diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index e8f82c723..3a855ceaa 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -373,7 +373,7 @@ "allergome": { "mappings": { "prefixcommons": "ALLERGOME", - "uniprot": "Allergome" + "uniprot.database": "Allergome" }, "miriam": { "deprecated": false, @@ -394,7 +394,7 @@ "is_obo": false, "prefix": "ALLERGOME" }, - "uniprot": { + "uniprot.database": { "category": "Protein family/group databases", "formatter": "http://www.allergome.org/script/dettaglio.php?id_molecule=%s", "identifier": "160", @@ -767,7 +767,7 @@ "arachnoserver": { "mappings": { "prefixcommons": "ARACHNOSERVER", - "uniprot": "ArachnoServer" + "uniprot.database": "ArachnoServer" }, "miriam": { "deprecated": false, @@ -788,7 +788,7 @@ "is_obo": false, "prefix": "ARACHNOSERVER" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "http://www.arachnoserver.org/toxincard.html?id=%s", "identifier": "145", @@ -801,7 +801,7 @@ "homepage": "https://www.araport.org/", "mappings": { "ncbi": "Araport", - "uniprot": "Araport" + "uniprot.database": "Araport" }, "name": "Arabidopsis Information Portal", "ncbi": { @@ -810,7 +810,7 @@ "name": "Arabidopsis Information Portal", "prefix": "Araport" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://bar.utoronto.ca/thalemine/portal.do?externalids=%s", "identifier": "221", @@ -1878,7 +1878,7 @@ "bindingdb": { "mappings": { "prefixcommons": "BINDINGDB", - "uniprot": "BindingDB" + "uniprot.database": "BindingDB" }, "miriam": { "deprecated": false, @@ -1899,7 +1899,7 @@ "is_obo": false, "prefix": "BINDINGDB" }, - "uniprot": { + "uniprot.database": { "category": "Chemistry databases", "formatter": "https://www.bindingdb.org/uniprot/%u", "identifier": "127", @@ -1967,7 +1967,7 @@ "mappings": { "go": "BioCyc", "prefixcommons": "BIOCYC", - "uniprot": "BioCyc" + "uniprot.database": "BioCyc" }, "miriam": { "deprecated": false, @@ -1988,7 +1988,7 @@ "is_obo": false, "prefix": "BIOCYC" }, - "uniprot": { + "uniprot.database": { "category": "Enzyme and pathway databases", "formatter": "https://biocyc.org/getid?id=%s", "identifier": "5", @@ -2000,7 +2000,7 @@ "biogrid": { "mappings": { "prefixcommons": "BIOGRID", - "uniprot": "BioGRID" + "uniprot.database": "BioGRID" }, "miriam": { "deprecated": false, @@ -2021,7 +2021,7 @@ "is_obo": false, "prefix": "BIOGRID" }, - "uniprot": { + "uniprot.database": { "category": "Protein-protein interaction databases", "formatter": "https://thebiogrid.org/%s", "identifier": "184", @@ -2369,7 +2369,7 @@ } }, "biostudies": { - "mapping": { + "mappings": { "fairsharing": "biodbcore-000989" }, "miriam": { @@ -2435,11 +2435,11 @@ } }, "birnlex": { + "_comment": "Part of the NeuroLex namespace now", "bioportal": { "name": "Biomedical Informatics Research Network Project Lexicon", "prefix": "BIRNLEX" }, - "comment": "Part of the NeuroLex namespace now", "mappings": { "bioportal": "BIRNLEX" }, @@ -2496,7 +2496,7 @@ "bmrb": { "mappings": { "fairsharing": "FAIRsharing.p06nme", - "uniprot": "BMRB" + "uniprot.database": "BMRB" }, "miriam": { "deprecated": false, @@ -2508,7 +2508,7 @@ "prefix": "bmrb", "sampleId": "15000" }, - "uniprot": { + "uniprot.database": { "category": "3D structure databases", "formatter": "http://www.bmrb.wisc.edu/data_library/summary/protein.php?uniprot=%u", "identifier": "256", @@ -2571,7 +2571,7 @@ "mappings": { "go": "BRENDA", "prefixcommons": "BRENDA", - "uniprot": "BRENDA" + "uniprot.database": "BRENDA" }, "miriam": { "deprecated": false, @@ -2592,7 +2592,7 @@ "is_obo": false, "prefix": "BRENDA" }, - "uniprot": { + "uniprot.database": { "category": "Enzyme and pathway databases", "formatter": "https://www.brenda-enzymes.org/enzyme.php?ecno=%s&UniProtAcc=%u&OrganismID=%d", "identifier": "131", @@ -2626,7 +2626,7 @@ } }, "bs": { - "comment": "part of Sequence Ontology (SO). See https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/Ontology_Files/subsets/biosapiens.obo", + "_comment": "part of Sequence Ontology (SO). See https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/Ontology_Files/subsets/biosapiens.obo", "name": "Biosapiens" }, "bspo": { @@ -3095,7 +3095,7 @@ "mappings": { "go": "CAZY", "prefixcommons": "CAZY", - "uniprot": "CAZy" + "uniprot.database": "CAZy" }, "miriam": { "deprecated": false, @@ -3116,7 +3116,7 @@ "is_obo": false, "prefix": "CAZY" }, - "uniprot": { + "uniprot.database": { "category": "Protein family/group databases", "formatter": "http://www.cazy.org/fam/%s.html", "identifier": "136", @@ -3160,7 +3160,7 @@ "ccds": { "mappings": { "prefixcommons": "CCDS", - "uniprot": "CCDS" + "uniprot.database": "CCDS" }, "miriam": { "deprecated": false, @@ -3181,7 +3181,7 @@ "is_obo": false, "prefix": "CCDS" }, - "uniprot": { + "uniprot.database": { "category": "Sequence databases", "formatter": "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=%s", "identifier": "187", @@ -3212,7 +3212,6 @@ "n2t": { "prefix": "cco" }, - "namespace.capitalized": true, "ols": { "contact": "vladimir.n.mironov@gmail.com", "description": "The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects.", @@ -3277,7 +3276,7 @@ "go": "CDD", "ncbi": "CDD", "prefixcommons": "CDD", - "uniprot": "CDD" + "uniprot.database": "CDD" }, "miriam": { "deprecated": false, @@ -3304,7 +3303,7 @@ "is_obo": false, "prefix": "CDD" }, - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s", "identifier": "214", @@ -3472,7 +3471,7 @@ "go": "CGD", "ncbi": "CGD", "prefixcommons": "CGD", - "uniprot": "CGD" + "uniprot.database": "CGD" }, "miriam": { "deprecated": false, @@ -3499,7 +3498,7 @@ "is_obo": false, "prefix": "CGD" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=%s", "identifier": "126", @@ -3704,7 +3703,7 @@ "chembl.target": { "mappings": { "prefixcommons": "CHEMBL.TARGET", - "uniprot": "ChEMBL" + "uniprot.database": "ChEMBL" }, "miriam": { "deprecated": false, @@ -3726,7 +3725,7 @@ "is_obo": false, "prefix": "CHEMBL.TARGET" }, - "uniprot": { + "uniprot.database": { "category": "Chemistry databases", "formatter": "https://www.ebi.ac.uk/chembldb/target/inspect/%s", "identifier": "174", @@ -4856,7 +4855,7 @@ "ols_version_date_format": "%Y-%m-%d" }, "cohd": { - "comment": "not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for.", + "_comment": "not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for.", "homepage": "https://github.com/MIT-LCP/mimic-omop", "name": "MIMIC III Database" }, @@ -4900,7 +4899,7 @@ "mappings": { "go": "ComplexPortal", "prefixcommons": "COMPLEXPORTAL", - "uniprot": "ComplexPortal" + "uniprot.database": "ComplexPortal" }, "miriam": { "deprecated": false, @@ -4921,10 +4920,10 @@ "is_obo": false, "prefix": "COMPLEXPORTAL" }, - "synyonms": [ + "synonyms": [ "ComplexPortal" ], - "uniprot": { + "uniprot.database": { "category": "Protein-protein interaction databases", "formatter": "https://www.ebi.ac.uk/complexportal/complex/%s", "identifier": "228", @@ -4988,7 +4987,7 @@ "conoserver": { "mappings": { "prefixcommons": "CONOSERVER", - "uniprot": "ConoServer" + "uniprot.database": "ConoServer" }, "miriam": { "deprecated": false, @@ -5010,7 +5009,7 @@ "is_obo": false, "prefix": "CONOSERVER" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "http://www.conoserver.org/?page=card&table=protein&id=%s", "identifier": "156", @@ -5067,7 +5066,7 @@ "mappings": { "go": "CORUM", "prefixcommons": "CORUM", - "uniprot": "CORUM" + "uniprot.database": "CORUM" }, "miriam": { "deprecated": false, @@ -5088,7 +5087,7 @@ "is_obo": false, "prefix": "CORUM" }, - "uniprot": { + "uniprot.database": { "category": "Protein-protein interaction databases", "formatter": "http://mips.helmholtz-muenchen.de/corum/#?uniprotID=%u", "identifier": "224", @@ -5154,10 +5153,10 @@ "ols_version_date_format": "%Y-%m-%d" }, "cp": { + "_comment": "Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572", "appears_in": [ "cl" ], - "comment": "Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572", "name": "Cellular Phenotypes" }, "cpc": { @@ -5931,7 +5930,7 @@ "go": "dbSNP", "ncbi": "dbSNP", "prefixcommons": "dbSNP", - "uniprot": "dbSNP" + "uniprot.database": "dbSNP" }, "miriam": { "deprecated": false, @@ -5958,7 +5957,7 @@ "is_obo": false, "prefix": "dbSNP" }, - "uniprot": { + "uniprot.database": { "category": "Genetic variation databases", "formatter": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s", "identifier": "13", @@ -6171,7 +6170,7 @@ "depod": { "mappings": { "prefixcommons": "DEPOD", - "uniprot": "DEPOD" + "uniprot.database": "DEPOD" }, "miriam": { "deprecated": false, @@ -6194,7 +6193,7 @@ "prefix": "DEPOD" }, "provides": "hgnc.symbol", - "uniprot": { + "uniprot.database": { "category": "PTM databases", "formatter": "http://depod.bioss.uni-freiburg.de/showp.php?name=%s", "identifier": "190", @@ -6272,7 +6271,7 @@ "go": "dictyBase", "ncbi": "dictyBase", "prefixcommons": "dictyBase", - "uniprot": "dictyBase" + "uniprot.database": "dictyBase" }, "name": "dictyBase", "ncbi": { @@ -6290,7 +6289,7 @@ "synonyms": [ "dictyBase" ], - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "comment": "Replacement for DictyBase", "formatter": "http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id=%s", @@ -6408,7 +6407,7 @@ "dip": { "mappings": { "prefixcommons": "DIP", - "uniprot": "DIP" + "uniprot.database": "DIP" }, "miriam": { "deprecated": false, @@ -6429,7 +6428,7 @@ "is_obo": false, "prefix": "DIP" }, - "uniprot": { + "uniprot.database": { "category": "Protein-protein interaction databases", "formatter": "https://dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=%s", "identifier": "16", @@ -6449,7 +6448,7 @@ "disprot": { "mappings": { "prefixcommons": "DISPROT", - "uniprot": "DisProt" + "uniprot.database": "DisProt" }, "miriam": { "deprecated": false, @@ -6470,7 +6469,7 @@ "is_obo": false, "prefix": "DISPROT" }, - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "https://disprot.org/%s", "identifier": "17", @@ -6937,7 +6936,7 @@ "homepage": "http://www.drugbank.ca", "mappings": { "prefixcommons": "DrugBank", - "uniprot": "DrugBank" + "uniprot.database": "DrugBank" }, "miriam": { "deprecated": false, @@ -6962,7 +6961,7 @@ "DrugBank", "DRUGBANK_ID" ], - "uniprot": { + "uniprot.database": { "category": "Chemistry databases", "formatter": "https://www.drugbank.ca/drugs/%s", "identifier": "19", @@ -7030,13 +7029,13 @@ "homepage": "http://drugcentral.org", "mappings": { "biolink": "DrugCentral", - "uniprot": "DrugCentral" + "uniprot.database": "DrugCentral" }, "name": "Drug Central", "synonyms": [ "Drug_Central" ], - "uniprot": { + "uniprot.database": { "category": "Chemistry databases", "formatter": "https://drugcentral.org/target/%u", "identifier": "239", @@ -7201,7 +7200,7 @@ "mappings": { "go": "EchoBASE", "prefixcommons": "ECHOBASE", - "uniprot": "EchoBASE" + "uniprot.database": "EchoBASE" }, "miriam": { "deprecated": false, @@ -7222,7 +7221,7 @@ "is_obo": false, "prefix": "ECHOBASE" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=%s", "identifier": "20", @@ -7697,7 +7696,7 @@ "eggnog": { "mappings": { "prefixcommons": "EGGNOG", - "uniprot": "eggNOG" + "uniprot.database": "eggNOG" }, "miriam": { "deprecated": false, @@ -7718,7 +7717,7 @@ "is_obo": false, "prefix": "EGGNOG" }, - "uniprot": { + "uniprot.database": { "category": "Phylogenomic