add back in go to the registry

prefixcommons · Jan 12, 2023 · d72e741 · d72e741
1 parent 423f5c9
commit d72e741
Show file tree

Hide file tree

Showing 2 changed files with 580 additions and 0 deletions.
diff --git a/prefixcommons/registry/go_context.jsonld b/prefixcommons/registry/go_context.jsonld
@@ -0,0 +1,212 @@
+{
+    "@context": {
+        "BIOMD": "http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=", 
+        "COG_Function": "http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=", 
+        "WB": "http://identifiers.org/wormbase/", 
+        "FBbt": "http://purl.obolibrary.org/obo/FBbt_", 
+        "KEGG_LIGAND": "http://www.genome.jp/dbget-bin/www_bget?cpd:", 
+        "PSO_GIT": "https://github.com/Planteome/plant-stress-ontology/issues/", 
+        "MaizeGDB_stock": "http://maizegdb.org/data_center/stock?id=", 
+        "EMAPA": "http://purl.obolibrary.org/obo/EMAPA_", 
+        "GO": "http://purl.obolibrary.org/obo/GO_", 
+        "NCBI_GP": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=", 
+        "NMPDR": "http://www.nmpdr.org/linkin.cgi?id=", 
+        "CASSPC": "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=", 
+        "TGD_REF": "http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=", 
+        "NCBIGene": "http://identifiers.org/ncbigene/", 
+        "KEGG_REACTION": "http://www.genome.jp/dbget-bin/www_bget?rn:", 
+        "PseudoCAP": "http://v2.pseudomonas.com/getAnnotation.do?locusID=", 
+        "UniPathway": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=", 
+        "MEROPS_fam": "http://merops.sanger.ac.uk/cgi-bin/famsum?family=", 
+        "GO_REF": "http://purl.obolibrary.org/obo/go/references/", 
+        "VEGA": "http://vega.sanger.ac.uk/id/", 
+        "ZFIN": "http://identifiers.org/zfin/", 
+        "AspGD_REF": "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=", 
+        "RO": "http://purl.obolibrary.org/obo/RO_", 
+        "Pfam": "http://pfam.xfam.org/family/", 
+        "UBERON": "http://purl.obolibrary.org/obo/UBERON_", 
+        "GR": "http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=", 
+        "PDB": "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=", 
+        "CORIELL": "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=", 
+        "JCVI_GenProp": "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=", 
+        "SGN": "http://identifiers.org/sgn/", 
+        "BFO": "http://purl.obolibrary.org/obo/BFO_", 
+        "Genesys-pgr": "https://www.genesys-pgr.org/acn/search?q=", 
+        "UniMod": "http://www.unimod.org/modifications_view.php?editid1=", 
+        "UM-BBD_reactionID": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=", 
+        "PubChem_Substance": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=", 
+        "EcoCyc": "http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=", 
+        "Reactome": "http://identifiers.org/reactome/", 
+        "InterPro": "http://identifiers.org/interpro/", 
+        "UniRule": "http://www.uniprot.org/unirule/", 
+        "MGCSC_GENETIC_STOCKS": "http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=", 
+        "dictyBase": "http://identifiers.org/dictybase.gene/", 
+        "PO_GIT": "https://github.com/Planteome/plant-ontology/issues/", 
+        "AspGD_LOCUS": "http://identifiers.org/aspgd.locus/", 
+        "SGD": "http://identifiers.org/sgd/", 
+        "COG_Pathway": "http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=", 
+        "ENZYME": "http://www.expasy.ch/cgi-bin/nicezyme.pl?", 
+        "PAMGO_MGG": "http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=", 
+        "AgBase": "http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=", 
+        "AraCyc": "http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=", 
+        "EcoCyc_REF": "http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=", 
+        "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", 
+        "HGNC": "http://identifiers.org/hgnc/", 
+        "dictyBase_gene_name": "http://dictybase.org/gene/", 
+        "TAIR": "http://identifiers.org/tair.locus/", 
+        "EnsemblFungi": "http://www.ensemblgenomes.org/id/", 
+        "Wikipedia": "http://en.wikipedia.org/wiki/", 
+        "SUPERFAMILY": "http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF", 
+        "SWALL": "http://ca.expasy.org/cgi-bin/sprot-search-de?S=1&amp;T=1&amp;SEARCH=", 
+        "PSI-MOD": "http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:", 
+        "FYPO": "http://purl.obolibrary.org/obo/FYPO_", 
+        "RGD": "http://identifiers.org/rgd/", 
+        "UM-BBD_enzymeID": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=", 
+        "Broad_MGG": "http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S", 
+        "Swiss-Prot": "http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=", 
+        "PMID": "http://www.ncbi.nlm.nih.gov/pubmed/", 
+        "Xenbase": "http://identifiers.org/xenbase/", 
+        "PR": "http://purl.obolibrary.org/obo/PR_", 
