{"id":"https://openalex.org/W2049346142","doi":"https://doi.org/10.1109/jbhi.2013.2248742","title":"Determining the Semantic Similarities Among Gene Ontology Terms","display_name":"Determining the Semantic Similarities Among Gene Ontology Terms","publication_year":2013,"publication_date":"2013-02-25","ids":{"openalex":"https://openalex.org/W2049346142","doi":"https://doi.org/10.1109/jbhi.2013.2248742","mag":"2049346142","pmid":"https://pubmed.ncbi.nlm.nih.gov/24592450"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2013.2248742","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2013.2248742","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074032096","display_name":"Kamal Taha","orcid":"https://orcid.org/0000-0002-6674-4614"},"institutions":[{"id":"https://openalex.org/I176601375","display_name":"Khalifa University of Science and Technology","ror":"https://ror.org/05hffr360","country_code":"AE","type":"education","lineage":["https://openalex.org/I176601375"]}],"countries":["AE"],"is_corresponding":true,"raw_author_name":"Kamal Taha","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Khalifa University of Science, Technology and Research, Abu Dhabi, UAE","Department of Electrical and Computer Engineering, Khalifa University of Science Technology and Research, Abu Dhabi, UAE"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Khalifa University of Science, Technology and Research, Abu Dhabi, UAE","institution_ids":["https://openalex.org/I176601375"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Khalifa University of Science Technology and Research, Abu Dhabi, UAE","institution_ids":["https://openalex.org/I176601375"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5074032096"],"corresponding_institution_ids":["https://openalex.org/I176601375"],"apc_list":null,"apc_paid":null,"fwci":2.0928,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.8687983,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"3","first_page":"512","last_page":"525"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9905999898910522,"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":0.7144407033920288},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5109373927116394},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.44928738474845886},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.4414639472961426},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.438149094581604},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4241727590560913},{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.4136693775653839},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3617812991142273},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.34667110443115234}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7144407033920288},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5109373927116394},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.44928738474845886},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.4414639472961426},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.438149094581604},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4241727590560913},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.4136693775653839},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3617812991142273},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.34667110443115234},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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":"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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2013.2248742","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2013.2248742","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:24592450","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24592450","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W173642147","https://openalex.org/W1659833910","https://openalex.org/W1830662877","https://openalex.org/W1831066781","https://openalex.org/W1981352196","https://openalex.org/W1999722941","https://openalex.org/W2026227080","https://openalex.org/W2042252652","https://openalex.org/W2059975159","https://openalex.org/W2103017472","https://openalex.org/W2109047523","https://openalex.org/W2110626682","https://openalex.org/W2126225210","https://openalex.org/W2127536416","https://openalex.org/W2128049108","https://openalex.org/W2128721091","https://openalex.org/W2134226301","https://openalex.org/W2149214683","https://openalex.org/W2160493020","https://openalex.org/W2161358836"],"related_works":["https://openalex.org/W4234886518","https://openalex.org/W2389591058","https://openalex.org/W2486541857","https://openalex.org/W2382112581","https://openalex.org/W3124036233","https://openalex.org/W2108840191","https://openalex.org/W2759366996","https://openalex.org/W2110679372","https://openalex.org/W2354081742","https://openalex.org/W2372661603"],"abstract_inverted_index":{"We":[0,16,129,146],"present":[1,147],"in":[2,20,53,61,87,120,182,206],"this":[3],"paper":[4],"novel":[5,131],"techniques":[6,19,132,154],"that":[7,133,198],"determine":[8,134],"the":[9,70,88,94,97,113,121,135,141,157,177,189,202],"semantic":[10,71,158,178],"relationships":[11],"among":[12,73,160,180],"GeneOntology":[13],"(GO)":[14],"terms.":[15],"implemented":[17],"these":[18,153],"a":[21,35,108,148],"prototype":[22],"system":[23],"called":[24],"GoSE,":[25],"which":[26,99],"resides":[27],"between":[28],"user":[29],"application":[30],"and":[31,82,166,184,191,208],"GO":[32,39,48,74,89,109,122,161],"database.":[33],"Given":[34],"set":[36,45,114],"S":[37],"of":[38,47,96,107,115,137,143,175],"terms,":[40,49,98,117],"GoSE":[41,164],"would":[42],"return":[43],"another":[44,86],"S'":[46,54],"where":[50],"each":[51,59],"term":[52,60,110],"is":[55,66,112,125],"semantically":[56],"related":[57],"to":[58,84,102],"S.":[62],"Most":[63],"current":[64],"research":[65],"focused":[67],"on":[68,79,127,140],"determining":[69,156],"similarities":[72,159,179],"ontology":[75],"terms":[76,138],"based":[77,139],"solely":[78],"their":[80],"IDs":[81],"proximity":[83],"one":[85],"graph":[90,123],"structure,":[91],"while":[92],"overlooking":[93],"contexts":[95,136],"may":[100],"lead":[101],"erroneous":[103],"results.":[104],"The":[105,173],"context":[106],"T":[111],"other":[116,203],"whose":[118],"existence":[119,144],"structure":[124],"dependent":[126],"T.":[128],"propose":[130],"concept":[142],"dependency.":[145],"stack-based":[149],"sort-merge":[150],"algorithm":[151],"employing":[152],"for":[155],"terms.We":[162],"evaluated":[163],"experimentally":[165],"compared":[167],"it":[168],"with":[169],"three":[170,204],"existing":[171],"methods.":[172],"results":[174],"measuring":[176],"genes":[181],"KEGG":[183],"Pfam":[185,193],"pathways":[186],"retrieved":[187],"from":[188],"DBGET":[190],"Sanger":[192],"databases,":[194],"respectively,":[195],"have":[196],"shown":[197],"our":[199],"method":[200],"outperforms":[201],"methods":[205],"recall":[207],"precision.":[209]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