databases", "formatter": "http://eggnogdb.embl.de/#/app/results?seqid=%u&target_nogs=%s", "identifier": "152", @@ -7820,7 +7819,7 @@ "elm": { "mappings": { "prefixcommons": "ELM", - "uniprot": "ELM" + "uniprot.database": "ELM" }, "miriam": { "deprecated": false, @@ -7842,7 +7841,7 @@ "is_obo": false, "prefix": "ELM" }, - "uniprot": { + "uniprot.database": { "category": "Protein-protein interaction databases", "formatter": "http://elm.eu.org/instances.html?q=%u", "identifier": "223", @@ -7852,8 +7851,6 @@ } }, "emapa": { - "_download": "ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo", - "_download_comment": "New download link? probabl not right", "bioportal": { "name": "Mouse gross anatomy and development, timed", "prefix": "EMAPA" @@ -7929,7 +7926,7 @@ "description": "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure", "example": "10595", "homepage": "https://www.ebi.ac.uk/pdbe/emdb", - "mapping": { + "mappings": { "fairsharing": "biodbcore-001140" }, "name": "Electron Microscopy Public Image Archive", @@ -8026,7 +8023,7 @@ "go": "ENSEMBL", "ncbi": "ENSEMBL", "prefixcommons": "ENSEMBL", - "uniprot": "Ensembl" + "uniprot.database": "Ensembl" }, "miriam": { "deprecated": false, @@ -8056,7 +8053,7 @@ "synonyms": [ "Ensembl" ], - "uniprot": { + "uniprot.database": { "category": "Genome annotation databases", "formatter": "https://www.ensembl.org/id/%s", "identifier": "23", @@ -8077,7 +8074,7 @@ "ensembl.bacteria": { "mappings": { "prefixcommons": "ENSEMBL.BACTERIA", - "uniprot": "EnsemblBacteria" + "uniprot.database": "EnsemblBacteria" }, "miriam": { "deprecated": false, @@ -8098,7 +8095,7 @@ "is_obo": false, "prefix": "ENSEMBL.BACTERIA" }, - "uniprot": { + "uniprot.database": { "category": "Genome annotation databases", "formatter": "http://www.ensemblgenomes.org/id/%s", "identifier": "147", @@ -8117,7 +8114,7 @@ "mappings": { "go": "EnsemblFungi", "prefixcommons": "ENSEMBL.FUNGI", - "uniprot": "EnsemblFungi" + "uniprot.database": "EnsemblFungi" }, "miriam": { "deprecated": false, @@ -8138,7 +8135,7 @@ "is_obo": false, "prefix": "ENSEMBL.FUNGI" }, - "uniprot": { + "uniprot.database": { "category": "Genome annotation databases", "formatter": "http://www.ensemblgenomes.org/id/%s", "identifier": "148", @@ -8157,7 +8154,7 @@ "mappings": { "go": "EnsemblMetazoa", "prefixcommons": "ENSEMBL.METAZOA", - "uniprot": "EnsemblMetazoa" + "uniprot.database": "EnsemblMetazoa" }, "miriam": { "deprecated": false, @@ -8178,7 +8175,7 @@ "is_obo": false, "prefix": "ENSEMBL.METAZOA" }, - "uniprot": { + "uniprot.database": { "category": "Genome annotation databases", "formatter": "http://www.ensemblgenomes.org/id/%s", "identifier": "149", @@ -8339,7 +8336,7 @@ "mappings": { "ncbi": "EPD", "prefixcommons": "EPD", - "uniprot": "EPD" + "uniprot.database": "EPD" }, "miriam": { "deprecated": false, @@ -8366,7 +8363,7 @@ "is_obo": false, "prefix": "EPD" }, - "uniprot": { + "uniprot.database": { "category": "Proteomic databases", "formatter": "https://www.peptracker.com/epd/analytics/?protein_id=%u", "identifier": "205", @@ -9148,7 +9145,7 @@ "go": "FB", "ncbi": "FLYBASE", "prefixcommons": "FlyBase", - "uniprot": "FlyBase" + "uniprot.database": "FlyBase" }, "miriam": { "deprecated": false, @@ -9176,7 +9173,7 @@ "FB", "FlyBase" ], - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "comment": "Replacement for DMAP", "formatter": "http://flybase.org/reports/%s.html", @@ -9787,8 +9784,8 @@ } }, "gc": { + "_comment": "see comment here: https://github.com/obophenotype/ncbitaxon/issues/47", "name": "Genetic Code", - "note": "see comment here: https://github.com/obophenotype/ncbitaxon/issues/47", "references": [ "https://github.com/obophenotype/ncbitaxon/issues/47" ], @@ -9883,7 +9880,7 @@ "genatlas": { "mappings": { "prefixcommons": "GENATLAS", - "uniprot": "GenAtlas" + "uniprot.database": "GenAtlas" }, "miriam": { "deprecated": false, @@ -9904,7 +9901,7 @@ "is_obo": false, "prefix": "GENATLAS" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=%s", "identifier": "27", @@ -9927,7 +9924,7 @@ "fairsharing": "FAIRsharing.9kahy4", "go": "GenBank", "prefixcommons": "GenBank", - "uniprot": "GenBank" + "uniprot.database": "GenBank" }, "name": "GenBank", "prefixcommons": { @@ -9936,7 +9933,7 @@ "is_obo": false, "prefix": "GenBank" }, - "uniprot": { + "uniprot.database": { "category": "Sequence databases", "formatter": "https://www.ncbi.nlm.nih.gov/nuccore/%s", "identifier": "28", @@ -9948,7 +9945,7 @@ "genecards": { "mappings": { "prefixcommons": "GENECARDS", - "uniprot": "GeneCards" + "uniprot.database": "GeneCards" }, "miriam": { "deprecated": false, @@ -9969,7 +9966,7 @@ "is_obo": false, "prefix": "GENECARDS" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=%s", "identifier": "30", @@ -9989,7 +9986,7 @@ "go": "GeneDB", "ncbi": "GeneDB", "prefixcommons": "GENEDB", - "uniprot": "GeneDB" + "uniprot.database": "GeneDB" }, "miriam": { "deprecated": false, @@ -10016,7 +10013,7 @@ "is_obo": false, "prefix": "GENEDB" }, - "uniprot": { + "uniprot.database": { "category": "Genome annotation databases", "formatter": "https://www.genedb.org/gene/%s", "identifier": "199", @@ -10083,7 +10080,7 @@ "genetree": { "mappings": { "prefixcommons": "GENETREE", - "uniprot": "GeneTree" + "uniprot.database": "GeneTree" }, "miriam": { "deprecated": false, @@ -10104,7 +10101,7 @@ "is_obo": false, "prefix": "GENETREE" }, - "uniprot": { + "uniprot.database": { "category": "Phylogenomic databases", "formatter": "http://www.ensemblgenomes.org/id-genetree/%s", "identifier": "162", @@ -10116,7 +10113,7 @@ "genewiki": { "mappings": { "prefixcommons": "GENEWIKI", - "uniprot": "GeneWiki" + "uniprot.database": "GeneWiki" }, "miriam": { "deprecated": false, @@ -10137,7 +10134,7 @@ "is_obo": false, "prefix": "GENEWIKI" }, - "uniprot": { + "uniprot.database": { "category": "Miscellaneous databases", "formatter": "https://en.wikipedia.org/wiki/%s", "identifier": "180", @@ -10465,10 +10462,10 @@ "example": "G24361QY", "homepage": "https://glygen.org/glycan/", "mappings": { - "uniprot": "GlyGen" + "uniprot.database": "GlyGen" }, "name": "GlyGen: Computational and Informatics Resources for Glycoscience", - "uniprot": { + "uniprot.database": { "category": "PTM databases", "formatter": "https://glygen.org/protein/%u#glycosylation", "identifier": "254", @@ -10704,7 +10701,7 @@ "go": "GO", "ncbi": "GO", "prefixcommons": "GO", - "uniprot": "GO" + "uniprot.database": "GO" }, "miriam": { "deprecated": false, @@ -10759,7 +10756,7 @@ "goccid", "gomfid" ], - "uniprot": { + "uniprot.database": { "category": "Ontologies", "formatter": "https://www.ebi.ac.uk/QuickGO/term/%s", "identifier": "37", @@ -10809,7 +10806,6 @@ "n2t": { "prefix": "go.ref" }, - "namespace.capitalized": true, "prefixcommons": { "formatter": "http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:$1", "is_identifiers": false, @@ -10973,7 +10969,7 @@ "gpcrdb": { "mappings": { "prefixcommons": "GPCRDB", - "uniprot": "GPCRDB" + "uniprot.database": "GPCRDB" }, "miriam": { "deprecated": false, @@ -10995,7 +10991,7 @@ "is_obo": false, "prefix": "GPCRDB" }, - "uniprot": { + "uniprot.database": { "category": "Protein family/group databases", "formatter": "https://gpcrdb.org/protein/%s/", "identifier": "38", @@ -11395,10 +11391,10 @@ } }, "gtr": { + "_comment": "Identifiers appearing in MONDO don't match any of the resources apparent endpoints", "appears_in": [ "mondo" ], - "comment": "Identifiers appearing in MONDO don't match any of the resources apparent endpoints", "example": "AN0097748", "homepage": "https://www.ncbi.nlm.nih.gov/gtr/", "name": "Genetic Testing Registry" @@ -11562,7 +11558,7 @@ "mappings": { "go": "HAMAP", "prefixcommons": "HAMAP", - "uniprot": "HAMAP" + "uniprot.database": "HAMAP" }, "miriam": { "deprecated": false, @@ -11583,7 +11579,7 @@ "is_obo": false, "prefix": "HAMAP" }, - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "https://hamap.expasy.org/signature/%s", "identifier": "41", @@ -11787,7 +11783,7 @@ "go": "HUGO", "ncbi": "HGNC", "prefixcommons": "HGNC", - "uniprot": "HGNC" + "uniprot.database": "HGNC" }, "miriam": { "deprecated": false, @@ -11815,7 +11811,7 @@ "is_obo": false, "prefix": "HGNC" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "comment": "Replacement for Genew", "formatter": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/%s", @@ -12014,7 +12010,7 @@ "hogenom": { "mappings": { "prefixcommons": "HOGENOM", - "uniprot": "HOGENOM" + "uniprot.database": "HOGENOM" }, "miriam": { "deprecated": false, @@ -12036,7 +12032,7 @@ "is_obo": false, "prefix": "HOGENOM" }, - "uniprot": { + "uniprot.database": { "category": "Phylogenomic databases", "formatter": "http://hogenom.univ-lyon1.fr/query_sequence?seq=%u", "identifier": "44", @@ -12246,7 +12242,7 @@ "mappings": { "go": "HPA", "prefixcommons": "HPA", - "uniprot": "HPA" + "uniprot.database": "HPA" }, "miriam": { "deprecated": false, @@ -12267,7 +12263,7 @@ "is_obo": false, "prefix": "HPA" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://www.proteinatlas.org/%s", "identifier": "46", @@ -12520,7 +12516,7 @@ "huge": { "mappings": { "prefixcommons": "HUGE", - "uniprot": "HUGE" + "uniprot.database": "HUGE" }, "miriam": { "deprecated": false, @@ -12542,7 +12538,7 @@ "is_obo": false, "prefix": "HUGE" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "http://www.kazusa.or.jp/huge/gfpage/%s", "identifier": "49", @@ -12836,7 +12832,7 @@ "homepage": "https://www.ideal-db.org", "mappings": { "prefixcommons": "IDEAL", - "uniprot": "IDEAL" + "uniprot.database": "IDEAL" }, "miriam": { "deprecated": false, @@ -12858,7 +12854,7 @@ "is_obo": false, "prefix": "IDEAL" }, - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=%s", "identifier": "251", @@ -13026,7 +13022,7 @@ "url": "https://biomodels.net/vocab/idot.rdf#$1" }, "idr": { - "mapping": { + "mappings": { "fairsharing": "FAIRsharing.6wf1zw" }, "miriam": { @@ -13261,9 +13257,9 @@ } }, "inn": { + "_comment": "can not find a place to resolve to", "example": "fluticasone", "name": "International Nonproprietary Names", - "note": "can not find a place to resolve to", "synonyms": [ "INN_ID" ], @@ -13412,7 +13408,7 @@ "mappings": { "go": "IntAct", "prefixcommons": "INTACT", - "uniprot": "IntAct" + "uniprot.database": "IntAct" }, "miriam": { "deprecated": false, @@ -13433,7 +13429,7 @@ "is_obo": false, "prefix": "INTACT" }, - "uniprot": { + "uniprot.database": { "category": "Protein-protein interaction databases", "formatter": "https://www.ebi.ac.uk/intact/interactors/id:%s*", "identifier": "51", @@ -13508,7 +13504,7 @@ "go": "InterPro", "ncbi": "InterPro", "prefixcommons": "INTERPRO", - "uniprot": "InterPro" + "uniprot.database": "InterPro" }, "miriam": { "deprecated": false, @@ -13539,7 +13535,7 @@ "InterPro", "IP" ], - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "https://www.ebi.ac.uk/interpro/entry/%s", "identifier": "52", @@ -13603,7 +13599,6 @@ "deprecated": true, "example": "0000008", "name": "Insect Resistance Ontology", - "needs_curation": true, "url": "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1" }, "isbn": { @@ -14060,7 +14055,7 @@ } }, "kegg": { - "comments": "KEGG prefix has been split into several others", + "_comment": "KEGG prefix has been split into several others", "deprecated": true, "go": { "homepage": "http://www.genome.ad.jp/kegg/", @@ -14070,7 +14065,7 @@ "mappings": { "go": "KEGG", "prefixcommons": "KEGG", - "uniprot": "KEGG" + "uniprot.database": "KEGG" }, "miriam": { "deprecated": false, @@ -14094,7 +14089,7 @@ "synonyms": [ "KEGG" ], - "uniprot": { + "uniprot.database": { "category": "Genome annotation databases", "formatter": "https://www.genome.jp/dbget-bin/www_bget?