{"id":"https://openalex.org/W2798361766","doi":"https://doi.org/10.1093/bioinformatics/bty933","title":"OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction","display_name":"OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction","publication_year":2018,"publication_date":"2018-11-07","ids":{"openalex":"https://openalex.org/W2798361766","doi":"https://doi.org/10.1093/bioinformatics/bty933","mag":"2798361766","pmid":"https://pubmed.ncbi.nlm.nih.gov/30407490"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty933","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty933","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/12/2133/48935045/bioinformatics_35_12_2133.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":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/12/2133/48935045/bioinformatics_35_12_2133.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 & Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, 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 & Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, 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 & Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, 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 & Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, 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 & Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0001-8149-5890","affiliations":[{"raw_affiliation_string":"Computer, Electrical & Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, 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":null,"fwci":0.4949,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.61107474,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"12","first_page":"2133","last_page":"2140"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9301000237464905,"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":0.9301000237464905,"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":0.061000000685453415,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.003000000026077032,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/ontology","display_name":"Ontology","score":0.7717316150665283},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6932708024978638},{"id":"https://openalex.org/keywords/axiom","display_name":"Axiom","score":0.6538593769073486},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6381392478942871},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6057158708572388},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.5536240935325623},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.5422109365463257},{"id":"https://openalex.org/keywords/formal-ontology","display_name":"Formal ontology","score":0.5350208282470703},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5284504890441895},{"id":"https://openalex.org/keywords/semantic-similarity","display_name":"Semantic similarity","score":0.5225445628166199},{"id":"https://openalex.org/keywords/word2vec","display_name":"Word2vec","score":0.4920622706413269},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.4898540675640106},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.4575466513633728},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.43432819843292236},{"id":"https://openalex.org/keywords/ontology-components","display_name":"Ontology components","score":0.4293109178543091},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.42908942699432373},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3617691695690155},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3234187364578247},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.2605239450931549},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12746739387512207}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7717316150665283},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6932708024978638},{"id":"https://openalex.org/C167729594","wikidata":"https://www.wikidata.org/wiki/Q17736","display_name":"Axiom","level":2,"score":0.6538593769073486},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6381392478942871},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6057158708572388},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.5536240935325623},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.5422109365463257},{"id":"https://openalex.org/C2778177438","wikidata":"https://www.wikidata.org/wiki/Q1437388","display_name":"Formal ontology","level":4,"score":0.5350208282470703},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5284504890441895},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.5225445628166199},{"id":"https://openalex.org/C2776461190","wikidata":"https://www.wikidata.org/wiki/Q22673982","display_name":"Word2vec","level":3,"score":0.4920622706413269},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4898540675640106},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.4575466513633728},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.43432819843292236},{"id":"https://openalex.org/C154210476","wikidata":"https://www.wikidata.org/wiki/Q7095057","display_name":"Ontology components","level":5,"score":0.4293109178543091},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.42908942699432373},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3617691695690155},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3234187364578247},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.2605239450931549},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12746739387512207},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","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/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"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":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","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":6,"locations":[{"id":"doi:10.1093/bioinformatics/bty933","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty933","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/12/2133/48935045/bioinformatics_35_12_2133.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:30407490","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30407490","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:1804.10922","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1804.10922","pdf_url":"https://arxiv.org/pdf/1804.10922","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":"mag:2798361766","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1804.10922","pdf_url":null,"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":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:repository.kaust.edu.sa:10754/629859","is_oa":false,"landing_page_url":"http://hdl.handle.net/10754/629859","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"},{"id":"doi:10.48550/arxiv.1804.10922","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1804.10922","pdf_url":null,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty933","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty933","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/12/2133/48935045/bioinformatics_35_12_2133.