{"id":"https://openalex.org/W2141541659","doi":"https://doi.org/10.1093/bioinformatics/btt113","title":"EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats","display_name":"EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats","publication_year":2013,"publication_date":"2013-03-11","ids":{"openalex":"https://openalex.org/W2141541659","doi":"https://doi.org/10.1093/bioinformatics/btt113","mag":"2141541659","pmid":"https://pubmed.ncbi.nlm.nih.gov/23479348"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt113","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt113","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/10/1325/48886384/bioinformatics_29_10_1325.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/10/1325/48886384/bioinformatics_29_10_1325.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080837511","display_name":"Jon Ison","orcid":"https://orcid.org/0000-0001-6666-1520"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["GB","NO"],"is_corresponding":true,"raw_author_name":"Jon Ison","raw_affiliation_strings":["1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007975575","display_name":"Mat\u00fa\u0161 Kala\u0161","orcid":"https://orcid.org/0000-0002-1509-4981"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["GB","NO"],"is_corresponding":false,"raw_author_name":"Mat\u00fa\u0161 Kala\u0161","raw_affiliation_strings":["1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012964587","display_name":"Inge Jonassen","orcid":"https://orcid.org/0000-0003-4110-0748"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["GB","NO"],"is_corresponding":false,"raw_author_name":"Inge Jonassen","raw_affiliation_strings":["1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005347238","display_name":"Dan Bolser","orcid":"https://orcid.org/0000-0002-3991-0859"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["GB","NO"],"is_corresponding":false,"raw_author_name":"Dan Bolser","raw_affiliation_strings":["1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044474509","display_name":"Mahmut Uluda\u011f","orcid":"https://orcid.org/0000-0001-8482-2172"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["GB","NO"],"is_corresponding":false,"raw_author_name":"Mahmut Uludag","raw_affiliation_strings":["1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084942657","display_name":"Hamish McWilliam","orcid":"https://orcid.org/0000-0003-1769-5032"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["GB","NO"],"is_corresponding":false,"raw_author_name":"Hamish McWilliam","raw_affiliation_strings":["1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037878913","display_name":"James Malone","orcid":"https://orcid.org/0000-0002-1615-2899"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["GB","NO"],"is_corresponding":false,"raw_author_name":"James Malone","raw_affiliation_strings":["1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018972787","display_name":"Rodrigo L\u00f3pez","orcid":"https://orcid.org/0000-0003-1256-7306"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["GB","NO"],"is_corresponding":false,"raw_author_name":"Rodrigo Lopez","raw_affiliation_strings":["1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081272754","display_name":"Steve Pettifer","orcid":"https://orcid.org/0000-0002-1809-5621"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["GB","NO"],"is_corresponding":false,"raw_author_name":"Steve Pettifer","raw_affiliation_strings":["1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109116797","display_name":"Peter Rice","orcid":null},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["GB","NO"],"is_corresponding":false,"raw_author_name":"Peter Rice","raw_affiliation_strings":["1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK, 2Computational Biology Unit, Uni Computing, 5008 Bergen, Norway, 3Department of Informatics, University of Bergen, 5008 Bergen, Norway and 4School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5080837511"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I28407311","https://openalex.org/I4432739"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.4642,"has_fulltext":true,"cited_by_count":296,"citation_normalized_percentile":{"value":0.97596759,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"29","issue":"10","first_page":"1325","last_page":"1332"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5975000262260437,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5975000262260437,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.17520000040531158,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.045099999755620956,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7403360605239868},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.709885835647583},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6890859603881836},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6368241310119629},{"id":"https://openalex.org/keywords/prot\u00e9g\u00e9","display_name":"Prot\u00e9g\u00e9","score":0.5794475674629211},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5631431341171265},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5016417503356934},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.485115647315979},{"id":"https://openalex.org/keywords/unique-identifier","display_name":"Unique