{"id":"https://openalex.org/W7121650478","doi":"https://doi.org/10.1038/s41746-025-02290-x","title":"Knowledge-graph embeddings for osteoarthritis candidate prediction","display_name":"Knowledge-graph embeddings for osteoarthritis candidate prediction","publication_year":2026,"publication_date":"2026-01-10","ids":{"openalex":"https://openalex.org/W7121650478","doi":"https://doi.org/10.1038/s41746-025-02290-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/41519968"},"language":"en","primary_location":{"id":"doi:10.1038/s41746-025-02290-x","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41746-025-02290-x","pdf_url":"https://www.nature.com/articles/s41746-025-02290-x.pdf","source":{"id":"https://openalex.org/S4210195431","display_name":"npj Digital Medicine","issn_l":"2398-6352","issn":["2398-6352"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"npj Digital Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.nature.com/articles/s41746-025-02290-x.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5122719177","display_name":"Zhenggang Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210160344","display_name":"Tongji Hospital","ror":"https://ror.org/04xy45965","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210160344"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenggang Wang","raw_affiliation_strings":["Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210160344","https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122715807","display_name":"Zhengyu Lu","orcid":null},"institutions":[{"id":"https://openalex.org/I173899330","display_name":"Henan University","ror":"https://ror.org/003xyzq10","country_code":"CN","type":"education","lineage":["https://openalex.org/I173899330"]},{"id":"https://openalex.org/I4210146051","display_name":"Anyang Institute of Technology","ror":"https://ror.org/03sd3t490","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210146051"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhengyu Lu","raw_affiliation_strings":["School of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, Henan, China","School of Software, Henan University, Kaifeng, Henan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, Henan, China","institution_ids":["https://openalex.org/I4210146051"]},{"raw_affiliation_string":"School of Software, Henan University, Kaifeng, Henan, China","institution_ids":["https://openalex.org/I173899330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122713603","display_name":"Meng Li","orcid":null},"institutions":[{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Meng Li","raw_affiliation_strings":["Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China. lmedu@smu.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China. lmedu@smu.edu.cn","institution_ids":["https://openalex.org/I58200834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122711161","display_name":"Peiqing Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150072","display_name":"Central Hospital of Zibo","ror":"https://ror.org/04n3h0p93","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210150072"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Peiqing Zhao","raw_affiliation_strings":["Zibo Central Hospital, Binzhou Medical University, Zibo, Shandong, China. bzjzzpq@sdu.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zibo Central Hospital, Binzhou Medical University, Zibo, Shandong, China. bzjzzpq@sdu.edu.cn","institution_ids":["https://openalex.org/I4210150072"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100601010","display_name":"Chengliang Zhang","orcid":"https://orcid.org/0000-0003-0072-8037"},"institutions":[{"id":"https://openalex.org/I4210160344","display_name":"Tongji Hospital","ror":"https://ror.org/04xy45965","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210160344"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chengliang Zhang","raw_affiliation_strings":["Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China. clzhang@tjh.tjmu.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China. clzhang@tjh.tjmu.edu.cn","institution_ids":["https://openalex.org/I4210160344","https://openalex.org/I47720641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100601010","https://openalex.org/A5122711161","https://openalex.org/A5122713603"],"corresponding_institution_ids":["https://openalex.org/I4210150072","https://openalex.org/I4210160344","https://openalex.org/I47720641","https://openalex.org/I58200834"],"apc_list":{"value":3060,"currency":"USD","value_usd":3590},"apc_paid":{"value":3060,"currency":"USD","value_usd":3590},"fwci":19.0575,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.98408757,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"9","issue":"1","first_page":"112","last_page":"112"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10105","display_name":"Osteoarthritis