{"id":"https://openalex.org/W3108053645","doi":"https://doi.org/10.1371/journal.pcbi.1008376","title":"Transforming the study of organisms: Phenomic data models and knowledge bases","display_name":"Transforming the study of organisms: Phenomic data models and knowledge bases","publication_year":2020,"publication_date":"2020-11-24","ids":{"openalex":"https://openalex.org/W3108053645","doi":"https://doi.org/10.1371/journal.pcbi.1008376","mag":"3108053645","pmid":"https://pubmed.ncbi.nlm.nih.gov/33232313"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008376","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008376","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008376&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008376&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028696519","display_name":"Anne Thessen","orcid":"https://orcid.org/0000-0002-2908-3327"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]},{"id":"https://openalex.org/I4210147267","display_name":"Ronin Institute","ror":"https://ror.org/04awze035","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210147267"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Anne E. Thessen","raw_affiliation_strings":["Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America","Ronin Institute for Independent Scholarship, Monclair, New Jersey, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2908-3327","affiliations":[{"raw_affiliation_string":"Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America","institution_ids":["https://openalex.org/I131249849"]},{"raw_affiliation_string":"Ronin Institute for Independent Scholarship, Monclair, New Jersey, United States of America","institution_ids":["https://openalex.org/I4210147267"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015253000","display_name":"Ramona Walls","orcid":"https://orcid.org/0000-0001-8815-0078"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ramona L. Walls","raw_affiliation_strings":["Bio5 Institute, University of Arizona, Tucson, Arizona, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-8815-0078","affiliations":[{"raw_affiliation_string":"Bio5 Institute, University of Arizona, Tucson, Arizona, United States of America","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022190846","display_name":"Lars Vogt","orcid":"https://orcid.org/0000-0002-8280-0487"},"institutions":[{"id":"https://openalex.org/I2802635041","display_name":"Technische Informationsbibliothek (TIB)","ror":"https://ror.org/04aj4c181","country_code":"DE","type":"archive","lineage":["https://openalex.org/I2802635041","https://openalex.org/I315704651"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lars Vogt","raw_affiliation_strings":["TIB Leibniz Information Centre for Science and Technology, Hannover, Germany"],"raw_orcid":"https://orcid.org/0000-0002-8280-0487","affiliations":[{"raw_affiliation_string":"TIB Leibniz Information Centre for Science and Technology, Hannover, Germany","institution_ids":["https://openalex.org/I2802635041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084325682","display_name":"Jessica Singer","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jessica Singer","raw_affiliation_strings":["Annex Agriculture Inc., Saskatchewan, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Annex Agriculture Inc., Saskatchewan, Canada","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075128999","display_name":"Robert Warren","orcid":"https://orcid.org/0000-0002-7066-1141"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robert Warren","raw_affiliation_strings":["Annex Agriculture Inc., Saskatchewan, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Annex Agriculture Inc., Saskatchewan, Canada","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091806083","display_name":"Pier Luigi Buttigieg","orcid":"https://orcid.org/0000-0002-4366-3088"},"institutions":[{"id":"https://openalex.org/I127251866","display_name":"Alfred-Wegener-Institut Helmholtz-Zentrum f\u00fcr Polar- und Meeresforschung","ror":"https://ror.org/032e6b942","country_code":"DE","type":"facility","lineage":["https://openalex.org/I127251866","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Pier Luigi Buttigieg","raw_affiliation_strings":["Alfred-Wegener-Institut, Helmholtz-Zentrum f\u00fcr Polar- und Meeresforschung, Bremerhaven, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4366-3088","affiliations":[{"raw_affiliation_string":"Alfred-Wegener-Institut, Helmholtz-Zentrum f\u00fcr Polar- und Meeresforschung, Bremerhaven, Germany","institution_ids":["https://openalex.org/I127251866"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021056529","display_name":"James P. Balhoff","orcid":"https://orcid.org/0000-0002-8688-6599"},"institutions":[{"id":"https://openalex.org/I69048370","display_name":"Renaissance Computing Institute","ror":"https://ror.org/01s91ey96","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535","https://openalex.org/I170897317","https://openalex.org/I69048370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James P. Balhoff","raw_affiliation_strings":["Renaissance Computing Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Renaissance Computing Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America","institution_ids":["https://openalex.org/I69048370"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002223413","display_name":"Chris Mungall","orcid":"https://orcid.org/0000-0002-6601-2165"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher J. Mungall","raw_affiliation_strings":["Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-6601-2165","affiliations":[{"raw_affiliation_string":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043699777","display_name":"Deborah