{"id":"https://openalex.org/W2132290594","doi":"https://doi.org/10.1145/1099554.1099658","title":"Semantic similarity over the gene ontology","display_name":"Semantic similarity over the gene ontology","publication_year":2005,"publication_date":"2005-10-31","ids":{"openalex":"https://openalex.org/W2132290594","doi":"https://doi.org/10.1145/1099554.1099658","mag":"2132290594"},"language":"en","primary_location":{"id":"doi:10.1145/1099554.1099658","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1099554.1099658","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM international conference on Information and knowledge management","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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":["Faculdade de Ci\u00eancias da Universidade de Lisboa"],"affiliations":[{"raw_affiliation_string":"Faculdade de Ci\u00eancias da Universidade de Lisboa","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043057704","display_name":"M\u00e1rio J. Silva","orcid":"https://orcid.org/0000-0002-5452-6185"},"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":false,"raw_author_name":"M\u00e1rio J. Silva","raw_affiliation_strings":["Faculdade de Ci\u00eancias da Universidade de Lisboa"],"affiliations":[{"raw_affiliation_string":"Faculdade de Ci\u00eancias da Universidade de Lisboa","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102987146","display_name":"Pedro M. Coutinho","orcid":"https://orcid.org/0000-0003-3992-0384"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210146787","display_name":"Architecture et Fonction des Macromol\u00e9cules Biologiques","ror":"https://ror.org/04jm8zw14","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I21491767","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210146787"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pedro M. Coutinho","raw_affiliation_strings":["AFMB, CNRS, Marseille","AFMB, CNRS, Marseille#TAB#"],"affiliations":[{"raw_affiliation_string":"AFMB, CNRS, Marseille","institution_ids":["https://openalex.org/I4210146787"]},{"raw_affiliation_string":"AFMB, CNRS, Marseille#TAB#","institution_ids":["https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014333753"],"corresponding_institution_ids":["https://openalex.org/I141596103"],"apc_list":null,"apc_paid":null,"fwci":2.405,"has_fulltext":false,"cited_by_count":103,"citation_normalized_percentile":{"value":0.88638956,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":null,"issue":null,"first_page":"343","last_page":"344"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9961000084877014,"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":0.9872000217437744,"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/semantic-similarity","display_name":"Semantic similarity","score":0.8396775722503662},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6913968324661255},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6030578017234802},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5387175679206848},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5176544785499573},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.4269505441188812},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.40572118759155273},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3720129132270813},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.36478573083877563},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16352158784866333},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09431597590446472}],"concepts":[{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.8396775722503662},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6913968324661255},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6030578017234802},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5387175679206848},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5176544785499573},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.4269505441188812},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40572118759155273},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3720129132270813},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.36478573083877563},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16352158784866333},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09431597590446472},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1099554.1099658","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1099554.1099658","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM international conference on Information and knowledge management","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1483118642","https://openalex.org/W1569415500","https://openalex.org/W1647729745","https://openalex.org/W1976097579","https://openalex.org/W2079665010","https://openalex.org/W2099100406","https://openalex.org/W2100935296","https://openalex.org/W2117805756","https://openalex.org/W2134226301","https://openalex.org/W6636975626"],"related_works":["https://openalex.org/W2003333417","https://openalex.org/W2378862226","https://openalex.org/W118236634","https://openalex.org/W2355326633","https://openalex.org/W2804669904","https://openalex.org/W2380654781","https://openalex.org/W2114797768","https://openalex.org/W2176214140","https://openalex.org/W2516873349","https://openalex.org/W1990601549"],"abstract_inverted_index":{"Many":[0],"bioinformatics":[1],"applications":[2],"would":[3],"benefit":[4],"from":[5,50],"comparing":[6],"proteins":[7,21,47,56],"based":[8],"on":[9],"their":[10,15,51],"biological":[11,19,59],"role":[12,60],"rather":[13,143],"than":[14,144,159],"sequence.":[16],"In":[17],"most":[18,148],"databases,":[20],"are":[22],"already":[23],"annotated":[24,52],"with":[25],"ontology":[26],"terms.":[27,54],"Previous":[28],"studies":[29],"identified":[30],"a":[31,58,65,93,106,126,154],"correlation":[32,74,95,158],"between":[33,75,96],"the":[34,38,73,85,112,115,119,131,139,147,160],"sequence":[35,88],"similarity":[36,40,45,81,133,157,163],"and":[37,77,98],"semantic":[39,44,132,162],"of":[41,46,72,84,87,118,122,134],"proteins.":[42],"The":[43],"was":[48],"computed":[49],"GO":[53,76,97],"However,":[55],"sharing":[57],"do":[61],"not":[62],"necessarily":[63],"have":[64],"similar":[66],"sequence.This":[67],"paper":[68,103],"introduces":[69,104],"our":[70],"study":[71],"family":[78,99,156],"similarity.":[79,100],"Family":[80],"overcomes":[82],"some":[83],"limitations":[86],"similarity,":[89],"thus":[90],"we":[91],"obtained":[92],"strong":[94],"Additionally,":[101],"this":[102],"GraSM,":[105],"novel":[107],"method":[108],"that":[109],"uses":[110],"all":[111],"information":[113],"in":[114],"graph":[116],"structure":[117],"GO,":[120],"instead":[121],"considering":[123],"it":[124],"as":[125],"hierarchical":[127],"tree.":[128],"When":[129],"calculating":[130],"two":[135],"concepts,":[136],"GraSM":[137,152],"selects":[138],"disjunctive":[140],"common":[141,150],"ancestors":[142],"only":[145],"using":[146],"informative":[149],"ancestor.":[151],"produced":[153],"higher":[155],"original":[161],"measures.":[164]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
