",
"assemblies":[
{
"ensemblVersion":"79_1",
"name":"PPYG2"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"mmulatta",
"scientificName":"Macaca mulatta",
"assemblies":[
{
"ensemblVersion":"79_10",
"name":"MMUL_1.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"csabaeus",
"scientificName":"Chlorocebus sabaeus",
"assemblies":[
{
"ensemblVersion":"79_1",
"name":"ChlSab1.1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"sscrofa",
"scientificName":"Sus scrofa",
"assemblies":[
{
"ensemblVersion":"79_102",
"name":"Sscrofa10.2"
}
],
"data":[
"genome",
"gene",
"variation",
"protein"
]
},
{
"id":"cfamiliaris",
"scientificName":"Canis familiaris",
"assemblies":[
{
"ensemblVersion":"79_31",
"name":"CanFam3.1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"ecaballus",
"scientificName":"Equus caballus",
"assemblies":[
{
"ensemblVersion":"79_2",
"name":"EquCab2"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"ocuniculus",
"scientificName":"Oryctolagus cuniculus",
"assemblies":[
{
"ensemblVersion":"79_2",
"name":"oryCun2.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"ggallus",
"scientificName":"Gallus gallus",
"assemblies":[
{
"ensemblVersion":"79_4",
"name":"Galgal4"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"btaurus",
"scientificName":"Bos taurus",
"assemblies":[
{
"ensemblVersion":"79_31",
"name":"UMD3.1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"fcatus",
"scientificName":"Felis catus",
"assemblies":[
{
"ensemblVersion":"79_62",
"name":"Felis_catus_6.2"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"cintestinalis",
"scientificName":"Ciona intestinalis",
"assemblies":[
{
"ensemblVersion":"79_3",
"name":"KH"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"oaries",
"scientificName":"Ovis aries",
"assemblies":[
{
"ensemblVersion":"79_31",
"name":"Oar_v3.1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"olatipes",
"scientificName":"Oryzias latipes",
"assemblies":[
{
"ensemblVersion":"79_1",
"name":"HdrR"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"ttruncatus",
"scientificName":"Tursiops truncatus",
"assemblies":[
{
"ensemblVersion":"79_1",
"name":"turTru1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"lafricana",
"scientificName":"Loxodonta africana",
"assemblies":[
{
"ensemblVersion":"79_3",
"name":"Loxafr3.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"cjacchus",
"scientificName":"Callithrix jacchus",
"assemblies":[
{
"ensemblVersion":"79_321",
"name":"C_jacchus3.2.1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"nleucogenys",
"scientificName":"Nomascus leucogenys",
"assemblies":[
{
"ensemblVersion":"79_1",
"name":"Nleu1.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"aplatyrhynchos",
"scientificName":"Anas platyrhynchos",
"assemblies":[
{
"ensemblVersion":"79_1",
"name":"BGI_duck_1.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"falbicollis",
"scientificName":"Ficedula albicollis",
"assemblies":[
{
"ensemblVersion":"79_1",
"name":"FicAlb_1.4"
}
],
"data":[
"genome",
"gene",
"variation"
]
}
],
"metazoa":[
{
"id":"celegans",
"scientificName":"Caenorhabditis elegans",
"assemblies":[
{
"ensemblVersion":"26_79_245",
"name":"WBcel235"
}
],
"data":[
"genome",
"gene",
"variation",
"protein"
]
},
{
"id":"dmelanogaster",
"scientificName":"Drosophila melanogaster",
"assemblies":[
{
"ensemblVersion":"26_79_6",
"name":"BDGP6"
}
],
"data":[
"genome",
"gene",
"variation",
"protein"
]
},
{
"id":"dsimulans",
"scientificName":"Drosophila simulans",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"WUGSC1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"dyakuba",
"scientificName":"Drosophila yakuba",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"dyak_r1.3"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"agambiae",
"scientificName":"Anopheles gambiae",
"assemblies":[
{
"ensemblVersion":"26_79_4",
"name":"AgamP4"
}
],
"data":[
"genome",
"gene",
"variation",
"protein"
]
},
{
"id":"adarlingi",
"scientificName":"Anopheles darlingi",
"assemblies":[
{
"ensemblVersion":"26_79_3",
"name":"AdarC1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"nvectensis",
"scientificName":"Nematostella vectensis",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"ASM20922v1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"spurpuratus",
"scientificName":"Strongylocentrotus purpuratus",
"assemblies":[
{
"ensemblVersion":"26_79_3",
"name":"GCA_000002235.2"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"bmori",
"scientificName":"Bombyx mori",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"Bmor1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"aaegypti",
"scientificName":"Aedes aegypti",
"assemblies":[
{
"ensemblVersion":"26_79_3",
"name":"AaegL3"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"apisum",
"scientificName":"Acyrthosiphon pisum",
"assemblies":[
{
"ensemblVersion":"26_79_2",
"name":"GCA_000142985.2"
}
],
"data":[
"genome",
"gene",
"variation"
]
}
],
"fungi":[
{
"id":"scerevisiae",
"scientificName":"Saccharomyces cerevisiae",
"assemblies":[
{
"ensemblVersion":"26_79_4",
"name":"R64_1_1"
}
],
"data":[
"genome",
"gene",
"variation",
"protein"
]
},
{
"id":"spombe",
"scientificName":"Schizosaccharomyces pombe",
"assemblies":[
{
"ensemblVersion":"26_79_2",
"name":"ASM294v2"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"afumigatus",
"scientificName":"Aspergillus fumigatus",
"assemblies":[
{
"ensemblVersion":"26_79_2",
"name":"CADRE"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"aniger",
"scientificName":"Aspergillus niger",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"CADRE"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"anidulans",
"scientificName":"Aspergillus nidulans",
"assemblies":[
{
"ensemblVersion":"26_79_6",
