{"id":"https://openalex.org/W4409356347","doi":"https://doi.org/10.1109/tkde.2025.3559023","title":"Ontology Embedding: A Survey of Methods, Applications and Resources","display_name":"Ontology Embedding: A Survey of Methods, Applications and Resources","publication_year":2025,"publication_date":"2025-04-11","ids":{"openalex":"https://openalex.org/W4409356347","doi":"https://doi.org/10.1109/tkde.2025.3559023"},"language":"en","primary_location":{"id":"doi:10.1109/tkde.2025.3559023","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tkde.2025.3559023","pdf_url":null,"source":{"id":"https://openalex.org/S30698027","display_name":"IEEE Transactions on Knowledge and Data Engineering","issn_l":"1041-4347","issn":["1041-4347","1558-2191","2326-3865"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320439","host_organization_name":"IEEE Computer Society","host_organization_lineage":["https://openalex.org/P4310320439","https://openalex.org/P4310319808"],"host_organization_lineage_names":["IEEE Computer Society","Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Knowledge and Data Engineering","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://research.manchester.ac.uk/en/publications/d4162497-795c-492d-93ff-6f5d84a5c4f7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085691361","display_name":"Jiaoyan Chen","orcid":"https://orcid.org/0000-0003-4643-6750"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"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":"Jiaoyan Chen","raw_affiliation_strings":["University of Manchester, Manchester, U.K","University of Manchester &amp; University of Oxford in the UK, U.K"],"raw_orcid":"https://orcid.org/0000-0003-4643-6750","affiliations":[{"raw_affiliation_string":"University of Manchester, Manchester, U.K","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"University of Manchester &amp; University of Oxford in the UK, U.K","institution_ids":["https://openalex.org/I28407311","https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5097357685","display_name":"Olga Mashkova","orcid":null},"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":"Olga Mashkova","raw_affiliation_strings":["King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","King Abdullah University of Science and Technology, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0002-4916-1660","affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046892245","display_name":"Fernando Zhapa-Camacho","orcid":"https://orcid.org/0000-0002-0710-2259"},"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":"Fernando Zhapa-Camacho","raw_affiliation_strings":["King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","King Abdullah University of Science and Technology, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0002-0710-2259","affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","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":false,"raw_author_name":"Robert Hoehndorf","raw_affiliation_strings":["King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","King Abdullah University of Science and Technology, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0001-8149-5890","affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","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":false,"raw_author_name":"Yuan He","raw_affiliation_strings":["University of Oxford, Oxford, U.K","University of Oxford in the UK, U.K"],"raw_orcid":"https://orcid.org/0000-0002-4486-1262","affiliations":[{"raw_affiliation_string":"University of Oxford, Oxford, U.K","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"University of Oxford in the UK, U.K","institution_ids":["https://openalex.org/I40120149"]}]},{"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":["University of Oxford, Oxford, U.K","University of Oxford in the UK, U.K"],"raw_orcid":"https://orcid.org/0000-0002-2685-7462","affiliations":[{"raw_affiliation_string":"University of Oxford, Oxford, U.K","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"University of Oxford in the UK, U.K","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5085691361"],"corresponding_institution_ids":["https://openalex.org/I28407311","https://openalex.org/I40120149"],"apc_list":null,"apc_paid":null,"fwci":32.5988,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.99612692,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"37","issue":"7","first_page":"4193","last_page":"4212"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9721999764442444,"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"}},"topics":[{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9721999764442444,"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":0.8269058465957642},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7196394205093384},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5389237403869629},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.45930254459381104},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.42113399505615234},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.39052918553352356},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.349476158618927},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1684936285018921}