Treatment and Mechanisms","score":0.3855000138282776,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10105","display_name":"Osteoarthritis Treatment and Mechanisms","score":0.3855000138282776,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.26759999990463257,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.13220000267028809,"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/drug-repositioning","display_name":"Drug repositioning","score":0.6715999841690063},{"id":"https://openalex.org/keywords/genome-wide-association-study","display_name":"Genome-wide association study","score":0.4235999882221222},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.3776000142097473},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.3774999976158142},{"id":"https://openalex.org/keywords/candidate-gene","display_name":"Candidate gene","score":0.35580000281333923},{"id":"https://openalex.org/keywords/regularization","display_name":"Regularization (linguistics)","score":0.3465999960899353},{"id":"https://openalex.org/keywords/genetic-association","display_name":"Genetic association","score":0.3005000054836273},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.2989000082015991}],"concepts":[{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.6715999841690063},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5683000087738037},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5325999855995178},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5250999927520752},{"id":"https://openalex.org/C106208931","wikidata":"https://www.wikidata.org/wiki/Q1098876","display_name":"Genome-wide association study","level":5,"score":0.4235999882221222},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.3776000142097473},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3774999976158142},{"id":"https://openalex.org/C69991583","wikidata":"https://www.wikidata.org/wiki/Q1423575","display_name":"Candidate gene","level":3,"score":0.35580000281333923},{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.3465999960899353},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3424000144004822},{"id":"https://openalex.org/C186413461","wikidata":"https://www.wikidata.org/wiki/Q744727","display_name":"Genetic association","level":5,"score":0.3005000054836273},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.2989000082015991},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.2897000014781952},{"id":"https://openalex.org/C74197172","wikidata":"https://www.wikidata.org/wiki/Q1195339","display_name":"Directed acyclic graph","level":2,"score":0.2849000096321106},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.28290000557899475},{"id":"https://openalex.org/C2776164576","wikidata":"https://www.wikidata.org/wiki/Q62736","display_name":"Osteoarthritis","level":3,"score":0.28029999136924744},{"id":"https://openalex.org/C2984324147","wikidata":"https://www.wikidata.org/wiki/Q3080021","display_name":"Gene selection","level":5,"score":0.27379998564720154},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.27149999141693115},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.2685999870300293},{"id":"https://openalex.org/C519536355","wikidata":"https://www.wikidata.org/wiki/Q21021151","display_name":"Repurposing","level":2,"score":0.26669999957084656},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.266400009393692},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.262800008058548},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.25999999046325684},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.25440001487731934}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1038/s41746-025-02290-x","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41746-025-02290-x","pdf_url":"https://www.nature.com/articles/s41746-025-02290-x.pdf","source":{"id":"https://openalex.org/S4210195431","display_name":"npj Digital Medicine","issn_l":"2398-6352","issn":["2398-6352"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"npj Digital Medicine","raw_type":"journal-article"},{"id":"pmid:41519968","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41519968","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":"NPJ digital medicine","raw_type":null},{"id":"pmh:oai:doaj.org/article:d1e5756776b84eb5897ecd7dc8fd46a0","is_oa":true,"landing_page_url":"https://doaj.org/article/d1e5756776b84eb5897ecd7dc8fd46a0","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":"npj Digital Medicine, Vol 9, Iss 1, Pp 1-13 (2026)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11672250","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12864741","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1038/s41746-025-02290-x","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41746-025-02290-x","pdf_url":"https://www.nature.com/articles/s41746-025-02290-x.pdf","source":{"id":"https://openalex.org/S4210195431","display_name":"npj Digital Medicine","issn_l":"2398-6352","issn":["2398-6352"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"npj Digital Medicine","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.8284645080566406}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7121650478.pdf","grobid_xml":"https://content.openalex.org/works/W7121650478.