{"id":"https://openalex.org/W2514438535","doi":"https://doi.org/10.3233/sw-160238","title":"A systematic analysis of term reuse and term overlap across biomedical ontologies","display_name":"A systematic analysis of term reuse and term overlap across biomedical ontologies","publication_year":2016,"publication_date":"2016-08-19","ids":{"openalex":"https://openalex.org/W2514438535","doi":"https://doi.org/10.3233/sw-160238","mag":"2514438535","pmid":"https://pubmed.ncbi.nlm.nih.gov/28819351"},"language":"en","primary_location":{"id":"doi:10.3233/sw-160238","is_oa":false,"landing_page_url":"https://doi.org/10.3233/sw-160238","pdf_url":null,"source":{"id":"https://openalex.org/S4210177235","display_name":"Semantic Web","issn_l":"1570-0844","issn":["1570-0844","2210-4968"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Semantic Web","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":null,"any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059142933","display_name":"Maulik R. Kamdar","orcid":"https://orcid.org/0000-0002-9898-0515"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Maulik R. Kamdar","raw_affiliation_strings":["Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, USA. E-mails:\u00a0tudorache@stanford.edu,\u00a0musen@stanford.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, USA. E-mails:\u00a0tudorache@stanford.edu,\u00a0musen@stanford.edu","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051690097","display_name":"Tania Tudorache","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tania Tudorache","raw_affiliation_strings":["Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, USA. E-mails:\u00a0tudorache@stanford.edu,\u00a0musen@stanford.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, USA. E-mails:\u00a0tudorache@stanford.edu,\u00a0musen@stanford.edu","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009128820","display_name":"Mark A. Musen","orcid":"https://orcid.org/0000-0003-3325-793X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark A. Musen","raw_affiliation_strings":["Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, USA. E-mails:\u00a0tudorache@stanford.edu,\u00a0musen@stanford.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, USA. E-mails:\u00a0tudorache@stanford.edu,\u00a0musen@stanford.edu","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5059142933"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":null,"apc_paid":null,"fwci":4.7841,"has_fulltext":false,"cited_by_count":74,"citation_normalized_percentile":{"value":0.95446586,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"8","issue":"6","first_page":"853","last_page":"871"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12881","display_name":"linguistics and terminology studies","score":0.983299970626831,"subfield":{"id":"https://openalex.org/subfields/1203","display_name":"Language and Linguistics"},"field":{"id":"https://openalex.org/fields/12","display_name":"Arts and Humanities"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.8754520416259766},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.5261613726615906},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48167097568511963},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3800444006919861},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33005377650260925},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13624915480613708},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07183462381362915},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.056469619274139404}],"concepts":[{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.8754520416259766},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.5261613726615906},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48167097568511963},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3800444006919861},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33005377650260925},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13624915480613708},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07183462381362915},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.056469619274139404},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3233/sw-160238","is_oa":false,"landing_page_url":"https://doi.org/10.3233/sw-160238","pdf_url":null,"source":{"id":"https://openalex.org/S4210177235","display_name":"Semantic Web","issn_l":"1570-0844","issn":["1570-0844","2210-4968"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Semantic Web","raw_type":"journal-article"},{"id":"pmid:28819351","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28819351","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":"Semantic web","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5555235","is_oa":true,"landing_page_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5555235","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5555235","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Semant