{"id":"https://openalex.org/W2794015366","doi":"https://doi.org/10.1093/bib/bby015","title":"Where to search top-K biomedical ontologies?","display_name":"Where to search top-K biomedical ontologies?","publication_year":2018,"publication_date":"2018-02-14","ids":{"openalex":"https://openalex.org/W2794015366","doi":"https://doi.org/10.1093/bib/bby015","mag":"2794015366"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby015","pdf_url":"https://academic.oup.com/bib/article-pdf/20/4/1477/30119637/bby015.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/20/4/1477/30119637/bby015.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072119046","display_name":"Daniela Oliveira","orcid":"https://orcid.org/0000-0003-0559-8737"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Daniela Oliveira","raw_affiliation_strings":["Insight Centre for Data Analytics, NUI Galway, Ireland"],"affiliations":[{"raw_affiliation_string":"Insight Centre for Data Analytics, NUI Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061546828","display_name":"Anila Sahar Butt","orcid":"https://orcid.org/0000-0002-3508-6049"},"institutions":[{"id":"https://openalex.org/I1292875679","display_name":"Commonwealth Scientific and Industrial Research Organisation","ror":"https://ror.org/03qn8fb07","country_code":"AU","type":"funder","lineage":["https://openalex.org/I1292875679","https://openalex.org/I2801453606","https://openalex.org/I4387156119"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Anila Sahar Butt","raw_affiliation_strings":["CSIRO, Canberra, Australia"],"affiliations":[{"raw_affiliation_string":"CSIRO, Canberra, Australia","institution_ids":["https://openalex.org/I1292875679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072221152","display_name":"Armin Haller","orcid":"https://orcid.org/0000-0003-3425-0780"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Armin Haller","raw_affiliation_strings":["Australian National University, Canberra, Australia"],"affiliations":[{"raw_affiliation_string":"Australian National University, Canberra, Australia","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006224704","display_name":"Dietrich Rebholz\u2010Schuhmann","orcid":"https://orcid.org/0000-0002-1018-0370"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Dietrich Rebholz-Schuhmann","raw_affiliation_strings":["Insight Centre for Data Analytics, NUI Galway, Ireland"],"affiliations":[{"raw_affiliation_string":"Insight Centre for Data Analytics, NUI Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058460371","display_name":"Ratnesh Sahay","orcid":"https://orcid.org/0000-0003-4864-4174"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Ratnesh Sahay","raw_affiliation_strings":["Insight Centre for Data Analytics, NUI Galway, Ireland"],"affiliations":[{"raw_affiliation_string":"Insight Centre for Data Analytics, NUI Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5058460371"],"corresponding_institution_ids":["https://openalex.org/I188760350"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.3711,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.59576868,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"20","issue":"4","first_page":"1477","last_page":"1491"},"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":0.9958000183105469,"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":0.9638000130653381,"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/computer-science","display_name":"Computer science","score":0.5766239166259766},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5238237977027893},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.39069968461990356}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5766239166259766},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5238237977027893},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.39069968461990356}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bby015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby015","pdf_url":"https://academic.oup.com/bib/article-pdf/20/4/1477/30119637/bby015.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:https://researchrepository.universityofgalway.ie:10379/7444","is_oa":true,"landing_page_url":"http://hdl.handle.net/10379/7444","pdf_url":"http://hdl.handle.net/10379/7444","source":{"id":"https://openalex.org/S4377196322","display_name":"ARAN (University of Galway Research Repository) (Ollscoil na Gaillimhe \u2013 University of Galway)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I188760350","host_organization_name":"Ollscoil na Gaillimhe \u2013 University of Galway","host_organization_lineage":["https://openalex.org/I188760350"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:openresearch-repository.anu.edu.au:1885/214160","is_oa":true,"landing_page_url":"http://hdl.handle.net/1885/214160","pdf_url":null,"source":{"id":"https://openalex.org/S4306402539","display_name":"ANU Open Research (Australian National University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I118347636","host_organization_name":"Australian National University","host_organization_lineage":["https://openalex.org/I118347636"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics","raw_type":"Journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6781604","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6781604","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bby015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby015","pdf_url":"https://academic.oup.com/bib/article-pdf/20/4/1477/30119637/bby015.