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/G1052733046","display_name":null,"funder_award_id":"URF/1/3007\u201001","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"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/G1632090538","display_name":null,"funder_award_id":"URF/1/2602\u201301","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G373881210","display_name":null,"funder_award_id":"URF/1/3412\u201001","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/W2798361766.pdf","grobid_xml":"https://content.openalex.org/works/W2798361766.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W55962619","https://openalex.org/W1482169241","https://openalex.org/W1529533208","https://openalex.org/W1555563750","https://openalex.org/W1601038846","https://openalex.org/W1659833910","https://openalex.org/W1678959094","https://openalex.org/W1974896839","https://openalex.org/W1983766967","https://openalex.org/W1989521494","https://openalex.org/W2012361142","https://openalex.org/W2084168100","https://openalex.org/W2093601562","https://openalex.org/W2098440497","https://openalex.org/W2103017472","https://openalex.org/W2113142309","https://openalex.org/W2117243134","https://openalex.org/W2123457740","https://openalex.org/W2124045889","https://openalex.org/W2124991490","https://openalex.org/W2125818553","https://openalex.org/W2131421168","https://openalex.org/W2132819807","https://openalex.org/W2133109597","https://openalex.org/W2136265964","https://openalex.org/W2136410628","https://openalex.org/W2136437513","https://openalex.org/W2139315672","https://openalex.org/W2140581050","https://openalex.org/W2144086069","https://openalex.org/W2146495783","https://openalex.org/W2149907293","https://openalex.org/W2152850487","https://openalex.org/W2155015104","https://openalex.org/W2155463318","https://openalex.org/W2158191506","https://openalex.org/W2159092541","https://openalex.org/W2170659225","https://openalex.org/W2329205227","https://openalex.org/W2398931073","https://openalex.org/W2534712034","https://openalex.org/W2537623931","https://openalex.org/W2557385283","https://openalex.org/W2559482520","https://openalex.org/W2562531153","https://openalex.org/W2605099106","https://openalex.org/W2615066396","https://openalex.org/W2624297474","https://openalex.org/W2695731692","https://openalex.org/W2705861159","https://openalex.org/W2770044072","https://openalex.org/W2779933443","https://openalex.org/W2782350151","https://openalex.org/W2786757148","https://openalex.org/W2799259690","https://openalex.org/W2950577311","https://openalex.org/W2951798058","https://openalex.org/W3099272318","https://openalex.org/W4300388893","https://openalex.org/W6683186658","https://openalex.org/W6739425016"],"related_works":["https://openalex.org/W3020814054","https://openalex.org/W2782350151","https://openalex.org/W3126162820","https://openalex.org/W2795007297","https://openalex.org/W2999954485","https://openalex.org/W1995642679","https://openalex.org/W2766608798","https://openalex.org/W2588397446","https://openalex.org/W1489291989","https://openalex.org/W2112036454","https://openalex.org/W593607171","https://openalex.org/W1996989641","https://openalex.org/W3153362321","https://openalex.org/W2149911752","https://openalex.org/W2038408384","https://openalex.org/W2771285622","https://openalex.org/W73228523","https://openalex.org/W3090253812","https://openalex.org/W2964167913","https://openalex.org/W2013483673"],"abstract_inverted_index":{"MOTIVATION:":[0],"Ontologies":[1],"are":[2,61,251],"widely":[3],"used":[4,41,228],"in":[5,22,42,87,131,144],"biology":[6],"for":[7,202,218],"data":[8,250],"annotation,":[9],"integration":[10],"and":[11,94,175,181,222],"analysis.":[12],"In":[13],"addition":[14],"to":[15,80,119,148,186,214,229],"formally":[16],"structured":[17],"axioms,":[18],"ontologies":[19,43,88],"contain":[20],"meta-data":[21,60],"the":[23,58,98,138,183],"form":[24],"of":[25,32,55,84,142,173,233,240],"annotation":[26,95],"axioms":[27,39,93,96],"which":[28],"provide":[29],"valuable":[30],"pieces":[31],"information":[33],"that":[34,106,196],"characterize":[35],"ontology":[36,59,92,99],"classes.":[37],"Annotation":[38],"commonly":[40],"include":[44],"class":[45],"labels,":[46],"descriptions":[47],"or":[48,114,116],"synonyms.":[49],"Despite":[50],"being":[51],"a":[52,76,103,112,145,178],"rich":[53],"source":[54],"semantic":[56,70],"information,":[57],"generally":[62],"unexploited":[63],"by":[64,89,169],"ontology-based":[65],"analysis":[66],"methods":[67,201],"such":[68],"as":[69],"similarity":[71,146,168],"measures.":[72],"RESULTS:":[73],"We":[74,101,127,194],"propose":[75],"novel":[77],"method,":[78],"OPA2Vec,":[79],"generate":[81],"vector":[82,140,171,231],"representations":[83,141,172,232],"biological":[85],"entities":[86],"combining":[90],"formal":[91],"from":[97,123,208],"meta-data.":[100],"apply":[102,212],"Word2Vec":[104],"model":[105,192],"has":[107],"been":[108],"pre-trained":[109],"on":[110,152,161,166],"either":[111],"corpus":[113],"abstracts":[115],"full-text":[117],"articles":[118],"produce":[120,230],"feature":[121],"vectors":[122,185],"our":[124,129,159],"collected":[125],"data.":[126],"validate":[128],"method":[130,160],"two":[132,153],"different":[133,154],"ways:":[134],"first,":[135],"we":[136,157,211],"use":[137],"obtained":[139,184],"proteins":[143],"measure":[147],"predict":[149,187],"protein-protein":[150],"interaction":[151],"datasets.":[155],"Second,":[156],"evaluate":[158],"predicting":[162,203],"gene-disease":[163,188,204],"associations":[164,189],"based":[165],"phenotype":[167,179],"generating":[170],"genes":[174,217],"diseases":[176],"using":[177,190],"ontology,":[180],"applying":[182],"mouse":[191,209],"phenotypes.":[193],"demonstrate":[195],"OPA2Vec":[197,213,225],"significantly":[198],"outperforms":[199],"existing":[200],"associations.":[205],"Using":[206],"evidence":[207],"models,":[210],"identify":[215],"candidate":[216],"several":[219],"thousand":[220],"rare":[221],"orphan":[223],"diseases.":[224],"can":[226],"be":[227],"any":[234,238],"biomedical":[235,241],"entity":[236],"given":[237],"type":[239],"ontology.":[242],"AVAILABILITY":[243],"AND":[244],"IMPLEMENTATION:":[245],"https://github.com/bio-ontology-research-group/opa2vec.":[246],"SUPPLEMENTARY":[247],"INFORMATION:":[248],"Supplementary":[249],"available":[252],"at":[253],"Bioinformatics":[254],"online.":[255]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}
