{"id":"https://openalex.org/W2786757148","doi":"https://doi.org/10.1093/bioinformatics/bty259","title":"Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations","display_name":"Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations","publication_year":2018,"publication_date":"2018-04-12","ids":{"openalex":"https://openalex.org/W2786757148","doi":"https://doi.org/10.1093/bioinformatics/bty259","mag":"2786757148","pmid":"https://pubmed.ncbi.nlm.nih.gov/29949999"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty259","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty259","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i52/25098468/bty259.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i52/25098468/bty259.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037662171","display_name":"Fatima Zohra Smaili","orcid":"https://orcid.org/0000-0001-6439-0659"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Fatima Zohra Smaili","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100618900","display_name":"Xin Gao","orcid":"https://orcid.org/0000-0002-7108-3574"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Xin Gao","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043808311","display_name":"Robert Hoehndorf","orcid":"https://orcid.org/0000-0001-8149-5890"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Robert Hoehndorf","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5043808311","https://openalex.org/A5100618900"],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.2793,"has_fulltext":true,"cited_by_count":131,"citation_normalized_percentile":{"value":0.96826427,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"34","issue":"13","first_page":"i52","last_page":"i60"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7197999954223633,"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":0.7197999954223633,"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":0.21250000596046448,"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":0.03970000147819519,"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":0.7675013542175293},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6768752336502075},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6667205691337585},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5947149395942688},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5484566688537598},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.49307772517204285},{"id":"https://openalex.org/keywords/joint","display_name":"Joint (building)","score":0.4799002408981323},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.47271865606307983},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.4710559546947479},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.41354331374168396},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4084751605987549},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3899478018283844},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3737887740135193}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7675013542175293},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6768752336502075},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6667205691337585},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5947149395942688},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5484566688537598},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.49307772517204285},{"id":"https://openalex.org/C18555067","wikidata":"https://www.wikidata.org/wiki/Q8375051","display_name":"Joint (building)","level":2,"score":0.4799002408981323},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47271865606307983},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.4710559546947479},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.41354331374168396},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4084751605987549},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3899478018283844},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3737887740135193},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C170154142","wikidata":"https://www.wikidata.org/wiki/Q150737","display_name":"Architectural engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","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":5,"locations":[{"id":"doi:10.1093/bioinformatics/bty259","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty259","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i52/25098468/bty259.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29949999","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29949999","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:arXiv.org:1802.00864","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1802.00864","pdf_url":"https://arxiv.org/pdf/1802.00864","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:europepmc.org:4991062","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6022543","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:repository.kaust.edu.sa:10754/627122","is_oa":false,"landing_page_url":"http://hdl.handle.net/10754/627122","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty259","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty259","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i52/25098468/bty259.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1118087459","display_name":null,"funder_award_id":"URF/1/3450-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G5123324070","display_name":null,"funder_award_id":"FCC/1/1976-06","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G5678844772","display_name":null,"funder_award_id":"FCC/1/1976\u201004","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2786757148.pdf","grobid_xml":"https://content.openalex.org/works/W2786757148.