{"id":"https://openalex.org/W4280604898","doi":"https://doi.org/10.1007/978-3-031-19433-7_33","title":"Machine Learning-Friendly Biomedical Datasets for\u00a0Equivalence and\u00a0Subsumption Ontology Matching","display_name":"Machine Learning-Friendly Biomedical Datasets for\u00a0Equivalence and\u00a0Subsumption Ontology Matching","publication_year":2022,"publication_date":"2022-01-01","ids":{"openalex":"https://openalex.org/W4280604898","doi":"https://doi.org/10.1007/978-3-031-19433-7_33"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-031-19433-7_33","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-19433-7_33","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1007/978-3-031-19433-7_33","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100461968","display_name":"Yuan He","orcid":"https://orcid.org/0000-0002-4486-1262"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Yuan He","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Oxford, UK"],"raw_orcid":"https://orcid.org/0000-0002-4486-1262","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085691361","display_name":"Jiaoyan Chen","orcid":"https://orcid.org/0000-0003-4643-6750"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jiaoyan Chen","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Oxford, UK"],"raw_orcid":"https://orcid.org/0000-0003-4643-6750","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035163413","display_name":"Hang Dong","orcid":"https://orcid.org/0000-0001-6828-6891"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Hang Dong","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Oxford, UK"],"raw_orcid":"https://orcid.org/0000-0001-6828-6891","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056324053","display_name":"Ernesto Jim\u00e9nez-Ruiz","orcid":"https://orcid.org/0000-0002-9083-4599"},"institutions":[{"id":"https://openalex.org/I180825142","display_name":"City, University of London","ror":"https://ror.org/04489at23","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I180825142"]},{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["GB","NO"],"is_corresponding":false,"raw_author_name":"Ernesto Jim\u00e9nez-Ruiz","raw_affiliation_strings":["City, University of London, London, UK","University of Oslo, Oslo, Norway"],"raw_orcid":"https://orcid.org/0000-0002-9083-4599","affiliations":[{"raw_affiliation_string":"City, University of London, London, UK","institution_ids":["https://openalex.org/I180825142"]},{"raw_affiliation_string":"University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022807561","display_name":"Ali Hadian","orcid":"https://orcid.org/0000-0003-2010-0765"},"institutions":[{"id":"https://openalex.org/I4210117523","display_name":"Samsung (United Kingdom)","ror":"https://ror.org/01w6gjq94","country_code":"GB","type":"company","lineage":["https://openalex.org/I2250650973","https://openalex.org/I4210117523"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ali Hadian","raw_affiliation_strings":["Samsung Research, Staines, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Samsung Research, Staines, UK","institution_ids":["https://openalex.org/I4210117523"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060350556","display_name":"Ian Horrocks","orcid":"https://orcid.org/0000-0002-2685-7462"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ian Horrocks","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Oxford, UK"],"raw_orcid":"https://orcid.org/0000-0002-2685-7462","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100461968"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":{"value":5000,"currency":"EUR","value_usd":5392},"fwci":null,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"575","last_page":"591"},"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":0.9980000257492065,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9786999821662903,"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":0.8625919222831726},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.7859055995941162},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5946047902107239},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5850487947463989},{"id":"https://openalex.org/keywords/equivalence","display_name":"Equivalence (formal languages)","score":0.5645784139633179},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.4885443150997162},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4540258049964905},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32270190119743347},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.3219650685787201},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.2314840853214264}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8625919222831726},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.7859055995941162},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5946047902107239},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5850487947463989},{"id":"https://openalex.org/C2780069185","wikidata":"https://www.wikidata.org/wiki/Q7977945","display_name":"Equivalence (formal