{"id":"https://openalex.org/W2165084475","doi":"https://doi.org/10.1142/s0219720013710017","title":"THE NEXT GENERATION OF SIMILARITY MEASURES THAT FULLY EXPLORE THE SEMANTICS IN BIOMEDICAL ONTOLOGIES","display_name":"THE NEXT GENERATION OF SIMILARITY MEASURES THAT FULLY EXPLORE THE SEMANTICS IN BIOMEDICAL ONTOLOGIES","publication_year":2013,"publication_date":"2013-06-11","ids":{"openalex":"https://openalex.org/W2165084475","doi":"https://doi.org/10.1142/s0219720013710017","mag":"2165084475","pmid":"https://pubmed.ncbi.nlm.nih.gov/24131058"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720013710017","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720013710017","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5014333753","display_name":"Francisco M. Couto","orcid":"https://orcid.org/0000-0003-0627-1496"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"FRANCISCO M. COUTO","raw_affiliation_strings":["Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, Lisboa 1749-016, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa, Lisboa 1749-016, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077227139","display_name":"H. Sofia Pinto","orcid":"https://orcid.org/0000-0001-9209-1349"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I4387152517","display_name":"Instituto Superior T\u00e9cnico","ror":"https://ror.org/03db2by73","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103","https://openalex.org/I4387152517"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"H. SOFIA PINTO","raw_affiliation_strings":["INESC-ID, Departamento de Engenharia Inform\u00e1tica, Instituto Superior T\u00e9cnico, Lisboa 1000-029, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC-ID, Departamento de Engenharia Inform\u00e1tica, Instituto Superior T\u00e9cnico, Lisboa 1000-029, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I4387152517"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5014333753"],"corresponding_institution_ids":["https://openalex.org/I141596103"],"apc_list":null,"apc_paid":null,"fwci":3.5893,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.93675157,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"11","issue":"05","first_page":"1371001","last_page":"1371001"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9940999746322632,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9922999739646912,"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/axiom","display_name":"Axiom","score":0.6657580137252808},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6475142240524292},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.6453905701637268},{"id":"https://openalex.org/keywords/semantic-similarity","display_name":"Semantic similarity","score":0.6228021383285522},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5904014706611633},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5540227890014648},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.5113577246665955},{"id":"https://openalex.org/keywords/formality","display_name":"Formality","score":0.4916754364967346},{"id":"https://openalex.org/keywords/extensional-definition","display_name":"Extensional definition","score":0.4388502538204193},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4190340042114258},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39976245164871216},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.37747904658317566},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35707783699035645},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2102651298046112},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.1862165927886963},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.1579788625240326},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14902576804161072},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.07510030269622803}],"concepts":[{"id":"https://openalex.org/C167729594","wikidata":"https://www.wikidata.org/wiki/Q17736","display_name":"Axiom","level":2,"score":0.6657580137252808},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6475142240524292},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.6453905701637268},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.6228021383285522},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5904014706611633},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5540227890014648},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.5113577246665955},{"id":"https://openalex.org/C2777159308","wikidata":"https://www.wikidata.org/wiki/Q1757948","display_name":"Formality","level":2,"score":0.4916754364967346},{"id":"https://openalex.org/C136137745","wikidata":"https://www.wikidata.org/wiki/Q19515659","display_name":"Extensional