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1383882326","display_name":null,"funder_award_id":"SFI/12/RC/","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G2881606312","display_name":null,"funder_award_id":"SFI/12/RC/2289","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G5098725405","display_name":null,"funder_award_id":"12/RC/","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G6712843611","display_name":null,"funder_award_id":"12/RC/228","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G7362007176","display_name":null,"funder_award_id":"12/RC/2289","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"}],"funders":[{"id":"https://openalex.org/F4320320386","display_name":"Commonwealth Scientific and Industrial Research Organisation","ror":"https://ror.org/03qn8fb07"},{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2794015366.pdf","grobid_xml":"https://content.openalex.org/works/W2794015366.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W19676100","https://openalex.org/W68970679","https://openalex.org/W171940191","https://openalex.org/W341877867","https://openalex.org/W971865635","https://openalex.org/W1528140876","https://openalex.org/W1601038846","https://openalex.org/W1757909678","https://openalex.org/W1854214752","https://openalex.org/W1937427849","https://openalex.org/W1966619306","https://openalex.org/W1972562845","https://openalex.org/W1974896839","https://openalex.org/W1978394996","https://openalex.org/W1978799369","https://openalex.org/W2002430005","https://openalex.org/W2008600054","https://openalex.org/W2022166150","https://openalex.org/W2022451103","https://openalex.org/W2037382435","https://openalex.org/W2058320302","https://openalex.org/W2087779040","https://openalex.org/W2093217971","https://openalex.org/W2095723013","https://openalex.org/W2097311303","https://openalex.org/W2097395913","https://openalex.org/W2103017472","https://openalex.org/W2103260426","https://openalex.org/W2117815774","https://openalex.org/W2123152121","https://openalex.org/W2126434293","https://openalex.org/W2126827435","https://openalex.org/W2128365672","https://openalex.org/W2140611297","https://openalex.org/W2141201603","https://openalex.org/W2141541659","https://openalex.org/W2143326402","https://openalex.org/W2147018385","https://openalex.org/W2147268363","https://openalex.org/W2152889283","https://openalex.org/W2156828625","https://openalex.org/W2156997379","https://openalex.org/W2159092541","https://openalex.org/W2163670493","https://openalex.org/W2165612380","https://openalex.org/W2168091868","https://openalex.org/W2170282111","https://openalex.org/W2178026535","https://openalex.org/W2252448679","https://openalex.org/W2293532363","https://openalex.org/W2401582930","https://openalex.org/W2404810405","https://openalex.org/W2479473169","https://openalex.org/W2490667291","https://openalex.org/W2559028527","https://openalex.org/W2964300898","https://openalex.org/W2996036406","https://openalex.org/W4285719527","https://openalex.org/W4376862038","https://openalex.org/W6683186658"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Searching":[2],"for":[3,46,66,118,193,252],"precise":[4],"terms":[5],"and":[6,22,70,91,111,132,136,163,200,210,231,241,266],"terminological":[7],"definitions":[8],"in":[9,26,74,93,219],"the":[10,54,59,67,75,125,133,143,166,187,215,235,249],"biomedical":[11,194,208],"data":[12],"space":[13],"is":[14,85,156,186],"problematic,":[15],"as":[16,169,171],"researchers":[17,230],"find":[18],"overlapping,":[19],"closely":[20],"related":[21],"even":[23],"equivalent":[24],"concepts":[25],"a":[27,47,152,173,201],"single":[28],"or":[29,64],"multiple":[30],"ontologies.":[31,119],"Search":[32],"engines":[33,84,117,138],"that":[34,155,205,225,242],"retrieve":[35],"ontological":[36,61],"resources":[37],"often":[38],"suggest":[39],"an":[40],"extensive":[41],"list":[42],"of":[43,57,81,176,183,189,203],"search":[44,83,95,108,116,137,177,191,198,221,237],"results":[45,268],"given":[48],"input":[49,68],"term,":[50],"which":[51],"leads":[52],"to":[53,87,107,159,165,213,233,247],"tedious":[55],"task":[56],"selecting":[58],"best-fit":[60],"resource":[62],"(class":[63],"property)":[65],"term":[69],"reduces":[71],"user":[72],"confidence":[73,164],"retrieval":[76,217],"engines.":[77],"A":[78],"systematic":[79],"evaluation":[80,227],"these":[82],"necessary":[86],"understand":[88],"their":[89,220,253],"strengths":[90],"weaknesses":[92],"different":[94],"requirements.":[96],"Result":[97],"We":[98,223],"have":[99,122,127,139],"implemented":[100],"seven":[101,261],"comparable":[102],"Information":[103],"Retrieval":[104],"ranking":[105,134,262],"algorithms":[106,135],"through":[109],"ontologies":[110,195],"compared":[112],"them":[113,246],"against":[114,142],"four":[115],"Free-text":[120],"queries":[121],"been":[123,128,140],"performed,":[124],"outcomes":[126],"judged":[129],"by":[130],"experts":[131,209],"evaluated":[141],"expert-based":[144,167],"ground":[145,264],"truth":[146],"(GT).":[147],"In":[148],"addition,":[149],"we":[150],"propose":[151],"probabilistic":[153],"GT":[154,168],"developed":[157],"automatically":[158],"provide":[160],"deeper":[161],"insights":[162],"well":[170],"evaluating":[172],"broader":[174],"range":[175],"queries.":[178],"Conclusion":[179],"The":[180,257],"main":[181],"outcome":[182],"this":[184,226],"work":[185],"identification":[188],"key":[190],"factors":[192],"together":[196],"with":[197],"requirements":[199],"set":[202],"recommendations":[204],"will":[206,228,244],"help":[207,245],"ontology":[211],"engineers":[212],"select":[214,248],"best-suited":[216],"mechanism":[218],"scenarios.":[222],"expect":[224],"allow":[229],"practitioners":[232],"apply":[234],"current":[236],"techniques":[238],"more":[239],"reliably":[240],"it":[243],"right":[250],"solution":[251],"daily":[254],"work.":[255],"Availability":[256],"source":[258],"code":[259],"(of":[260],"algorithms),":[263],"truths":[265],"experimental":[267],"are":[269],"available":[270],"at":[271],"https://github.com/danielapoliveira/bioont-search-benchmark":[272]},"counts_by_year":[{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