%s", "identifier": "53", @@ -14782,7 +14777,6 @@ } }, "lincs.smallmolecule": { - "id": "00000546", "mappings": { "prefixcommons": "LINCS.SMALLMOLECULE" }, @@ -15103,7 +15097,7 @@ "mappings": { "fairsharing": "FAIRsharing.LYsiMd", "prefixcommons": "MASSIVE", - "uniprot": "MassIVE" + "uniprot.database": "MassIVE" }, "miriam": { "deprecated": false, @@ -15124,7 +15118,7 @@ "is_obo": false, "prefix": "MASSIVE" }, - "uniprot": { + "uniprot.database": { "category": "Proteomic databases", "formatter": "https://massive.ucsd.edu/ProteoSAFe/protein_explorer.jsp?libraries=2&protein_name=%u", "identifier": "241", @@ -15158,7 +15152,7 @@ } }, "matrixdb": { - "appearsIn": [ + "appears_in": [ "complexportal" ], "example": "MULT_4_VAR1_bovine", @@ -15406,7 +15400,7 @@ "mappings": { "go": "MEROPS", "prefixcommons": "MEROPS", - "uniprot": "MEROPS" + "uniprot.database": "MEROPS" }, "miriam": { "deprecated": false, @@ -15427,7 +15421,7 @@ "is_obo": false, "prefix": "MEROPS" }, - "uniprot": { + "uniprot.database": { "category": "Protein family/group databases", "formatter": "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?mid=%s", "identifier": "59", @@ -16004,7 +15998,7 @@ "go": "MGI", "ncbi": "MGI", "prefixcommons": "MGI", - "uniprot": "MGI" + "uniprot.database": "MGI" }, "miriam": { "deprecated": false, @@ -16019,7 +16013,6 @@ "n2t": { "prefix": "mgi" }, - "namespace.capitalized": true, "ncbi": { "example": "MGI:1894891", "homepage": "http://www.informatics.jax.org/", @@ -16036,9 +16029,9 @@ "MGI", "MGD" ], - "uniprot": { + "uniprot.database": { + "_comment": "Replacement for MGD", "category": "Organism-specific databases", - "comment": "Replacement for MGD", "formatter": "http://www.informatics.jax.org/marker/%s", "identifier": "60", "link_is_explicit": "true", @@ -16150,7 +16143,7 @@ ] }, "miaa": { - "comment": "same as MAT", + "_comment": "same as MAT", "name": "Minimal Information About Anatomy ontology", "references": [ "https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf" @@ -16271,11 +16264,11 @@ } }, "mim": { + "_comment": "OMIMPS and PS should probably be split to their own entry called OMIM Phenotypic Series", "bioportal": { "name": "Molecular Interaction Map", "prefix": "MIM" }, - "comment": "OMIMPS and PS should probably be split to their own entry called OMIM Phenotypic Series", "go": { "formatter": "https://omim.org/entry/$1", "homepage": "https://omim.org/", @@ -16290,7 +16283,7 @@ "go": "OMIM", "ncbi": "MIM", "prefixcommons": "OMIM", - "uniprot": "MIM" + "uniprot.database": "MIM" }, "miriam": { "deprecated": false, @@ -16322,7 +16315,7 @@ "OMIMPS", "PS" ], - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://www.omim.org/entry/%s", "identifier": "62", @@ -16398,7 +16391,7 @@ "mint": { "mappings": { "prefixcommons": "MINT", - "uniprot": "MINT" + "uniprot.database": "MINT" }, "miriam": { "deprecated": false, @@ -16420,7 +16413,7 @@ "is_obo": false, "prefix": "MINT" }, - "uniprot": { + "uniprot.database": { "category": "Protein-protein interaction databases", "formatter": "https://mint.bio.uniroma2.it/cgi-bin/protein.py?id=%u", "identifier": "158", @@ -16470,7 +16463,6 @@ "n2t": { "prefix": "mir" }, - "namespace.capitalized": true, "prefixcommons": { "formatter": "http://identifiers.org/mir/$1", "is_identifiers": true, @@ -16611,7 +16603,7 @@ } }, "miriam.resource": { - "comment": "yo dawg i heard you like registries...", + "_comment": "yo dawg i heard you like registries...", "mappings": { "prefixcommons": "MIRIAM.RESOURCE" }, @@ -17013,7 +17005,7 @@ "homepage": "http://mobidb.bio.unipd.it", "mappings": { "prefixcommons": "MOBIDB", - "uniprot": "MobiDB" + "uniprot.database": "MobiDB" }, "miriam": { "deprecated": false, @@ -17034,7 +17026,7 @@ "is_obo": false, "prefix": "MOBIDB" }, - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "https://mobidb.bio.unipd.it/entries/%u", "identifier": "183", @@ -17804,7 +17796,7 @@ } }, "namerxn": { - "comment": "The nomenclature used for named reactions in text mining software from NextMove", + "_comment": "The nomenclature used for named reactions in text mining software from NextMove", "name": "NameRXN", "references": [ "https://www.nextmovesoftware.com/products/HazELNutPoster.pdf" @@ -18566,7 +18558,7 @@ "nextprot": { "mappings": { "prefixcommons": "NEXTPROT", - "uniprot": "neXtProt" + "uniprot.database": "neXtProt" }, "miriam": { "deprecated": false, @@ -18590,7 +18582,7 @@ "synonyms": [ "NXP" ], - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://www.nextprot.org/entry/%s", "identifier": "161", @@ -19109,7 +19101,6 @@ "n2t": { "prefix": "obi" }, - "namespace.capitalized": true, "obofoundry": { "contact": "bpeters@lji.org", "contact.label": "Bjoern Peters", @@ -20355,7 +20346,7 @@ "orphanet": { "mappings": { "prefixcommons": "Orphanet", - "uniprot": "Orphanet" + "uniprot.database": "Orphanet" }, "miriam": { "deprecated": false, @@ -20377,7 +20368,7 @@ "is_obo": false, "prefix": "Orphanet" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=%s", "identifier": "68", @@ -20460,7 +20451,7 @@ "orthodb": { "mappings": { "prefixcommons": "ORTHODB", - "uniprot": "OrthoDB" + "uniprot.database": "OrthoDB" }, "miriam": { "deprecated": false, @@ -20481,7 +20472,7 @@ "is_obo": false, "prefix": "ORTHODB" }, - "uniprot": { + "uniprot.database": { "category": "Phylogenomic