{"id":"https://openalex.org/W4311053242","doi":"https://doi.org/10.3390/make4040056","title":"Ontology Completion with Graph-Based Machine Learning: A Comprehensive Evaluation","display_name":"Ontology Completion with Graph-Based Machine Learning: A Comprehensive Evaluation","publication_year":2022,"publication_date":"2022-12-01","ids":{"openalex":"https://openalex.org/W4311053242","doi":"https://doi.org/10.3390/make4040056"},"language":"en","primary_location":{"id":"doi:10.3390/make4040056","is_oa":true,"landing_page_url":"https://doi.org/10.3390/make4040056","pdf_url":"https://www.mdpi.com/2504-4990/4/4/56/pdf?version=1669882603","source":{"id":"https://openalex.org/S4210213891","display_name":"Machine Learning and Knowledge Extraction","issn_l":"2504-4990","issn":["2504-4990"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning and Knowledge Extraction","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2504-4990/4/4/56/pdf?version=1669882603","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074094097","display_name":"Sebastian Me\u017enar","orcid":"https://orcid.org/0000-0002-0469-6696"},"institutions":[{"id":"https://openalex.org/I3006985408","display_name":"Jo\u017eef Stefan Institute","ror":"https://ror.org/05060sz93","country_code":"SI","type":"facility","lineage":["https://openalex.org/I3006985408"]},{"id":"https://openalex.org/I4210113529","display_name":"Jo\u017eef Stefan International Postgraduate School","ror":"https://ror.org/01hdkb925","country_code":"SI","type":"education","lineage":["https://openalex.org/I4210113529"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Sebastian Me\u017enar","raw_affiliation_strings":["Jo\u017eef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia","Jo\u017eef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia"],"raw_orcid":"https://orcid.org/0000-0002-0469-6696","affiliations":[{"raw_affiliation_string":"Jo\u017eef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I3006985408"]},{"raw_affiliation_string":"Jo\u017eef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210113529"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006422389","display_name":"Matej Bevec","orcid":"https://orcid.org/0000-0001-8746-469X"},"institutions":[{"id":"https://openalex.org/I3006985408","display_name":"Jo\u017eef Stefan Institute","ror":"https://ror.org/05060sz93","country_code":"SI","type":"facility","lineage":["https://openalex.org/I3006985408"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Matej Bevec","raw_affiliation_strings":["Jo\u017eef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia"],"raw_orcid":"https://orcid.org/0000-0001-8746-469X","affiliations":[{"raw_affiliation_string":"Jo\u017eef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I3006985408"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060174190","display_name":"Nada Lavra\u010d","orcid":"https://orcid.org/0000-0002-9995-7093"},"institutions":[{"id":"https://openalex.org/I192455894","display_name":"University of Nova Gorica","ror":"https://ror.org/00mw0tw28","country_code":"SI","type":"education","lineage":["https://openalex.org/I192455894"]},{"id":"https://openalex.org/I3006985408","display_name":"Jo\u017eef Stefan Institute","ror":"https://ror.org/05060sz93","country_code":"SI","type":"facility","lineage":["https://openalex.org/I3006985408"]},{"id":"https://openalex.org/I4210113529","display_name":"Jo\u017eef Stefan International Postgraduate School","ror":"https://ror.org/01hdkb925","country_code":"SI","type":"education","lineage":["https://openalex.org/I4210113529"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Nada Lavra\u010d","raw_affiliation_strings":["Jo\u017eef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia","Jo\u017eef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia","School of Engineering and Management, University of Nova Gorica, Glavni trg 8, 5271 Vipava, Slovenia"],"raw_orcid":"https://orcid.org/0000-0002-9995-7093","affiliations":[{"raw_affiliation_string":"Jo\u017eef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I3006985408"]},{"raw_affiliation_string":"Jo\u017eef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210113529"]},{"raw_affiliation_string":"School of Engineering and Management, University of Nova Gorica, Glavni trg 8, 5271 Vipava, Slovenia","institution_ids":["https://openalex.org/I192455894"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007096285","display_name":"Bla\u017e \u0160krlj","orcid":"https://orcid.org/0000-0002-9916-8756"},"institutions":[{"id":"https://openalex.org/I3006985408","display_name":"Jo\u017eef