definition","level":3,"score":0.4388502538204193},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4190340042114258},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39976245164871216},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.37747904658317566},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35707783699035645},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2102651298046112},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.1862165927886963},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.1579788625240326},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14902576804161072},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.07510030269622803},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C77928131","wikidata":"https://www.wikidata.org/wiki/Q193343","display_name":"Tectonics","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","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":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","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":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","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":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720013710017","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720013710017","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:24131058","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24131058","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W80737574","https://openalex.org/W158759942","https://openalex.org/W172116272","https://openalex.org/W1482253003","https://openalex.org/W1505548477","https://openalex.org/W1535708631","https://openalex.org/W1549853718","https://openalex.org/W1555811341","https://openalex.org/W1582964678","https://openalex.org/W1598707686","https://openalex.org/W1599231733","https://openalex.org/W1605533097","https://openalex.org/W1773139785","https://openalex.org/W1806630989","https://openalex.org/W1806783651","https://openalex.org/W1967446680","https://openalex.org/W2012361142","https://openalex.org/W2025452874","https://openalex.org/W2032319966","https://openalex.org/W2033377040","https://openalex.org/W2045729458","https://openalex.org/W2048024098","https://openalex.org/W2048947602","https://openalex.org/W2057119643","https://openalex.org/W2059975159","https://openalex.org/W2065936280","https://openalex.org/W2067375208","https://openalex.org/W2082380079","https://openalex.org/W2084168100","https://openalex.org/W2084377579","https://openalex.org/W2087739686","https://openalex.org/W2088561970","https://openalex.org/W2091729411","https://openalex.org/W2095869976","https://openalex.org/W2099100406","https://openalex.org/W2103017472","https://openalex.org/W2103260426","https://openalex.org/W2112946624","https://openalex.org/W2113142309","https://openalex.org/W2117805756","https://openalex.org/W2123023820","https://openalex.org/W2123402141","https://openalex.org/W2124758832","https://openalex.org/W2124834853","https://openalex.org/W2124957697","https://openalex.org/W2126276057","https://openalex.org/W2127563440","https://openalex.org/W2134967412","https://openalex.org/W2150378591","https://openalex.org/W2158714788","https://openalex.org/W2166718065","https://openalex.org/W2169179075","https://openalex.org/W2171206351","https://openalex.org/W2337512840","https://openalex.org/W2398193230","https://openalex.org/W2745750801","https://openalex.org/W2913616910","https://openalex.org/W2914271914"],"related_works":["https://openalex.org/W25517187","https://openalex.org/W2480381080","https://openalex.org/W2329847998","https://openalex.org/W2193232575","https://openalex.org/W2500726251","https://openalex.org/W138719379","https://openalex.org/W1838148781","https://openalex.org/W4250466770","https://openalex.org/W2963469174","https://openalex.org/W2303098424"],"abstract_inverted_index":{"There":[0],"is":[1,17,44,91,96],"a":[2,163,166],"prominent":[3],"trend":[4],"to":[5,121],"augment":[6],"and":[7,67,130,147,174],"improve":[8],"the":[9,20,33,45,60,81,109,123,149,157,177],"formality":[10],"of":[11,32,41,52,83,105,111,125,151,168],"biomedical":[12,57,99,116,158,169,181],"ontologies.":[13,182],"For":[14],"example,":[15],"this":[16,42,128],"shown":[18],"by":[19,87],"current":[21,61],"effort":[22,43],"on":[23],"adding":[24],"description":[25,53,84],"logic":[26,54,85],"axioms,":[27],"such":[28],"as":[29],"disjointness.":[30],"One":[31],"key":[34],"ontology":[35],"applications":[36],"that":[37,101,154,172],"can":[38,133],"take":[39,122],"advantage":[40],"conceptual":[46],"(functional)":[47],"similarity":[48,74,89,118,170],"measurement.":[49],"The":[50],"presence":[51],"axioms":[55,86],"in":[56,78,108,162,180],"ontologies":[58,100],"make":[59],"structural":[62],"or":[63],"extensional":[64],"approaches":[65],"weaker":[66],"further":[68],"away":[69],"from":[70],"providing":[71],"sound":[72],"semantics-based":[73,88],"measures.":[75],"Although":[76],"beneficial":[77],"small":[79],"ontologies,":[80],"exploration":[82],"measures":[90,119,171],"computational":[92,140],"expensive.":[93],"This":[94,142],"limitation":[95],"critical":[97],"for":[98],"normally":[102],"contain":[103],"thousands":[104],"concepts.":[106],"Thus":[107],"process":[110],"gaining":[112],"their":[113],"rightful":[114],"place,":[115],"functional":[117],"have":[120],"journey":[124],"finding":[126],"how":[127],"rich":[129],"powerful":[131],"knowledge":[132],"be":[134],"fully":[135,175],"explored":[136],"while":[137],"keeping":[138],"feasible":[139],"costs.":[141],"manuscript":[143],"aims":[144],"at":[145],"promoting":[146],"guiding":[148],"development":[150],"compelling":[152],"tools":[153],"deliver":[155],"what":[156],"community":[159],"will":[160],"require":[161],"near":[164],"future:":[165],"next-generation":[167],"efficiently":[173],"explore":[176],"semantics":[178],"present":[179]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
