{"id":"https://openalex.org/W4393762023","doi":"https://doi.org/10.5281/zenodo.6946466","title":"Bio-ML: Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching","display_name":"Bio-ML: Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching","publication_year":2022,"publication_date":"2022-07-28","ids":{"openalex":"https://openalex.org/W4393762023","doi":"https://doi.org/10.5281/zenodo.6946466"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:6946466","is_oa":true,"landing_page_url":"https://zenodo.org/record/6946466","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"type":"dataset","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://zenodo.org/record/6946466","any_repository_has_fulltext":true},"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":"He, Yuan","raw_affiliation_strings":["University of Oxford"],"affiliations":[{"raw_affiliation_string":"University of Oxford","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":"Chen, Jiaoyan","raw_affiliation_strings":["University of Oxford"],"affiliations":[{"raw_affiliation_string":"University of Oxford","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":"Dong, Hang","raw_affiliation_strings":["University of Oxford"],"affiliations":[{"raw_affiliation_string":"University of Oxford","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"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jim\u00e9nez-Ruiz, Ernesto","raw_affiliation_strings":["City, University of London"],"affiliations":[{"raw_affiliation_string":"City, University of London","institution_ids":["https://openalex.org/I180825142"]}]},{"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":"Hadian, Ali","raw_affiliation_strings":["Samsung Research UK"],"affiliations":[{"raw_affiliation_string":"Samsung Research 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":"Horrocks, Ian","raw_affiliation_strings":["University of Oxford"],"affiliations":[{"raw_affiliation_string":"University of Oxford","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100461968"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9811000227928162,"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":0.9811000227928162,"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":0.9024999737739563,"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/equivalence","display_name":"Equivalence (formal languages)","score":0.7037731409072876},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.662065863609314},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6579533815383911},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5895460247993469},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48167407512664795},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.4340248107910156},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3775229752063751},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34420961141586304},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1967809796333313},{"id":"https://openalex.org/keywords/process-ontology","display_name":"Process ontology","score":0.15689459443092346},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.09007391333580017},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.08182746171951294},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.0780055820941925},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.047382503747940063}],"concepts":[{"id":"https://openalex.org/C2780069185","wikidata":"https://www.wikidata.org/wiki/Q7977945","display_name":"Equivalence (formal languages)","level":2,"score":0.7037731409072876},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.662065863609314},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6579533815383911},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5895460247993469},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48167407512664795},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.4340248107910156},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3775229752063751},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34420961141586304},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1967809796333313},{"id":"https://openalex.org/C137003198","wikidata":"https://www.wikidata.org/wiki/Q7247296","display_name":"Process