+        "MIPS_funcat": "http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=", 
+        "GR_REF": "http://www.gramene.org/db/literature/pub_search?ref_id=", 
+        "MaizeGDB": "http://maizegdb.org/gene_center/gene/", 
+        "HAMAP": "http://hamap.expasy.org/unirule/", 
+        "SGN_ref": "http://www.sgn.cornell.edu/chado/publication.pl?pub_id=", 
+        "TO_GIT": "https://github.com/Planteome/plant-trait-ontology/issues/", 
+        "MeSH": "http://n2t.net/MESH:", 
+        "GR_PROTEIN": "http://identifiers.org/gramene.protein/", 
+        "MaizeGDB_REF": "http://maizegdb.org/data_center/reference?id=", 
+        "GEO": "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=", 
+        "PO": "http://purl.obolibrary.org/obo/PO_", 
+        "PomBase": "http://identifiers.org/pombase/", 
+        "ENA": "http://www.ebi.ac.uk/ena/data/view/", 
+        "PIRSF": "http://pir.georgetown.edu/cgi-bin/ipcSF?id=", 
+        "EMBL": "http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=", 
+        "Prosite": "http://www.expasy.ch/cgi-bin/prosite-search-ac?", 
+        "H-invDB_cDNA": "http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=", 
+        "EC": "http://www.expasy.org/enzyme/", 
+        "MACSC_REF": "http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=", 
+        "PAMGO_VMD": "http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=", 
+        "IRGC": "https://www.genesys-pgr.org/acn/search?q=IRGC+", 
+        "NASC_code": "http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=", 
+        "COG_Cluster": "http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=", 
+        "TreeGenes": "http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=", 
+        "WB_REF": "http://www.wormbase.org/db/misc/paper?name=", 
+        "TGD_LOCUS": "http://db.ciliate.org/cgi-bin/locus.pl?locus=", 
+        "MA": "http://purl.obolibrary.org/obo/MA_", 
+        "UniProtKB": "http://identifiers.org/uniprot/", 
+        "MGI": "http://identifiers.org/mgi/", 
+        "GRINDesc": "https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=", 
+        "DDANAT": "http://purl.obolibrary.org/obo/DDANAT_", 
+        "RAP-DB": "http://rapdb.dna.affrc.go.jp/tools/search/run?id=on&attr=desc&attr=cgs&attr=cgn&attr=cgss&attr=cgns&attr=rgss&attr=rgns&keyword=", 
+        "gomodel": "http://model.geneontology.org/", 
+        "KEGG_PATHWAY": "http://identifiers.org/kegg.pathway/", 
+        "BTO": "http://purl.obolibrary.org/obo/BTO_", 
+        "JCVI_CMR": "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=", 
+        "dictyBase_REF": "http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=", 
+        "DOI": "http://dx.doi.org/", 
+        "LIFEdb": "http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=", 
+        "PANTHER": "http://identifiers.org/panther.family/", 
+        "Gene3D": "http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=", 
+        "PATRIC": "http://patric.vbi.vt.edu/gene/overview.php?fid=", 
+        "FB": "http://identifiers.org/flybase/", 
+        "PAINT_REF": "http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR", 
+        "CASREF": "http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=", 
+        "ENSEMBL": "http://identifiers.org/ensembl/", 
+        "SMART": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=", 
+        "RefSeq": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=", 
+        "WBls": "http://purl.obolibrary.org/obo/WBls_", 
+        "MaizeGDB_QTL": "http://www.maizegdb.org/data_center/trait?id=", 
+        "SOY_ref": "http://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=", 
+        "ECO": "http://purl.obolibrary.org/obo/ECO_", 
+        "CGD_REF": "http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=", 
+        "ECK": "http://www.ecogene.org/geneInfo.php?eck_id=", 
+        "CGD": "http://identifiers.org/cgd/", 
+        "GR_GENE": "http://identifiers.org/gramene.gene/", 
+        "RNAmods": "http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?", 
+        "KEGG_ENZYME": "http://identifiers.org/kegg.enzyme/", 
+        "CACAO": "http://gowiki.tamu.edu/wiki/index.php/", 
+        "IUPHAR_GPCR": "http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=", 
+        "JCVI_TIGRFAMS": "http://search.jcvi.org/search?p&q=", 
+        "SOY_QTL": "http://soybase.org/sbt/search/search_results.php?category=QTLName&search_term=", 
+        "DDBJ": "http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=", 
+        "PRINTS": "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=", 
+        "PO_REF": "http://planteome.org/po_ref/", 
+        "IMG": "http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=", 
+        "CL": "http://purl.obolibrary.org/obo/CL_", 
+        "UniProtKB-SubCell": "http://www.uniprot.org/locations/", 
+        "NIF_Subcellular": "http://www.neurolex.org/wiki/", 
+        "GeneDB": "http://identifiers.org/genedb/", 
+        "ApiDB_PlasmoDB": "http://www.plasmodb.org/gene/", 