languages)","level":2,"score":0.5645784139633179},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4885443150997162},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4540258049964905},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32270190119743347},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.3219650685787201},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.2314840853214264},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","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/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}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1007/978-3-031-19433-7_33","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-19433-7_33","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmh:oai:openaccess.city.ac.uk:28706","is_oa":false,"landing_page_url":"https://openaccess.city.ac.uk/view/creators_id/ernesto=2Ejimenez-ruiz.html>","pdf_url":null,"source":{"id":"https://openalex.org/S4306401940","display_name":"City Research Online (City University London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I180825142","host_organization_name":"City, University of London","host_organization_lineage":["https://openalex.org/I180825142"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Conference or Workshop Item"},{"id":"pmh:oai:www.duo.uio.no:10852/97769","is_oa":false,"landing_page_url":"http://hdl.handle.net/10852/97769","pdf_url":null,"source":{"id":"https://openalex.org/S4306401717","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"0302-9743","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1007/978-3-031-19433-7_33","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-19433-7_33","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7097328358","display_name":null,"funder_award_id":"EP/S019111/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7513764588","display_name":null,"funder_award_id":"EP/V050869/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W102861580","https://openalex.org/W2013093146","https://openalex.org/W2087779040","https://openalex.org/W2118100588","https://openalex.org/W2141985222","https://openalex.org/W2148014577","https://openalex.org/W2159583324","https://openalex.org/W2162151166","https://openalex.org/W2184957013","https://openalex.org/W2336088163","https://openalex.org/W2404369708","https://openalex.org/W2774466664","https://openalex.org/W2803524328","https://openalex.org/W2899915536","https://openalex.org/W2963716420","https://openalex.org/W2984102990","https://openalex.org/W2988630324","https://openalex.org/W3101571553","https://openalex.org/W3120491054","https://openalex.org/W3136802089","https://openalex.org/W3153694186","https://openalex.org/W3166265964","https://openalex.org/W3211159667","https://openalex.org/W4212919921","https://openalex.org/W4283819412","https://openalex.org/W4367670019"],"related_works":["https://openalex.org/W2127299687","https://openalex.org/W2386232412","https://openalex.org/W274732444","https://openalex.org/W149627178","https://openalex.org/W22148886","https://openalex.org/W4206428734","https://openalex.org/W152870918","https://openalex.org/W1794266373","https://openalex.org/W2365397974","https://openalex.org/W2357882026"],"abstract_inverted_index":{"Ontology":[0,35,170],"Matching":[1,171],"(OM)":[2],"plays":[3],"an":[4,41],"important":[5],"role":[6],"in":[7],"many":[8],"domains":[9],"such":[10],"as":[11,158],"bioinformatics":[12],"and":[13,17,66,91,98,114,131],"the":[14,26,34,45,70,101,147,161],"Semantic":[15],"Web,":[16],"its":[18],"research":[19],"is":[20,106,119],"becoming":[21],"increasingly":[22],"popular,":[23],"especially":[24],"with":[25],"application":[27],"of":[28,48,60,72,103,142,149,153,160],"machine":[29],"learning":[30],"(ML)":[31],"techniques.":[32],"Although":[33],"Alignment":[36],"Evaluation":[37],"Initiative":[38],"(OAEI)":[39],"represents":[40],"impressive":[42],"effort":[43],"for":[44,69,128,139],"systematic":[46],"evaluation":[47,59,71,117,137],"OM":[49,84,123,133,140],"systems,":[50],"it":[51],"still":[52],"suffers":[53],"from":[54,89,125],"several":[55],"limitations":[56],"including":[57],"limited":[58,67],"subsumption":[61,99],"mappings,":[62,65],"suboptimal":[63],"reference":[64,104],"support":[68],"ML-based":[73,130],"systems.":[74,134],"To":[75],"tackle":[76],"these":[77,150],"limitations,":[78],"we":[79],"introduce":[80],"five":[81],"new":[82,162],"biomedical":[83],"tasks":[85],"involving":[86],"ontologies":[87],"extracted":[88],"Mondo":[90],"UMLS.":[92],"Each":[93],"task":[94],"includes":[95],"both":[96,129],"equivalence":[97],"matching;":[100],"quality":[102],"mappings":[105],"ensured":[107],"by":[108],"human":[109],"curation,":[110],"ontology":[111],"pruning,":[112],"etc.;":[113],"a":[115],"comprehensive":[116],"framework":[118],"proposed":[120],"to":[121,145],"measure":[122],"performance":[124],"various":[126],"perspectives":[127],"non-ML-based":[132],"We":[135],"report":[136],"results":[138],"systems":[141],"different":[143],"types":[144],"demonstrate":[146],"usage":[148],"resources,":[151],"all":[152],"which":[154],"are":[155],"publicly":[156],"available":[157],"part":[159],"Bio-ML":[163],"track":[164],"at":[165],"OAEI":[166,182],"2022.":[167],"Resource":[168],"type:":[169],"Dataset":[172],"License:":[173],"CC":[174],"BY":[175],"4.0":[176],"International":[177],"DOI:":[178],"https://doi.org/10.5281/zenodo.6510086":[179],"Documentation:":[180],"https://krr-oxford.github.io/DeepOnto/#/om_resources":[181],"track:":[183],"https://www.cs.ox.ac.uk/isg/projects/ConCur/oaei/":[184]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":7}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
