Commit 601521ba authored by Xavier Watkins's avatar Xavier Watkins
Browse files

Update xref file

parent f7a1603c
......@@ -433,7 +433,7 @@ module.exports = function (grunt) {
cwd: '<%= yeoman.app %>',
dest: '<%= yeoman.dist %>',
src: [
'*.{ico,png,txt}',
'*.{ico,png,txt,json}',
'.htaccess',
'{,*/}*.html',
'images/{,*/}*.{webp}',
......
[
{
"database": "AgBase",
"name": "AgBase resource for functional analysis of agricultural plant and animal gene products",
"generic_urls": [
"http://www.agbase.msstate.edu/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"example_id": "P02264",
"url_syntax": "https://agbase.arizona.edu/cgi-bin/getEntry.pl?db_pick=all&database=Swiss-Prot&gb_acc=[example_id]"
}
]
},
{
"database": "AGI_LocusCode",
"name": "Arabidopsis Genome Initiative",
"description": "Comprises TAIR, TIGR and MIPS",
"generic_urls": [
"http://www.arabidopsis.org"
],
"entity_types": [
{
"type_name": "gene",
"type_id": "SO:0000704",
"id_syntax": "A[Tt][MmCc0-5][Gg][0-9]{5}(\\.[0-9]{1})?",
"url_syntax": "http://arabidopsis.org/servlets/TairObject?type=locus&name=[example_id]",
"example_id": "AGI_LocusCode:At2g17950",
"example_url": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950"
}
]
},
{
"database": "AGRICOLA_ID",
"name": "AGRICultural OnLine Access",
"generic_urls": [
"http://agricola.nal.usda.gov/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"example_id": "AGRICOLA_NAL:TP248.2 P76 v.14"
}
]
},
{
"database": "AGRICOLA_IND",
"name": "AGRICultural OnLine Access",
"generic_urls": [
"http://agricola.nal.usda.gov/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"example_id": "AGRICOLA_IND:IND23252955"
}
]
},
{
"database": "Alzheimers_University_of_Toronto",
"name": "Alzheimers Project at University of Toronto",
"generic_urls": [
"http://www.ims.utoronto.ca/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000"
}
]
},
{
"database": "ApiDB_PlasmoDB",
"name": "PlasmoDB Plasmodium Genome Resource",
"generic_urls": [
"http://plasmodb.org/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://www.plasmodb.org/gene/[example_id]",
"example_id": "ApiDB_PlasmoDB:PF11_0344",
"example_url": "https://plasmodb.org/plasmo/app/record/gene/PF11_0344"
}
]
},
{
"database": "APweb",
"name": "Angiosperm Phylogeny Website",
"generic_urls": [
"http://www.mobot.org/mobot/research/apweb/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html",
"example_id": "APweb:Glossary",
"example_url": "http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html"
}
]
},
{
"database": "ARUK-UCL",
"name": "Alzheimers Research Gene Ontology Initiative",
"generic_urls": [
"https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene-0"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000"
}
]
},
{
"database": "ASAP",
"name": "A Systematic Annotation Package for Community Analysis of Genomes",
"generic_urls": [
"https://asap.genetics.wisc.edu/asap/ASAP1.htm"
],
"entity_types": [
{
"type_name": "gene",
"type_id": "SO:0000704",
"url_syntax": "https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=[example_id]",
"example_id": "ASAP:ABF-0014586",
"example_url": "https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=ABF-0014586"
}
]
},
{
"database": "AspGD",
"name": "Aspergillus Genome Database",
"synonyms": [
"ASPGD",
"AspGDID"
],
"generic_urls": [
"http://www.aspergillusgenome.org/"
],
"entity_types": [
{
"type_name": "gene",
"type_id": "SO:0000704",
"id_syntax": "ASPL[0-9]{10}",
"url_syntax": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=[example_id]",
"example_id": "AspGD:ASPL0000067538",
"example_url": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=ASPL0000067538"
}
]
},
{
"database": "AspGD_LOCUS",
"name": "Aspergillus Genome Database",
"rdf_uri_prefix": "http://identifiers.org/aspgd.locus/",
"generic_urls": [
"http://www.aspergillusgenome.org/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=[example_id]",
"example_id": "AspGD_LOCUS:AN10942",
"example_url": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=AN10942"
}
]
},
{
"database": "AspGD_REF",
"name": "Aspergillus Genome Database",
"generic_urls": [
"http://www.aspergillusgenome.org/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]",
"example_id": "AspGD_REF:90",
"example_url": "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=90"
}
]
},
{
"database": "BFO",
"name": "Basic Formal Ontology",
"description": "An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050)",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/BFO_",
"generic_urls": [