Stefan Institute","ror":"https://ror.org/05060sz93","country_code":"SI","type":"facility","lineage":["https://openalex.org/I3006985408"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Bla\u017e \u0160krlj","raw_affiliation_strings":["Jo\u017eef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia"],"raw_orcid":"https://orcid.org/0000-0002-9916-8756","affiliations":[{"raw_affiliation_string":"Jo\u017eef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I3006985408"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074094097"],"corresponding_institution_ids":["https://openalex.org/I3006985408","https://openalex.org/I4210113529"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.7796,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.69834809,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"4","issue":"4","first_page":"1107","last_page":"1123"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.9957000017166138,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7918177843093872},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7605763077735901},{"id":"https://openalex.org/keywords/process-ontology","display_name":"Process ontology","score":0.5388789176940918},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.5384182333946228},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.5353496670722961},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.5198026895523071},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.5110489130020142},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4869135618209839},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4536530077457428},{"id":"https://openalex.org/keywords/suggested-upper-merged-ontology","display_name":"Suggested Upper Merged Ontology","score":0.4526292681694031},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34553414583206177},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.3218543529510498},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3211621940135956},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2811915874481201}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7918177843093872},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7605763077735901},{"id":"https://openalex.org/C137003198","wikidata":"https://www.wikidata.org/wiki/Q7247296","display_name":"Process ontology","level":3,"score":0.5388789176940918},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.5384182333946228},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.5353496670722961},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.5198026895523071},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.5110489130020142},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4869135618209839},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4536530077457428},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.4526292681694031},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34553414583206177},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.3218543529510498},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3211621940135956},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2811915874481201},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/make4040056","is_oa":true,"landing_page_url":"https://doi.org/10.3390/make4040056","pdf_url":"https://www.mdpi.com/2504-4990/4/4/56/pdf?version=1669882603","source":{"id":"https://openalex.org/S4210213891","display_name":"Machine Learning and Knowledge Extraction","issn_l":"2504-4990","issn":["2504-4990"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning and Knowledge Extraction","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:03722ffab5a24d4582e367c232ffe6b9","is_oa":true,"landing_page_url":"https://doaj.org/article/03722ffab5a24d4582e367c232ffe6b9","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Machine Learning and Knowledge Extraction, Vol 4, Iss 4, Pp 1107-1123 (2022)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2504-4990/4/4/56/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/make4040056","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Machine Learning and Knowledge Extraction; Volume 4; Issue 4; Pages: 1107-1123","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/make4040056","is_oa":true,"landing_page_url":"https://doi.org/10.3390/make4040056","pdf_url":"https://www.mdpi.com/2504-4990/4/4/56/pdf?version=1669882603","source":{"id":"https://openalex.org/S4210213891","display_name":"Machine Learning and Knowledge Extraction","issn_l":"2504-4990","issn":["2504-4990"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning and Knowledge