{"id":"https://openalex.org/W2261245081","doi":"https://doi.org/10.1093/bioinformatics/btv755","title":"simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes","display_name":"simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes","publication_year":2015,"publication_date":"2015-12-26","ids":{"openalex":"https://openalex.org/W2261245081","doi":"https://doi.org/10.1093/bioinformatics/btv755","mag":"2261245081","pmid":"https://pubmed.ncbi.nlm.nih.gov/26708333"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv755","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv755","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/9/1380/49019250/bioinformatics_32_9_1380.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/9/1380/49019250/bioinformatics_32_9_1380.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062453139","display_name":"Ahmad Pesaranghader","orcid":"https://orcid.org/0000-0002-0739-8475"},"institutions":[{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Ahmad Pesaranghader","raw_affiliation_strings":["1 Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada,","2 Institute for Big Data Analytics, Halifax, NS B3H 4R2, Canada,"],"affiliations":[{"raw_affiliation_string":"1 Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada,","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"2 Institute for Big Data Analytics, Halifax, NS B3H 4R2, Canada,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042893723","display_name":"Stan Matwin","orcid":"https://orcid.org/0000-0001-6629-8434"},"institutions":[{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"funder","lineage":["https://openalex.org/I99542240"]},{"id":"https://openalex.org/I4210087266","display_name":"Institute of Computer Science","ror":"https://ror.org/003fvp964","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210087266","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA","PL"],"is_corresponding":false,"raw_author_name":"Stan Matwin","raw_affiliation_strings":["1 Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada,","2 Institute for Big Data Analytics, Halifax, NS B3H 4R2, Canada,","3 Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland and"],"affiliations":[{"raw_affiliation_string":"1 Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada,","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"2 Institute for Big Data Analytics, Halifax, NS B3H 4R2, Canada,","institution_ids":[]},{"raw_affiliation_string":"3 Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland and","institution_ids":["https://openalex.org/I99542240","https://openalex.org/I4210087266"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027087230","display_name":"Marina Sokolova","orcid":"https://orcid.org/0000-0002-7719-9615"},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Marina Sokolova","raw_affiliation_strings":["2 Institute for Big Data Analytics, Halifax, NS B3H 4R2, Canada,","4 Faculty of Medicine and Faculty of Engineering, University of Ottawa, Ottawa, ON K1H 8M5, Canada"],"affiliations":[{"raw_affiliation_string":"2 Institute for Big Data Analytics, Halifax, NS B3H 4R2, Canada,","institution_ids":[]},{"raw_affiliation_string":"4 Faculty of Medicine and Faculty of Engineering, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063083987","display_name":"Robert G. Beiko","orcid":"https://orcid.org/0000-0002-5065-4980"},"institutions":[{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Robert G. Beiko","raw_affiliation_strings":["1 Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada,"],"affiliations":[{"raw_affiliation_string":"1 Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada,","institution_ids":["https://openalex.org/I129902397"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5062453139"],"corresponding_institution_ids":["https://openalex.org/I129902397"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.5657,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.90115595,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"32","issue":"9","first_page":"1380","last_page":"1387"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10887","display_name":"Bioinformatics and Genomic Networks","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9972000122070312,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/semantic-similarity","display_name":"Semantic similarity","score":0.742536187171936},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6116848587989807},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5348286628723145},{"id":"https://openalex.org/keywords/similarity-measure","display_name":"Similarity measure","score":0.4937191903591156},{"id":"https://openalex.org/keywords/cosine-similarity","display_name":"Cosine similarity","score":0.45622381567955017},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.424331396818161},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.4225623607635498},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4178951680660248},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39036282896995544},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.38924360275268555},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.36678552627563477},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33313193917274475},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24562129378318787},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.24480915069580078},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.10560327768325806}],"concepts":[{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.742536187171936},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6116848587989807},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5348286628723145},{"id":"https://openalex.org/C2776517306","wikidata":"https://www.wikidata.org/wiki/Q29017317","display_name":"Similarity measure","level":2,"score":0.4937191903591156},{"id":"https://openalex.org/C2780762811","wikidata":"https://www.wikidata.org/wiki/Q1784941","display_name":"Cosine similarity","level":3,"score":0.45622381567955017},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.424331396818161},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.4225623607635498},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4178951680660248},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39036282896995544},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.38924360275268555},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.36678552627563477},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33313193917274475},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24562129378318787},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.24480915069580078},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.10560327768325806},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv755","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv755","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/9/1380/49019250/bioinformatics_32_9_1380.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26708333","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26708333","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/9/1380","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/9/1380","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv755","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv755","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/9/1380/49019250/bioinformatics_32_9_1380.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2165548363","display_name":null,"funder_award_id":"Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G4472667909","display_name":null,"funder_award_id":"CREATE","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G5784215521","display_name":null,"funder_award_id":"Chair","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6804633385","display_name":null,"funder_award_id":"210812-151799-2001","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G919846122","display_name":null,"funder_award_id":"Chair","funder_id":"https://openalex.org/F4320320994","funder_display_name":"Canada Research Chairs"}],"funders":[{"id":"https://openalex.org/F4320320994","display_name":"Canada Research Chairs","ror":"https://ror.org/0517h6h17"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2261245081.pdf","grobid_xml":"https://content.openalex.org/works/W2261245081.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W14390591","https://openalex.org/W96703012","https://openalex.org/W166231430","https://openalex.org/W321018677","https://openalex.org/W1495712943","https://openalex.org/W1506427777","https://openalex.org/W1647729745","https://openalex.org/W1970239938","https://openalex.org/W1978073536","https://openalex.org/W1980948656","https://openalex.org/W1985213868","https://openalex.org/W1989034333","https://openalex.org/W2017936606","https://openalex.org/W2042301222","https://openalex.org/W2042330903","https://openalex.org/W2058290061","https://openalex.org/W2066846405","https://openalex.org/W2095722560","https://openalex.org/W2097795961","https://openalex.org/W2100935296","https://openalex.org/W2103017472","https://openalex.org/W2109047523","https://openalex.org/W2121343862","https://openalex.org/W2123023820","https://openalex.org/W2126225210","https://openalex.org/W2127563440","https://openalex.org/W2128049108","https://openalex.org/W2130687290","https://openalex.org/W2136480620","https://openalex.org/W2138255346","https://openalex.org/W2142120379","https://openalex.org/W2142643924","https://openalex.org/W2148853951","https://openalex.org/W2158714788","https://openalex.org/W2161062388","https://openalex.org/W2162891889","https://openalex.org/W2163118979","https://openalex.org/W2165858555","https://openalex.org/W2171690228","https://openalex.org/W2176033110","https://openalex.org/W2318028114","https://openalex.org/W2505157755","https://openalex.org/W2950225692","https://openalex.org/W2953332543","https://openalex.org/W4211054902","https://openalex.org/W6611147966","https://openalex.org/W6675339850","https://openalex.org/W6699618779"],"related_works":["https://openalex.org/W4248020907","https://openalex.org/W57923944","https://openalex.org/W1992371859","https://openalex.org/W2518415416","https://openalex.org/W3182591145","https://openalex.org/W2358805260","https://openalex.org/W1020482675","https://openalex.org/W2399932691","https://openalex.org/W2102964821","https://openalex.org/W4239349090"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":3}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}
