{"id":"https://openalex.org/W3044820918","doi":"https://doi.org/10.1186/s12859-020-03637-9","title":"BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint","display_name":"BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint","publication_year":2020,"publication_date":"2020-07-23","ids":{"openalex":"https://openalex.org/W3044820918","doi":"https://doi.org/10.1186/s12859-020-03637-9","mag":"3044820918","pmid":"https://pubmed.ncbi.nlm.nih.gov/32703160"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03637-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03637-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03637-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03637-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102780086","display_name":"Vincent Henry","orcid":"https://orcid.org/0000-0002-9281-1665"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent Henry","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France","Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas]","Universit\u00e9 Paris-Saclay"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210088668"]},{"raw_affiliation_string":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas]","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay","institution_ids":["https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082193370","display_name":"Fatiha Sa\u00efs","orcid":"https://orcid.org/0000-0002-6995-2785"},"institutions":[{"id":"https://openalex.org/I102197404","display_name":"Universit\u00e9 Paris-Sud","ror":"https://ror.org/028rypz17","country_code":"FR","type":"education","lineage":["https://openalex.org/I102197404"]},{"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/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210144804","display_name":"Laboratoire de Recherche en Informatique","ror":"https://ror.org/04e3ktk27","country_code":"FR","type":"facility","lineage":["https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210144804","https://openalex.org/I4210159245"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fatiha Sa\u00efs","raw_affiliation_strings":["LRI, UMR 8623, CNRS, Universit\u00e9 Paris-Sud, Universit\u00e9 Paris Saclay, Orsay, France","Donn\u00e9es et Connaissances Massives et H\u00e9t\u00e9rog\u00e8nes (LRI)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LRI, UMR 8623, CNRS, Universit\u00e9 Paris-Sud, Universit\u00e9 Paris Saclay, Orsay, France","institution_ids":["https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210144804"]},{"raw_affiliation_string":"Donn\u00e9es et Connaissances Massives et H\u00e9t\u00e9rog\u00e8nes (LRI)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059563571","display_name":"Olivier Inizan","orcid":"https://orcid.org/0000-0002-1137-5794"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Olivier Inizan","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France","Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas]","Universit\u00e9 Paris-Saclay"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210088668"]},{"raw_affiliation_string":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas]","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay","institution_ids":["https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090236938","display_name":"Elodie Marchadier","orcid":"https://orcid.org/0000-0001-5618-6471"},"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/I22248866","display_name":"AgroParisTech","ror":"https://ror.org/02kbmgc12","country_code":"FR","type":"education","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210098344","display_name":"G\u00e9n\u00e9tique Quantitative et \u00c9volution Le Moulon","ror":"https://ror.org/012fqzm33","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4210098344"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Elodie Marchadier","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, 91190, France","G\u00e9n\u00e9tique Quantitative et Evolution - Le Moulon (G\u00e9n\u00e9tique V\u00e9g\u00e9tale)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, 91190, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4210098344"]},{"raw_affiliation_string":"G\u00e9n\u00e9tique Quantitative et Evolution - Le Moulon (G\u00e9n\u00e9tique V\u00e9g\u00e9tale)","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210088668","https://openalex.org/I4210098344"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062329271","display_name":"Juliette Dibie-Barth\u00e9lemy","orcid":"https://orcid.org/0000-0003-0395-1306"},"institutions":[{"id":"https://openalex.org/I22248866","display_name":"AgroParisTech","ror":"https://ror.org/02kbmgc12","country_code":"FR","type":"education","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210102957","display_name":"D\u00e9partement math\u00e9matiques, informatique, sciences de la donn\u00e9e et technologies du num\u00e9rique","ror":"https://ror.org/011emb038","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210102957"]},{"id":"https://openalex.org/I4387153087","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es","ror":"https://ror.org/00780az30","country_code":null,"type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4387153087"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Juliette