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W124940209","https://openalex.org/W192221291","https://openalex.org/W1484701502","https://openalex.org/W1529533208","https://openalex.org/W1566952502","https://openalex.org/W1614298861","https://openalex.org/W1659833910","https://openalex.org/W1821527815","https://openalex.org/W1969271108","https://openalex.org/W1974896839","https://openalex.org/W1980948656","https://openalex.org/W2015191210","https://openalex.org/W2084168100","https://openalex.org/W2103017472","https://openalex.org/W2103260426","https://openalex.org/W2113072832","https://openalex.org/W2113142309","https://openalex.org/W2125818553","https://openalex.org/W2127006085","https://openalex.org/W2127563440","https://openalex.org/W2127795553","https://openalex.org/W2130410032","https://openalex.org/W2132819807","https://openalex.org/W2136961946","https://openalex.org/W2137450588","https://openalex.org/W2139315672","https://openalex.org/W2143962926","https://openalex.org/W2145544171","https://openalex.org/W2154851992","https://openalex.org/W2156997379","https://openalex.org/W2158698691","https://openalex.org/W2187089797","https://openalex.org/W2523679382","https://openalex.org/W2537623931","https://openalex.org/W2562531153","https://openalex.org/W2588397446","https://openalex.org/W2604272474","https://openalex.org/W2606379926","https://openalex.org/W2621103247","https://openalex.org/W2767656849","https://openalex.org/W2782350151","https://openalex.org/W2912996760","https://openalex.org/W2949972983","https://openalex.org/W2950133940","https://openalex.org/W2950577311","https://openalex.org/W3104097132","https://openalex.org/W4294170691","https://openalex.org/W4300388893","https://openalex.org/W4386450904","https://openalex.org/W6654155348"],"related_works":["https://openalex.org/W2003333417","https://openalex.org/W4298130764","https://openalex.org/W2804364458","https://openalex.org/W2378862226","https://openalex.org/W118236634","https://openalex.org/W2355326633","https://openalex.org/W2132641928","https://openalex.org/W4310225030","https://openalex.org/W2090259340","https://openalex.org/W1926736923"],"abstract_inverted_index":{"Motivation:":[0],"Biological":[1],"knowledge":[2,59],"is":[3,65],"widely":[4,66],"represented":[5],"in":[6,44,82,166,186,258,262],"the":[7,14,23,37,89,143,155,164,197,251,256],"form":[8],"of":[9,34,117,125,130,153,183],"ontology-based":[10,75],"annotations:":[11],"ontologies":[12,45,264],"describe":[13],"phenomena":[15,35],"assumed":[16],"to":[17,68,94,105,113,158,210,223,253],"exist":[18],"within":[19,36],"a":[20,26,32,114],"domain,":[21],"and":[22,41,46,58,74,147,163,188,247,268],"annotations":[24,48,76,104],"associate":[25],"(kind":[27],"of)":[28],"biological":[29,72,99,245],"entity":[30],"with":[31],"set":[33],"domain.":[38],"The":[39],"structure":[40],"information":[42],"contained":[43],"their":[47,103,229],"make":[49],"them":[50],"valuable":[51],"for":[52,98,199],"developing":[53],"machine":[54,83],"learning,":[55,135],"data":[56,274],"analysis":[57],"extraction":[60],"algorithms;":[61],"notably,":[62],"semantic":[63,203],"similarity":[64,204],"used":[67,79,209],"identify":[69,211,224],"relations":[70,213],"between":[71,127,214],"entities,":[73],"are":[77,161,265,275],"frequently":[78],"as":[80,122],"features":[81],"learning":[84],"applications.":[85],"Results:":[86],"We":[87,190],"propose":[88],"Onto2Vec":[90,194,237,249],"method,":[91],"an":[92,219],"approach":[93,222],"learn":[95],"feature":[96,177,242],"vectors":[97,178,243],"entities":[100,246],"based":[101,227],"on":[102,228],"biomedical":[106],"ontologies.":[107,248],"Our":[108,233],"method":[109],"can":[110,179,207,238],"be":[111,208],"applied":[112],"wide":[115],"range":[116],"bioinformatics":[118],"research":[119],"problems":[120],"such":[121],"similarity-based":[123],"prediction":[124,182],"interactions":[126,185],"proteins,":[128,154],"classification":[129],"interaction":[131],"types":[132],"using":[133],"supervised":[134],"or":[136],"clustering.":[137],"To":[138],"evaluate":[139],"Onto2Vec,":[140],"we":[141,173,217],"use":[142,218],"gene":[144],"ontology":[145],"(GO)":[146],"jointly":[148],"produce":[149],"dense":[150],"vector":[151],"representations":[152,195],"GO":[156,167],"classes":[157],"which":[159,263],"they":[160],"annotated,":[162],"axioms":[165],"that":[168,175,206,236],"constrain":[169],"these":[170],"classes.":[171],"First,":[172],"demonstrate":[174,235],"Onto2Vec-generated":[176],"significantly":[180,254],"improve":[181],"protein-protein":[184],"human":[187],"yeast.":[189],"then":[191],"illustrate":[192],"how":[193],"provide":[196],"means":[198],"constructing":[200],"data-driven,":[201],"trainable":[202],"measures":[205],"particular":[212],"proteins.":[215],"Finally,":[216],"unsupervised":[220],"clustering":[221],"protein":[225],"families":[226],"Enzyme":[230],"Commission":[231],"numbers.":[232],"results":[234],"generate":[239],"high":[240],"quality":[241],"from":[244],"has":[250],"potential":[252],"outperform":[255],"state-of-the-art":[257],"several":[259],"predictive":[260],"applications":[261],"involved.":[266],"Availability":[267],"implementation:":[269],"https://github.com/bio-ontology-research-group/onto2vec.":[270],"Supplementary":[271,273],"information:":[272],"available":[276],"at":[277],"Bioinformatics":[278],"online.":[279]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":24},{"year":2020,"cited_by_count":19},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":6}],"updated_date":"2026-08-09T07:27:16.801131","created_date":"2025-10-10T00:00:00"}
