{"id":"https://openalex.org/W4401821897","doi":"https://doi.org/10.3233/shti240526","title":"Merging Biomedical Ontologies with BioSTransformers","display_name":"Merging Biomedical Ontologies with BioSTransformers","publication_year":2024,"publication_date":"2024-08-22","ids":{"openalex":"https://openalex.org/W4401821897","doi":"https://doi.org/10.3233/shti240526","pmid":"https://pubmed.ncbi.nlm.nih.gov/39176907"},"language":"en","primary_location":{"id":"doi:10.3233/shti240526","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti240526","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI240526","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI240526","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092761739","display_name":"Safaa Menad","orcid":"https://orcid.org/0009-0009-2204-7786"},"institutions":[{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4210108118","display_name":"Laboratoire d'Informatique, du Traitement de l'Information et des Syst\u00e8mes","ror":"https://ror.org/01f1vfy95","country_code":"FR","type":"facility","lineage":["https://openalex.org/I141576021","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210108118","https://openalex.org/I62396329","https://openalex.org/I88814501"]},{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Safaa Menad","raw_affiliation_strings":["Univ Rouen Normandie, Normandie Univ, LITIS UR 4108 F-76000 Rouen, France"],"raw_orcid":"https://orcid.org/0009-0009-2204-7786","affiliations":[{"raw_affiliation_string":"Univ Rouen Normandie, Normandie Univ, LITIS UR 4108 F-76000 Rouen, France","institution_ids":["https://openalex.org/I62396329","https://openalex.org/I4210108118","https://openalex.org/I4210105918"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066934424","display_name":"Sa\u00efd Abdedda\u00efm","orcid":"https://orcid.org/0000-0002-7521-7955"},"institutions":[{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4210108118","display_name":"Laboratoire d'Informatique, du Traitement de l'Information et des Syst\u00e8mes","ror":"https://ror.org/01f1vfy95","country_code":"FR","type":"facility","lineage":["https://openalex.org/I141576021","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210108118","https://openalex.org/I62396329","https://openalex.org/I88814501"]},{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sa\u00efd Abdedda\u00efm","raw_affiliation_strings":["Univ Rouen Normandie, Normandie Univ, LITIS UR 4108 F-76000 Rouen, France"],"raw_orcid":"https://orcid.org/0000-0002-7521-7955","affiliations":[{"raw_affiliation_string":"Univ Rouen Normandie, Normandie Univ, LITIS UR 4108 F-76000 Rouen, France","institution_ids":["https://openalex.org/I62396329","https://openalex.org/I4210108118","https://openalex.org/I4210105918"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047697321","display_name":"Lina F. Soualmia","orcid":"https://orcid.org/0000-0001-7668-2819"},"institutions":[{"id":"https://openalex.org/I4210105918","display_name":"Normandie Universit\u00e9","ror":"https://ror.org/01k40cz91","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918"]},{"id":"https://openalex.org/I4210108118","display_name":"Laboratoire d'Informatique, du Traitement de l'Information et des Syst\u00e8mes","ror":"https://ror.org/01f1vfy95","country_code":"FR","type":"facility","lineage":["https://openalex.org/I141576021","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210105918","https://openalex.org/I4210108118","https://openalex.org/I62396329","https://openalex.org/I88814501"]},{"id":"https://openalex.org/I62396329","display_name":"Universit\u00e9 de Rouen Normandie","ror":"https://ror.org/03nhjew95","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210105918","https://openalex.org/I62396329"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Lina F. Soualmia","raw_affiliation_strings":["Univ Rouen Normandie, Normandie Univ, LITIS UR 4108 F-76000 Rouen, France"],"raw_orcid":"https://orcid.org/0000-0001-7668-2819","affiliations":[{"raw_affiliation_string":"Univ Rouen Normandie, Normandie Univ, LITIS UR 4108 F-76000 Rouen, France","institution_ids":["https://openalex.org/I62396329","https://openalex.org/I4210108118","https://openalex.org/I4210105918"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5092761739"],"corresponding_institution_ids":["https://openalex.org/I4210105918","https://openalex.org/I4210108118","https://openalex.org/I62396329"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.31361874,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"316","issue":null,"first_page":"771","last_page":"775"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8021073341369629},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6518882513046265},{"id":"https://openalex.org/keywords/unified-medical-language-system","display_name":"Unified Medical Language