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8269058465957642},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7196394205093384},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5389237403869629},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.45930254459381104},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.42113399505615234},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.39052918553352356},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.349476158618927},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1684936285018921},{"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":2,"locations":[{"id":"doi:10.1109/tkde.2025.3559023","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tkde.2025.3559023","pdf_url":null,"source":{"id":"https://openalex.org/S30698027","display_name":"IEEE Transactions on Knowledge and Data Engineering","issn_l":"1041-4347","issn":["1041-4347","1558-2191","2326-3865"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320439","host_organization_name":"IEEE Computer Society","host_organization_lineage":["https://openalex.org/P4310320439","https://openalex.org/P4310319808"],"host_organization_lineage_names":["IEEE Computer Society","Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Knowledge and Data Engineering","raw_type":"journal-article"},{"id":"pmh:oai:pure.atira.dk:openaire/d4162497-795c-492d-93ff-6f5d84a5c4f7","is_oa":true,"landing_page_url":"https://research.manchester.ac.uk/en/publications/d4162497-795c-492d-93ff-6f5d84a5c4f7","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Chen, J, Mashkova, O, Zhapa-Camacho, F, Hoehndorf, R, He, Y & Horrocks, I 2025, 'Ontology Embedding: A Survey of Methods, Applications and Resources', IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 37, no. 7, pp. 4193 - 4212. https://doi.org/10.1109/TKDE.2025.3559023","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"pmh:oai:pure.atira.dk:openaire/d4162497-795c-492d-93ff-6f5d84a5c4f7","is_oa":true,"landing_page_url":"https://research.manchester.ac.uk/en/publications/d4162497-795c-492d-93ff-6f5d84a5c4f7","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Chen, J, Mashkova, O, Zhapa-Camacho, F, Hoehndorf, R, He, Y & Horrocks, I 2025, 'Ontology Embedding: A Survey of Methods, Applications and Resources', IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 37, no. 7, pp. 4193 - 4212. https://doi.org/10.1109/TKDE.2025.3559023","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":142,"referenced_works":["https://openalex.org/W102708294","https://openalex.org/W153886719","https://openalex.org/W1501531009","https://openalex.org/W1555563750","https://openalex.org/W1596295448","https://openalex.org/W1601038846","https://openalex.org/W1662144952","https://openalex.org/W2081580037","https://openalex.org/W2110324082","https://openalex.org/W2115958581","https://openalex.org/W2136410628","https://openalex.org/W2163922914","https://openalex.org/W2164508904","https://openalex.org/W2250539671","https://openalex.org/W2251878275","https://openalex.org/W2523679382","https://openalex.org/W2557074642","https://openalex.org/W2562531153","https://openalex.org/W2596142952","https://openalex.org/W2626137579","https://openalex.org/W2728059831","https://openalex.org/W2759136286","https://openalex.org/W2786757148","https://openalex.org/W2803524328","https://openalex.org/W2883780523","https://openalex.org/W2886905685","https://openalex.org/W2890216969","https://openalex.org/W2896457183","https://openalex.org/W2896538705","https://openalex.org/W2903298154","https://openalex.org/W2910965811","https://openalex.org/W2945254433","https://openalex.org/W2950595506","https://openalex.org/W2954820957","https://openalex.org/W2958214433","https://openalex.org/W2962756421","https://openalex.org/W2962869320","https://openalex.org/W2962969117","https://openalex.org/W2963690776","https://openalex.org/W2964990093","https://openalex.org/W2965778154","https://openalex.org/W2972535098","https://openalex.org/W2973180967","https://openalex.org/W2979669231","https://openalex.org/W2981612821","https://openalex.org/W3010336026","https://openalex.org/W3034332260","https://openalex.org/W3050693196","https://openalex.org/W3080269789","https://openalex.org/W3080628425","https://openalex.org/W3092613928","https://openalex.org/W3093526682","https://openalex.org/W3094537309","https://openalex.org/W3116286104","https://openalex.org/W3136802089","https://openalex.org/W3153385943","https://openalex.org/W3153694186","https://openalex.org/W3164540570","https://openalex.org/W3166265964","https://openalex.org/W3171177851","https://openalex.org/W3174142355","https://openalex.org/W3174584874","https://openalex.org/W3175052898","https://openalex.org/W3175988714","https://openalex.org/W3177500196","https://openalex.org/W3189514847","https://openalex.org/W3189827190","https://openalex.org/W3199714630","https://openalex.org/W3211454967","https://openalex.org/W3211645405","https://openalex.org/W3216178672","https://openalex.org/W4210547400","https://openalex.org/W4210858491","https://openalex.org/W4213437488","https://openalex.org/W4225687252","https://openalex.org/W4226203366","https://openalex.org/W4239696231","https://openalex.org/W4244275182