Dibie","raw_affiliation_strings":["UMR MIA-Paris, AgroParisTech, INRAE, Universit\u00e9 Paris Saclay, Paris, France","Math\u00e9matiques et Informatique Appliqu\u00e9es","Universit\u00e9 Paris-Saclay"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UMR MIA-Paris, AgroParisTech, INRAE, Universit\u00e9 Paris Saclay, Paris, France","institution_ids":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I4210088668"]},{"raw_affiliation_string":"Math\u00e9matiques et Informatique Appliqu\u00e9es","institution_ids":["https://openalex.org/I4210102957","https://openalex.org/I4387153087"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay","institution_ids":["https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080851047","display_name":"Anne Goelzer","orcid":"https://orcid.org/0000-0003-2222-6142"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Anne Goelzer","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France. anne.goelzer@inrae.fr","Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas]","Universit\u00e9 Paris-Saclay"],"raw_orcid":"https://orcid.org/0000-0003-2222-6142","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France. anne.goelzer@inrae.fr","institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas]","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay","institution_ids":["https://openalex.org/I277688954"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026415146","display_name":"Vincent Fromion","orcid":"https://orcid.org/0000-0002-9194-5426"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent Fromion","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France","Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas]","Universit\u00e9 Paris-Saclay"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210088668"]},{"raw_affiliation_string":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas]","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay","institution_ids":["https://openalex.org/I277688954"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5080851047"],"corresponding_institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4210159481"],"apc_list":{"value":2170,"currency":"USD","value_usd":2170},"apc_paid":{"value":1745,"currency":"EUR","value_usd":1881},"fwci":0.1512,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.45687473,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":94},"biblio":{"volume":"21","issue":"1","first_page":"327","last_page":"327"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.8474000096321106,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.8474000096321106,"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/T11445","display_name":"Origins and Evolution of Life","score":0.024700000882148743,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.02290000021457672,"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/ontology","display_name":"Ontology","score":0.7541797161102295},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7343703508377075},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6097351908683777},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5822477340698242},{"id":"https://openalex.org/keywords/knowledge-representation-and-reasoning","display_name":"Knowledge representation and reasoning","score":0.5244170427322388},{"id":"https://openalex.org/keywords/description-logic","display_name":"Description logic","score":0.4139830470085144},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3580842614173889},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30818456411361694},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21877548098564148}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7541797161102295},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7343703508377075},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6097351908683777},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5822477340698242},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.5244170427322388},{"id":"https://openalex.org/C102993220","wikidata":"https://www.wikidata.org/wiki/Q387196","display_name":"Description logic","level":2,"score":0.4139830470085144},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3580842614173889},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30818456411361694},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21877548098564148},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"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},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-020-03637-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03637-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03637-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32703160","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32703160","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7376860","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7376860","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:HAL:hal-02907978v1","is_oa":false,"landing_page_url":"https://hal.science/hal-02907978","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2020, 21 (1), pp.327. &#x27E8;10.1186/s12859-020-03637-9&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:e73f4a39ba654f7aa44486cc5cf88a17","is_oa":true,"landing_page_url":"https://doaj.org/article/e73f4a39ba654f7aa44486cc5cf88a17","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":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-18 (2020)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03637-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03637-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03637-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5199999809265137,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320324252","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503"},{"id":"https://openalex.org/F4320331560","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3044820918.pdf","grobid_xml":"https://content.openalex.org/works/W3044820918.