{"id":"https://openalex.org/W4299316047","doi":"https://doi.org/10.7287/peerj.preprints.3140v1","title":"PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units","display_name":"PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units","publication_year":2017,"publication_date":"2017-08-11","ids":{"openalex":"https://openalex.org/W4299316047","doi":"https://doi.org/10.7287/peerj.preprints.3140v1"},"language":"en","primary_location":{"id":"doi:10.7287/peerj.preprints.3140v1","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.3140v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.7287/peerj.preprints.3140v1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088952442","display_name":"Pierre Monnin","orcid":"https://orcid.org/0000-0002-2017-8426"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210121838","display_name":"Laboratoire Lorrain de Recherche en Informatique et ses Applications","ror":"https://ror.org/02vnf0c38","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I277688954","https://openalex.org/I4210107720","https://openalex.org/I4210121838","https://openalex.org/I4210159245","https://openalex.org/I90183372"]},{"id":"https://openalex.org/I90183372","display_name":"Universit\u00e9 de Lorraine","ror":"https://ror.org/04vfs2w97","country_code":"FR","type":"education","lineage":["https://openalex.org/I90183372"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre Monnin","raw_affiliation_strings":["LORIA (CNRS, Inria Nancy-Grand Est, Universit\u00e9 de Lorraine), Vandoeuvre-l\u00e8s-Nancy, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LORIA (CNRS, Inria Nancy-Grand Est, Universit\u00e9 de Lorraine), Vandoeuvre-l\u00e8s-Nancy, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210121838","https://openalex.org/I90183372"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064022148","display_name":"Cl\u00e9ment Jonquet","orcid":"https://orcid.org/0000-0002-2404-1582"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"Cl\u00e9ment Jonquet","raw_affiliation_strings":["BMIR (Stanford University), Stanford, USA","LIRMM (CNRS, Universit\u00e9 de Montpellier), Montpellier, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BMIR (Stanford University), Stanford, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"LIRMM (CNRS, Universit\u00e9 de Montpellier), Montpellier, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210101743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034466727","display_name":"Jo\u00ebl Legrand","orcid":"https://orcid.org/0000-0002-6508-7421"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210121838","display_name":"Laboratoire Lorrain de Recherche en Informatique et ses Applications","ror":"https://ror.org/02vnf0c38","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I277688954","https://openalex.org/I4210107720","https://openalex.org/I4210121838","https://openalex.org/I4210159245","https://openalex.org/I90183372"]},{"id":"https://openalex.org/I90183372","display_name":"Universit\u00e9 de Lorraine","ror":"https://ror.org/04vfs2w97","country_code":"FR","type":"education","lineage":["https://openalex.org/I90183372"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jo\u00ebl Legrand","raw_affiliation_strings":["LORIA (CNRS, Inria Nancy-Grand Est, Universit\u00e9 de Lorraine), Vandoeuvre-l\u00e8s-Nancy, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LORIA (CNRS, Inria Nancy-Grand Est, Universit\u00e9 de Lorraine), Vandoeuvre-l\u00e8s-Nancy, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210121838","https://openalex.org/I90183372"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026515643","display_name":"Amedeo Napoli","orcid":"https://orcid.org/0000-0001-5236-9561"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210121838","display_name":"Laboratoire Lorrain de Recherche en Informatique et ses Applications","ror":"https://ror.org/02vnf0c38","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I277688954","https://openalex.org/I4210107720","https://openalex.org/I4210121838","https://openalex.org/I4210159245","https://openalex.org/I90183372"]},{"id":"https://openalex.org/I90183372","display_name":"Universit\u00e9 de Lorraine","ror":"https://ror.org/04vfs2w97","country_code":"FR","type":"education","lineage":["https://openalex.org/I90183372"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Amedeo Napoli","raw_affiliation_strings":["LORIA (CNRS, Inria Nancy-Grand Est, Universit\u00e9 de Lorraine), Vandoeuvre-l\u00e8s-Nancy, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LORIA (CNRS, Inria Nancy-Grand Est, Universit\u00e9 de Lorraine), Vandoeuvre-l\u00e8s-Nancy, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210121838","https://openalex.org/I90183372"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082641159","display_name":"Adrien Coulet","orcid":"https://orcid.org/0000-0002-1466-062X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210121838","display_name":"Laboratoire Lorrain de Recherche en Informatique et ses Applications","ror":"https://ror.org/02vnf0c38","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I277688954","https://openalex.org/I4210107720","https://openalex.org/I4210121838","https://openalex.org/I4210159245","https://openalex.org/I90183372"]},{"id":"https://openalex.org/I90183372","display_name":"Universit\u00e9 de