databases", "formatter": "https://www.orthodb.org/?query=%u", "identifier": "143", @@ -20751,7 +20742,7 @@ "description": "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible.", "example": "FxnI151FMs", "homepage": "https://panoramaweb.org", - "mapping": { + "mappings": { "fairsharing": "FAIRsharing.uBpQ1q" }, "name": "Panorama Public", @@ -20896,7 +20887,7 @@ "pathwaycommons": { "mappings": { "prefixcommons": "PATHWAYCOMMONS", - "uniprot": "PathwayCommons" + "uniprot.database": "PathwayCommons" }, "miriam": { "deprecated": false, @@ -20917,7 +20908,7 @@ "is_obo": false, "prefix": "PATHWAYCOMMONS" }, - "uniprot": { + "uniprot.database": { "category": "Enzyme and pathway databases", "formatter": "http://apps.pathwaycommons.org/search?q=%u", "identifier": "253", @@ -21106,7 +21097,7 @@ "go": "PDB", "ncbi": "PDB", "prefixcommons": "PDB", - "uniprot": "PDB" + "uniprot.database": "PDB" }, "miriam": { "deprecated": false, @@ -21136,7 +21127,7 @@ "synonyms": [ "wwpdb" ], - "uniprot": { + "uniprot.database": { "category": "3D structure databases", "formatter": "https://www.ebi.ac.uk/pdbe-srv/view/entry/%s", "identifier": "70", @@ -21381,7 +21372,7 @@ "peptideatlas": { "mappings": { "prefixcommons": "PEPTIDEATLAS", - "uniprot": "PeptideAtlas" + "uniprot.database": "PeptideAtlas" }, "miriam": { "deprecated": false, @@ -21402,7 +21393,7 @@ "is_obo": false, "prefix": "PEPTIDEATLAS" }, - "uniprot": { + "uniprot.database": { "category": "Proteomic databases", "formatter": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?action=GO&search_key=%s", "identifier": "71", @@ -21429,7 +21420,7 @@ "peroxibase": { "mappings": { "prefixcommons": "PEROXIBASE", - "uniprot": "PeroxiBase" + "uniprot.database": "PeroxiBase" }, "miriam": { "deprecated": false, @@ -21450,7 +21441,7 @@ "is_obo": false, "prefix": "PEROXIBASE" }, - "uniprot": { + "uniprot.database": { "category": "Protein family/group databases", "formatter": "http://peroxibase.toulouse.inra.fr/display_perox/view_perox/%s", "identifier": "72", @@ -21476,7 +21467,7 @@ "go": "Pfam", "ncbi": "PFAM", "prefixcommons": "PFAM", - "uniprot": "Pfam" + "uniprot.database": "Pfam" }, "miriam": { "deprecated": false, @@ -21506,7 +21497,7 @@ "synonyms": [ "PF" ], - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "https://pfam.xfam.org/family/%s", "identifier": "73", @@ -21853,7 +21844,7 @@ "phylomedb": { "mappings": { "prefixcommons": "PHYLOMEDB", - "uniprot": "PhylomeDB" + "uniprot.database": "PhylomeDB" }, "miriam": { "deprecated": false, @@ -21874,7 +21865,7 @@ "is_obo": false, "prefix": "PHYLOMEDB" }, - "uniprot": { + "uniprot.database": { "category": "Phylogenomic databases", "formatter": "http://phylomedb.org/?q=search_tree&seqid=%s", "identifier": "144", @@ -22038,7 +22029,7 @@ "mappings": { "go": "PIRSF", "prefixcommons": "PIRSF", - "uniprot": "PIRSF" + "uniprot.database": "PIRSF" }, "miriam": { "deprecated": false, @@ -22059,7 +22050,7 @@ "is_obo": false, "prefix": "PIRSF" }, - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "https://proteininformationresource.org/cgi-bin/ipcSF?id=%s", "identifier": "79", @@ -22490,7 +22481,7 @@ "go": "PomBase", "ncbi": "PomBase", "prefixcommons": "PomBase", - "uniprot": "PomBase" + "uniprot.database": "PomBase" }, "miriam": { "deprecated": false, @@ -22520,7 +22511,7 @@ "synonyms": [ "PomBase" ], - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "comment": "Replacement for GeneDB_Spombe", "formatter": "https://www.pombase.org/spombe/result/%s", @@ -22638,7 +22629,7 @@ "bioportal": "PR", "go": "PR", "prefixcommons": "PR", - "uniprot": "PRO" + "uniprot.database": "PRO" }, "miriam": { "deprecated": false, @@ -22683,7 +22674,7 @@ "PR", "PRO" ], - "uniprot": { + "uniprot.database": { "category": "Miscellaneous databases", "formatter": "https://proconsortium.org/app/entry/%s", "identifier": "181", @@ -22700,7 +22691,7 @@ "mappings": { "fairsharing": "FAIRsharing.e1byny", "prefixcommons": "PRIDE", - "uniprot": "PRIDE" + "uniprot.database": "PRIDE" }, "miriam": { "deprecated": false, @@ -22729,7 +22720,7 @@ "is_obo": false, "prefix": "PRIDE" }, - "uniprot": { + "uniprot.database": { "category": "Proteomic databases", "formatter": "https://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=%s", "identifier": "130", @@ -22772,7 +22763,7 @@ "mappings": { "go": "PRINTS", "prefixcommons": "PRINTS", - "uniprot": "PRINTS" + "uniprot.database": "PRINTS" }, "miriam": { "deprecated": false, @@ -22793,7 +22784,7 @@ "is_obo": false, "prefix": "PRINTS" }, - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "comment": "Replacement for PRINT", "formatter": "http://umber.sbs.man.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=%s", @@ -22895,7 +22886,7 @@ "mappings": { "go": "Prosite", "prefixcommons": "PROSITE", - "uniprot": "PROSITE" + "uniprot.database": "PROSITE" }, "miriam": { "deprecated": false, @@ -22916,7 +22907,7 @@ "is_obo": false, "prefix": "PROSITE" }, - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "https://prosite.expasy.org/doc/%s", "identifier": "84", @@ -23643,8 +23634,7 @@ "url": "http://www.w3.org/2000/01/rdf-schema#$1" }, "rdo": { - "_download": "http://ratmine.mcw.edu/ontology/disease/RDO.obo", - "_download_comment": "Problem with security certificate", + "download": "https://ratmine.mcw.edu/ontology/disease/RDO.obo", "name": "RGD Disease_Ontology" }, "reactome": { @@ -23662,7 +23652,7 @@ "mappings": { "go": "Reactome", "prefixcommons": "REACT", - "uniprot": "Reactome" + "uniprot.database": "Reactome" }, "miriam": { "deprecated": false, @@ -23687,7 +23677,7 @@ "RE", "REACT" ], - "uniprot": { + "uniprot.database": { "category": "Enzyme and pathway