"name":"ASM1142v1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"aoryzae",
"scientificName":"Aspergillus oryzae",
"assemblies":[
{
"ensemblVersion":"26_79_2",
"name":"CADRE2"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"foxysporum",
"scientificName":"Fusarium oxysporum",
"assemblies":[
{
"ensemblVersion":"26_79_2",
"name":"FO2"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"pgraminis",
"scientificName":"Puccinia graminis",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"ASM14992v1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"ptriticina",
"scientificName":"Puccinia triticina",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"ASM15152v1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"moryzae",
"scientificName":"Magnaporthe oryzae",
"assemblies":[
{
"ensemblVersion":"26_79_8",
"name":"MG8"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"umaydis",
"scientificName":"Ustilago maydis",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"UM1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"ssclerotiorum",
"scientificName":"Sclerotinia sclerotiorum",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"ASM14694v1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"cneoformans",
"scientificName":"Cryptococcus neoformans",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"GCA_000091045.1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"ztritici",
"scientificName":"Zymoseptoria tritici",
"assemblies":[
{
"ensemblVersion":"26_79_2",
"name":"MG2"
}
],
"data":[
"genome",
"gene",
"variation"
]
}
],
"protist":[
{
"id":"pfalciparum",
"scientificName":"Plasmodium falciparum",
"assemblies":[
{
"ensemblVersion":"26_79_3",
"name":"ASM276v1"
}
],
"data":[
"genome",
"gene",
"variation",
"protein"
]
},
{
"id":"lmajor",
"scientificName":"Leishmania major",
"assemblies":[
{
"ensemblVersion":"26_79_2",
"name":"ASM272v2"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"ddiscoideum",
"scientificName":"Dictyostelium discoideum",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"dictybase.01"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"glamblia",
"scientificName":"Giardia lamblia",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"GCA_000002435.1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"pultimum",
"scientificName":"Pythium ultimum",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"pug"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"alaibachii",
"scientificName":"Albugo laibachii",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"ENA1"
}
],
"data":[
"genome",
"gene",
"variation"
]
}
],
"plants":[
{
"id":"athaliana",
"scientificName":"Arabidopsis thaliana",
"assemblies":[
{
"ensemblVersion":"26_79_10",
"name":"TAIR10"
}
],
"data":[
"genome",
"gene",
"variation",
"protein"
]
},
{
"id":"alyrata",
"scientificName":"Arabidopsis lyrata",
"assemblies":[
{
"ensemblVersion":"26_79_10",
"name":"v.1.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"bdistachyon",
"scientificName":"Brachypodium distachyon",
"assemblies":[
{
"ensemblVersion":"26_79_12",
"name":"v1.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"osativa",
"scientificName":"Oryza sativa",
"assemblies":[
{
"ensemblVersion":"26_79_7",
"name":"IRGSP-1.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"gmax",
"scientificName":"Glycine max",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"V1.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"vvinifera",
"scientificName":"Vitis vinifera",
"assemblies":[
{
"ensemblVersion":"26_79_3",
"name":"IGGP_12x"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"zmays",
"scientificName":"Zea mays",
"assemblies":[
{
"ensemblVersion":"26_79_6",
"name":"AGPv3"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"hvulgare",
"scientificName":"Hordeum vulgare",
"assemblies":[
{
"ensemblVersion":"26_79_2",
"name":"030312v2"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"macuminata",
"scientificName":"Musa acuminata",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"MA1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"sbicolor",
"scientificName":"Sorghum bicolor",
"assemblies":[
{
"ensemblVersion":"26_79_14",
"name":"Sorbi1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"sitalica",
"scientificName":"Setaria italica",
"assemblies":[
{
"ensemblVersion":"26_79_21",
"name":"JGIv2.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"taestivum",
"scientificName":"Triticum aestivum",
"assemblies":[
{
"ensemblVersion":"26_79_2",
"name":"IWGSC2"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"brapa",
"scientificName":"Brassica rapa",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"IVFCAASv1"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"ptrichocarpa",
"scientificName":"Populus trichocarpa",
"assemblies":[
{
"ensemblVersion":"26_79_20",
"name":"JGI2.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"slycopersicum",
"scientificName":"Solanum lycopersicum",
"assemblies":[
{
"ensemblVersion":"26_79_240",
"name":"SL2.40"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"stuberosum",
"scientificName":"Solanum tuberosum",
"assemblies":[
{
"ensemblVersion":"26_79_4",
"name":"3.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"smoellendorffii",
"scientificName":"Selaginella moellendorffii",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"v1.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"creinhardtii",
"scientificName":"Chlamydomonas reinhardtii",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"v3.0"
}
],
"data":[
"genome",
"gene",
"variation"
]
},
{
"id":"cmerolae",
"scientificName":"Cyanidioschyzon merolae",
"assemblies":[
{
"ensemblVersion":"26_79_1",
"name":"ASM9120v1"
}
],
"data":[
"genome",
"gene",
"variation"
]
}
]
}
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