identifier","score":0.43746697902679443},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3954426050186157},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.316625714302063},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2492489218711853},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1193968653678894},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11165136098861694}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7403360605239868},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.709885835647583},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6890859603881836},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6368241310119629},{"id":"https://openalex.org/C2779247653","wikidata":"https://www.wikidata.org/wiki/Q2066865","display_name":"Prot\u00e9g\u00e9","level":3,"score":0.5794475674629211},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5631431341171265},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5016417503356934},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.485115647315979},{"id":"https://openalex.org/C119839945","wikidata":"https://www.wikidata.org/wiki/Q6545185","display_name":"Unique identifier","level":3,"score":0.43746697902679443},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3954426050186157},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.316625714302063},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2492489218711853},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1193968653678894},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11165136098861694},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btt113","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt113","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/10/1325/48886384/bioinformatics_29_10_1325.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3654706","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3654706","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:23479348","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23479348","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:bora.uib.no:1956/10659","is_oa":true,"landing_page_url":"http://hdl.handle.net/1956/10659","pdf_url":null,"source":{"id":"https://openalex.org/S4306401716","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/b95dccd5-fc5c-4724-8983-d81731207cee","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/b95dccd5-fc5c-4724-8983-d81731207cee","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Ison, J, Kala\u0161, M, Jonassen, I, Bolser, D, Uludag, M, McWilliam, H, Malone, J, Lopez, R, Pettifer, S & Rice, P 2013, 'EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics and formats', Bioinformatics, vol. 29, no. 10, pp. 1325-1332. https://doi.org/10.1093/bioinformatics/btt113","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pure.atira.dk:publications/b95dccd5-fc5c-4724-8983-d81731207cee","is_oa":false,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/edam-an-ontology-of-bioinformatics-operations-types-of-data-and-identifiers-topics-and-formats(b95dccd5-fc5c-4724-8983-d81731207cee).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Ison, J, Kala\u0161, M, Jonassen, I, Bolser, D, Uludag, M, McWilliam, H, Malone, J, Lopez, R, Pettifer, S & Rice, P 2013, 'EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics and formats', Bioinformatics, vol. 29, no. 10, pp. 1325-1332. https://doi.org/10.1093/bioinformatics/btt113","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.25504/fairsharing.a6r7zs","is_oa":true,"landing_page_url":"https://doi.org/10.25504/fairsharing.a6r7zs","pdf_url":null,"source":{"id":"https://openalex.org/S7407053452","display_name":"FAIRsharing.org","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt113","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt113","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/10/1325/48886384/bioinformatics_29_10_1325.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G214953350","display_name":null,"funder_award_id":"208481","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G5697113605","display_name":"European Life-science Infrastructure for Biological Information","funder_award_id":"211601","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7546909933","display_name":"Building data bridges between biological and medical infrastructures in Europe","funder_award_id":"284209","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8045596080","display_name":null,"funder_award_id":"178885/V30","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G8128737203","display_name":"EMBOSS: European Molecular Biology Open Software Suite","funder_award_id":"BB/G02264X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320323299","display_name":"Norges Forskningsr\u00e5d","ror":"https://ror.org/00epmv149"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2141541659.pdf","grobid_xml":"https://content.openalex.org/works/W2141541659.