"http://purl.obolibrary.org/obo/bfo"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://purl.obolibrary.org/obo/BFO_[example_id]",
"example_id": "BFO:0000066",
"example_url": "http://purl.obolibrary.org/obo/BFO_0000066"
}
]
},
{
"database": "BHF-UCL",
"name": "Cardiovascular Gene Ontology Annotation Initiative",
"description": "The Cardiovascular Gene Ontology Annotation Initiative is supported by the British Heart Foundation (BHF) and located at University College London (UCL).",
"generic_urls": [
"https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/cardiovascular-gene"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000"
}
]
},
{
"database": "BioCyc",
"name": "BioCyc collection of metabolic pathway databases",
"generic_urls": [
"http://biocyc.org/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=[example_id]",
"example_id": "BioCyc:PWY-5271",
"example_url": "http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5271"
}
]
},
{
"database": "BIOMD",
"name": "BioModels Database",
"synonyms": [
"BIOMDID"
],
"generic_urls": [
"https://www.ebi.ac.uk/biomodels/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "https://www.ebi.ac.uk/biomodels/[example_id]",
"example_id": "BIOMD:BIOMD0000000045",
"example_url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000045"
}
]
},
{
"database": "bioRxiv",
"name": "bioRxiv",
"synonyms": [
"BIORXIV"
],
"generic_urls": [
"https://www.biorxiv.org/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"id_syntax": "[0-9]+",
"url_syntax": "https://www.biorxiv.org/content/[example_id]",
"example_id": "bioRxiv:10.1101/530881v2",
"example_url": "https://www.biorxiv.org/content/10.1101/530881v2"
}
]
},
{
"database": "BRENDA",
"name": "BRENDA, The Comprehensive Enzyme Information System",
"generic_urls": [
"http://www.brenda-enzymes.info"
],
"entity_types": [
{
"type_name": "catalytic activity",
"type_id": "GO:0003824",
"url_syntax": "https://www.brenda-enzymes.info/enzyme.php?ecno=[example_id]",
"example_id": "BRENDA:4.2.1.3",
"example_url": "https://www.brenda-enzymes.info/enzyme.php?ecno=4.2.1.3"
}
]
},
{
"database": "BTO",
"name": "BRENDA tissue / enzyme ontology",
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/BTO_",
"generic_urls": [
"http://purl.obolibrary.org/obo/bto"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://purl.obolibrary.org/obo/BTO_[example_id]",
"example_id": "BTO_0002164",
"example_url": "http://purl.obolibrary.org/obo/BTO_0002164"
}
]
},
{
"database": "CACAO",
"name": "Community Assessment of Community Annotation with Ontologies",
"description": "The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition.",
"generic_urls": [
"http://gowiki.tamu.edu/wiki/index.php/Category:CACAO"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "https://gowiki.tamu.edu/wiki/index.php/[example_id]",
"example_id": "MYCS2:A0QNF5",
"example_url": "https://gowiki.tamu.edu/wiki/index.php/MYCS2:A0QNF5"
}
]
},
{
"database": "CAFA",
"name": "Critical Assessment of Protein Function Annotation",
"generic_urls": [
"http://biofunctionprediction.org/cafa/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000"
}
]
},
{
"database": "CARO",
"name": "Common Anatomy Reference Ontology",
"description": "An upper ontology for anatomy used by OBO Foundry ontologies. Used to facilitate interoperability between existing anatomy ontologies for different species",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/CARO_",
"generic_urls": [
"http://purl.obolibrary.org/obo/caro"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://purl.obolibrary.org/obo/CARO_[example_id]",
"example_id": "CARO:0020003",
"example_url": "http://purl.obolibrary.org/obo/CARO_0020003"
}
]
},
{
"database": "CAS",
"name": "CAS Chemical Registry",
"description": "CAS REGISTRY is the most authoritative collection of disclosed chemical substance information, containing more than 54 million organic and inorganic substances and 62 million sequences. CAS REGISTRY covers substances identified from the scientific literature from 1957 to the present, with additional substances going back to the early 1900s.",
"rdf_uri_prefix": "http://identifiers.org/cas/",
"generic_urls": [
"http://www.cas.org/expertise/cascontent/registry/index.html"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"example_id": "CAS:58-08-2"
}
]
},
{
"database": "CASGEN",
"name": "Catalog of Fishes genus database",
"synonyms": [
"CAS_GEN"
],
"generic_urls": [
"http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=[example_id]",
"example_id": "CASGEN:1040",
"example_url": "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=1040"
}
]
},
{