L. McGuinness","orcid":"https://orcid.org/0000-0001-7037-4567"},"institutions":[{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Deborah L. McGuinness","raw_affiliation_strings":["Rensselaer Polytechnic Institute, Troy, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7037-4567","affiliations":[{"raw_affiliation_string":"Rensselaer Polytechnic Institute, Troy, New York, United States of America","institution_ids":["https://openalex.org/I165799507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102833422","display_name":"Brian J. Stucky","orcid":"https://orcid.org/0000-0003-0769-2970"},"institutions":[{"id":"https://openalex.org/I1313142568","display_name":"Florida Museum of Natural History","ror":"https://ror.org/02pjdv450","country_code":"US","type":"archive","lineage":["https://openalex.org/I1313142568","https://openalex.org/I33213144"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian J. Stucky","raw_affiliation_strings":["Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America","institution_ids":["https://openalex.org/I1313142568","https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067021279","display_name":"Matthew Yoder","orcid":"https://orcid.org/0000-0002-5640-5491"},"institutions":[{"id":"https://openalex.org/I4210156743","display_name":"Illinois Archaeological Survey","ror":"https://ror.org/04gczvb13","country_code":"US","type":"other","lineage":["https://openalex.org/I4210156743"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew J. Yoder","raw_affiliation_strings":["Illinois Natural History Survey, Champaign, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Illinois Natural History Survey, Champaign, Illinois, United States of America","institution_ids":["https://openalex.org/I4210156743"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064320417","display_name":"Melissa Haendel","orcid":"https://orcid.org/0000-0001-9114-8737"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melissa A. Haendel","raw_affiliation_strings":["Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-9114-8737","affiliations":[{"raw_affiliation_string":"Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America","institution_ids":["https://openalex.org/I131249849"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5028696519"],"corresponding_institution_ids":["https://openalex.org/I131249849","https://openalex.org/I4210147267"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.9196,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.73841999,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"16","issue":"11","first_page":"e1008376","last_page":"e1008376"},"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":0.9965999722480774,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9886999726295471,"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/interoperability","display_name":"Interoperability","score":0.699653148651123},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6051226854324341},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5678434371948242},{"id":"https://openalex.org/keywords/phenotypic-trait","display_name":"Phenotypic trait","score":0.5578005909919739},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5470526814460754},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.5233004689216614},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5066595673561096},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.46382585167884827},{"id":"https://openalex.org/keywords/semantic-heterogeneity","display_name":"Semantic heterogeneity","score":0.46293821930885315},{"id":"https://openalex.org/keywords/semantic-integration","display_name":"Semantic integration","score":0.4541364312171936},{"id":"https://openalex.org/keywords/phenome","display_name":"Phenome","score":0.452719509601593},{"id":"https://openalex.org/keywords/trait","display_name":"Trait","score":0.4394261837005615},{"id":"https://openalex.org/keywords/biobank","display_name":"Biobank","score":0.4270053803920746},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.42393773794174194},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.4210563600063324},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.3377370238304138},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.31572425365448},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29247787594795227},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2580428719520569},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24504002928733826},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.23251023888587952},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.22380253672599792},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.18151599168777466},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13372069597244263},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11773872375488281}],"concepts":[{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.699653148651123},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6051226854324341},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5678434371948242},{"id":"https://openalex.org/C130073038","wikidata":"https://www.wikidata.org/wiki/Q1211967","display_name":"Phenotypic trait","level":4,"score":0.5578005909919739},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5470526814460754},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.5233004689216614},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5066595673561096},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.46382585167884827},{"id":"https://openalex.org/C2778180026","wikidata":"https://www.wikidata.org/wiki/Q18378163","display_name":"Semantic heterogeneity","level":4,"score":0.46293821930885315},{"id":"https://openalex.org/C110903229","wikidata":"https://www.wikidata.org/wiki/Q7449064","display_name":"Semantic