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1905058580","https://openalex.org/W2073836327","https://openalex.org/W2099085143","https://openalex.org/W2113699335","https://openalex.org/W2161633633","https://openalex.org/W2324862792","https://openalex.org/W2728059831","https://openalex.org/W2766208765","https://openalex.org/W2767891136","https://openalex.org/W2803072880","https://openalex.org/W2805712258","https://openalex.org/W2889583850","https://openalex.org/W2900569176","https://openalex.org/W2949275660","https://openalex.org/W2949311246","https://openalex.org/W2962886429","https://openalex.org/W3027865872","https://openalex.org/W3035403290","https://openalex.org/W3042068575","https://openalex.org/W3103802158","https://openalex.org/W3132471123","https://openalex.org/W3133859624","https://openalex.org/W3154252255","https://openalex.org/W3194108800","https://openalex.org/W3202212354","https://openalex.org/W4285029539","https://openalex.org/W4317566725","https://openalex.org/W4376618023","https://openalex.org/W4385577954","https://openalex.org/W4386042200","https://openalex.org/W4387344358","https://openalex.org/W4392857278","https://openalex.org/W4402900312","https://openalex.org/W4403454303","https://openalex.org/W4408353384","https://openalex.org/W4413100503"],"related_works":[],"abstract_inverted_index":{"Osteoarthritis":[0,34],"(OA)":[1],"is":[2],"a":[3,16,37,67,88,193],"prevalent,":[4],"disabling":[5],"joint":[6],"disease":[7,11],"with":[8,49,115,201],"no":[9],"approved":[10],"modifying":[12],"treatments.":[13],"We":[14,31,64],"present":[15],"knowledge-graph":[17,68,184],"based":[18,90],"approach":[19],"to":[20,93,105,125,196],"discover":[21],"candidate":[22],"treatments":[23],"for":[24,119,134],"OA":[25,54,82,97,148],"by":[26],"integrating":[27],"large-scale":[28],"biomedical":[29],"data.":[30],"introduce":[32],"the":[33,42,188],"Knowledge-graph":[35,45],"(OKG),":[36],"comprehensive":[38],"network":[39],"derived":[40],"from":[41,53],"Drug":[43],"Repurposing":[44],"(DRKG)":[46],"and":[47,109,141,155,170],"enriched":[48],"causal":[50,98],"genetic":[51,181],"associations":[52],"genome-wide":[55],"association":[56],"study":[57],"(GWAS)":[58],"involving":[59],"nearly":[60],"2":[61],"million":[62],"individuals.":[63],"propose":[65],"CausalPathKG,":[66],"embedding":[69],"model":[70],"built":[71],"upon":[72],"RotatE":[73,142],"that":[74,161,179],"integrates":[75],"domain":[76],"specific":[77],"innovations:":[78],"(i)":[79],"weighted":[80],"gene":[81,96],"edges":[83,133],"reflecting":[84],"GWAS":[85],"significance,":[86],"(ii)":[87],"path":[89],"regularization":[91],"term":[92],"encourage":[94],"drug":[95,202],"connectivity,":[99],"(iii)":[100],"multi":[101],"hop":[102],"graph":[103],"attention":[104],"prioritize":[106],"informative":[107],"paths,":[108],"(iv)":[110],"self":[111],"adversarial":[112],"negative":[113],"sampling":[114],"type":[116],"consistent":[117],"corruptions":[118],"robust":[120],"training.":[121],"CausalPathKG":[122,138],"was":[123],"trained":[124],"predict":[126],"missing":[127],"links,":[128],"while":[129],"withholding":[130],"known":[131],"OA-related":[132],"testing.":[135],"In":[136],"experiments,":[137],"outperformed":[139],"TransE":[140],"baselines":[143],"in":[144,173],"predicting":[145],"held":[146],"out":[147],"treatments,":[149],"achieving":[150],"higher":[151],"link":[152],"prediction":[153],"accuracy":[154],"classification":[156],"performance.":[157],"Case":[158],"studies":[159],"highlight":[160],"top":[162],"ranked":[163],"repurposed":[164],"drugs":[165],"engage":[166],"key":[167],"OA-associated":[168],"genes":[169],"pathways":[171],"identified":[172],"human":[174,198],"genetics.":[175],"These":[176],"results":[177],"demonstrate":[178],"incorporating":[180],"evidence":[182],"into":[183],"models":[185],"can":[186],"improve":[187],"discovery":[189],"of":[190],"therapeutics,":[191],"offering":[192],"computational":[194],"strategy":[195],"bridge":[197],"genomic":[199],"data":[200],"repurposing.":[203]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2026-01-11T00:00:00"}