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W217162355","https://openalex.org/W647408738","https://openalex.org/W1527927437","https://openalex.org/W1562643504","https://openalex.org/W1577783107","https://openalex.org/W1799738555","https://openalex.org/W1965091013","https://openalex.org/W1969709265","https://openalex.org/W1974252038","https://openalex.org/W1989277387","https://openalex.org/W2022451103","https://openalex.org/W2049762689","https://openalex.org/W2050604932","https://openalex.org/W2052116093","https://openalex.org/W2070962276","https://openalex.org/W2081781433","https://openalex.org/W2095869976","https://openalex.org/W2113142309","https://openalex.org/W2116472408","https://openalex.org/W2123152121","https://openalex.org/W2123171788","https://openalex.org/W2124737787","https://openalex.org/W2124915144","https://openalex.org/W2130367921","https://openalex.org/W2130962401","https://openalex.org/W2134923619","https://openalex.org/W2140611297","https://openalex.org/W2143916531","https://openalex.org/W2168120333","https://openalex.org/W2175849758","https://openalex.org/W2202347610","https://openalex.org/W2261812172","https://openalex.org/W2345996245","https://openalex.org/W2441893520","https://openalex.org/W2482187735","https://openalex.org/W2545591455","https://openalex.org/W2559588208","https://openalex.org/W2580888539","https://openalex.org/W2604808360","https://openalex.org/W2730330710","https://openalex.org/W2739999456","https://openalex.org/W2749963879","https://openalex.org/W2767914218","https://openalex.org/W2770944789","https://openalex.org/W2807615161","https://openalex.org/W2907374855","https://openalex.org/W2948606836","https://openalex.org/W4233698560","https://openalex.org/W4241685680"],"related_works":["https://openalex.org/W2911529331","https://openalex.org/W2045726866","https://openalex.org/W2354320020","https://openalex.org/W4244275182","https://openalex.org/W2749819226","https://openalex.org/W2057110953","https://openalex.org/W1998044538","https://openalex.org/W1862275504","https://openalex.org/W2309581826","https://openalex.org/W2104750878"],"abstract_inverted_index":{"BACKGROUND:":[0],"Managing":[1],"and":[2,87,101],"organizing":[3],"biological":[4,196],"knowledge":[5,162,188],"remains":[6],"a":[7,26,40,52,82,159,176,181],"major":[8],"challenge,":[9],"due":[10],"to":[11,50,74,144,164,194],"the":[12,29,35,56,92,95,99,102,105,110,121,172,185,192,195],"complexity":[13],"of":[14,43,55,59,85,104,113,123,187],"living":[15],"systems.":[16],"Recently,":[17],"systemic":[18,57],"representations":[19],"have":[20],"been":[21],"promising":[22],"in":[23],"tackling":[24],"such":[25,33,125],"challenge":[27],"at":[28,203],"whole-cell":[30],"scale.":[31],"In":[32],"representations,":[34],"cell":[36],"is":[37,48,189],"considered":[38],"as":[39,78,107,109,126,175],"system":[41,174],"composed":[42],"interlocked":[44,67,79],"subsystems.":[45],"The":[46,141],"need":[47],"now":[49],"define":[51],"relevant":[53],"formalization":[54],"description":[58],"cellular":[60,167,173],"processes.":[61],"RESULTS:":[62],"We":[63,89,117],"introduce":[64],"BiPOm":[65,146,157,199],"(Biological":[66],"Process":[68],"Ontology":[69],"for":[70],"metabolism)":[71],"an":[72],"ontology":[73],"represent":[75],"metabolic":[76],"processes":[77],"subsystems":[80],"using":[81,138],"limited":[83],"number":[84],"classes":[86],"properties.":[88],"explicitly":[90],"formalized":[91],"relations":[93],"between":[94],"enzyme,":[96],"its":[97],"activity,":[98],"substrates":[100],"products":[103],"reaction,":[106],"well":[108],"active":[111],"state":[112],"all":[114,166],"involved":[115],"molecules.":[116],"further":[118],"showed":[119],"that":[120],"information":[122,142],"molecules":[124],"molecular":[127,130],"types":[128],"or":[129,153],"properties":[131],"can":[132,147,200],"be":[133,148,201],"deduced":[134],"by":[135,170],"automatic":[136],"reasoning":[137],"logical":[139],"rules.":[140],"necessary":[143],"populate":[145],"extracted":[149],"from":[150,191],"existing":[151,154],"databases":[152],"bio-ontologies.":[155],"CONCLUSION:":[156],"provides":[158],"formal":[160],"rule-based":[161],"representation":[163],"relate":[165],"components":[168],"together":[169],"considering":[171],"whole.":[177],"It":[178],"relies":[179],"on":[180],"paradigm":[182],"shift":[183],"where":[184],"anchorage":[186],"rerouted":[190],"molecule":[193],"process.":[197],"AVAILABILITY:":[198],"downloaded":[202],"https://github.com/SysBioInra/SysOnto.":[204]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
