{"id":"https://openalex.org/W2138088864","doi":"https://doi.org/10.1093/database/bau060","title":"A controlled vocabulary for pathway entities and events","display_name":"A controlled vocabulary for pathway entities and events","publication_year":2014,"publication_date":"2014-06-20","ids":{"openalex":"https://openalex.org/W2138088864","doi":"https://doi.org/10.1093/database/bau060","mag":"2138088864","pmid":"https://pubmed.ncbi.nlm.nih.gov/24951798"},"language":"en","primary_location":{"id":"doi:10.1093/database/bau060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau060","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau060/8246425/bau060.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau060/8246425/bau060.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007029298","display_name":"S Jupe","orcid":"https://orcid.org/0000-0001-5807-0069"},"institutions":[{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"funder","lineage":["https://openalex.org/I87048295"]},{"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"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"S. Jupe","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK sjupe@ebi.ac.uk","European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK sjupe@ebi.ac.uk","institution_ids":[]},{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045359895","display_name":"Bijay Jassal","orcid":"https://orcid.org/0000-0002-5039-5405"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"B. Jassal","raw_affiliation_strings":["Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada","Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"],"affiliations":[{"raw_affiliation_string":"Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada","institution_ids":["https://openalex.org/I112260969"]},{"raw_affiliation_string":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada","institution_ids":["https://openalex.org/I112260969"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001790294","display_name":"Mark Williams","orcid":"https://orcid.org/0000-0002-1294-1110"},"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/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"funder","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"M. Williams","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006718188","display_name":"Guanming Wu","orcid":"https://orcid.org/0000-0001-8196-1177"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"G. Wu","raw_affiliation_strings":["Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada","Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada"],"affiliations":[{"raw_affiliation_string":"Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada","institution_ids":["https://openalex.org/I112260969"]},{"raw_affiliation_string":"Ontario Institute for Cancer Research, Toronto, ON\u00a0M5G0A3, Canada","institution_ids":["https://openalex.org/I112260969"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007029298"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.8556,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.73560379,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"2014","issue":"0","first_page":"bau060","last_page":"bau060"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"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":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9973999857902527,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8206143975257874},{"id":"https://openalex.org/keywords/readability","display_name":"Readability","score":0.6034953594207764},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5882039070129395},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.5784791111946106},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.545305073261261},{"id":"https://openalex.org/keywords/controlled-vocabulary","display_name":"Controlled vocabulary","score":0.5424680113792419},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5118395686149597},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.4912809729576111},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4246380031108856},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.4188106656074524},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2521402835845947},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18452772498130798},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.09457394480705261}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8206143975257874},{"id":"https://openalex.org/C2778143727","wikidata":"https://www.wikidata.org/wiki/Q1820650","display_name":"Readability","level":2,"score":0.6034953594207764},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5882039070129395},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.5784791111946106},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.545305073261261},{"id":"https://openalex.org/C110615152","wikidata":"https://www.wikidata.org/wiki/Q1469824","display_name":"Controlled vocabulary","level":2,"score":0.5424680113792419},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5118395686149597},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.4912809729576111},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4246380031108856},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.4188106656074524},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2521402835845947},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18452772498130798},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.09457394480705261},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/bau060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau060","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau060/8246425/bau060.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:24951798","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24951798","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4064568","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4064568","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bau060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau060","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau060/8246425/bau060.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.41999998688697815}],"awards":[{"id":"https://openalex.org/G3619172963","display_name":null,"funder_award_id":"U41 HG003751","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3732942959","display_name":null,"funder_award_id":"U41 HG003751","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320313288","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2138088864.pdf","grobid_xml":"https://content.openalex.org/works/W2138088864.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1976097579","https://openalex.org/W1981215030","https://openalex.org/W1989962769","https://openalex.org/W1999615477","https://openalex.org/W2009341227","https://openalex.org/W2096560421","https://openalex.org/W2125904022","https://openalex.org/W2159482845","https://openalex.org/W2415462974","https://openalex.org/W2605068739","https://openalex.org/W2999820612","https://openalex.org/W4212920271","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W1964661231","https://openalex.org/W3110264473","https://openalex.org/W4254960163","https://openalex.org/W2032810564","https://openalex.org/W2370831213","https://openalex.org/W2972807713","https://openalex.org/W4315704968","https://openalex.org/W1989811317","https://openalex.org/W3202867831","https://openalex.org/W1597990569"],"abstract_inverted_index":{"Entities":[0],"involved":[1],"in":[2,9,20,44,94],"pathways":[3],"and":[4,12,48,54,75,82,104,115,122,126],"the":[5,21,84],"events":[6],"they":[7,87],"participate":[8],"require":[10],"descriptive":[11],"unambiguous":[13,74],"names":[14,77,98],"that":[15,71],"are":[16,99],"often":[17],"not":[18],"available":[19,41],"literature":[22],"or":[23],"elsewhere.":[24],"Reactome":[25],"is":[26,36],"a":[27,39,67],"manually":[28],"curated":[29],"open-source":[30],"resource":[31],"of":[32,107],"human":[33],"pathways.":[34],"It":[35],"accessible":[37],"via":[38,49],"website,":[40],"as":[42],"downloads":[43],"standard":[45],"reusable":[46],"formats":[47],"Representational":[50],"State":[51],"Transfer":[52],"(REST)-ful":[53],"Simple":[55],"Object":[56],"Access":[57],"Protocol":[58],"(SOAP)":[59],"application":[60],"programming":[61],"interfaces":[62],"(APIs).":[63],"We":[64],"have":[65],"devised":[66],"controlled":[68],"vocabulary":[69],"(CV)":[70],"creates":[72],"concise,":[73],"unique":[76],"for":[78,101,120],"reactions":[79],"(pathway":[80],"events)":[81],"all":[83],"molecular":[85],"entities":[86,103],"involve.":[88],"The":[89],"CV":[90,109],"could":[91],"be":[92],"reapplied":[93],"any":[95],"situation":[96],"where":[97],"used":[100],"pathway":[102],"events.":[105],"Adoption":[106],"this":[108],"would":[110],"significantly":[111],"improve":[112],"naming":[113],"consistency":[114],"readability,":[116],"with":[117],"consequent":[118],"benefits":[119],"searching":[121],"data":[123],"mining":[124],"within":[125],"between":[127],"databases.":[128],"Database":[129],"URL:":[130],"http://www.reactome.org.":[131]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