+        "RNAcentral": "http://rnacentral.org/rna/", 
+        "CGD_LOCUS": "http://www.candidagenome.org/cgi-bin/locus.pl?locus=", 
+        "Rfam": "http://rfam.sanger.ac.uk/family/", 
+        "Broad_NEUROSPORA": "http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S", 
+        "AGI_LocusCode": "http://arabidopsis.org/servlets/TairObject?type=locus&name=", 
+        "OBO_SF2_PO": "http://sourceforge.net/p/obo/plant-ontology-po-term-requests/", 
+        "FMA": "http://purl.obolibrary.org/obo/FMA_", 
+        "CDD": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=", 
+        "PubChem_Compound": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=", 
+        "HGNC_gene": "http://www.genenames.org/data/hgnc_data.php?app_sym=", 
+        "PharmGKB": "http://www.pharmgkb.org/do/serve?objId=", 
+        "VMD": "http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=", 
+        "UniParc": "http://www.uniprot.org/uniparc/", 
+        "MEROPS": "http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=", 
+        "GDB": "http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:", 
+        "SEED": "http://www.theseed.org/linkin.cgi?id=", 
+        "SO": "http://purl.obolibrary.org/obo/SO_", 
+        "Soy_gene": "http://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=", 
+        "CORUM": "http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=", 
+        "RHEA": "http://www.rhea-db.org/reaction.xhtml?id=", 
+        "dbSNP": "http://identifiers.org/dbsnp/", 
+        "MaizeGDB_Locus": "http://identifiers.org/maizegdb.locus/", 
+        "MO": "http://mged.sourceforge.net/ontologies/MGEDontology.php#", 
+        "PLANA_REF": "http://purl.obolibrary.org/obo/plana/references/", 
+        "ISBN": "https://www.worldcat.org/search?q=bn%3A", 
+        "BRENDA": "http://www.brenda-enzymes.info/php/result_flat.php4?ecno=", 
+        "ASAP": "https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=", 
+        "CAS": "http://identifiers.org/cas/", 
+        "H-invDB_locus": "http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=", 
+        "UM-BBD_ruleID": "http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=", 
+        "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", 
+        "ComplexPortal": "https://www.ebi.ac.uk/complexportal/complex/", 
+        "JSTOR": "http://www.jstor.org/stable/", 
+        "GRIMS": "https://www.genesys-pgr.org/acn/search2?q=IRGC+", 
+        "PATO": "http://purl.obolibrary.org/obo/PATO_", 
+        "GR_QTL": "http://identifiers.org/gramene.qtl/", 
+        "ECOGENE": "http://www.ecogene.org/geneInfo.php?eg_id=", 
+        "HPA_antibody": "http://www.proteinatlas.org/antibody_info.php?antibody_id=", 
+        "VBRC": "http://vbrc.org/query.asp?web_id=VBRC:", 
+        "EO_GIT": "https://github.com/Planteome/plant-environment-ontology/issues/", 
+        "EchoBASE": "http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=", 
+        "CASGEN": "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=", 
+        "IUPHAR_RECEPTOR": "http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=", 
+        "IRIC": "http://oryzasnp.org/_variety.zul?irisid=", 
+        "GenBank": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=", 
+        "TGD": "http://identifiers.org/tgd/", 
+        "JCVI_EGAD": "http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=", 
+        "PubChem_BioAssay": "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=", 
+        "TC": "http://www.tcdb.org/tcdb/index.php?tc=", 
+        "SABIO-RK": "http://sabio.villa-bosch.de/reacdetails.jsp?reactid=", 
+        "OBO_SF2_PECO": "https://sourceforge.net/p/obo/plant-environment-ontology-eo/", 
+        "MetaCyc": "http://identifiers.org/metacyc/", 
+        "PAMGO_GAT": "http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=", 
+        "ModBase": "http://salilab.org/modbase/searchbyid?databaseID=", 
+        "OMIM": "http://omim.org/entry/", 
+        "GR_MUT": "http://www.gramene.org/db/genes/search_gene?acc=", 
+        "HPA": "http://www.proteinatlas.org/tissue_profile.php?antibody_id=", 
+        "IntAct": "http://identifiers.org/intact/", 
+        "ProDom": "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=", 
+        "GRIN": "https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=", 
+        "WBPhenotype": "http://purl.obolibrary.org/obo/WBPhenotype_", 
+        "BioCyc": "http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=", 
+        "ENSEMBL_GeneID": "http://www.ensembl.org/id/", 
+        "PIR": "http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=", 
+        "UniProtKB-KW": "http://www.uniprot.org/keywords/", 
+        "Planteome_gene": "https://www.google.com/search?q=", 
+        "AspGD": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=", 
+        "JCVI_Medtr": "http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=", 
+        "EuPathDB": "http://eupathdb.org/gene/", 
+        "PMCID": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term="
+    }
+}