integration","level":4,"score":0.4541364312171936},{"id":"https://openalex.org/C7952369","wikidata":"https://www.wikidata.org/wiki/Q844116","display_name":"Phenome","level":4,"score":0.452719509601593},{"id":"https://openalex.org/C106934330","wikidata":"https://www.wikidata.org/wiki/Q1971873","display_name":"Trait","level":2,"score":0.4394261837005615},{"id":"https://openalex.org/C116567970","wikidata":"https://www.wikidata.org/wiki/Q864217","display_name":"Biobank","level":2,"score":0.4270053803920746},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.42393773794174194},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.4210563600063324},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3377370238304138},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.31572425365448},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29247787594795227},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2580428719520569},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24504002928733826},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.23251023888587952},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.22380253672599792},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.18151599168777466},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13372069597244263},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11773872375488281},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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/C167379230","wikidata":"https://www.wikidata.org/wiki/Q1026884","display_name":"Semantic Web Stack","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000080444","descriptor_name":"Phenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000080444","descriptor_name":"Phenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000080444","descriptor_name":"Phenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059647","descriptor_name":"Gene-Environment Interaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059647","descriptor_name":"Gene-Environment Interaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059647","descriptor_name":"Gene-Environment Interaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1008376","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008376","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008376&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:33232313","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33232313","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":"PLoS computational biology","raw_type":null},{"id":"pmh:ark:/13030/qt76j2g4bf","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:4b8bcdf688004a8fa2f478e5a611892e","is_oa":true,"landing_page_url":"https://doaj.org/article/4b8bcdf688004a8fa2f478e5a611892e","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 11, p e1008376 (2020)","raw_type":"article"},{"id":"pmh:oai:epic.awi.de:54711","is_oa":false,"landing_page_url":"https://epic.awi.de/id/eprint/54711/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400378","display_name":"Helmholtz-Zentrum f\u00fcr Polar-und Meeresforschung (Alfred-Wegener-Institut)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2799732068","host_organization_name":"Royal Prince Alfred Hospital","host_organization_lineage":["https://openalex.org/I2799732068"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"EPIC3PLoS Computational Biology, PUBLIC LIBRARY SCIENCE, 16(11), pp. e1008376, ISSN: 1553-734X","raw_type":"Article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt76j2g4bf","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/76j2g4bf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS computational biology, vol 16, iss 11","raw_type":"article"},{"id":"pmh:oai:osti.gov:1828551","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1828551","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7685442","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7685442","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008376","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008376","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008376&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.5600000023841858,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G4121577249","display_name":null,"funder_award_id":"5R24OD011883","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5783761093","display_name":null,"funder_award_id":"SAW-2016-SGN-2","funder_id":"https://openalex.org/F4320334763","funder_display_name":"Leibniz-Gemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334763","display_name":"Leibniz-Gemeinschaft","ror":"https://ror.org/01n6r0e97"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3108053645.pdf","grobid_xml":"https://content.openalex.org/works/W3108053645.grobid-xml"},"referenced_works_count":131,"referenced_works":["https://openalex.org/W220935706","https://openalex.org/W839878123","https://openalex.org/W1505770165","https://openalex.org/W1577783107","https://openalex.org/W1661858205","https://openalex.org/W1831548991","https://openalex.org/W1852821313","https://openalex.org/W1964255443","https://openalex.org/W1971097461","https://openalex.org/W1976043669","https://openalex.org/W1987248861","https://openalex.org/W1989104313","https://openalex.org/W1994474588","https://openalex.org/W2001306005","https://openalex.org/W2002507929","https://openalex.org/W2007859640","https://openalex.org/W2009324633","https://openalex.org/W2020152108","https://openalex.org/W2022451103","https://openalex.org/W2030217765","https://openalex.org/W2040712196","https://openalex.org/W2048024098","https://openalex.org/W2053551770","https://openalex.org/W2054688372","https://openalex.org/W2059313072","https://openalex.org/W2067227875","https://openalex