{"id":"https://openalex.org/W4403799156","doi":"https://doi.org/10.48550/arxiv.2409.18659","title":"Explainable Enrichment-Driven GrAph Reasoner (EDGAR) for Large Knowledge Graphs with Applications in Drug Repurposing","display_name":"Explainable Enrichment-Driven GrAph Reasoner (EDGAR) for Large Knowledge Graphs with Applications in Drug Repurposing","publication_year":2024,"publication_date":"2024-09-27","ids":{"openalex":"https://openalex.org/W4403799156","doi":"https://doi.org/10.48550/arxiv.2409.18659"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2409.18659","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2409.18659","pdf_url":"https://arxiv.org/pdf/2409.18659","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2409.18659","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114420098","display_name":"Olawumi Olasunkanmi","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Olasunkanmi, Olawumi","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087984939","display_name":"Erick J. Morris","orcid":"https://orcid.org/0000-0002-3566-5630"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Morris, Evan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056177526","display_name":"Yaphet Kebede","orcid":"https://orcid.org/0000-0002-5046-0246"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kebede, Yaphet","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055567952","display_name":"Harlin Lee","orcid":"https://orcid.org/0000-0001-6128-9942"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lee, Harlin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072157766","display_name":"Stanley C. Ahalt","orcid":"https://orcid.org/0000-0002-8395-1279"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ahalt, Stanley","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078536199","display_name":"Alexander Tropsha","orcid":"https://orcid.org/0000-0003-3802-8896"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tropsha, Alexander","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5043972221","display_name":"Chris Bizon","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bizon, Chris","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5114420098"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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":0.942300021648407,"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":0.942300021648407,"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":0.9228000044822693,"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/semantic-reasoner","display_name":"Semantic reasoner","score":0.8059909343719482},{"id":"https://openalex.org/keywords/repurposing","display_name":"Repurposing","score":0.7982947826385498},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.6996972560882568},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5030795931816101},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49190735816955566},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.48364388942718506},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.43082961440086365},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.26128363609313965},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.25428104400634766},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.21469011902809143},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.21037286520004272},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18304917216300964},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15770405530929565}],"concepts":[{"id":"https://openalex.org/C9616225","wikidata":"https://www.wikidata.org/wiki/Q3929429","display_name":"Semantic reasoner","level":2,"score":0.8059909343719482},{"id":"https://openalex.org/C519536355","wikidata":"https://www.wikidata.org/wiki/Q21021151","display_name":"Repurposing","level":2,"score":0.7982947826385498},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.6996972560882568},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5030795931816101},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49190735816955566},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.48364388942718506},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.43082961440086365},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.26128363609313965},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25428104400634766},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.21469011902809143},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.21037286520004272},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18304917216300964},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15770405530929565},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2409.18659","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2409.18659","pdf_url":"https://arxiv.org/pdf/2409.18659","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2409.18659","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2409.18659","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2409.18659","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2409.18659","pdf_url":"https://arxiv.org/pdf/2409.18659","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7849883208","display_name":null,"funder_award_id":"3OT2TR003441","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403799156.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2899096130","https://openalex.org/W3190782215","https://openalex.org/W2902729297","https://openalex.org/W3110500039","https://openalex.org/W4255531208","https://openalex.org/W4396858017","https://openalex.org/W4400165188","https://openalex.org/W4206422705","https://openalex.org/W4320009247","https://openalex.org/W3186872001"],"abstract_inverted_index":{"Knowledge":[0],"graphs":[1],"(KGs)":[2],"represent":[3],"connections":[4],"and":[5,57,101,171],"relationships":[6],"between":[7],"real-world":[8],"entities.":[9],"We":[10,69],"propose":[11],"a":[12,36,75,89,154],"link":[13],"prediction":[14],"framework":[15],"for":[16,84,117,133],"KGs":[17],"named":[18],"Enrichment-Driven":[19],"GrAph":[20],"Reasoner":[21],"(EDGAR),":[22],"which":[23],"infers":[24],"new":[25],"edges":[26],"by":[27],"mining":[28],"entity-local":[29],"rules.":[30],"This":[31,158],"approach":[32],"leverages":[33],"enrichment":[34,107,124,165],"analysis,":[35,108],"well-established":[37],"statistical":[38,63],"method":[39],"used":[40],"to":[41,45,113,163,167],"identify":[42],"mechanisms":[43],"common":[44],"sets":[46],"of":[47,65],"differentially":[48],"expressed":[49],"genes.":[50],"EDGAR's":[51],"inference":[52],"results":[53],"are":[54],"inherently":[55],"explainable":[56],"rankable,":[58],"with":[59,153],"p-values":[60],"indicating":[61],"the":[62,71,99,121,160],"significance":[64],"each":[66],"enrichment-based":[67],"rule.":[68],"demonstrate":[70],"framework's":[72],"effectiveness":[73],"on":[74,81],"large-scale":[76],"biomedical":[77],"KG,":[78],"ROBOKOP,":[79,151],"focusing":[80],"drug":[82,115,131,172],"repurposing":[83],"Alzheimer":[85],"disease":[86],"(AD)":[87],"as":[88],"case":[90],"study.":[91],"Initially,":[92],"we":[93],"extracted":[94],"14":[95],"known":[96],"drugs":[97],"from":[98,144],"KG":[100],"identified":[102,128],"20":[103],"contextual":[104],"biomarkers":[105],"through":[106],"revealing":[109],"functional":[110],"pathways":[111],"relevant":[112],"shared":[114],"efficacy":[116],"AD.":[118],"Subsequently,":[119],"using":[120,142],"top":[122,137],"1000":[123],"results,":[125],"our":[126],"system":[127],"1246":[129],"additional":[130],"candidates":[132,139],"AD":[134],"treatment.":[135],"The":[136],"10":[138],"were":[140],"validated":[141],"evidence":[143],"medical":[145],"literature.":[146],"EDGAR":[147],"is":[148,159],"deployed":[149],"within":[150],"complete":[152],"web":[155],"user":[156],"interface.":[157],"first":[161],"study":[162],"apply":[164],"analysis":[166],"large":[168],"graph":[169],"completion":[170],"repurposing.":[173]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2024-10-27T00:00:00"}