Lorraine","ror":"https://ror.org/04vfs2w97","country_code":"FR","type":"education","lineage":["https://openalex.org/I90183372"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Adrien Coulet","raw_affiliation_strings":["LORIA (CNRS, Inria Nancy-Grand Est, Universit\u00e9 de Lorraine), Vandoeuvre-l\u00e8s-Nancy, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LORIA (CNRS, Inria Nancy-Grand Est, Universit\u00e9 de Lorraine), Vandoeuvre-l\u00e8s-Nancy, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210121838","https://openalex.org/I90183372"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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":0.9994000196456909,"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":0.9994000196456909,"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":0.9962999820709229,"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/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.9696000218391418,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pharmacogenomics","display_name":"Pharmacogenomics","score":0.7674504518508911},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7221723794937134},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.42159369587898254},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.358479380607605},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.1621445119380951},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1400197148323059},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1256205439567566},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.08806660771369934}],"concepts":[{"id":"https://openalex.org/C170734499","wikidata":"https://www.wikidata.org/wiki/Q1152227","display_name":"Pharmacogenomics","level":2,"score":0.7674504518508911},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7221723794937134},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.42159369587898254},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.358479380607605},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.1621445119380951},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1400197148323059},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1256205439567566},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.08806660771369934}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.7287/peerj.preprints.3140v1","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.3140v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"pmh:oai:HAL:hal-01593184v2","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-01593184","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"http://www.igst.it/nettab/2017/","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"doi:10.7287/peerj.preprints.3140v1","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.3140v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3776455082","display_name":"Practice-based evidences for actioning Knowledge in Pharmacogenomics","funder_award_id":"ANR-15-CE23-0028","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2362192218","https://openalex.org/W2381477132","https://openalex.org/W1867395701","https://openalex.org/W2377000990","https://openalex.org/W2386636980","https://openalex.org/W2120460904","https://openalex.org/W1602573413","https://openalex.org/W2369157347","https://openalex.org/W2373434917","https://openalex.org/W2773694660"],"abstract_inverted_index":{"We":[0],"present":[1],"in":[2,38,43,85,93,115],"this":[3],"article":[4],"a":[5,11,22],"lightweight":[6],"ontology":[7],"named":[8],"PGxO":[9],"and":[10,26,98,150],"set":[12],"of":[13,48,54],"rules":[14],"for":[15,24,67,146],"its":[16],"instantiation,":[17],"which":[18],"we":[19],"developed":[20],"as":[21,89,108],"frame":[23],"reconciling":[25],"tracing":[27],"pharmacogenomics":[28],"(PGx)":[29],"knowledge.":[30],"PGx":[31,44,116],"studies":[32],"how":[33],"genomic":[34],"variations":[35,37],"impact":[36],"drug":[39],"response":[40],"phenotypes.":[41],"Knowledge":[42],"is":[45,117,128],"typically":[46],"composed":[47],"units":[49,81],"that":[50,61],"have":[51],"the":[52,70,77,94],"form":[53],"ternary":[55],"relationships":[56],"gene":[57,71],"variant\u2013drug\u2013adverse":[58],"event,":[59],"stating":[60],"an":[62],"adverse":[63],"event":[64],"may":[65,100],"occur":[66],"patients":[68],"having":[69],"variant":[72],"when":[73,153],"being":[74],"exposed":[75],"to":[76,131],"drug.":[78],"These":[79],"knowledge":[80,114,148],"(i)":[82],"are":[83,91],"available":[84],"reference":[86],"databases,":[87],"such":[88,107],"PharmGKB,":[90],"reported":[92],"scientific":[95],"biomedical":[96],"literature":[97],"(ii)":[99],"be":[101],"discovered":[102],"by":[103],"mining":[104],"clinical":[105],"data":[106],"Electronic":[109],"Health":[110],"Records":[111],"(EHRs).":[112],"Therefore,":[113],"heterogeneously":[118],"described":[119],"(i.e.,":[120],"with":[121],"various":[122],"quality,":[123],"granularity,":[124],"vocabulary,":[125],"etc.).":[126],"It":[127],"consequently":[129],"worth":[130],"extract,":[132],"then":[133],"compare,":[134],"assertions":[135],"from":[136,156],"distinct":[137,157],"resources.":[138],"Using":[139],"PGxO,":[140],"one":[141],"can":[142],"represent":[143],"multiple":[144],"provenances":[145],"pharmacogenomic":[147],"units,":[149],"reconcile":[151],"duplicates":[152],"they":[154],"come":[155],"sources.":[158]},"counts_by_year":[],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2022-10-02T00:00:00"}