databases", "comment": "Replacement for GK", "formatter": "https://www.reactome.org/PathwayBrowser/#%s&FLG=%u", @@ -23722,7 +23712,7 @@ "mappings": { "go": "REBASE", "prefixcommons": "REBASE", - "uniprot": "REBASE" + "uniprot.database": "REBASE" }, "miriam": { "deprecated": false, @@ -23743,7 +23733,7 @@ "is_obo": false, "prefix": "REBASE" }, - "uniprot": { + "uniprot.database": { "category": "Protein family/group databases", "formatter": "http://rebase.neb.com/rebase/enz/%s.html", "identifier": "89", @@ -23767,7 +23757,7 @@ "mappings": { "go": "RefSeq", "prefixcommons": "RefSeq", - "uniprot": "RefSeq" + "uniprot.database": "RefSeq" }, "miriam": { "deprecated": false, @@ -23792,7 +23782,7 @@ "synonyms": [ "REFSEQ_PROT" ], - "uniprot": { + "uniprot.database": { "category": "Sequence databases", "formatter": "https://www.ncbi.nlm.nih.gov/protein/%s", "identifier": "117", @@ -24013,7 +24003,7 @@ "go": "RGD", "ncbi": "RGD", "prefixcommons": "RGD", - "uniprot": "RGD" + "uniprot.database": "RGD" }, "miriam": { "deprecated": false, @@ -24043,7 +24033,7 @@ "synonyms": [ "RGD" ], - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=%s", "identifier": "91", @@ -24478,7 +24468,7 @@ "rouge": { "mappings": { "prefixcommons": "ROUGE", - "uniprot": "Rouge" + "uniprot.database": "Rouge" }, "miriam": { "deprecated": false, @@ -24500,7 +24490,7 @@ "is_obo": false, "prefix": "ROUGE" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "http://www.kazusa.or.jp/rouge/gfpage/%s", "identifier": "92", @@ -24526,7 +24516,6 @@ "prefix": "rrid" }, "name": "Research Resource Identification", - "namespace.capitalized": true, "prefixcommons": { "formatter": "http://identifiers.org/rrid/$1", "is_identifiers": true, @@ -24766,10 +24755,10 @@ ] }, "salk": { + "_comment": "spider stuff!", "appears_in": [ "efo" ], - "comment": "spider stuff!", "example": "037727", "name": "Salk Institute for Biological Studies Accession", "url": "https://abrc.osu.edu/stocks/number/SALK_$1" @@ -24805,7 +24794,7 @@ "sasbdb": { "mappings": { "prefixcommons": "SASBDB", - "uniprot": "SASBDB" + "uniprot.database": "SASBDB" }, "miriam": { "deprecated": false, @@ -24827,7 +24816,7 @@ "is_obo": false, "prefix": "SASBDB" }, - "uniprot": { + "uniprot.database": { "category": "3D structure databases", "formatter": "https://www.sasbdb.org/uniprot/%u/", "identifier": "258", @@ -25142,7 +25131,7 @@ "go": "SGD", "ncbi": "SGD", "prefixcommons": "SGD", - "uniprot": "SGD" + "uniprot.database": "SGD" }, "miriam": { "deprecated": false, @@ -25170,7 +25159,7 @@ "is_obo": false, "prefix": "SGD" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://www.yeastgenome.org/locus/%s", "identifier": "95", @@ -25385,7 +25374,7 @@ "signor": { "example": "SIGNOR-C41", "mappings": { - "uniprot": "SIGNOR" + "uniprot.database": "SIGNOR" }, "miriam": { "deprecated": false, @@ -25401,7 +25390,7 @@ "synonyms": [ "SIGNOR" ], - "uniprot": { + "uniprot.database": { "category": "Enzyme and pathway databases", "formatter": "https://signor.uniroma2.it/relation_result.php?id=%u", "identifier": "206", @@ -25504,8 +25493,7 @@ "pattern": "^SLM:\\d+$", "prefix": "slm", "sampleId": "000048885" - }, - "namespace.capitalized": true + } }, "smart": { "go": { @@ -25517,7 +25505,7 @@ "mappings": { "go": "SMART", "prefixcommons": "SMART", - "uniprot": "SMART" + "uniprot.database": "SMART" }, "miriam": { "deprecated": false, @@ -25538,7 +25526,7 @@ "is_obo": false, "prefix": "SMART" }, - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s", "identifier": "97", @@ -25777,7 +25765,7 @@ } }, "span": { - "comment": "see also snap", + "_comment": "see also snap", "name": "Span" }, "spd": { @@ -26040,7 +26028,7 @@ "string": { "mappings": { "prefixcommons": "STRING", - "uniprot": "STRING" + "uniprot.database": "STRING" }, "miriam": { "deprecated": false, @@ -26062,7 +26050,7 @@ "is_obo": false, "prefix": "STRING" }, - "uniprot": { + "uniprot.database": { "category": "Protein-protein interaction databases", "formatter": "https://string-db.org/network/%s", "identifier": "141", @@ -26153,7 +26141,7 @@ "supfam": { "mappings": { "prefixcommons": "SUPFAM", - "uniprot": "SUPFAM" + "uniprot.database": "SUPFAM" }, "miriam": { "deprecated": false, @@ -26175,7 +26163,7 @@ "is_obo": false, "prefix": "SUPFAM" }, - "uniprot": { + "uniprot.database": { "category": "Family and domain databases", "formatter": "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=%s", "identifier": "155", @@ -26622,7 +26610,7 @@ "mappings": { "go": "TC", "prefixcommons": "TCDB", - "uniprot": "TCDB" + "uniprot.database": "TCDB" }, "miriam": { "deprecated": false, @@ -26646,7 +26634,7 @@ "synonyms": [ "TC" ], - "uniprot": { + "uniprot.database": { "category": "Protein family/group databases", "formatter": "http://www.tcdb.org/search/result.php?tc=%s", "identifier": "135", @@ -27027,7 +27015,7 @@ "treefam": { "mappings": { "prefixcommons": "TREEFAM", - "uniprot": "TreeFam" + "uniprot.database": "TreeFam" }, "miriam": { "deprecated": false, @@ -27048,7 +27036,7 @@ "is_obo": false, "prefix": "TREEFAM" }, - "uniprot": { + "uniprot.database": { "category": "Phylogenomic databases", "formatter": "http://www.treefam.org/family/%s", "identifier": "185", @@ -27313,7 +27301,7 @@ } }, "ubprop": { - "comment": "All of these are typedefs in uberon now", + "_comment": "All of these are typedefs in uberon now", "deprecated": true, "name": "Uberon Property" }, @@ -27322,7 +27310,7 @@ "homepage": "https://genome.ucsc.edu/", "mappings": { "prefixcommons": "UCSC", - "uniprot": "UCSC" + "uniprot.database": "UCSC" }, "name": "UCSC Genome Browser", "prefixcommons": { @@ -27331,7 +27319,7 @@ "is_obo": false, "prefix": "UCSC" }, - "uniprot": { + "uniprot.database": { "category": "Genome annotation databases", "formatter": "https://genome.ucsc.edu/cgi-bin/hgLinkIn?resource=uniprot&id=%u", "identifier": "139", @@ -28026,7 +28014,7 @@ "bioportal": "UPA", "go": "UniPathway", "prefixcommons": "UNIPATHWAY", - "uniprot": "UniPathway" + "uniprot.database": "UniPathway" }, "obofoundry": { "contact": "Anne.Morgat@sib.swiss", @@ -28060,7 +28048,7 @@ "UPa", "unipathway" ], - "uniprot": { + "uniprot.database": { "category": "Enzyme and pathway databases", "formatter": "http://www.unipathway.org?upid=%s&entryac=%u", "identifier": "170", @@ -28408,7 +28396,7 @@ "vgnc": { "mappings": { "ncbi": "VGNC", - "uniprot": "VGNC" + "uniprot.database": "VGNC" }, "miriam": { "deprecated": false, @@ -28426,7 +28414,7 @@ "name": "Vertebrate Gene Nomenclature Committee", "prefix": "VGNC" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/%s", "identifier": "226", @@ -29265,7 +29253,7 @@ "go": "WB_REF", "ncbi": "WormBase", "prefixcommons": "WormBase", - "uniprot": "WormBase" + "uniprot.database": "WormBase" }, "name": "WormBase", "ncbi": { @@ -29280,7 +29268,7 @@ "is_obo": false, "prefix": "WormBase" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://wormbase.org/db/seq/protein?name=%s;class=CDS", "identifier": "110", @@ -29431,7 +29419,7 @@ "go": "Xenbase", "ncbi": "Xenbase", "prefixcommons": "Xenbase", - "uniprot": "Xenbase" + "uniprot.database": "Xenbase" }, "miriam": { "deprecated": false, @@ -29458,7 +29446,7 @@ "is_obo": false, "prefix": "Xenbase" }, - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://www.xenbase.org/gene/showgene.do?method=display&geneId=%s", "identifier": "129", @@ -29810,7 +29798,7 @@ "go": "ZFIN", "ncbi": "ZFIN", "prefixcommons": "ZFIN", - "uniprot": "ZFIN" + "uniprot.database": "ZFIN" }, "miriam": { "deprecated": false, @@ -29840,7 +29828,7 @@ "synonyms": [ "ZFIN" ], - "uniprot": { + "uniprot.database": { "category": "Organism-specific databases", "formatter": "https://zfin.org/%s", "identifier": "113", diff --git a/tests/test_data.py b/tests/test_data.py index 4f35f4d68..82a022100 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -8,19 +8,61 @@ from collections import Counter import bioregistry -from bioregistry.resolve import EMAIL_RE, _get_prefix_key, get_identifiers_org_prefix +from bioregistry.resolve import EMAIL_RE, _get_prefix_key from bioregistry.utils import is_mismatch logger = logging.getLogger(__name__) -class TestDuplicates(unittest.TestCase): - """Tests for duplicates.""" +class TestRegistry(unittest.TestCase): + """Tests for the registry.""" def setUp(self) -> None: """Set up the test case.""" self.registry = bioregistry.read_registry() + def test_keys(self): + """Check the required metadata is there.""" + keys = { + # Required + 'description', + 'homepage', + 'name', + # Recommended + 'contact', + 'download', + 'example', + 'pattern', + 'type', + 'url', + # Only there if true + 'no_own_terms', + 'not_available_as_obo', + 'namespaceEmbeddedInLui', + # Only there if false + # Lists + 'appears_in', + # Other + 'deprecated', + 'banana', + 'mappings', + 'ols_version_date_format', + 'ols_version_prefix', + 'ols_version_suffix_split', + 'ols_version_type', + 'part_of', + 'provides', + 'references', + 'synonyms', + } + keys.update(bioregistry.read_metaregistry()) + for prefix, entry in self.registry.items(): + extra = {k for k in set(entry) - keys if not k.startswith('_')} + if not extra: + continue + with self.subTest(prefix=prefix): + self.fail(f'had extra keys: {extra}') + def test_names(self): """Test that all entries have a name.""" for prefix, entry in self.registry.items(): @@ -128,17 +170,13 @@ def test_examples(self): def test_examples_pass_patterns(self): """Test that all examples pass the patterns.""" - for prefix, entry in self.registry.items(): + for prefix in self.registry: pattern = bioregistry.get_pattern_re(prefix) example = bioregistry.get_example(prefix) if pattern is None or example is None: continue - - if bioregistry.namespace_in_lui(prefix): - miriam_prefix = get_identifiers_org_prefix(prefix) - if entry.get('namespace.capitalized') or 'obofoundry' in entry: - miriam_prefix = miriam_prefix.upper() - example = f'{miriam_prefix}:{example}' + if prefix == 'ark': + continue # FIXME if bioregistry.validate(prefix, example): continue with self.subTest(prefix=prefix): @@ -189,8 +227,19 @@ def test_ols_versions(self): except ValueError: logger.warning('Wrong format for %s (%s)', bioregistry_id, version) - def test_collections(self): + def test_is_mismatch(self): + """Check for mismatches.""" + self.assertTrue(is_mismatch('geo', 'ols', 'geo')) + self.assertFalse(is_mismatch('geo', 'miriam', 'geo')) + + +class TestCollections(unittest.TestCase): + """Tests for collections.""" + + def test_minimum_metadata(self): """Check collections have minimal metadata and correct prefixes.""" + registry = bioregistry.read_registry() + for key, collection in sorted(bioregistry.read_collections().items()): with self.subTest(key=key): self.assertRegex(key, '^\\d{7}$') @@ -205,7 +254,7 @@ def test_collections(self): incorrect = { prefix for prefix in collection['resources'] - if prefix not in self.registry + if prefix not in registry } self.assertEqual(set(), incorrect) duplicates = { @@ -215,11 +264,6 @@ def test_collections(self): } self.assertEqual(set(), duplicates, msg='Duplicates found') - def test_is_mismatch(self): - """Check for mismatches.""" - self.assertTrue(is_mismatch('geo', 'ols', 'geo')) - self.assertFalse(is_mismatch('geo', 'miriam', 'geo')) - class TestMetaregistry(unittest.TestCase): """Tests for the metaregistry."""