Web","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:5555235","is_oa":true,"landing_page_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[{"score":0.5199999809265137,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1728561560","display_name":null,"funder_award_id":"R01 GM103316","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2641238297","display_name":null,"funder_award_id":"R01 GM086587","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W31461794","https://openalex.org/W91108659","https://openalex.org/W99023140","https://openalex.org/W110497164","https://openalex.org/W326451266","https://openalex.org/W1481690646","https://openalex.org/W1483357098","https://openalex.org/W1527627804","https://openalex.org/W1577293923","https://openalex.org/W1600120165","https://openalex.org/W1654805921","https://openalex.org/W1806386184","https://openalex.org/W1816056598","https://openalex.org/W1983569077","https://openalex.org/W2002043951","https://openalex.org/W2026705124","https://openalex.org/W2030197114","https://openalex.org/W2031752570","https://openalex.org/W2042281163","https://openalex.org/W2062558911","https://openalex.org/W2074944495","https://openalex.org/W2087779040","https://openalex.org/W2091729411","https://openalex.org/W2103017472","https://openalex.org/W2113142309","https://openalex.org/W2114112915","https://openalex.org/W2123152121","https://openalex.org/W2128975000","https://openalex.org/W2136593687","https://openalex.org/W2156997379","https://openalex.org/W2159583324","https://openalex.org/W2164947858","https://openalex.org/W2165874743","https://openalex.org/W2178026535","https://openalex.org/W2293690484","https://openalex.org/W2295596860","https://openalex.org/W2395623484","https://openalex.org/W2395648879","https://openalex.org/W2405181880","https://openalex.org/W2407779602","https://openalex.org/W4285719527","https://openalex.org/W4407802416","https://openalex.org/W6743505604"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2384475851","https://openalex.org/W2000444236","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109"],"abstract_inverted_index":{"Reusing":[0],"ontologies":[1,59,91,118],"and":[2,8,28,48,65,71,183,187,226],"their":[3,97],"terms":[4,98,111,130,155,191,216],"is":[5,86],"a":[6,38,100,114,147,176,195,202],"principle":[7],"best":[9],"practice":[10],"that":[11,109,124,131,150,179,188,207,209,221,238],"most":[12,90,160],"ontology":[13,125,210,244],"development":[14],"methodologies":[15],"strongly":[16],"encourage.":[17],"Reuse":[18],"comes":[19],"with":[20,89],"the":[21,25,42,55,62,83,110,143,167,171,233,243],"promise":[22],"to":[23,29,128,153,214],"support":[24],"semantic":[26,121],"interoperability":[27],"reduce":[30],"engineering":[31,245],"costs.":[32],"In":[33],"this":[34,139],"paper,":[35],"we":[36,75],"present":[37],"descriptive":[39],"study":[40],"of":[41,45,57,69,96,103,117,170,197,204],"current":[43],"extent":[44],"term":[46,79,84,196,240],"reuse":[47,70,85,129,154,161,181,215,241],"overlap":[49,72,80,184],"among":[50,185],"biomedical":[51,58],"ontologies.":[52,105],"We":[53,137,158,174,199],"use":[54],"corpus":[56],"stored":[60],"in":[61,242],"BioPortal":[63,193],"repository,":[64],"analyze":[66],"different":[67,225],"types":[68],"constructs.":[73],"While":[74],"find":[76,159],"an":[77],"approximate":[78],"between":[81],"25-31%,":[82],"only":[87],"<9%,":[88],"reusing":[92],"fewer":[93],"than":[94],"5%":[95],"from":[99,146,156,192,217],"small":[101],"set":[102,116,203],"popular":[104],"Clustering":[106],"analysis":[107],"shows":[108],"reused":[112],"by":[113,141],"common":[115],"have":[119],">90%":[120],"similarity,":[122],"hinting":[123],"developers":[126,152,211],"tend":[127],"are":[132],"sibling":[133],"or":[134],"parent-child":[135],"nodes.":[136],"validate":[138],"finding":[140],"analysing":[142],"logs":[144],"generated":[145],"Prot\u00e9g\u00e9":[148],"plugin":[149],"enables":[151],"BioPortal.":[157],"constructs":[162],"were":[163,223],"2-level":[164],"subtrees":[165],"on":[166],"higher":[168],"levels":[169],"class":[172],"hierarchy.":[173],"developed":[175],"Web":[177],"application":[178],"visualizes":[180],"dependencies":[182],"ontologies,":[186,219],"proposes":[189],"similar":[190],"for":[194,235],"interest.":[198],"also":[200],"identified":[201],"error":[205],"patterns":[206],"indicate":[208],"did":[212],"intend":[213],"other":[218],"but":[220],"they":[222],"using":[224],"sometimes":[227],"incorrect":[228],"representations.":[229],"Our":[230],"results":[231],"stipulate":[232],"need":[234],"semi-automated":[236],"tools":[237],"augment":[239],"process":[246],"through":[247],"personalized":[248],"recommendations.":[249]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