ontology","level":3,"score":0.15689459443092346},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.09007391333580017},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.08182746171951294},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0780055820941925},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.047382503747940063},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:6946466","is_oa":true,"landing_page_url":"https://zenodo.org/record/6946466","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},{"id":"doi:10.5281/zenodo.6946466","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.6946466","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"dataset"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:6946466","is_oa":true,"landing_page_url":"https://zenodo.org/record/6946466","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2142963442","https://openalex.org/W274732444","https://openalex.org/W149627178","https://openalex.org/W2386232412","https://openalex.org/W2793451634","https://openalex.org/W4206428734","https://openalex.org/W152870918","https://openalex.org/W2394920388","https://openalex.org/W2223008607","https://openalex.org/W2391790737"],"abstract_inverted_index":{"<strong>NOTE</strong>:":[0],"This":[1],"version":[2,15],"is":[3,30,101],"used":[4],"in":[5,215],"the":[6,10,17,112,116,122,182,202,210,216],"Bio-ML":[7,184],"track":[8,185],"of":[9,27],"<strong>OAEI":[11],"2022</strong>;":[12],"a":[13],"new":[14],"for":[16,118,124,133,229,232],"OAEI":[18,183],"2023":[19],"will":[20],"be":[21],"available":[22],"soon.":[23],"<strong>About</strong>":[24],"The":[25],"purpose":[26],"these":[28],"datasets":[29],"to":[31,111,238],"support":[32],"<em>equivalence</em>":[33],"and":[34,46,108,121,135,141,144,147,150,153,199],"<em>subsumption</em>":[35],"ontology":[36,41],"matching.":[37,126],"There":[38],"are":[39,219,236],"five":[40],"pairs":[42],"extracted":[43],"from":[44],"MONDO":[45],"UMLS:":[47],"<strong>Source</strong>":[48],"<strong>Task</strong>":[49],"<strong>Category</strong>":[50],"<strong>#SrcCls</strong>":[51],"<strong>#TgtCls</strong>":[52],"<strong>#TgtCls":[53],"(subs)</strong>":[54,58],"<strong>#Ref":[55,57],"(equiv)</strong>":[56],"Mondo":[59,67],"OMIM-ORDO":[60],"Disease":[61,69],"9,642":[62],"8,838":[63],"8,735":[64],"3,721":[65],"103":[66],"NCIT-DOID":[68],"6,835":[70],"8,448":[71],"5,113":[72],"4,686":[73],"3,339":[74],"UMLS":[75,83,91],"SNOMED-FMA":[76],"Body":[77],"24,182":[78],"64,726":[79],"59,567":[80],"7,256":[81],"5,506":[82],"SNOMED-NCIT":[84,92],"Pharm":[85],"16,045":[86],"15,250":[87],"12,462":[88],"5,803":[89],"4,225":[90],"Neoplas":[93],"11,271":[94],"13,956":[95],"13,790":[96],"3,804":[97],"213":[98],"Each":[99],"pair":[100],"associated":[102],"with":[103],"three":[104],"folders:":[105],"\"raw_data\",":[106],"\"equiv_match\",":[107],"\"subs_match\",":[109],"corresponding":[110],"downloaded":[113],"source":[114],"ontologies,":[115],"package":[117,123],"equivalence":[119],"matching,":[120],"subsumption":[125],"<strong>Citation</strong>":[127],"<pre><code>@inproceedings{he2022machine,":[128],"title={Machine":[129],"Learning-Friendly":[130],"Biomedical":[131],"Datasets":[132],"Equivalence":[134],"Subsumption":[136],"Ontology":[137],"Matching},":[138],"author={He,":[139],"Yuan":[140],"Chen,":[142],"Jiaoyan":[143],"Dong,":[145],"Hang":[146],"Jim{\\'e}nez-Ruiz,":[148],"Ernesto":[149],"Hadian,":[151],"Ali":[152],"Horrocks,":[154],"Ian},":[155],"booktitle={The":[156],"Semantic":[157,162],"Web--ISWC":[158],"2022:":[159],"21st":[160],"International":[161],"Web":[163],"Conference,":[164],"Virtual":[165],"Event,":[166],"October":[167],"23--27,":[168],"2022,":[169],"Proceedings},":[170],"pages={575--591},":[171],"year={2022},":[172],"organization={Springer}":[173],"}</code></pre>":[174],"<strong>Links</strong>":[175],"See":[176,181,188],"detailed":[177],"instructions":[178],"at:":[179,186],"https://krr-oxford.github.io/DeepOnto/bio-ml.":[180],"https://www.cs.ox.ac.uk/isg/projects/ConCur/oaei/":[187],"our":[189],"resource":[190,204],"paper":[191,205],"at":[192],"arxiv":[193],"or":[194],"springer":[195],"(accepted":[196],"by":[197],"<em>ISWC-2022</em>":[198],"nominated":[200],"as":[201],"<em>best":[203],"candidate</em>).":[206],"<strong>Changelog</strong>":[207],"Update":[208],"against":[209],"previous":[211],"versions:":[212],"Class":[213],"entities":[214],"mapping":[217],"files":[218],"now":[220],"represented":[221],"using":[222],"their":[223],"full":[224],"IRIs":[225],"(against":[226],"v2).":[227],"Files":[228],"candidate":[230],"mappings":[231],"local":[233],"ranking":[234],"evaluation":[235],"simplified":[237],"just":[239],"one":[240],"<strong>.tsv</strong>":[241],"file.":[242]},"counts_by_year":[],"updated_date":"2026-02-05T00:54:17.221276","created_date":"2025-10-10T00:00:00"}
