From 70a14b1d6f4ed5828d25421ed9be30de6219a2bd Mon Sep 17 00:00:00 2001 From: Harshad Date: Tue, 18 Jul 2023 14:43:56 -0500 Subject: [PATCH] Removes unnecessary `external_context.py`, clean Makefile & update dependencies. (#394) * Removes unnecessary `external_context.py` and clean Makefile. * Fixed get_external_jsonld_context() * test change * Moved scipy to extras * Changed package dependencies from ^ to >= fixes #392 * flake8 ed * ran poetry update and all work. --- Makefile | 24 +- poetry.lock | 410 ++++++------ pyproject.toml | 22 +- src/sssom/constants.py | 1 + src/sssom/context.py | 7 +- ...ntext.py => sssom.external.context.jsonld} | 609 +++++++++++++----- tests/test_parsers.py | 2 +- 7 files changed, 671 insertions(+), 404 deletions(-) rename src/sssom/{external_context.py => sssom.external.context.jsonld} (71%) diff --git a/Makefile b/Makefile index c07d2924..933a4157 100644 --- a/Makefile +++ b/Makefile @@ -20,7 +20,7 @@ schema/cliquesummary.py: schema/cliquesummary.yaml gen-py-classes $< > $@ schema/%.schema.json: .FORCE wget $(SSSOM_JSON_SCHEMA) -O $@ -schema/sssom.external.context.jsonld: +src/sssom/sssom.external.context.jsonld: wget $(DEFAULT_PREFIX_MAP) -O $@ schema/%.context.jsonld: .FORCE wget $(SSSOM_JSONLD_CONTEXT) -O $@ @@ -33,28 +33,8 @@ test: tox sh tests/tests.sh -src/sssom/external_context.py: schema/sssom.external.context.jsonld - echo "\"\"\"This module contains an autogenerated copy of the external SSSOM context.\"\"\"" > $@ - echo "" >> $@ - echo "# This is autogenerated and super hacky." >> $@ - echo "sssom_external_context = \"\"\"" >> $@ - cat $< >> $@ - echo "\"\"\"" >> $@ - black $@ - -src/sssom/internal_context.py: schema/sssom.context.jsonld - echo "\"\"\"This module contains an autogenerated copy of the internal SSSOM context.\"\"\"" > $@ - echo "" >> $@ - echo "sssom_context = \"\"\"" >> $@ - cat $< >> $@ - echo "\"\"\"" >> $@ - -deploy-dm: src/sssom/external_context.py src/sssom/internal_context.py - cp schema/sssom_datamodel.py src/sssom/ - cp schema/sssom.context.jsonld src/sssom/ - cp schema/sssom.external.context.jsonld src/sssom/ +deploy-dm: src/sssom/sssom.external.context.jsonld - install: pip install .[test,docs] diff --git 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a/src/sssom/constants.py b/src/sssom/constants.py index e0ac78a0..e313ee0e 100644 --- a/src/sssom/constants.py +++ b/src/sssom/constants.py @@ -14,6 +14,7 @@ HERE = pathlib.Path(__file__).parent.resolve() SCHEMA_YAML = pkg_resources.resource_filename("sssom_schema", "schema/sssom_schema.yaml") +EXTERNAL_CONTEXT = HERE / "sssom.external.context.jsonld" # SCHEMA_VIEW = package_schemaview("sssom_schema") diff --git a/src/sssom/context.py b/src/sssom/context.py index 045bf7f8..1a4813cc 100644 --- a/src/sssom/context.py +++ b/src/sssom/context.py @@ -7,7 +7,8 @@ import pkg_resources -from .external_context import sssom_external_context +from sssom.constants import EXTERNAL_CONTEXT + from .typehints import Metadata, MetadataType, PrefixMap # HERE = pathlib.Path(__file__).parent.resolve() @@ -41,7 +42,9 @@ def get_external_jsonld_context(): :return: JSON-LD context """ - return json.loads(sssom_external_context, strict=False) + with open(str(EXTERNAL_CONTEXT), "r") as f: + data = json.load(f, strict=False) + return data def get_built_in_prefix_map() -> PrefixMap: diff --git a/src/sssom/external_context.py b/src/sssom/sssom.external.context.jsonld similarity index 71% rename from src/sssom/external_context.py rename to src/sssom/sssom.external.context.jsonld index f9f3ec80..60731ae7 100644 --- a/src/sssom/external_context.py +++ b/src/sssom/sssom.external.context.jsonld @@ -1,7 +1,3 @@ -"""This module contains an autogenerated copy of the external SSSOM context.""" - -# This is autogenerated and super hacky. -sssom_external_context = """ { "@context": { "3dmet": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=", @@ -9,7 +5,7 @@ "4dn.replicate": "https://data.4dnucleome.org/experiment-set-replicates/", "AAO": "http://purl.obolibrary.org/obo/AAO_", "ADO": "http://purl.obolibrary.org/obo/ADO_", - "ADW": "https://animaldiversity.org/accounts/", + "ADW": "http://purl.obolibrary.org/obo/ADW_", "AEO": "http://purl.obolibrary.org/obo/AEO_", "AERO": "http://purl.obolibrary.org/obo/AERO_", "AGRO": "http://purl.obolibrary.org/obo/AGRO_", @@ -47,21 +43,56 @@ "CMO": "http://purl.obolibrary.org/obo/CMO_", "COB": "http://purl.obolibrary.org/obo/COB_", "COLAO": "http://purl.obolibrary.org/obo/COLAO_", + "CO_320": "https://cropontology.org/rdf/CO_320:", + "CO_321": "https://cropontology.org/rdf/CO_321:", + "CO_322": "https://cropontology.org/rdf/CO_322:", + "CO_323": "https://cropontology.org/rdf/CO_323:", + "CO_324": "https://cropontology.org/rdf/CO_324:", + "CO_325": "https://cropontology.org/rdf/CO_325:", + "CO_326": "https://cropontology.org/rdf/CO_326:", + "CO_327": "https://cropontology.org/rdf/CO_327:", + "CO_330": "https://cropontology.org/rdf/CO_330:", + "CO_331": "https://cropontology.org/rdf/CO_331:", + "CO_333": "https://cropontology.org/rdf/CO_333:", + "CO_334": "https://cropontology.org/rdf/CO_334:", + "CO_335": "https://cropontology.org/rdf/CO_335:", + "CO_336": "https://cropontology.org/rdf/CO_336:", + "CO_337": "https://cropontology.org/rdf/CO_337:", + "CO_338": "https://cropontology.org/rdf/CO_338:", + "CO_339": "https://cropontology.org/rdf/CO_339:", + "CO_340": "https://cropontology.org/rdf/CO_340:", + "CO_341": "https://cropontology.org/rdf/CO_341:", + "CO_343": "https://cropontology.org/rdf/CO_343:", + "CO_345": "https://cropontology.org/rdf/CO_345:", + "CO_346": "https://cropontology.org/rdf/CO_346:", + "CO_347": "https://cropontology.org/rdf/CO_347:", + "CO_348": "https://cropontology.org/rdf/CO_348:", + "CO_350": "https://cropontology.org/rdf/CO_350:", + "CO_356": "https://cropontology.org/rdf/CO_356:", + "CO_357": "https://cropontology.org/rdf/CO_357:", + "CO_358": "https://cropontology.org/rdf/CO_358:", + "CO_359": "https://cropontology.org/rdf/CO_359:", + "CO_360": "https://cropontology.org/rdf/CO_360:", + "CO_365": "https://cropontology.org/rdf/CO_365:", + "CO_366": "https://cropontology.org/rdf/CO_366:", + "CO_367": "https://cropontology.org/rdf/CO_367:", + "CO_370": "https://cropontology.org/rdf/CO_370:", "CRO": "http://purl.obolibrary.org/obo/CRO_", "CTENO": "http://purl.obolibrary.org/obo/CTENO_", "CTO": "http://purl.obolibrary.org/obo/CTO_", "CVDO": "http://purl.obolibrary.org/obo/CVDO_", + "ChEMROF": "https://chemkg.github.io/chemrof/", "CiTO": "http://purl.org/spar/cito/", "DC_CL": "http://purl.obolibrary.org/obo/DC_CL_", "DDANAT": "http://purl.obolibrary.org/obo/DDANAT_", "DDPHENO": "http://purl.obolibrary.org/obo/DDPHENO_", "DEO": "http://purl.org/spar/deo/", + "DHBA": "https://biopragmatics.github.io/providers/dhba/", "DIDEO": "http://purl.obolibrary.org/obo/DIDEO_", "DINTO": "http://purl.obolibrary.org/obo/DINTO_", "DISDRIV": "http://purl.obolibrary.org/obo/DISDRIV_", - "DOI": "https://doi.org/", + "DMBA": "https://biopragmatics.github.io/providers/dmba/", "DOID": "http://purl.obolibrary.org/obo/DOID_", - "DPO": "http://purl.obolibrary.org/obo/FBcv_", "DRON": "http://purl.obolibrary.org/obo/DRON_", "DUO": "http://purl.obolibrary.org/obo/DUO_", "DataCite": "http://purl.org/spar/datacite/", @@ -77,9 +108,10 @@ "EHDAA2": "http://purl.obolibrary.org/obo/EHDAA2_", "EMAP": "http://purl.obolibrary.org/obo/EMAP_", "EMAPA": "http://purl.obolibrary.org/obo/EMAPA_", - "ENSEMBL": "https://www.ensembl.org/id/", + "EMAPS": "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:", + "ENSEMBL": "http://rdf.ebi.ac.uk/resource/ensembl/", "ENVO": "http://purl.obolibrary.org/obo/ENVO_", - "EO": "http://archive.gramene.org/db/ontology/search?query=EO:", + "EO": "http://purl.obolibrary.org/obo/EO_", "EPIO": "http://purl.obolibrary.org/obo/EPIO_", "EPO": "http://purl.obolibrary.org/obo/EPO_", "ERO": "http://purl.obolibrary.org/obo/ERO_", @@ -108,19 +140,24 @@ "GECKO": "http://purl.obolibrary.org/obo/GECKO_", "GENEPIO": "http://purl.obolibrary.org/obo/GENEPIO_", "GENO": "http://purl.obolibrary.org/obo/GENO_", - "GEOGEO": "http://purl.obolibrary.org/obo/GEO_", + "GEO": "http://purl.obolibrary.org/obo/GEO_", "GNO": "http://purl.obolibrary.org/obo/GNO_", "GO": "http://purl.obolibrary.org/obo/GO_", + "GOCHE": "https://biopragmatics.github.io/providers/goche/", + "GRO": "http://purl.obolibrary.org/obo/GRO_", "GSSO": "http://purl.obolibrary.org/obo/GSSO_", "HABRONATTUS": "http://purl.obolibrary.org/obo/HABRONATTUS_", "HANCESTRO": "http://purl.obolibrary.org/obo/HANCESTRO_", "HAO": "http://purl.obolibrary.org/obo/HAO_", + "HBA": "https://biopragmatics.github.io/providers/hba/", + "HEPRO": "http://purl.obolibrary.org/obo/HEPRO_", "HOM": "http://purl.obolibrary.org/obo/HOM_", "HP": "http://purl.obolibrary.org/obo/HP_", "HSO": "http://purl.obolibrary.org/obo/HSO_", "HTN": "http://purl.obolibrary.org/obo/HTN_", "HsapDv": "http://purl.obolibrary.org/obo/HsapDv_", "IAO": "http://purl.obolibrary.org/obo/IAO_", + "ICD10WHO": "https://icd.who.int/browse10/2019/en#/", "ICEO": "http://purl.obolibrary.org/obo/ICEO_", "ICO": "http://purl.obolibrary.org/obo/ICO_", "IDO": "http://purl.obolibrary.org/obo/IDO_", @@ -128,6 +165,7 @@ "IEV": "http://purl.obolibrary.org/obo/IEV_", "IMR": "http://purl.obolibrary.org/obo/IMR_", "INO": "http://purl.obolibrary.org/obo/INO_", + "IPR": "http://purl.obolibrary.org/obo/IPR_", "KISAO": "http://purl.obolibrary.org/obo/KISAO_", "LABO": "http://purl.obolibrary.org/obo/LABO_", "LEPAO": "http://purl.obolibrary.org/obo/LEPAO_", @@ -138,6 +176,7 @@ "MAO": "http://purl.obolibrary.org/obo/MAO_", "MAT": "http://purl.obolibrary.org/obo/MAT_", "MAXO": "http://purl.obolibrary.org/obo/MAXO_", + "MBA": "https://biopragmatics.github.io/providers/mba/", "MCO": "http://purl.obolibrary.org/obo/MCO_", "MF": "http://purl.obolibrary.org/obo/MF_", "MFMO": "http://purl.obolibrary.org/obo/MFMO_", @@ -162,15 +201,16 @@ "MS": "http://purl.obolibrary.org/obo/MS_", "MmusDv": "http://purl.obolibrary.org/obo/MmusDv_", "NBO": "http://purl.obolibrary.org/obo/NBO_", - "NCBIGene": "https://www.ncbi.nlm.nih.gov/gene/", + "NCBIGene": "http://purl.uniprot.org/geneid/", "NCBIProtein": "https://www.ncbi.nlm.nih.gov/protein/", "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", "NCIT": "http://purl.obolibrary.org/obo/NCIT_", "NCRO": "http://purl.obolibrary.org/obo/NCRO_", + "NGBO": "http://purl.obolibrary.org/obo/NGBO_", "NIF_CELL": "http://purl.obolibrary.org/obo/NIF_CELL_", "NIF_DYSFUNCTION": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_", "NIF_GROSSANATOMY": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_", - "NMR": "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:", + "NMR": "http://purl.obolibrary.org/obo/NMR_", "NOMEN": "http://purl.obolibrary.org/obo/NOMEN_", "OAE": "http://purl.obolibrary.org/obo/OAE_", "OARCS": "http://purl.obolibrary.org/obo/OARCS_", @@ -202,6 +242,7 @@ "OlatDv": "http://purl.obolibrary.org/obo/OlatDv_", "PAO": "http://purl.obolibrary.org/obo/PAO_", "PATO": "http://purl.obolibrary.org/obo/PATO_", + "PBA": "https://biopragmatics.github.io/providers/pba/", "PCL": "http://purl.obolibrary.org/obo/PCL_", "PCO": "http://purl.obolibrary.org/obo/PCO_", "PDRO": "http://purl.obolibrary.org/obo/PDRO_", @@ -212,6 +253,7 @@ "PLANA": "http://purl.obolibrary.org/obo/PLANA_", "PLANP": "http://purl.obolibrary.org/obo/PLANP_", "PLO": "http://purl.obolibrary.org/obo/PLO_", + "PMID": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/", "PO": "http://purl.obolibrary.org/obo/PO_", "PORO": "http://purl.obolibrary.org/obo/PORO_", "PPO": "http://purl.obolibrary.org/obo/PPO_", @@ -225,26 +267,29 @@ "PdumDv": "http://purl.obolibrary.org/obo/PdumDv_", "PuRO": "http://purl.org/spar/pro/", "RBO": "http://purl.obolibrary.org/obo/RBO_", - "RESID": "https://proteininformationresource.org/cgi-bin/resid?id=", + "RESID": "http://purl.obolibrary.org/obo/RESID_", "REX": "http://purl.obolibrary.org/obo/REX_", "RNAO": "http://purl.obolibrary.org/obo/RNAO_", "RO": "http://purl.obolibrary.org/obo/RO_", "RS": "http://purl.obolibrary.org/obo/RS_", "RXNO": "http://purl.obolibrary.org/obo/RXNO_", - "SAO": "http://uri.neuinfo.org/nif/nifstd/sao", + "RoleO": "http://purl.obolibrary.org/obo/RoleO_", + "SAO": "http://purl.obolibrary.org/obo/SAO_", "SBO": "http://purl.obolibrary.org/obo/SBO_", "SCDO": "http://purl.obolibrary.org/obo/SCDO_", - "SCTID": "http://www.snomedbrowser.com/Codes/Details/", + "SCTID": "http://snomed.info/id/", "SCoRO": "http://purl.org/spar/scoro/", "SEP": "http://purl.obolibrary.org/obo/SEP_", "SEPIO": "http://purl.obolibrary.org/obo/SEPIO_", "SIBO": "http://purl.obolibrary.org/obo/SIBO_", + "SLM": "https://www.swisslipids.org/#/entity/SLM:", "SO": "http://purl.obolibrary.org/obo/SO_", "SOPHARM": "http://purl.obolibrary.org/obo/SOPHARM_", "SPD": "http://purl.obolibrary.org/obo/SPD_", "STATO": "http://purl.obolibrary.org/obo/STATO_", "SWO": "http://purl.obolibrary.org/obo/SWO_", "SYMP": "http://purl.obolibrary.org/obo/SYMP_", + "T4FS": "http://purl.obolibrary.org/obo/T4FS_", "TADS": "http://purl.obolibrary.org/obo/TADS_", "TAHE": "http://purl.obolibrary.org/obo/TAHE_", "TAHH": "http://purl.obolibrary.org/obo/TAHH_", @@ -258,8 +303,9 @@ "UBERON": "http://purl.obolibrary.org/obo/UBERON_", "UMLS": "http://linkedlifedata.com/resource/umls/id/", "UO": "http://purl.obolibrary.org/obo/UO_", - "UPA": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=", + "UPA": "http://purl.obolibrary.org/obo/UPA_", "UPHENO": "http://purl.obolibrary.org/obo/UPHENO_", + "VBO": "http://purl.obolibrary.org/obo/VBO_", "VHOG": "http://purl.obolibrary.org/obo/VHOG_", "VO": "http://purl.obolibrary.org/obo/VO_", "VSAO": "http://purl.obolibrary.org/obo/VSAO_", @@ -274,27 +320,38 @@ "XCO": "http://purl.obolibrary.org/obo/XCO_", "XLMOD": "http://purl.obolibrary.org/obo/XLMOD_", "XPO": "http://purl.obolibrary.org/obo/XPO_", + "YPO": "http://purl.obolibrary.org/obo/YPO_", "ZEA": "http://purl.obolibrary.org/obo/ZEA_", "ZECO": "http://purl.obolibrary.org/obo/ZECO_", "ZFA": "http://purl.obolibrary.org/obo/ZFA_", "ZFS": "http://purl.obolibrary.org/obo/ZFS_", "ZP": "http://purl.obolibrary.org/obo/ZP_", + "aaindex": "http://www.genome.jp/dbget-bin/www_bget?aaindex:", "abcd": "https://web.expasy.org/abcd/ABCD_", - "abm": "https://www.abmgood.com/catalogsearch/result/?cat=&q=", + "abm": "https://www.abmgood.com/search?query=", + "abs": "https://identifiers.org/abs:", "ac": "http://www.w3.org/ns/activitystreams#", "aceview.worm": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=", + "adcad": "https://purl.dataone.org/odo/ADCAD_", "addexbio": "https://www.addexbio.com/productdetail?pid=", "addgene": "http://addgene.org/", + "adms": "http://www.w3.org/ns/adms#", + "aeon": "http://purl.obolibrary.org/obo/AEON_", "affy.probeset": "https://www.affymetrix.com/LinkServlet?probeset=", "aftol.taxonomy": "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=", "agricola": "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=", "agrkb": "https://www.alliancegenome.org/accession/", - "agrovoc": "http://aims.fao.org/aos/agrovoc/c_", + "agrovoc": "http://aims.fao.org/aos/agrovoc/", + "agsd": "http://www.genomesize.com/result_species.php?id=", + "aio": "https://w3id.org/aio/", + "alfred": "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=", "allergome": "http://www.allergome.org/script/dettaglio.php?id_molecule=", "alzforum.mutation": "https://www.alzforum.org/mutations/", + "alzgene": "http://www.alzgene.org/geneoverview.asp?geneid=", "amoebadb": "https://amoebadb.org/amoeba/app/record/gene/", "antibodyregistry": "http://antibodyregistry.org/AB_", "antweb": "http://www.antweb.org/specimen.do?name=", + "anzctr": "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=", "aop": "https://aopwiki.org/aops/", "aop.events": "https://aopwiki.org/events/", "aop.relationships": "https://aopwiki.org/relationships/", @@ -302,9 +359,9 @@ "apaonto": "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#", "apd": "http://aps.unmc.edu/AP/database/query_output.php?ID=", "aphidbase.transcript": "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=", - "apid.interactions": "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=", "arachnoserver": "http://www.arachnoserver.org/toxincard.html?id=", "araport": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=", + "archdb": "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=", "ardb": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=", "ark": "http://n2t.net/ark:", "arrayexpress": "https://www.ebi.ac.uk/arrayexpress/experiments/", @@ -316,53 +373,63 @@ "asin": "https://amzn.com/", "aspgd.locus": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=", "aspgd.protein": "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=", + "asrp": "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=", "atc": "http://www.whocc.no/atc_ddd_index/?code=", "atcc": "https://www.atcc.org/products/", "atcvet": "http://www.whocc.no/atcvet/atcvet_index/?code=", "atfdb.family": "http://www.bioguo.org/AnimalTFDB/family.php?fam=", + "atol": "http://opendata.inra.fr/ATOL/ATOL_", "autdb": "http://autism.mindspec.org/GeneDetail/", + "babelon": "https://w3id.org/babelon/", "bacdive": "https://bacdive.dsmz.de/strain/", "bacmap.biog": "http://bacmap.wishartlab.com/organisms/", + "bacmap.map": "https://identifiers.org/bacmap.map:", "bactibase": "http://bactibase.hammamilab.org/", "bao": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_", + "bartoc": "https://bartoc.org/en/node/", "bbkg": "https://bbp.epfl.ch/nexus/web/studios/public/", "bbtp": "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:", + "bcio": "https://w3id.org/BCI-ontology#", "bcrc": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=", "bcrj": "http://bcrj.org.br/celula/", - "bdgp.est": "https://www.ncbi.nlm.nih.gov/nucest/", "bdgp.insertion": "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=", "bdsc": "https://bdsc.indiana.edu/stocks/", "beetlebase": "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=", "begdb": "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=", "bgee.family": "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=", - "bgee.gene": "https://bgee.org/?page=gene&gene_id=", "bgee.organ": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=", "bgee.stage": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=", + "bibo": "http://purl.org/ontology/bibo/", "bigg.compartment": "http://bigg.ucsd.edu/compartments/", "bigg.metabolite": "http://bigg.ucsd.edu/models/universal/metabolites/", "bigg.model": "http://bigg.ucsd.edu/models/", "bigg.reaction": "http://bigg.ucsd.edu/models/universal/reactions/", + "bind": "http://www.bind.ca/Action?identifier=bindid&idsearch=", "bindingdb": "http://www.bindingdb.org/compact/", "biocarta.pathway": "https://cgap.nci.nih.gov/Pathways/BioCarta/", "biocatalogue.service": "https://www.biocatalogue.org/services/", "biocyc": "http://biocyc.org/getid?id=", + "biofactoid": "https://biofactoid.org/document/", "biogrid": "http://thebiogrid.org/", "biogrid.interaction": "https://thebiogrid.org/interaction/", + "biokc": "https://biokb.lcsb.uni.lu/fact/", "biolegend": "https://www.biolegend.com/Default.aspx?ID=6664&productid=", "biolink": "https://w3id.org/biolink/vocab/", + "biomagresbank": "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=", "biominder": "https://datalab.rwth-aachen.de/MINDER/resource/", "biomodels.db": "https://www.ebi.ac.uk/biomodels/", "biomodels.teddy": "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_", "biomodels.vocabulary": "http://biomodels.net/rdf/vocabulary.rdf#", "bionumbers": "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=", + "biopixie": "http://avis.princeton.edu/pixie/viewgraph.php?graphID=", "bioportal": "http://bioportal.bioontology.org/ontologies/", - "bioproject": "https://www.ncbi.nlm.nih.gov/bioproject/?term=", "bioregistry": "https://bioregistry.io/registry/", "bioregistry.collection": "https://bioregistry.io/collection/", "bioregistry.registry": "https://bioregistry.io/metaregistry/", "bioregistry.schema": "https://bioregistry.io/schema/#", - "biorxiv": "https://www.biorxiv.org/content/10.1101/", + "biorxiv": "http://dx.doi.org/10.1101/", "biosample": "https://www.ebi.ac.uk/biosamples/sample/", + "bioschemas": "https://bioschemas.org/profiles/", "biosimulations": "https://biosimulations.org/projects/", "biosimulators": "https://biosimulators.org/simulators/", "biostudies": "https://www.ebi.ac.uk/biostudies/studies/", @@ -374,25 +441,33 @@ "bitterdb.cpd": "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=", "bitterdb.rec": "http://bitterdb.agri.huji.ac.il/Receptor.php?id=", "bko": "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:", + "bmrb": "https://identifiers.org/bmrb:", "bmrb.restraint": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=", "bold.taxonomy": "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=", - "brenda": "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=", "brenda.ligand": "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=", "brenda.ligandgroup": "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=", + "bridgedb": "http://vocabularies.bridgedb.org/ops#", "broad": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=", + "bs": "https://biopragmatics.github.io/providers/bs/", + "bugbase.expt": "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=", + "bugbase.protocol": "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id=", + "cabri": "https://identifiers.org/cabri:", + "cadsr": "https://identifiers.org/cadsr:", + "caloha": "https://www.nextprot.org/term/", "cameo": "https://www.cameo3d.org/sp/targets/target/", "caps": "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=", - "cas": "https://commonchemistry.cas.org/detail?ref=", + "cas": "https://commonchemistry.cas.org/detail?cas_rn=", "casspc": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=", "cath": "http://www.cathdb.info/cathnode/", "cath.domain": "http://www.cathdb.info/domain/", - "cath.superfamily": "http://www.cathdb.info/cathnode/", - "cattleqtldb": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:", + "cazy": "https://identifiers.org/cazy:", "cba": "https://europepmc.org/article/CBA/", "cbioportal": "https://www.cbioportal.org/study/summary?id=", + "ccdc": "https://identifiers.org/ccdc:", "ccds": "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=", + "ccf": "http://purl.org/ccf/", "ccle": "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=", - "cco": "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:", + "cco": "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:", "ccrid": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=", "cdd": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=", "cdpd": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=", @@ -400,73 +475,57 @@ "cell_model_passport": "https://cellmodelpassports.sanger.ac.uk/passports/", "cellimage": "http://cellimagelibrary.org/images/", "cellopub": "https://web.expasy.org/cellosaurus/cellopub/", - "cellosaurus": "https://web.expasy.org/cellosaurus/CVCL_", + "cellosaurus": "https://www.cellosaurus.org/CVCL_", "cellosaurus.resource": "https://bioregistry.io/metaregistry/cellosaurus/", "cellrepo": "https://cellrepo.ico2s.org/repositories/", + "cemo": "https://biopragmatics.github.io/providers/cemo/", "cgd": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=", "cgnc": "http://birdgenenames.org/cgnc/GeneReport?id=", "cgsc": "http://cgsc.biology.yale.edu/Site.php?ID=", "charprot": "http://www.jcvi.org/charprotdb/index.cgi/view/", + "chembank": "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=", "chembl": "https://www.ebi.ac.uk/chembl/entity/", "chembl.cell": "https://www.ebi.ac.uk/chembl/cell_line_report_card/", - "chembl.compound": "https://www.ebi.ac.uk/chembl/compound/inspect/", - "chembl.target": "https://www.ebi.ac.uk/chembl/target/inspect/", + "chembl.compound": "http://rdf.ebi.ac.uk/resource/chembl/molecule/", "chemdb": "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=", "chemidplus": "https://chem.nlm.nih.gov/chemidplus/rn/", - "chickenqtldb": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:", + "chemspider": "http://rdf.chemspider.com/", "citexplore": "https://europepmc.org/article/CTX/", "civic.aid": "https://civicdb.org/links/assertions/", + "civic.did": "https://civicdb.org/links/diseases/", "civic.eid": "https://civicdb.org/links/evidence/", + "civic.gid": "https://civicdb.org/links/gene/", + "civic.mpid": "https://civicdb.org/links/molecular_profile/", + "civic.sid": "https://civicdb.org/links/sources/", + "civic.tid": "https://civicdb.org/links/drugs/", + "civic.vgid": "https://civicdb.org/links/variant_group/", + "civic.vid": "https://civicdb.org/links/variant/", "classyfire": "http://classyfire.wishartlab.com/tax_nodes/C", + "clb": "https://www.checklistbank.org/dataset/", + "cldb": "https://identifiers.org/cldb:", "clingene": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=", - "clinicaltrials": "https://clinicaltrials.gov/ct2/show/", + "clinicaltrials": "https://www.clinicaltrials.gov/study/", "clinvar": "https://www.ncbi.nlm.nih.gov/clinvar/variation/", "clinvar.record": "http://www.ncbi.nlm.nih.gov/clinvar/", "clinvar.submission": "http://www.ncbi.nlm.nih.gov/clinvar?term=", "clinvar.submitter": "https://www.ncbi.nlm.nih.gov/clinvar/submitters/", "cls": "https://cls.shop/", - "co_320": "https://www.cropontology.org/rdf/CO_320:", - "co_321": "https://www.cropontology.org/rdf/CO_321:", - "co_322": "https://www.cropontology.org/rdf/CO_322:", - "co_323": "https://www.cropontology.org/rdf/CO_323:", - "co_324": "https://www.cropontology.org/rdf/CO_324:", - "co_325": "https://www.cropontology.org/rdf/CO_325:", - "co_327": "https://www.cropontology.org/rdf/CO_327:", - "co_330": "https://www.cropontology.org/rdf/CO_330:", - "co_331": "https://www.cropontology.org/rdf/CO_331:", - "co_333": "https://www.cropontology.org/rdf/CO_333:", - "co_334": "https://www.cropontology.org/rdf/CO_334:", - "co_335": "https://www.cropontology.org/rdf/CO_335:", - "co_336": "https://www.cropontology.org/rdf/CO_336:", - "co_337": "https://www.cropontology.org/rdf/CO_337:", - "co_338": "https://www.cropontology.org/rdf/CO_338:", - "co_339": "https://www.cropontology.org/rdf/CO_339:", - "co_340": "https://www.cropontology.org/rdf/CO_340:", - "co_341": "https://www.cropontology.org/rdf/CO_341:", - "co_343": "https://www.cropontology.org/rdf/CO_343:", - "co_345": "https://www.cropontology.org/rdf/CO_345:", - "co_346": "https://www.cropontology.org/rdf/CO_346:", - "co_347": "https://www.cropontology.org/rdf/CO_347:", - "co_348": "https://www.cropontology.org/rdf/CO_348:", - "co_350": "https://www.cropontology.org/rdf/CO_350:", - "co_356": "https://www.cropontology.org/rdf/CO_356:", - "co_357": "https://www.cropontology.org/rdf/CO_357:", - "co_358": "https://www.cropontology.org/rdf/CO_358:", - "co_359": "https://www.cropontology.org/rdf/CO_359:", - "co_360": "https://www.cropontology.org/rdf/CO_360:", - "co_365": "https://www.cropontology.org/rdf/CO_365:", - "co_366": "https://www.cropontology.org/rdf/CO_366:", + "cmpo": "http://www.ebi.ac.uk/cmpo/CMPO_", "coconut": "https://coconut.naturalproducts.net/compound/coconut_id/", "cog": "https://www.ncbi.nlm.nih.gov/research/cog/cog/", "cog.category": "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/", "cog.pathway": "https://www.ncbi.nlm.nih.gov/research/cog/pathway/", + "col": "https://www.checklistbank.org/dataset/3LR/taxon/", "col.taiwan": "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=", "colonatlas": "http://www.coloncanceratlas.org/search_cell_line?cell_line=", - "combine.specifications": "https://co.mbine.org/specifications/", + "combine.specifications": "https://identifiers.org/combine.specifications:", "come": "https://www.flymine.org/come/entry?gn=", + "commoncoreontology": "http://www.ontologyrepository.com/CommonCoreOntologies/", "complexportal": "https://www.ebi.ac.uk/complexportal/complex/", "comptox": "https://comptox.epa.gov/dashboard/", - "compulyeast": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=", + "conference": "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#", + "confident.event": "https://www.confident-conference.org/index.php/Event:", + "confident.series": "https://www.confident-conference.org/index.php/Event_Series:", "conoserver": "http://www.conoserver.org/?page=card&table=protein&id=", "conso": "https://pharmacome.github.io/conso/", "cordis.article": "https://cordis.europa.eu/article/id/", @@ -477,30 +536,42 @@ "cosmic": "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=", "cosmic.cell": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=", "covid19": "https://covid19.sfb.uit.no/api/records/", + "covoc": "http://purl.obolibrary.org/obo/COVOC_", "cpc": "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=", "cpt": "https://www.aapc.com/codes/cpt-codes/", "crisprdb": "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=", + "crop2ml": "http://www.crop2ml.org/cropmdb/", + "cryoem": "http://scipion.i2pc.es/ontology/CRYOEM_", "cryptodb": "https://cryptodb.org/cryptodb/app/record/gene/", "csa": "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=", - "ctd.chemical": "http://ctdbase.org/detail.go?type=chem&acc=", - "ctd.disease": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=", - "ctd.gene": "http://ctdbase.org/detail.go?type=gene&acc=", + "csd": "https://identifiers.org/csd:", + "csp": "http://purl.bioontology.org/ontology/CSP/", + "cst": "https://identifiers.org/cst:", + "cst.ab": "https://identifiers.org/cst.ab:", + "cstr": "https://cstr.cn/", + "ctis": "https://euclinicaltrials.eu/app/#/view/", + "cubedb": "https://identifiers.org/cubedb:", + "d1id": "https://identifiers.org/d1id:", "dailymed": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=", "dandi": "https://dandiarchive.org/dandiset/", "darc": "http://darcsite.genzentrum.lmu.de/darc/view.php?id=", "dashr": "http://lisanwanglab.org/DASHR/entry/", + "dashr.expression": "https://identifiers.org/dashr.expression:", + "datacommons": "https://datacommons.org/browser/", "datanator.gene": "https://www.datanator.info/gene/", "datanator.metabolite": "https://www.datanator.info/metabolite/", "datanator.reaction": "https://datanator.info/reaction/", "datf": "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=", + "dbd": "https://identifiers.org/dbd:", "dbest": "https://www.ncbi.nlm.nih.gov/nucest/", "dbg2introns": "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=", "dbgap": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=", + "dbo": "https://dbpedia.org/ontology/", "dbprobe": "https://www.ncbi.nlm.nih.gov/probe/?term=", "dbsnp": "https://www.ncbi.nlm.nih.gov/snp/", "dbvar.study": "https://www.ncbi.nlm.nih.gov/dbvar/studies/", "dbvar.variant": "https://www.ncbi.nlm.nih.gov/dbvar/variants/", - "dc": "http://purl.org/dc/terms/", + "dc": "http://purl.org/dc/elements/1.1/", "dcat": "http://www.w3.org/ns/dcat#", "dcterms": "http://purl.org/dc/terms/", "dctypes": "http://purl.org/dc/dcmitype/", @@ -509,7 +580,7 @@ "decipher": "https://www.deciphergenomics.org/syndrome/", "degradome": "http://degradome.uniovi.es/cgi-bin/protease/", "depmap": "https://depmap.org/portal/cell_line/", - "depod": "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=", + "dermo": "http://purl.obolibrary.org/obo/DERMO_", "dev.ga4ghdos": "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/", "dg.4503": "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/", "dg.4dfc": "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/", @@ -518,20 +589,29 @@ "dg.f82a1a": "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/", "dg5b0d": "https://data.bloodpac.org/ga4gh/drs/v1/objects/", "dgrc": "https://dgrc.bio.indiana.edu/product/View?product=", + "dicom": "http://dicom.nema.org/resources/ontology/DCM/", "dictybase": "http://dictybase.org/gene/", "dictybase.est": "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=", - "dictybase.gene": "http://dictybase.org/gene/", "did": "https://uniresolver.io/#did:", "dip": "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=", + "diseaseclass": "https://biopragmatics.github.io/providers/diseaseclass/", "disprot": "https://disprot.org/", - "disprot.region": "https://www.disprot.org/", "dlxb": "https://doulix.com/biomodules/", "dlxc": "https://doulix.com/constructs/", + "doap": "http://usefulinc.com/ns/doap#", + "doi": "http://dx.doi.org/", "dommino": "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/", "door": "http://csbl.bmb.uga.edu/DOOR/operon.php?id=", "doqcs.model": "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=", "doqcs.pathway": "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=", "dpv": "http://www.dpvweb.net/dpv/showdpv.php?dpvno=", + "dragondb.allele": "https://identifiers.org/dragondb.allele:", + "dragondb.dna": "https://identifiers.org/dragondb.dna:", + "dragondb.locus": "https://identifiers.org/dragondb.locus:", + "dragondb.protein": "https://identifiers.org/dragondb.protein:", + "drduke": "https://phytochem.nal.usda.gov/phytochem/chemicals/show/", + "drks": "https://drks.de/search/en/trial/", + "drsanv0": "https://data.terra.bio/ga4gh/drs/v1/objects/", "drsc": "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=", "drugbank": "http://www.drugbank.ca/drugs/", "drugbank.category": "https://www.drugbank.ca/categories/", @@ -539,16 +619,22 @@ "drugbankv4.target": "http://www.drugbank.ca/biodb/bio_entities/", "drugcentral": "http://drugcentral.org/drugcard/", "dsmz": "https://www.dsmz.de/collection/catalogue/details/culture/", + "dso": "https://www.datascienceontology.org/concept/", + "dto": "http://www.drugtargetontology.org/dto/DTO_", "eaglei": "http://hawaii.eagle-i.net/i/", "easychair.cfp": "https://easychair.org/cfp/", "easychair.topic": "https://easychair.org/cfp/topic.cgi?tid=", "ebisc": "https://cells.ebisc.org/", "ecacc": "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=", "eccode": "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=", + "ecg": "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_", + "echinobase": "https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=", "echobase": "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=", "ecmdb": "http://ecmdb.ca/compounds/", - "ecocyc": "https://biocyc.org/gene?id=", + "ecocyc": "https://ecocyc.org/gene?id=", "ecogene": "http://www.ecogene.org/gene/", + "ecoliwiki": "https://identifiers.org/ecoliwiki:", + "ecso": "http://purl.dataone.org/odo/ECSO_", "ecyano.entity": "https://www.e-cyanobacterium.org/bcs/entity/", "ecyano.experiment": "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=", "ecyano.model": "https://e-cyanobacterium.org/models/model/", @@ -558,46 +644,65 @@ "edam.format": "http://edamontology.org/format_", "edam.operation": "http://edamontology.org/operation_", "edam.topic": "http://edamontology.org/topic_", + "edda": "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#", "ega.dataset": "https://www.ebi.ac.uk/ega/datasets/", "ega.study": "https://www.ebi.ac.uk/ega/studies/", "eggnog": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=", + "elm": "https://identifiers.org/elm:", "emdb": "https://www.ebi.ac.uk/pdbe/entry/emdb/", + "emmo": "http://emmo.info/emmo#EMMO_", + "emmo.cif": "http://emmo.info/emmo/cif-core#", "emolecules": "https://reaxys.emolecules.com/cgi-bin/more?vid=", "empiar": "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/", + "emsl.project": "https://www.emsl.pnnl.gov/project/", "ena.embl": "https://www.ebi.ac.uk/ena/browser/view/", "encode": "https://www.encodeproject.org/", - "ensembl.bacteria": "https://bacteria.ensembl.org/id/", - "ensembl.fungi": "https://fungi.ensembl.org/id/", + "enm": "http://purl.enanomapper.org/onto/ENM_", "ensembl.metazoa": "https://metazoa.ensembl.org/id/", "ensembl.plant": "https://plants.ensembl.org/id/", "ensembl.protist": "https://protists.ensembl.org/id/", + "ensemblglossary": "http://ensembl.org/glossary/ENSGLOSSARY_", "envipath": "https://envipath.org/package/", "enzo": "https://www.enzolifesciences.com/", + "eol": "http://purl.org/obo/owlEOL_", "eolife": "https://eol.org/pages/", - "epd": "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=", + "epd": "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=", + "epso": "http://www.case.edu/EpilepsyOntology.owl#", "erm": "https://nanocommons.github.io/identifiers/registry#", + "eropmoscow": "http://erop.inbi.ras.ru/result2.php?PepName=", "erv": "https://herv.img.cas.cz/s/", + "esldb": "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=", "estdab": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-", "eu89h": "http://data.europa.eu/89h/", "euclinicaltrials": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=", + "eugenes": "http://eugenes.org:7072/.bin/fbidq.html?", "exac.gene": "http://exac.broadinstitute.org/gene/", "exac.transcript": "http://exac.broadinstitute.org/transcript/", "exac.variant": "http://exac.broadinstitute.org/variant/", "fabio": "https://sparontologies.github.io/fabio/current/fabio.html#", "facebase": "https://www.facebase.org/data/record/#1/isa:dataset/accession=", "fairsharing": "https://fairsharing.org/", + "fairsharing.organization": "https://fairsharing.org/organisations/", + "fairsharing.user": "https://fairsharing.org/users/", "faldo": "http://biohackathon.org/resource/faldo#", + "fao.asfis": "https://www.fao.org/fishery/en/species/", + "fbol": "https://identifiers.org/fbol:", "fbrf": "https://flybase.org/reports/FBrf", "fbtc": "https://flybase.org/reports/FBtc", "fcb": "https://w3id.org/faircookbook/", "fcsfree": "https://fcs-free.org/fcs-database?", + "fhir.implementation": "https://hl7.org/fhir/us/", + "fishbase.species": "https://www.fishbase.ca/summary/", "flowrepository": "https://flowrepository.org/id/", + "flymine.chromosome": "https://www.flymine.org/flymine/report/ChromosomeBand/", "foaf": "http://xmlns.com/foaf/0.1/", "foodb.compound": "http://foodb.ca/compounds/", "foodb.food": "https://foodb.ca/foods/", + "foodex2": "http://data.food.gov.uk/codes/foodtype/id/", "fossilworks.journal": "http://fossilworks.org/?a=referenceInfo&reference_no=", "fossilworks.taxon": "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=", "fplx": "https://sorgerlab.github.io/famplex/", + "frbrer": "http://iflastandards.info/ns/fr/frbr/frbrer/", "fsnp": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=", "ftt": "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=", "funcbase.fly": "http://func.mshri.on.ca/fly/genes/list_functional_scores/", @@ -608,23 +713,30 @@ "fungidb": "https://fungidb.org/fungidb/app/record/gene/", "fungorum": "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=", "ga4ghdos": "https://dataguids.org/ga4gh/dos/v1/dataobjects/", + "gabi": "https://identifiers.org/gabi:", + "gainesville.core": "http://purl.org/gc/", + "galen": "http://www.co-ode.org/ontologies/galen#", "gateway": "https://web.www.healthdatagateway.org/dataset/", "gbif": "https://www.gbif.org/species/", "gc": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG", "gcst": "https://www.ebi.ac.uk/gwas/studies/", "gdc": "https://portal.gdc.cancer.gov/cases/", "gdsc": "https://www.cancerrxgene.org/translation/Drug/", + "gear": "https://umgear.org/p?id=", "gemet": "https://www.eionet.europa.eu/gemet/en/concept/", "genatlas": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=", "genbank": "https://www.ncbi.nlm.nih.gov/nucleotide/", + "gendis": "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=", "genecards": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=", + "genecards.geneloc": "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=", "genedb": "https://www.genedb.org/gene/", "genefarm": "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=", "genetree": "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=", - "genewiki": "http://plugins.biogps.org/cgi-bin/wp.cgi?id=", + "genpept": "https://identifiers.org/genpept:", "genprop": "https://www.ebi.ac.uk/interpro/genomeproperties/#", "geo": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=", "geonames": "https://www.geonames.org/", + "gfo": "http://www.onto-med.de/ontologies/gfo.owl#", "ghr": "https://medlineplus.gov/genetics/condition/", "giardiadb": "https://giardiadb.org/giardiadb/app/record/gene/", "github": "https://github.com/", @@ -634,37 +746,47 @@ "glida.gpcr": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=", "glida.ligand": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=", "glycoepitope": "https://www.glycoepitope.jp/epitopes/", - "glycomedb": "https://glytoucan.org/Structures/Glycans/", + "glycomapsdb": "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=", "glyconavi": "https://glyconavi.org/hub/?id=", "glycopost": "https://glycopost.glycosmos.org/entry/", + "glycosciencesdb": "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=", "glygen": "https://glygen.org/glycan/", "glytoucan": "https://glytoucan.org/Structures/Glycans/", + "gmd": "https://identifiers.org/gmd:", "gmd.analyte": "http://gmd.mpimp-golm.mpg.de/Analytes/", "gmd.gcms": "http://gmd.mpimp-golm.mpg.de/Spectrums/", "gmd.profile": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=", "gmd.ref": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/", + "gnd": "https://lobid.org/gnd/", + "gnomad": "https://gnomad.broadinstitute.org/variant/", "gnpis": "https://urgi.versailles.inra.fr/gnpis/#result/term=", + "gnps.task": "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=", + "go.gpi": "http://geneontology.org/docs/gene-product-information-gpi-format/#", "go.model": "http://noctua.geneontology.org/editor/graph/gomodel:", + "go.ref": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref", "go.resource": "https://bioregistry.io/metaregistry/go/", - "goa": "https://www.ebi.ac.uk/QuickGO/GProtein?ac=", "gold": "https://gold.jgi.doe.gov/resolver?id=", "gold.genome": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=", - "gold.meta": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=", + "goldbook": "http://dx.doi.org/10.1351/goldbook.", + "google.book": "https://books.google.com/books?id=", "google.patent": "https://www.google.com/patents/", + "gorel": "http://purl.obolibrary.org/obo/GOREL_", "gpcrdb": "https://gpcrdb.org/protein/", + "gpcrnava": "http://nava.liacs.nl/cgi-bin/nava.py?id=", "gpmdb": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=", "graingenes.reference": "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=", "graingenes.symbol": "http://wheat.pw.usda.gov/report?class=gene;name=", "gramene.gene": "http://www.gramene.org/db/genes/search_gene?acc=", - "gramene.growthstage": "http://www.gramene.org/db/ontology/search?id=GRO:", "gramene.protein": "http://www.gramene.org/db/protein/protein_search?protein_id=", "gramene.qtl": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=", "gramene.reference": "http://www.gramene.org/db/literature/pub_search?ref_id=", - "gramene.taxonomy": "http://www.gramene.org/db/ontology/search?id=", + "gramene.taxonomy": "https://archive.gramene.org/db/ontology/search?id=GR_tax:", "grassbase": "https://www.kew.org/data/grasses-db/www/", "greengenes": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=", "grid": "https://www.grid.ac/institutes/", + "grin": "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=", "grin.taxonomy": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?", + "gro": "http://www.bootstrep.eu/ontology/GRO#", "grsdb": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=", "gsfa": "http://www.fao.org/gsfaonline/additives/details.html?id=", "gtex": "https://www.gtexportal.org/home/gene/", @@ -675,44 +797,64 @@ "gwascentral.study": "https://www.gwascentral.org/study/", "gxa.expt": "https://www.ebi.ac.uk/gxa/experiments/", "gxa.gene": "https://www.ebi.ac.uk/gxa/genes/", + "hagr.genage": "http://genomics.senescence.info/genes/details.php?id=", + "hagr.gendr": "http://genomics.senescence.info/diet/details.php?id=", "hamap": "https://hamap.expasy.org/unirule/", + "hathitrust": "https://catalog.hathitrust.org/Record/", + "hbvar": "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=", + "hc.npn": "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=", + "hcpcs": "http://purl.bioontology.org/ontology/HCPCS/", "hcvdb": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=", + "hdl": "http://hdl.handle.net/", "hdr": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=", "hgmd": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=", "hgnc": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/", - "hgnc.genefamily": "https://www.genenames.org/cgi-bin/genefamilies/set/", "hgnc.genegroup": "https://www.genenames.org/cgi-bin/genefamilies/set/", "hgnc.symbol": "https://www.genenames.org/cgi-bin/gene_symbol_report?match=", "hinv.locus": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=", "hinv.protein": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=", "hinv.transcript": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=", - "hipsci": "http://www.hipsci.org/lines/#/lines/", + "hipsci": "https://www.hipsci.org/lines/#/lines/", + "hl7.v2codesystem": "http://terminology.hl7.org/CodeSystem/v2-", + "hl7.v3codesystem": "https://terminology.hl7.org/CodeSystem-v3-", "hmdb": "http://www.hmdb.ca/metabolites/", + "hms.lincs.antibody": "https://lincs.hms.harvard.edu/db/antibodies/", + "hms.lincs.cell": "https://lincs.hms.harvard.edu/db/cells/", "hms.lincs.compound": "https://lincs.hms.harvard.edu/db/sm/", + "hms.lincs.dataset": "https://lincs.hms.harvard.edu/db/datasets/", + "hog": "https://biopragmatics.github.io/providers/hog/", "hogenom": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=", + "hoip": "http://purl.bioontology.org/ontology/HOIP/HOIP_", "homd.seq": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=", - "homd.taxon": "www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=", + "homd.taxon": "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=", "homologene": "https://www.ncbi.nlm.nih.gov/homologene/", "horizon_discovery": "https://horizondiscovery.com/en/search?searchterm=", + "hovergen": "https://identifiers.org/hovergen:", "hpa": "http://www.proteinatlas.org/", + "hpath": "http://purl.obolibrary.org/obo/MC_", "hpm.peptide": "http://www.humanproteomemap.org/spectrum.php?pep_id=", "hpm.protein": "http://www.humanproteomemap.org/protein.php?hpm_id=", "hprd": "http://www.hprd.org/protein/", "hpscreg": "https://hpscreg.eu/cell-line/", "hsdb": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/", + "hssp": "https://identifiers.org/hssp:", "huge": "https://www.kazusa.or.jp/huge/gfpage/", - "icd10": "http://apps.who.int/classifications/icd10/browse/2010/en#/", "icd10cm": "https://icd.codes/icd10cm/", "icd10pcs": "https://www.findacode.com/code.php?set=ICD10PCS&c=", "icd11": "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/", - "icd9": "http://www.icd9data.com/getICD9Code.ashx?icd9=", "icd9cm": "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=", "icdc": "https://caninecommons.cancer.gov/#/study/", "icdo": "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=", - "iceberg.element": "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=", - "iceberg.family": "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=", + "iceberg.element": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=", + "iceberg.family": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=", + "icepo": "https://biopragmatics.github.io/providers/icepo/", + "icf": "http://id.who.int/icd/entity/", "iclc": "http://www.iclc.it/details/det_list.php?line_id=", + "icldb": "https://entomology.ca.uky.edu/content/", "ideal": "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=", + "idocovid19": "http://purl.obolibrary.org/obo/COVIDO_", + "idoden": "http://purl.bioontology.org/ontology/IDODEN_", + "idog": "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=", "idoo": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#", "idot": "https://biomodels.net/vocab/idot.rdf#", "idpo": "https://www.disprot.org/idpo/IDPO:", @@ -722,66 +864,69 @@ "igsn": "http://igsn.org/", "igsr": "https://www.internationalgenome.org/data-portal/sample/", "imanis": "https://www.imanislife.com/?s=", - "imex": "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=", + "imex": "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-", "img.gene": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=", "img.taxon": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=", "imgt.hla": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?", "imgt.ligm": "http://www.imgt.org/ligmdb/view?id=", + "imotdb": "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=", + "inaturalist.observation": "https://www.inaturalist.org/observations/", + "inaturalist.place": "https://www.inaturalist.org/places/", "inaturalist.taxon": "https://www.inaturalist.org/taxa/", + "inaturalist.user": "https://www.inaturalist.org/users/", "inchi": "http://www.chemspider.com/", "inchikey": "http://www.chemspider.com/inchikey=", "inn": "https://mednet-communities.net/inn/db/ViewINN.aspx?i=", + "innatedb": "http://www.innatedb.ca/getGeneCard.do?id=", "insdc": "https://www.ncbi.nlm.nih.gov/nuccore/", - "insdc.cds": "http://getentry.ddbj.nig.ac.jp/getentry/dad/", - "insdc.gca": "https://www.ebi.ac.uk/ena/data/view/", - "insdc.run": "https://www.ebi.ac.uk/ena/browser/view/", "insdc.sra": "https://www.ncbi.nlm.nih.gov/sra/", "intact": "https://www.ebi.ac.uk/intact/interaction/", - "intact.molecule": "https://www.ebi.ac.uk/intact/molecule/", + "intact.molecule": "https://www.ebi.ac.uk/intact/search?query=", + "interfil": "http://www.interfil.org/details.php?id=", "interlex": "https://scicrunch.org/scicrunch/interlex/view/ilx_", - "interpro": "https://www.ebi.ac.uk/interpro/entry/", + "iobc": "http://purl.jp/bio/4/id/", "ird.segment": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=", "irefweb": "http://wodaklab.org/iRefWeb/interaction/show/", + "iresite": "http://www.iresite.org/IRESite_web.php?page=view&entry_id=", "iro": "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:", "isbn": "http://isbndb.com/search-all.html?kw=", "isfinder": "https://www-is.biotoul.fr/scripts/ficheIS.php?name=", "isni": "http://www.isni.org/isni/", + "iso15926": "http://standards.iso.org/iso/15926/part14/", + "isrctn": "https://www.isrctn.com/", "issn": "https://portal.issn.org/resource/ISSN/", "itis": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=", - "ito": "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https%3A%2F%2Fai-strategies.org%2Fontology%2F", + "ito": "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_", "iuphar.family": "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=", "iuphar.ligand": "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=", "iuphar.receptor": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=", + "ivdb": "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=", "jax": "https://www.jax.org/strain/", + "jaxmice": "https://identifiers.org/jaxmice:", "jcggdb": "http://jcggdb.jp/idb/jcggdb/", "jcm": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=", "jcrb": "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=", "jcsd": "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=", + "jgi.proposal": "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=", + "jrct": "https://jrct.niph.go.jp/en-latest-detail/", "jstor": "http://www.jstor.org/stable/", "jws": "https://jjj.bio.vu.nl/models/", "kaggle": "https://www.kaggle.com/", "kclb": "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=", "kegg": "http://www.kegg.jp/entry/", - "kegg.compound": "https://www.kegg.jp/entry/", - "kegg.disease": "http://www.kegg.jp/entry/", - "kegg.drug": "https://www.kegg.jp/entry/", - "kegg.environ": "http://www.kegg.jp/entry/", - "kegg.enzyme": "http://www.genome.jp/dbget-bin/www_bget?ec:", - "kegg.genes": "http://www.kegg.jp/entry/", - "kegg.genome": "http://www.kegg.jp/entry/", - "kegg.glycan": "https://www.kegg.jp/entry/", - "kegg.ligand": "http://www.genome.jp/dbget-bin/www_bget?cpd:", - "kegg.metagenome": "http://www.kegg.jp/entry/", - "kegg.module": "http://www.kegg.jp/entry/", - "kegg.orthology": "http://www.kegg.jp/entry/", - "kegg.pathway": "https://www.kegg.jp/entry/", - "kegg.reaction": "https://www.kegg.jp/entry/", + "kegg.brite": "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br", + "kestrelo": "http://purl.obolibrary.org/obo/kestrelo_", "knapsack": "http://www.knapsackfamily.com/knapsack_core/information.php?word=", + "langual": "https://www.langual.org/langual_thesaurus.asp?termid=", + "lbo": "http://purl.obolibrary.org/obo/LBO_", + "lcsh": "http://id.loc.gov/authorities/names/", "lei": "https://www.gleif.org/lei/", "lgai.cede": "https://s3.us-east-2.amazonaws.com/lg.cede/", + "lgic": "https://identifiers.org/lgic:", "licebase": "https://licebase.org/?q=", "ligandbook": "https://ligandbook.org/package/", "ligandbox": "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=", + "ligandexpo": "https://identifiers.org/ligandexpo:", "ligea": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/", "limore": "https://www.picb.ac.cn/limore/cellLines/single?para=", "lincs.cell": "http://lincsportal.ccs.miami.edu/cells/#/view/", @@ -789,33 +934,43 @@ "lincs.protein": "https://lincs.hms.harvard.edu/db/proteins/", "lincs.smallmolecule": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/", "linguist": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#", + "linkml": "https://w3id.org/linkml/", "lipidbank": "http://lipidbank.jp/cgi-bin/detail.cgi?id=", "lipidmaps": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=", - "loinc": "https://loinc.org/", + "loinc": "http://loinc.org/rdf/", "lonza": "https://knowledge.lonza.com/cell?id=", + "loqate": "http://www.weizmann.ac.il/molgen/loqate/gene/view/", "lotus": "https://lotus.naturalproducts.net/compound/lotus_id/", "lpt": "http://purl.obolibrary.org/obo/LPT_", + "lrg": "https://identifiers.org/lrg:", "lspci": "https://labsyspharm.github.io/lspci/", "lter": "https://vocab.lternet.edu/vocab/vocab/index.php?tema=", "macie": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=", "maizegdb.locus": "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=", - "massbank": "http://www.massbank.jp/RecordDisplay?id=", + "mampol": "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=", + "massbank": "https://massbank.jp/RecordDisplay?id=", "massive": "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=", "matrixdb": "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=", + "matrixdb.association": "https://identifiers.org/matrixdb.association:", + "mcc": "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#", "mdm": "https://medical-data-models.org/forms/", - "meddra": "http://purl.bioontology.org/ontology/MEDDRA/", + "meddra": "http://purl.bioontology.org/ontology/MDRFRE/", "medgen": "https://www.ncbi.nlm.nih.gov/medgen/", + "medlineplus": "https://identifiers.org/medlineplus:", "merops.clan": "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=", "merops.entry": "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=", "merops.family": "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=", - "mesh": "https://meshb.nlm.nih.gov/record/ui?ui=", + "mesh": "http://id.nlm.nih.gov/mesh/", + "mesh.vocab": "http://id.nlm.nih.gov/mesh/vocab#", "metabolights": "https://www.ebi.ac.uk/metabolights/", "metacyc.compound": "https://metacyc.org/compound?orgid=META&id=", "metacyc.reaction": "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=", "metanetx.chemical": "https://www.metanetx.org/chem_info/", "metanetx.compartment": "https://www.metanetx.org/comp_info/", "metanetx.reaction": "https://www.metanetx.org/equa_info/", + "metatlas": "https://metabolicatlas.org/identifier/MetabolicAtlas/", "metlin": "http://metlin.scripps.edu/metabo_info.php?molid=", + "metnetdb": "http://metnetonline.org/browse_pathway2.php?pthID=", "mex": "https://www.metabolome-express.org/datasetview.php?datasetid=", "mge": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:", "mgnify.analysis": "https://www.ebi.ac.uk/metagenomics/analyses/", @@ -827,16 +982,19 @@ "mimodb": "http://immunet.cn/bdb/index.php/mimoset/", "minid": "https://hdl.handle.net/hdl:20.500.12582/", "minid.test": "https://hdl.handle.net/hdl:20.500.12633/", - "mint": "http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=", + "mint": "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-", "mipmod": "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=", + "mir": "https://registry.identifiers.org/registry?query=MIR:", "mirbase": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=", "mirbase.family": "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=", "mirbase.mature": "http://mirbase.org/cgi-bin/mature.pl?mature_acc=", + "mirex": "https://identifiers.org/mirex:", "miriam": "https://registry.identifiers.org/registry/", "miriam.collection": "https://www.ebi.ac.uk/miriam/main/", "miriam.resource": "https://www.ebi.ac.uk/miriam/main/resources/", "mirnest": "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=", "mirtarbase": "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=", + "mixs": "https://w3id.org/mixs/", "mlc": "https://www.mlcommons.org/mlc-id/", "mmdb": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=", "mmmp.biomaps": "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=", @@ -845,17 +1003,19 @@ "mmp.fun": "https://mmp.sfb.uit.no/databases/marfun/#/records/", "mmp.ref": "https://mmp.sfb.uit.no/databases/marref/#/records/", "mmrrc": "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=", - "mobidb": "https://mobidb.org/", - "modeldb": "http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=", + "mmsinc": "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode=", + "modeldb": "https://modeldb.science/", + "modeldb.concept": "https://senselab.med.yale.edu/ModelDB/ModelList?id=", "molbase": "http://www.molbase.com/en/index.php?app=search&search_keyword=", "molmedb": "https://molmedb.upol.cz/mol/", + "molmovdb": "http://www.molmovdb.org/cgi-bin/morph.cgi?ID=", "morpheus": "https://morpheus.gitlab.io/models/", + "mosaic": "https://purl.dataone.org/odo/MOSAIC_", "mpid": "http://www.jcvi.org/mpidb/experiment.php?interaction_id=", "msigdb": "https://biopragmatics.github.io/providers/msigdb/", + "msio": "http://purl.obolibrary.org/obo/MSIO_", + "mtbd": "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=", "multicellds": "http://multicellds.org/MultiCellDB/", - "multicellds.cell_line": "http://multicellds.org/MultiCellDB/", - "multicellds.collection": "http://multicellds.org/MultiCellDB/", - "multicellds.snapshot": "http://multicellds.org/MultiCellDB/", "mw.project": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=", "mw.study": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=", "myco.lepra": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=", @@ -864,21 +1024,27 @@ "myco.tuber": "http://tuberculist.epfl.ch/quicksearch.php?gene+name=", "mycobank": "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=", "mzspec": "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:", + "nando": "https://nanbyodata.jp/disease/NANDO:", "napdi": "https://repo.napdi.org/study/", "napp": "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=", "narcis": "http://www.narcis.nl/publication/RecordID/", "nasc": "http://arabidopsis.info/StockInfo?NASC_id=", + "nbn": "https://identifiers.org/nbn:", "nbrc": "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=", "ncats.bioplanet": "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_", "ncats.drug": "https://drugs.ncats.io/drug/", - "ncbi.assembly": "https://www.ncbi.nlm.nih.gov/assembly/", + "ncbi.assembly": "https://www.ncbi.nlm.nih.gov/datasets/genome/", "ncbi.genome": "https://www.ncbi.nlm.nih.gov/genome/", "ncbi.resource": "https://bioregistry.io/metaregistry/ncbi/", "ncbibook": "https://www.ncbi.nlm.nih.gov/books/", "ncim": "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=", "ndc": "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/", + "nddf": "http://purl.bioontology.org/ontology/NDDF/", "ndex": "https://www.ndexbio.org/viewer/networks/", + "ndfrt": "http://purl.bioontology.org/ontology/NDFRT/", + "nembase": "http://www.nematodes.org/nembase4/cluster.php?cluster=", "nemo": "https://assets.nemoarchive.org/", + "nemo2": "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_", "neurolex": "http://uri.neuinfo.org/nif/nifstd/nlx_", "neuromorpho": "http://neuromorpho.org/neuron_info.jsp?neuron_name=", "neuronames": "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=", @@ -888,12 +1054,16 @@ "nextdb": "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=", "nextprot": "https://www.nextprot.org/db/entry/", "nextprot.family": "https://www.nextprot.org/term/FA-", + "nfdi4chem.cao": "http://champ-project.org/images/ontology/cao.owl#CAO_", "ngl": "https://genelab-data.ndc.nasa.gov/genelab/accession/", "nhcdr": "https://stemcells.nindsgenetics.org?line=", "niaest": "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=", "nif.ext": "http://uri.neuinfo.org/nif/nifstd/nifext_", "nif.std": "http://uri.neuinfo.org/nif/nifstd/", + "nihhesc": "https://grants.nih.gov/stem_cells/registry/current.htm?ID=", "nihreporter.project": "https://reporter.nih.gov/project-details/", + "nkos": "http://w3id.org/nkos/", + "nlfff": "http://database.deepsolar.space:18080/dbs/nlfff/", "nlm": "https://www.ncbi.nlm.nih.gov/nlmcatalog/", "nlx.anat": "http://uri.neuinfo.org/nif/nifstd/nlx_anat_", "nlx.br": "http://uri.neuinfo.org/nif/nifstd/nlx_br_", @@ -909,6 +1079,7 @@ "nlx.res": "http://uri.neuinfo.org/nif/nifstd/nlx_res_", "nlx.sub": "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_", "nmdc": "https://drs.microbiomedata.org/objects/", + "nmpdr": "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=", "nmrshiftdb2": "https://nmrshiftdb.nmr.uni-koeln.de/molecule/", "noaa": "https://www.fisheries.noaa.gov/species/", "noncodev3": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=", @@ -916,25 +1087,36 @@ "noncodev4.rna": "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=", "norine": "http://bioinfo.lifl.fr/norine/result.jsp?ID=", "novus": "https://www.novusbio.com/products/", - "nuclearbd": "http://www.receptors.org/nucleardb/proteins/", - "nucleotide": "https://www.ncbi.nlm.nih.gov/nuccore/", + "npo": "http://purl.bioontology.org/ontology/npo#NPO_", + "nsc": "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=", + "nsf.award": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=", + "nucleardb": "http://www.receptors.org/nucleardb/proteins/", "oa": "http://www.w3.org/ns/oa#", - "obo": "http://purl.obolibrary.org/obo/", + "oban": "http://purl.org/oban/", "oboInOwl": "http://www.geneontology.org/formats/oboInOwl#", + "obv": "https://permalink.obvsg.at/", "occ": "https://w3id.org/oc/corpus/", "oci": "https://w3id.org/oc/oci/", "ocid": "https://ocid.ontochem.com/prefname?ocid=", "oclc": "https://www.worldcat.org/oclc/", + "odam": "https://identifiers.org/odam:", "odc.sci": "https://odc-sci.org/data/", "odc.tbi": "https://odc-tbi.org/data/", + "odor": "https://identifiers.org/odor:", + "odrl": "http://www.w3.org/ns/odrl/2/", + "oid": "http://oid-info.com/get/", "om": "http://www.ontology-of-units-of-measure.org/resource/om-2/", "oma.grp": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=", "oma.hog": "https://omabrowser.org/oma/hog/HOG:", "oma.protein": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=", - "omim": "https://omim.org/entry/", - "omim.ps": "https://omim.org/phenotypicSeries/", + "omia": "https://omia.org/OMIA", + "omid": "https://w3id.org/oc/meta/", + "omim": "https://omim.org/MIM:", + "omim.ps": "https://omim.org/MIM:PS", + "omop": "https://athena.ohdsi.org/search-terms/terms/", "oncotree": "http://oncotree.mskcc.org/api/tumorTypes/search/code/", - "opb": "http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_", + "ontie": "https://ontology.iedb.org/ontology/ONTIE_", + "opb": "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_", "openalex": "https://openalex.org/", "opm": "http://opm.phar.umich.edu/protein.php?pdbid=", "orcid": "https://orcid.org/", @@ -943,15 +1125,19 @@ "oridb.schizo": "http://pombe.oridb.org/details.php?id=", "orphanet": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=", "orphanet.ordo": "http://www.orpha.net/ORDO/Orphanet_", - "orthodb": "http://cegg.unige.ch/orthodb/results?searchtext=", + "orth": "http://purl.org/net/orth#", "oryzabase.gene": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/", "oryzabase.mutant": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/", "oryzabase.reference": "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/", "oryzabase.stage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/", "oryzabase.strain": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/", + "oslc": "http://open-services.net/ns/core#", "otl": "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=", "otol": "https://tree.opentreeoflife.org/taxonomy/browse?id=", "owl": "http://www.w3.org/2002/07/owl#", + "owlstar": "http://w3id.org/owlstar/", + "p3db.protein": "https://identifiers.org/p3db.protein:", + "p3db.site": "https://identifiers.org/p3db.site:", "paleodb": "http://fossilworks.org/?a=taxonInfo&taxon_no=", "panther.family": "http://www.pantherdb.org/panther/family.do?clsAccession=", "panther.node": "http://www.pantree.org/node/annotationNode.jsp?id=", @@ -959,23 +1145,26 @@ "panther.pthcmp": "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=", "pass2": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=", "pathbank": "https://pathbank.org/view/", + "pathguide": "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=", + "pathoplant": "http://www.pathoplant.de/detail.php?accNo=", "pathwaycommons": "http://www.pathwaycommons.org/pc/record2.do?id=", "pav": "http://purl.org/pav/", "paxdb.organism": "http://pax-db.org/#!species/", "paxdb.protein": "http://pax-db.org/#!protein/", "pazar": "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=", - "pdb": "https://www.wwpdb.org/pdb?id=", - "pdb-ccd": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/", + "pdb": "https://rdf.wwpdb.org/pdb/", "pdb.ligand": "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=", "pdc.study": "https://pdc.cancer.gov/pdc/study/", "ped": "https://proteinensemble.org/", - "ped.ensemble": "https://proteinensemble.org/", + "peff": "https://biopragmatics.github.io/providers/peff/", + "pennsieve": "https://discover.pennsieve.io/package/", + "pepbank": "http://pepbank.mgh.harvard.edu/interactions/details/", "peptideatlas": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=", "peptideatlas.dataset": "http://www.peptideatlas.org/PASS/", "perkinelmer": "https://www.perkinelmer.com/searchresult?searchName=", "peroxibase": "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=", - "pfam": "https://pfam.xfam.org/family/", - "pfam.clan": "https://pfam.xfam.org/clan/", + "pfam": "https://www.ebi.ac.uk/interpro/entry/pfam/", + "pfam.clan": "https://www.ebi.ac.uk/interpro/set/pfam/", "pfr": "http://repository.topdownproteomics.org/proteoforms/", "pgs": "https://www.pgscatalog.org/pgs/", "pgx": "https://progenetix.org/services/ids/", @@ -988,231 +1177,317 @@ "pharmgkb.pathways": "http://www.pharmgkb.org/pathway/", "phenolexplorer": "http://phenol-explorer.eu/foods/", "phenx": "https://www.phenxtoolkit.org/protocols/view/", + "phosphopoint.kinase": "https://identifiers.org/phosphopoint.kinase:", + "phosphopoint.protein": "https://identifiers.org/phosphopoint.protein:", "phosphosite.protein": "http://www.phosphosite.org/proteinAction.do?id=", "phosphosite.residue": "http://www.phosphosite.org/siteAction.do?id=", "phylomedb": "http://phylomedb.org/?seqid=", "phytozome.locus": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:", + "pibase": "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=", "pid.pathway": "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=", - "pigqtldb": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:", - "pina": "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=", "piroplasma": "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=", "pirsf": "https://pir.georgetown.edu/cgi-bin/ipcSF?id=", "pkdb": "https://pk-db.com/data/", "planttfdb": "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=", "plasmodb": "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=", "pmap.cutdb": "http://cutdb.burnham.org/relation/show/", + "pmap.substratedb": "https://identifiers.org/pmap.substratedb:", "pmc": "http://europepmc.org/articles/", "pmdb": "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=", - "pmp": "http://www.proteinmodelportal.org/query/uniprot/", "pmr": "https://models.physiomeproject.org/exposure/", - "pombase": "http://www.pombase.org/spombe/result/", + "pmr.workspace": "https://models.physiomeproject.org/workspace/", + "pocketome": "https://identifiers.org/pocketome:", + "polbase": "https://identifiers.org/polbase:", + "pombase": "https://www.pombase.org/gene/", "ppr": "https://europepmc.org/article/ppr/", "prefixcommons": "https://bioregistry.io/metaregistry/prefixcommons/", - "pride": "https://www.ebi.ac.uk/pride/archive/assays/", + "pride": "http://purl.obolibrary.org/obo/PRIDE_", "pride.project": "https://www.ebi.ac.uk/pride/archive/projects/", - "probonto": "https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=", + "prints": "https://identifiers.org/prints:", + "probesanddrugs": "https://www.probes-drugs.org/compound/", + "probonto": "http://www.probonto.org/ontology#PROB_", "prodom": "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=", "proglyc": "http://www.proglycprot.org/detail.aspx?ProId=", "prosite": "https://prosite.expasy.org/", "protclustdb": "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=", + "protcom": "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=", "proteomicsdb.peptide": "https://www.proteomicsdb.org/#human/proteinDetails/", + "proteomicsdb.protein": "https://identifiers.org/proteomicsdb.protein:", "protonet.cluster": "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=", "protonet.proteincard": "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=", "prov": "http://www.w3.org/ns/prov#", + "pscdb": "https://identifiers.org/pscdb:", + "pseudogene": "http://tables.pseudogene.org/[?species_name]/", "pseudomonas": "http://www.pseudomonas.com/feature/show/?locus_tag=", - "psipar": "https://www.ebi.ac.uk/ontology-lookup/?termId=", + "psipar": "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:", "pubchem.bioassay": "https://pubchem.ncbi.nlm.nih.gov/bioassay/", "pubchem.cell": "https://pubchem.ncbi.nlm.nih.gov/cell/", "pubchem.classification": "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=", - "pubchem.compound": "https://pubchem.ncbi.nlm.nih.gov/compound/", + "pubchem.compound": "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID", "pubchem.element": "https://pubchem.ncbi.nlm.nih.gov/element/", - "pubchem.substance": "https://pubchem.ncbi.nlm.nih.gov/substance/", + "pubchem.substance": "http://rdf.ncbi.nlm.nih.gov/pubchem/substance/SID", + "publons.publication": "https://publons.com/publon/", "publons.researcher": "https://publons.com/researcher/", - "pubmed": "https://www.ncbi.nlm.nih.gov/pubmed/", "px": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=", "pypi": "https://pypi.org/project/", + "qb": "http://purl.org/linked-data/cube#", "qtldb": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:", "qudt": "http://qudt.org/schema/qudt#", + "radiomics": "http://www.radiomics.org/RO/", + "radlex": "https://radlex.org/RID/", "rapdb.locus": "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=", "rapdb.transcript": "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=", + "ratmap": "http://ratmap.org/Showgene.php?gene_stable_id=", "rbk": "https://www.rebuildingakidney.org/id/", "rcb": "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "rdo": "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#", "re3data": "https://www.re3data.org/repository/", "reactome": "https://reactome.org/content/detail/", + "rebase": "https://identifiers.org/rebase:", + "rebec": "https://ensaiosclinicos.gov.br/rg/", "receptome.family": "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=", - "refseq": "https://www.ncbi.nlm.nih.gov/protein/", - "repeatsdb.protein": "https://repeatsdb.org/protein/", + "redfly": "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=", "repeatsdb.structure": "https://repeatsdb.org/structure/", + "repec": "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=", + "reproduceme": "https://w3id.org/reproduceme#", "rfam": "https://rfam.xfam.org/family/", + "rfc": "https://tools.ietf.org/rfc/rfc", + "rgap": "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=", "rgd": "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=", "rgd.qtl": "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=", "rgd.strain": "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=", "rhea": "https://www.rhea-db.org/rhea/", + "ribocentre": "https://www.ribocentre.org/docs/", + "ricecyc": "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=", "ricegap": "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=", "ricenetdb.compound": "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=", "ricenetdb.gene": "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=", "ricenetdb.mirna": "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=", "ricenetdb.protein": "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=", "ricenetdb.reaction": "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=", + "rism": "https://rism.online/", + "rna_sstrand": "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=", "rnacentral": "https://rnacentral.org/rna/", + "rnajunction": "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=", + "rnaloops": "https://rnaloops.cs.put.poznan.pl/search/details/", "rnamod": "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?", "rnamods": "http://mods.rna.albany.edu/mods/modifications/view/", + "rnavdb": "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=", + "ror": "https://ror.org/", "rouge": "https://www.kazusa.or.jp/rouge/gfpage/", + "rpcec": "https://rpcec.sld.cu/en/trials/", "rrid": "https://scicrunch.org/resolver/RRID:", "runbiosimulations": "https://run.biosimulations.org/simulations/", "rxnorm": "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=", + "s_mart_db": "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?", "sabiork.compound": "http://sabiork.h-its.org/newSearch?q=", - "sabiork.ec": "http://sabiork.h-its.org/newSearch?q=ecnumber:", "sabiork.kineticrecord": "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=", "sabiork.reaction": "http://sabiork.h-its.org/reacdetails.jsp?reactid=", "salk": "https://abrc.osu.edu/stocks/number/SALK_", + "salmon": "https://purl.dataone.org/odo/SALMON_", + "sasap": "https://purl.dataone.org/odo/SASAP_", "sasbdb": "http://www.sasbdb.org/data/", "schem": "https://biopragmatics.github.io/providers/schem/", "schema": "https://schema.org/", "scholia.resource": "https://bioregistry.io/metaregistry/scholia/", + "sciflection": "https://sciflection.com/", "scomp": "https://biopragmatics.github.io/providers/scomp/", - "scop": "http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=", + "scop": "http://scop.berkeley.edu/sunid=", + "scop.sccs": "http://scop.berkeley.edu/sccs=", + "scop.sid": "http://scop.berkeley.edu/sid=", + "scopus": "https://www.scopus.com/authid/detail.uri?authorId=", + "scopus.affiliation": "https://www.scopus.com/affil/profile.uri?afid=", + "scopus.publication": "https://www.scopus.com/sourceid/", + "scopus.work": "http://www.scopus.com/record/display.url?origin=inward&eid=", + "scpd": "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?", "scr": "http://scicrunch.org/resolver/SCR_", "scretf": "http://stormo.wustl.edu/ScerTF/details/", + "sdap": "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=", "sdbs": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=", + "sdgio": "http://purl.unep.org/sdg/SDGIO_", "sdis": "https://biopragmatics.github.io/providers/sdis/", "sedml.format": "https://sed-ml.org/urns.html#format:", "sedml.language": "https://sed-ml.org/urns.html#language:", "seed": "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=", "seed.compound": "http://modelseed.org/biochem/compounds/", "seed.reaction": "http://modelseed.org/biochem/reactions/", + "seinet": "https://swbiodiversity.org/seinet/taxa/index.php?taxon=", + "semapv": "https://w3id.org/semapv/vocab/", + "senso": "http://purl.dataone.org/odo/SENSO_", + "seo": "https://w3id.org/seo#", "sfam": "https://biopragmatics.github.io/providers/sfam/", "sgd": "https://www.yeastgenome.org/locus/", "sgd.pathways": "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=", "sgn": "http://solgenomics.net/phenome/locus_display.pl?locus_id=", - "sheepqtldb": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:", + "sh": "http://www.w3.org/ns/shacl#", + "shareloc": "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_", + "sharkipedia.species": "https://www.sharkipedia.org/species/", + "sharkipedia.trait": "https://www.sharkipedia.org/traits/", + "sharkipedia.trend": "https://www.sharkipedia.org/trends/", + "shex": "http://www.w3.org/ns/shex#", + "shibase": "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=", "sider.drug": "http://sideeffects.embl.de/drugs/", - "sider.effect": "http://sideeffects.embl.de/se/", "sigmaaldrich": "https://www.sigmaaldrich.com/US/en/product/sigma/", "signaling-gateway": "http://www.signaling-gateway.org/molecule/query?afcsid=", "signor": "https://signor.uniroma2.it/relation_result.php?id=", - "sio": "https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=", + "sio": "https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form=", "sisu": "http://search.sisuproject.fi/#/variant/", "sitex": "http://www-bionet.sscc.ru/sitex/index.php?siteid=", "skip": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=", + "skm": "https://identifiers.org/skm:", "skos": "http://www.w3.org/2004/02/skos/core#", + "skosxl": "http://www.w3.org/2008/05/skos-xl#", "slkbase": "https://sumlineknowledgebase.com/?page_id=", "smart": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=", "smid": "https://smid-db.org/smid/", + "smiles": "https://chemapps.stolaf.edu/jmol/jmol.php?model=", "smpdb": "https://smpdb.ca/view/", - "snp2tfbs": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=", + "snap": "http://www.ifomis.org/bfo/1.1/snap#", + "snornabase": "http://www-snorna.biotoul.fr/plus.php?id=", + "snp500cancer": "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=", "soybase": "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=", + "spbase": "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=", "spdx": "https://spdx.org/licenses/", + "sphn": "https://biomedit.ch/rdf/sphn-ontology/sphn#", + "spike.map": "https://identifiers.org/spike.map:", "splash": "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/", + "splicenest": "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=", "spp": "https://www.signalingpathways.org/datasets/dataset.jsf?doi=", - "sprint": "http://130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=", + "srao": "http://www.fairsharing.org/ontology/subject/SRAO_", "ssbd.dataset": "https://ssbd.riken.jp/database/dataset/", "ssbd.project": "https://ssbd.riken.jp/database/project/", + "sssom": "https://w3id.org/sssom/", + "sstoss": "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=", "stap": "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=", "stitch": "http://stitch.embl.de/interactions/", "storedb": "https://www.storedb.org/?", "storedb.dataset": "https://www.storedb.org/?STOREDB:DATASET", "storedb.file": "https://www.storedb.org/store_v3/download.jsp?fileId=", "storedb.study": "https://www.storedb.org/store_v3/study.jsp?studyId=", - "string": "http://string.embl.de/interactions/", - "sty": "http://purl.bioontology.org/ontology/STY/", + "sty": "https://uts.nlm.nih.gov/uts/umls/semantic-network/", "subtilist": "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+", "subtiwiki": "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/", "sugarbind": "http://sugarbind.expasy.org/", "supfam": "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=", + "sweetrealm": "http://sweetontology.net/matrMineral/", "swh": "https://archive.softwareheritage.org/browse/swh:", - "swiss-model": "https://swissmodel.expasy.org/repository/uniprot/", - "swisslipid": "https://www.swisslipids.org/#/entity/SLM:", "swissregulon": "http://swissregulon.unibas.ch/query/", + "swrl": "http://www.w3.org/2003/11/swrl#", "t3db": "http://www.t3db.org/toxins/", "tair.gene": "http://arabidopsis.org/servlets/TairObject?accession=Gene:", "tair.locus": "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:", "tair.protein": "http://arabidopsis.org/servlets/TairObject?accession=AASequence:", "tarbase": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=", "tcb": "https://www.pirbright.ac.uk/node/", + "tccd": "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=", "tcdb": "http://www.tcdb.org/search/result.php?tc=", + "tctr": "https://www.thaiclinicaltrials.org/show/", "tfclass": "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=", "tgd": "http://ciliate.org/index.php/feature/details/", "tgn": "http://vocab.getty.edu/page/tgn/", "thermofisher": "https://www.thermofisher.com/antibody/product/", "tigrfam": "https://www.ncbi.nlm.nih.gov/cdd?term=", + "time": "http://www.w3.org/2006/time#", "tngb": "http://biobanknetwork.telethon.it/Sample/View?sampleId=", + "togovar": "https://grch38.togovar.org/variant/", "tol": "http://tolweb.org/", "topdb": "http://topdb.enzim.hu/?m=show&id=", - "topfind": "http://clipserve.clip.ubc.ca/topfind/proteins/", "toxoplasma": "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=", + "transportdb": "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=", "transyt": "https://transyt.bio.di.uminho.pt/reactions/", + "tred": "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=", + "treebase": "https://identifiers.org/treebase:", "treefam": "http://www.treefam.org/family/", "trichdb": "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=", "tritrypdb": "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=", + "trnadbce": "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=", "ttd.drug": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=", "ttd.target": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=", "ubio.namebank": "http://www.ubio.org/browser/details.php?namebankID=", "ucsc": "ftp://hgdownload.cse.ucsc.edu/goldenPath/", + "ucum": "https://units-of-measurement.org/", "umbbd.compound": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=", "umbbd.enzyme": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=", + "umbbd.pathway": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=", "umbbd.reaction": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=", "umbbd.rule": "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=", + "unichem": "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=", "unigene": "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=", - "unii": "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=", + "unii": "https://precision.fda.gov/uniisearch/srs/unii/", "unimod": "http://www.unimod.org/modifications_view.php?editid1=", "uniparc": "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=", "unipathway.compound": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=", "unipathway.reaction": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=", "uniprot": "http://purl.uniprot.org/uniprot/", + "uniprot.arba": "https://www.uniprot.org/arba/", "uniprot.chain": "http://purl.uniprot.org/annotation/", "uniprot.disease": "https://www.uniprot.org/diseases/", - "uniprot.isoform": "http://www.uniprot.org/uniprot/", - "uniprot.journal": "https://www.uniprot.org/journals/", + "uniprot.isoform": "http://purl.uniprot.org/isoforms/", + "uniprot.journal": "http://purl.uniprot.org/journals/", "uniprot.keyword": "https://www.uniprot.org/keywords/", "uniprot.location": "https://www.uniprot.org/locations/", + "uniprot.proteome": "https://www.uniprot.org/proteomes/", "uniprot.ptm": "https://biopragmatics.github.io/providers/uniprot.ptm/", "uniprot.resource": "https://www.uniprot.org/database/", "uniprot.tissue": "https://www.uniprot.org/tissues/", + "uniprot.var": "http://purl.uniprot.org/annotation/VAR_", "uniref": "https://www.uniprot.org/uniref/", "unirule": "https://www.uniprot.org/unirule/", "unists": "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=", "unite": "http://unite.ut.ee/bl_forw.php?nimi=", "uspto": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/", - "validatordb": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/", + "utrdb": "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=", + "vac": "https://vac.niaid.nih.gov/view?id=", + "vandf": "http://purl.bioontology.org/ontology/VANDF/", + "vann": "https://vocab.org/vann/", "vbase2": "http://www.vbase2.org/vgene.php?id=", "vbrc": "http://vbrc.org/gene_detail.asp?gene_id=", "vcell": "https://vcell.org/biomodel-", - "vectorbase": "https://vectorbase.org/vectorbase/app/record/gene/", + "vectorbase": "https://vectorbase.org/gene/", + "vega": "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=", "vegbank": "http://vegbank.org/cite/", "vfb": "http://virtualflybrain.org/reports/", "vfdb.gene": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=", "vfdb.genus": "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=", "vgnc": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/", "viaf": "http://viaf.org/viaf/", + "vido": "http://purl.obolibrary.org/obo/VIDO_", + "violinnet": "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=", + "vipr": "https://identifiers.org/vipr:", + "viralzone": "https://viralzone.expasy.org/", + "viroligo": "http://viroligo.okstate.edu/main.php?vid=", "virsirna": "http://crdd.osdd.net/servers/virsirnadb/record.php?details=", + "vita": "http://vita.mbc.nctu.edu.tw/search.php?acc=", "vmhgene": "https://www.vmh.life/#gene/", "vmhmetabolite": "https://www.vmh.life/#metabolite/", "vmhreaction": "https://www.vmh.life/#reaction/", "void": "http://rdfs.org/ns/void#", + "vsmo": "http://purl.obolibrary.org/obo/VSMO_", "vso": "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_", - "vz": "https://viralzone.expasy.org/", "wb.rnai": "https://www.wormbase.org/species/c_elegans/rnai/", "webelements": "https://www.webelements.com/", "wgs84": "http://www.w3.org/2003/01/geo/wgs84_pos#", "wikidata": "http://www.wikidata.org/entity/", "wikidata.property": "https://www.wikidata.org/wiki/Property:", - "wikipathways": "http://www.wikipathways.org/instance/", + "wikipathways": "http://identifiers.org/wikipathways/", + "wikipathways.vocab": "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23", "wikipedia.en": "http://en.wikipedia.org/wiki/", "worfdb": "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=", + "world2dpage": "https://world-2dpage.expasy.org/repository/", + "worldavatar.kin": "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#", "wormpep": "https://www.wormbase.org/db/seq/protein?name=", "worms": "http://www.marinespecies.org/aphia.php?p=taxdetails&id=", "wwf.ecoregion": "https://www.worldwildlife.org/ecoregions/", "xenbase": "https://www.xenbase.org/entry/", "ximbio": "https://ximbio.com/reagent/", - "xl": "http://purl.obolibrary.org/obo/XL_", "xmetdb": "http://www.xmetdb.org/xmetdb/protocol/", "xml": "http://www.w3.org/XML/1998/namespace#", "xsd": "http://www.w3.org/2001/XMLSchema#", "ydpm": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=", "yeastintron": "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=", + "yeastract": "http://www.yeastract.com/view.php?existing=locus&orfname=", "yetfasco": "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=", "yid": "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=", "ymdb": "http://www.ymdb.ca/compounds/", @@ -1221,4 +1496,4 @@ "zfin": "http://zfin.org/", "zinc": "http://zinc15.docking.org/substances/" } -}""" +} \ No newline at end of file diff --git a/tests/test_parsers.py b/tests/test_parsers.py index ffb58e91..eb0a48a7 100644 --- a/tests/test_parsers.py +++ b/tests/test_parsers.py @@ -117,7 +117,7 @@ def test_parse_obographs(self): write_table(msdf, file) self.assertEqual( len(msdf.df), - 9880, + 9879, f"{self.obographs_file} has the wrong number of mappings.", )