","https://openalex.org/W4280604898","https://openalex.org/W4283819412","https://openalex.org/W4292722771","https://openalex.org/W4293690910","https://openalex.org/W4300129298","https://openalex.org/W4309440997","https://openalex.org/W4311940841","https://openalex.org/W4315779631","https://openalex.org/W4327550249","https://openalex.org/W4328122254","https://openalex.org/W4367670019","https://openalex.org/W4379382656","https://openalex.org/W4383215259","https://openalex.org/W4385245566","https://openalex.org/W4385570720","https://openalex.org/W4385571479","https://openalex.org/W4385812212","https://openalex.org/W4387055551","https://openalex.org/W4387898221","https://openalex.org/W4388024660","https://openalex.org/W4388144292","https://openalex.org/W4390692489","https://openalex.org/W4391136507","https://openalex.org/W4391821988","https://openalex.org/W4392500231","https://openalex.org/W4396572199","https://openalex.org/W4396736534","https://openalex.org/W4401812371","https://openalex.org/W4402364082","https://openalex.org/W4407737073","https://openalex.org/W4408633660","https://openalex.org/W4409402815","https://openalex.org/W6631964550","https://openalex.org/W6636152709","https://openalex.org/W6636510571","https://openalex.org/W6678830454","https://openalex.org/W6683861112","https://openalex.org/W6685183736","https://openalex.org/W6713634263","https://openalex.org/W6731893219","https://openalex.org/W6734862562","https://openalex.org/W6739076403","https://openalex.org/W6748125048","https://openalex.org/W6750599894","https://openalex.org/W6750637371","https://openalex.org/W6751264767","https://openalex.org/W6757037870","https://openalex.org/W6758276435","https://openalex.org/W6765954368","https://openalex.org/W6767121309","https://openalex.org/W6767684514","https://openalex.org/W6768769356","https://openalex.org/W6777615688","https://openalex.org/W6779039908","https://openalex.org/W6780896692","https://openalex.org/W6784187067","https://openalex.org/W6794592399","https://openalex.org/W6810128082","https://openalex.org/W6810793449","https://openalex.org/W6850625674","https://openalex.org/W6856169278","https://openalex.org/W6857253652","https://openalex.org/W6860708153","https://openalex.org/W7000567287"],"related_works":["https://openalex.org/W2081900870","https://openalex.org/W2003333417","https://openalex.org/W2037549926","https://openalex.org/W2345479200","https://openalex.org/W2183306018","https://openalex.org/W2378862226","https://openalex.org/W2849310602","https://openalex.org/W3006008237","https://openalex.org/W118236634","https://openalex.org/W2355326633"],"abstract_inverted_index":{"Ontologies":[0],"are":[1,35],"widely":[2,73],"used":[3],"for":[4,61],"representing":[5],"domain":[6],"knowledge":[7,62],"and":[8,23,41,51,117,135,152,161,179,187,191],"meta":[9],"data,":[10],"playing":[11],"an":[12,64],"increasingly":[13],"important":[14],"role":[15],"in":[16,38,173],"Information":[17],"Systems,":[18],"the":[19,147,168,189],"Semantic":[20],"Web,":[21],"Bioinformatics":[22],"many":[24],"other":[25],"domains.":[26],"However,":[27],"logical":[28],"reasoning":[29],"that":[30],"ontologies":[31,116,148],"can":[32],"directly":[33],"support":[34],"quite":[36],"limited":[37],"learning,":[39],"approximation":[40],"prediction.":[42],"One":[43],"straightforward":[44],"solution":[45],"is":[46],"to":[47,146],"integrate":[48],"statistical":[49],"analysis":[50],"machine":[52,176],"learning.":[53],"To":[54,99],"this":[55,97,101,105],"end,":[56],"automatically":[57],"learning":[58,177],"vector":[59],"representation":[60],"of":[63,86,96,113,115,127,141,170],"ontology":[65,81,120,171,174],"i.e.,":[66],"<italic":[67],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[68],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">ontology":[69],"embedding</i>":[70],"has":[71],"been":[72,78],"investigated.":[74],"Numerous":[75],"papers":[76],"have":[77],"published":[79],"on":[80,130],"embedding,":[82],"but":[83],"a":[84,93,137,183],"lack":[85],"systematic":[87],"reviews":[88],"hinders":[89],"researchers":[90],"from":[91],"gaining":[92],"comprehensive":[94],"understanding":[95],"field.":[98],"bridge":[100],"gap,":[102],"we":[103],"write":[104],"survey":[106,165],"paper,":[107],"which":[108],"first":[109],"introduces":[110,167],"different":[111],"kinds":[112],"semantics":[114],"formally":[118],"defines":[119],"embedding":[121,172],"as":[122,124],"well":[123],"its":[125],"property":[126],"faithfulness.":[128],"Based":[129],"this,":[131],"it":[132],"systematically":[133],"categorizes":[134],"analyses":[136],"relatively":[138],"complete":[139],"set":[140],"over":[142],"80":[143],"papers,":[144],"according":[145],"they":[149],"aim":[150],"at":[151],"their":[153],"technical":[154],"solutions":[155],"including":[156],"geometric":[157],"modeling,":[158],"sequence":[159],"modeling":[160],"graph":[162],"propagation.":[163],"This":[164],"also":[166],"applications":[169],"engineering,":[175],"augmentation":[178],"life":[180],"sciences,":[181],"presents":[182],"new":[184],"library":[185],"mOWL":[186],"discusses":[188],"challenges":[190],"future":[192],"directions.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":10}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