Extraction","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7699999809265137,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4311053242.pdf"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W21052363","https://openalex.org/W1979104937","https://openalex.org/W2008620264","https://openalex.org/W2048164849","https://openalex.org/W2053545516","https://openalex.org/W2084168100","https://openalex.org/W2103017472","https://openalex.org/W2127795553","https://openalex.org/W2129934604","https://openalex.org/W2138399168","https://openalex.org/W2149350752","https://openalex.org/W2150766729","https://openalex.org/W2154454189","https://openalex.org/W2154851992","https://openalex.org/W2175849758","https://openalex.org/W2186667348","https://openalex.org/W2338910273","https://openalex.org/W2519887557","https://openalex.org/W2572147858","https://openalex.org/W2591108329","https://openalex.org/W2614580676","https://openalex.org/W2618851150","https://openalex.org/W2743104969","https://openalex.org/W2767792127","https://openalex.org/W2770093575","https://openalex.org/W2786757148","https://openalex.org/W2792504918","https://openalex.org/W2802433760","https://openalex.org/W2888828233","https://openalex.org/W2889804191","https://openalex.org/W2903298154","https://openalex.org/W2909137510","https://openalex.org/W2918428907","https://openalex.org/W2933602294","https://openalex.org/W2962756421","https://openalex.org/W2962969117","https://openalex.org/W2980532801","https://openalex.org/W2991479679","https://openalex.org/W2999905431","https://openalex.org/W3084036021","https://openalex.org/W3091928167","https://openalex.org/W3092613928","https://openalex.org/W3100330855","https://openalex.org/W3102777254","https://openalex.org/W3104097132","https://openalex.org/W3166265964","https://openalex.org/W3201736551","https://openalex.org/W4210494925","https://openalex.org/W4210580280","https://openalex.org/W4232932184","https://openalex.org/W6600865458","https://openalex.org/W6636880475","https://openalex.org/W6639055396","https://openalex.org/W6682059071","https://openalex.org/W6731801563","https://openalex.org/W6745537798","https://openalex.org/W6754929296","https://openalex.org/W6761444737","https://openalex.org/W6790587931"],"related_works":["https://openalex.org/W2015306306","https://openalex.org/W2911326759","https://openalex.org/W2384240228","https://openalex.org/W22148886","https://openalex.org/W2805287566","https://openalex.org/W2184133400","https://openalex.org/W2064503500","https://openalex.org/W2293073117","https://openalex.org/W3197023343","https://openalex.org/W2373434917"],"abstract_inverted_index":{"Increasing":[0],"quantities":[1],"of":[2,8,18,25,32,108,115,126,129,132,151,161],"semantic":[3,76,137],"resources":[4,138],"offer":[5,96],"a":[6,33,53,91,97,106],"wealth":[7],"human":[9],"knowledge,":[10,117],"but":[11],"their":[12],"growth":[13],"also":[14],"increases":[15],"the":[16,113,121,127,152],"probability":[17],"wrong":[19],"knowledge":[20,35,71],"base":[21,36],"entries.":[22],"The":[23],"development":[24],"approaches":[26],"that":[27,48,90,144],"identify":[28],"potentially":[29,163],"spurious":[30],"parts":[31],"given":[34],"is":[37,119],"therefore":[38],"highly":[39],"relevant.":[40],"We":[41],"propose":[42],"an":[43,50],"approach":[44,104],"for":[45,70,105],"ontology":[46,51,102],"completion":[47,103],"transforms":[49],"into":[52],"graph":[54],"and":[55,85,99],"recommends":[56],"missing":[57],"edges":[58],"using":[59],"structure-only":[60,92],"link":[61,93,133],"analysis":[62,94,134],"methods.":[63,168],"By":[64],"systematically":[65],"evaluating":[66],"thirteen":[67],"methods":[68,135,162],"(some":[69],"graphs)":[72],"on":[73],"eight":[74],"different":[75,130,140],"resources,":[77],"including":[78],"Gene":[79],"Ontology,":[80,82,84],"Food":[81],"Marine":[83],"similar":[86],"ontologies,":[87],"we":[88],"demonstrate":[89],"can":[95,155],"scalable":[98],"computationally":[100],"efficient":[101],"subset":[107],"analyzed":[109],"data":[110],"sets.":[111],"To":[112],"best":[114],"our":[116],"this":[118,159],"currently":[120],"most":[122],"extensive":[123],"systematic":[124],"study":[125],"applicability":[128],"types":[131],"across":[136],"from":[139],"domains.":[141],"It":[142],"demonstrates":[143],"by":[145],"considering":[146],"symbolic":[147],"node":[148],"embeddings,":[149],"explanations":[150],"predictions":[153],"(links)":[154],"be":[156],"obtained,":[157],"making":[158],"branch":[160],"more":[164],"valuable":[165],"than":[166],"black-box":[167]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2022-12-23T00:00:00"}