"database": "CASREF",
"name": "Catalog of Fishes publications database",
"generic_urls": [
"http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=[example_id]",
"example_id": "CASREF:2031",
"example_url": "http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=2031"
}
]
},
{
"database": "CASSPC",
"name": "Catalog of Fishes species database",
"synonyms": [
"CAS_SPC"
],
"generic_urls": [
"http://research.calacademy.org/research/ichthyology/catalog/fishcatsearch.html"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=[example_id]",
"example_url": "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979"
}
]
},
{
"database": "CAZY",
"name": "Carbohydrate Active EnZYmes",
"description": "The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.",
"generic_urls": [
"http://www.cazy.org/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"id_syntax": "(CE|GH|GT|PL)\\d+",
"url_syntax": "http://www.cazy.org/[example_id].html",
"example_id": "CAZY:PL11",
"example_url": "http://www.cazy.org/PL11.html"
}
]
},
{
"database": "DTU",
"name": "DTU Health Tech Services",
"description": "Formerly CBS (Center for Biological Sequence Analysis)",
"generic_urls": [
"http://www.cbs.dtu.dk/services"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"example_id": "CBS:TMHMM",
"example_url": "http://www.cbs.dtu.dk/services/TMHMM/"
}
]
},
{
"database": "CDD",
"name": "Conserved Domain Database at NCBI",
"generic_urls": [
"https://www.ncbi.nlm.nih.gov/cdd"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=[example_id]",
"example_id": "CDD:34222",
"example_url": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=34222"
}
]
},
{
"database": "CGD",
"name": "Candida Genome Database",
"synonyms": [
"CGDID"
],
"rdf_uri_prefix": "http://identifiers.org/cgd/",
"generic_urls": [
"http://www.candidagenome.org/"
],
"entity_types": [
{
"type_name": "gene",
"type_id": "SO:0000704",
"id_syntax": "(CAL|CAF)[0-9]{10}",
"url_syntax": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=[example_id]",
"example_id": "CGD:CAL0000179664",
"example_url": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=CAL0000179664"
}
]
},
{
"database": "CGD_LOCUS",
"name": "Candida Genome Database",
"generic_urls": [
"http://www.candidagenome.org/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://www.candidagenome.org/cgi-bin/locus.pl?locus=[example_id]",
"example_id": "CGD_LOCUS:HWP1",
"example_url": "http://www.candidagenome.org/cgi-bin/locus.pl?locus=HWP1"
}
]
},
{
"database": "CGD_REF",
"name": "Candida Genome Database",
"generic_urls": [
"http://www.candidagenome.org/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"url_syntax": "http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]",
"example_id": "CGD_REF:1490",
"example_url": "http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=1490"
}
]
},
{
"database": "CGSC",
"name": "CGSC",
"generic_urls": [
"http://cgsc.biology.yale.edu/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"example_id": "CGSC:rbsK",
"example_url": "http://cgsc.biology.yale.edu/Site.php?ID=315"
}
]
},
{
"database": "CHEBI",
"name": "Chemical Entities of Biological Interest",
"synonyms": [
"ChEBI"
],
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/CHEBI_",
"generic_urls": [
"http://www.ebi.ac.uk/chebi/"
],
"entity_types": [
{
"type_name": "chemical entity",
"type_id": "CHEBI:24431",
"id_syntax": "[0-9]{1,6}",
"url_syntax": "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:[example_id]",
"example_id": "CHEBI:17234",
"example_url": "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17234"
}
]
},
{
"database": "CL",
"name": "Cell Type Ontology",
"rdf_uri_prefix": "http://purl.obolibrary.org/obo/CL_",
"generic_urls": [
"http://cellontology.org"
],
"entity_types": [
{
"type_name": "cell",
"type_id": "GO:0005623",
"id_syntax": "[0-9]{7}",
"url_syntax": "http://purl.obolibrary.org/obo/CL_[example_id]",
"example_id": "CL:0000041",
"example_url": "http://purl.obolibrary.org/obo/CL_0000041"
}
]
},
{
"database": "CO_125",
"name": "Crop Ontology CGIAR Musa Anatomy",
"generic_urls": [
"http://www.cropontology.org/ontology/CO_125:0000000/CGIAR_Musa_anatomy"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000",
"example_id": "CO_125:0000002",
"example_url": "http://www.cropontology.org/ontology/CO_125:0000000"
}
]
},
{
"database": "COG",
"name": "NCBI Clusters of Orthologous Groups",
"generic_urls": [
"http://www.ncbi.nlm.nih.gov/COG/"
],
"entity_types": [
{
"type_name": "entity",
"type_id": "BET:0000000"
}
]
},
{
"database": "COG_Cluster",
"name": "NCBI COG cluster",
"generic_urls": [