System","score":0.642046332359314},{"id":"https://openalex.org/keywords/structuring","display_name":"Structuring","score":0.636755108833313},{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.5745134353637695},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.5209149718284607},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4951306879520416},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.46047866344451904},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.44427186250686646},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.44182777404785156},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.41591113805770874},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.41582220792770386},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32734063267707825},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.2780297100543976},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.21656540036201477},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.15748831629753113}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8021073341369629},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6518882513046265},{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.642046332359314},{"id":"https://openalex.org/C2775945657","wikidata":"https://www.wikidata.org/wiki/Q381442","display_name":"Structuring","level":2,"score":0.636755108833313},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.5745134353637695},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.5209149718284607},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4951306879520416},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.46047866344451904},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.44427186250686646},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.44182777404785156},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.41591113805770874},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.41582220792770386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32734063267707825},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.2780297100543976},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.21656540036201477},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.15748831629753113},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","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},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"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/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"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":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","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},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.3233/shti240526","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti240526","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI240526","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},{"id":"pmid:39176907","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39176907","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":"Studies in health technology and informatics","raw_type":null}],"best_oa_location":{"id":"doi:10.3233/shti240526","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti240526","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI240526","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4401821897.pdf"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1592629787","https://openalex.org/W1791148566","https://openalex.org/W2159092541","https://openalex.org/W2168091868","https://openalex.org/W2193153316","https://openalex.org/W2803524328","https://openalex.org/W2970641574","https://openalex.org/W3123800493","https://openalex.org/W4387942588","https://openalex.org/W4388860692"],"related_works":["https://openalex.org/W2064177607","https://openalex.org/W2127299687","https://openalex.org/W1801798365","https://openalex.org/W1506177826","https://openalex.org/W2532736362","https://openalex.org/W2157272674","https://openalex.org/W2726617685","https://openalex.org/W2103987857","https://openalex.org/W2914601452","https://openalex.org/W1562796463"],"abstract_inverted_index":{"Ontologies":[0,54],"play":[1],"a":[2,70,115],"key":[3],"role":[4],"in":[5,65,123],"representing":[6],"and":[7,27,40,59,77,91,104,130,140],"structuring":[8],"domain":[9],"knowledge.":[10],"In":[11,42],"the":[12,15,37,47,61,66,85,110,127,131,137,141],"biomedical":[13,94],"domain,":[14,68],"need":[16],"for":[17,24,52,150],"this":[18,43],"type":[19],"of":[20],"representation":[21],"is":[22],"crucial":[23],"structuring,":[25],"coding,":[26],"retrieving":[28],"data.":[29],"However,":[30],"available":[31],"ontologies":[32,64],"do":[33],"not":[34],"encompass":[35],"all":[36],"relevant":[38,63,100],"concepts":[39,103],"relationships.":[41],"paper,":[44],"we":[45,89,134],"propose":[46,81],"framework":[48],"SiMHOMer":[49],"(Siamese":[50],"Models":[51],"Health":[53],"Merging)":[55],"to":[56,82,97,105,113],"semantically":[57],"merge":[58],"integrate":[60],"most":[62],"healthcare":[67],"with":[69],"first":[71,145],"focus":[72],"on":[73,84,93,136],"diseases,":[74],"symptoms,":[75],"drugs,":[76],"adverse":[78],"events.":[79],"We":[80],"rely":[83],"siamese":[86],"neural":[87],"models":[88],"developed":[90],"trained":[92],"data,":[95],"BioSTransformers,":[96],"identify":[98],"new":[99,107,116,132],"relations":[101],"between":[102],"create":[106],"semantic":[108],"relations,":[109,133],"objective":[111],"being":[112],"build":[114],"merging":[117],"ontology":[118],"that":[119],"could":[120],"be":[121],"used":[122],"applications.":[124],"To":[125],"validate":[126],"proposed":[128],"approach":[129],"relied":[135],"UMLS":[138],"Metathesaurus":[139],"Semantic":[142],"Network.":[143],"Our":[144],"results":[146],"show":[147],"promising":[148],"improvements":[149],"future":[151],"research.":[152]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