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W7060617","https://openalex.org/W1493945330","https://openalex.org/W1501546233","https://openalex.org/W1526965011","https://openalex.org/W1556177080","https://openalex.org/W1571433676","https://openalex.org/W1673404489","https://openalex.org/W1681831155","https://openalex.org/W1714132059","https://openalex.org/W1940888119","https://openalex.org/W1957356093","https://openalex.org/W1967176062","https://openalex.org/W1969709265","https://openalex.org/W1976894668","https://openalex.org/W1985468994","https://openalex.org/W1991056282","https://openalex.org/W1996423252","https://openalex.org/W2009569628","https://openalex.org/W2010605118","https://openalex.org/W2013571328","https://openalex.org/W2033377040","https://openalex.org/W2038777423","https://openalex.org/W2040704692","https://openalex.org/W2049625541","https://openalex.org/W2050554833","https://openalex.org/W2069435157","https://openalex.org/W2071221957","https://openalex.org/W2075123415","https://openalex.org/W2091162763","https://openalex.org/W2095612098","https://openalex.org/W2102883811","https://openalex.org/W2103017472","https://openalex.org/W2103260426","https://openalex.org/W2107658650","https://openalex.org/W2108234281","https://openalex.org/W2109904151","https://openalex.org/W2113142309","https://openalex.org/W2120772351","https://openalex.org/W2121237412","https://openalex.org/W2121792371","https://openalex.org/W2123171788","https://openalex.org/W2123854454","https://openalex.org/W2127770193","https://openalex.org/W2129687578","https://openalex.org/W2131660156","https://openalex.org/W2132247062","https://openalex.org/W2136482257","https://openalex.org/W2138608730","https://openalex.org/W2140157849","https://openalex.org/W2141541659","https://openalex.org/W2156467546","https://openalex.org/W2160943260","https://openalex.org/W2162094394","https://openalex.org/W2162832420","https://openalex.org/W2169231369","https://openalex.org/W2169826929","https://openalex.org/W2172194140","https://openalex.org/W2328044450","https://openalex.org/W2537627201","https://openalex.org/W2917476117","https://openalex.org/W4243251992","https://openalex.org/W6630000427","https://openalex.org/W6640387716","https://openalex.org/W6877228366"],"related_works":["https://openalex.org/W2413568490","https://openalex.org/W1913624564","https://openalex.org/W3130054399","https://openalex.org/W4301062032","https://openalex.org/W2343500026","https://openalex.org/W2319837024","https://openalex.org/W2390627310","https://openalex.org/W2413664130","https://openalex.org/W2051731675","https://openalex.org/W2164947858"],"abstract_inverted_index":{"MOTIVATION:":[0],"Advancing":[1],"the":[2,133,137],"search,":[3],"publication":[4],"and":[5,10,40,44,68,76,80,82,98,105,121,136,144],"integration":[6,86],"of":[7,30,38,51,112],"bioinformatics":[8,31],"tools":[9,79],"resources":[11],"demands":[12],"consistent":[13],"machine-understandable":[14],"descriptions.":[15],"A":[16],"comprehensive":[17],"ontology":[18,29],"allowing":[19],"such":[20,54],"descriptions":[21],"is":[22,27,114],"therefore":[23],"required.":[24],"RESULTS:":[25],"EDAM":[26,47,72,113],"an":[28],"operations":[32],"(tool":[33],"or":[34,90],"workflow":[35],"functions),":[36],"types":[37],"data":[39,45,65,81],"identifiers,":[41],"application":[42],"domains":[43],"formats.":[46],"supports":[48],"semantic":[49],"annotation":[50],"diverse":[52],"entities":[53],"as":[55],"Web":[56],"services,":[57],"databases,":[58],"programmatic":[59],"libraries,":[60],"standalone":[61],"tools,":[62],"interactive":[63],"applications,":[64],"schemas,":[66],"datasets":[67],"publications":[69],"within":[70],"bioinformatics.":[71],"applies":[73],"to":[74,83,148],"organizing":[75],"finding":[77],"suitable":[78],"automating":[84],"their":[85],"into":[87],"complex":[88],"applications":[89],"workflows.":[91],"It":[92,127],"includes":[93],"over":[94],"2200":[95],"defined":[96],"concepts":[97],"has":[99],"successfully":[100],"been":[101],"used":[102],"for":[103],"annotations":[104],"implementations.":[106],"AVAILABILITY:":[107],"The":[108],"latest":[109],"stable":[110],"version":[111,153],"available":[115,155],"in":[116,122],"OWL":[117],"format":[118,124],"from":[119,125],"http://edamontology.org/EDAM.owl":[120],"OBO":[123],"http://edamontology.org/EDAM.obo.":[126],"can":[128],"be":[129],"viewed":[130],"online":[131],"at":[132,156],"NCBO":[134],"BioPortal":[135],"EBI":[138],"Ontology":[139],"Lookup":[140],"Service.":[141],"For":[142],"documentation":[143],"license":[145],"please":[146],"refer":[147],"http://edamontology.org.":[149],"This":[150],"article":[151],"describes":[152],"1.2":[154],"http://edamontology.org/EDAM_1.2.owl.":[157],"CONTACT:":[158],"jison@ebi.ac.uk.":[159]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":27},{"year":2023,"cited_by_count":34},{"year":2022,"cited_by_count":42},{"year":2021,"cited_by_count":28},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":33},{"year":2018,"cited_by_count":17},{"year":2017,"cited_by_count":24},{"year":2016,"cited_by_count":22},{"year":2015,"cited_by_count":13},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2016-06-24T00:00:00"}