.org/W2073122003","https://openalex.org/W2076381052","https://openalex.org/W2078355959","https://openalex.org/W2081781433","https://openalex.org/W2082382448","https://openalex.org/W2086330580","https://openalex.org/W2089857530","https://openalex.org/W2095723013","https://openalex.org/W2097591011","https://openalex.org/W2100277744","https://openalex.org/W2100895966","https://openalex.org/W2113142309","https://openalex.org/W2116027790","https://openalex.org/W2116034137","https://openalex.org/W2117752917","https://openalex.org/W2120080235","https://openalex.org/W2124879678","https://openalex.org/W2125004669","https://openalex.org/W2127507437","https://openalex.org/W2131067724","https://openalex.org/W2131660156","https://openalex.org/W2136291980","https://openalex.org/W2138900077","https://openalex.org/W2143389435","https://openalex.org/W2146495783","https://openalex.org/W2147163359","https://openalex.org/W2151397621","https://openalex.org/W2151690004","https://openalex.org/W2152164604","https://openalex.org/W2152299024","https://openalex.org/W2152304671","https://openalex.org/W2153456016","https://openalex.org/W2157523980","https://openalex.org/W2159033162","https://openalex.org/W2159327312","https://openalex.org/W2159771235","https://openalex.org/W2162584119","https://openalex.org/W2162891889","https://openalex.org/W2166972836","https://openalex.org/W2168452914","https://openalex.org/W2168670121","https://openalex.org/W2177375219","https://openalex.org/W2195352021","https://openalex.org/W2200941093","https://openalex.org/W2205735312","https://openalex.org/W2278113653","https://openalex.org/W2281806033","https://openalex.org/W2297145735","https://openalex.org/W2337221773","https://openalex.org/W2464106564","https://openalex.org/W2479501825","https://openalex.org/W2494806197","https://openalex.org/W2502051256","https://openalex.org/W2508904198","https://openalex.org/W2519950442","https://openalex.org/W2527799432","https://openalex.org/W2531883117","https://openalex.org/W2552612469","https://openalex.org/W2557385283","https://openalex.org/W2558643140","https://openalex.org/W2562274706","https://openalex.org/W2567676418","https://openalex.org/W2580152911","https://openalex.org/W2593215024","https://openalex.org/W2598807615","https://openalex.org/W2605731854","https://openalex.org/W2624086276","https://openalex.org/W2731055327","https://openalex.org/W2760544538","https://openalex.org/W2765384588","https://openalex.org/W2768308516","https://openalex.org/W2769436351","https://openalex.org/W2770044072","https://openalex.org/W2772877400","https://openalex.org/W2779928889","https://openalex.org/W2784573484","https://openalex.org/W2799793824","https://openalex.org/W2804457431","https://openalex.org/W2808117961","https://openalex.org/W2897443710","https://openalex.org/W2899669628","https://openalex.org/W2900255713","https://openalex.org/W2922350609","https://openalex.org/W2922994503","https://openalex.org/W2949292628","https://openalex.org/W2951918413","https://openalex.org/W2954521347","https://openalex.org/W2961673996","https://openalex.org/W2963784716","https://openalex.org/W2963923670","https://openalex.org/W2978057278","https://openalex.org/W2993873509","https://openalex.org/W3001450467","https://openalex.org/W3001864233","https://openalex.org/W3006289070","https://openalex.org/W3016218187","https://openalex.org/W3108858082","https://openalex.org/W3125577063","https://openalex.org/W3217405741","https://openalex.org/W4212919921","https://openalex.org/W4234674830","https://openalex.org/W4247276974","https://openalex.org/W4285719527","https://openalex.org/W6769298621","https://openalex.org/W6812244948"],"related_works":["https://openalex.org/W2383706660","https://openalex.org/W2389860946","https://openalex.org/W2739100381","https://openalex.org/W4307158935","https://openalex.org/W2381211535","https://openalex.org/W1997451603","https://openalex.org/W3007667068","https://openalex.org/W2369581909","https://openalex.org/W2375662764","https://openalex.org/W2385643360"],"abstract_inverted_index":{"The":[0,45],"rapidly":[1],"decreasing":[2],"cost":[3],"of":[4,12,19,47,70,74,96,155],"gene":[5],"sequencing":[6],"has":[7,103],"resulted":[8],"in":[9,32,52,107,118],"a":[10,23,119],"deluge":[11],"genomic":[13,28],"data":[14,29,49,57,86,88,102,115,142,157,169],"from":[15,122],"across":[16],"the":[17],"tree":[18],"life;":[20],"however,":[21],"outside":[22],"few":[24],"model":[25],"organism":[26],"databases,":[27],"are":[30,38,50,60,116,127],"limited":[31],"their":[33],"scientific":[34],"impact":[35],"because":[36,69],"they":[37],"not":[39,129],"accompanied":[40],"by":[41],"computable":[42,92],"phenomic":[43,48],"data.":[44],"majority":[46],"contained":[51],"countless":[53],"small,":[54],"heterogeneous":[55],"phenotypic":[56,85,101,112,156,168],"sets":[58],"that":[59],"very":[61],"difficult":[62],"or":[63],"impossible":[64],"to":[65,83,153],"integrate":[66],"at":[67],"scale":[68],"variable":[71],"formats,":[72],"lack":[73],"digitization,":[75],"and":[76,109,113,137,141,148,158],"linguistic":[77],"problems.":[78],"One":[79],"powerful":[80],"solution":[81],"is":[82],"represent":[84],"using":[87],"models":[89],"with":[90],"precise,":[91],"semantics,":[93],"but":[94,125],"adoption":[95],"semantic":[97,120],"standards":[98],"for":[99,161],"representing":[100],"been":[104],"slow,":[105],"especially":[106],"biodiversity":[108],"ecology.":[110],"Some":[111],"trait":[114],"available":[117],"language":[121],"knowledge":[123],"bases,":[124],"these":[126],"often":[128],"interoperable.":[130],"In":[131],"this":[132],"review,":[133],"we":[134],"will":[135],"compare":[136],"contrast":[138],"existing":[139],"ontology":[140],"models,":[143],"focusing":[144],"on":[145],"nonhuman":[146],"phenotypes":[147],"traits.":[149],"We":[150],"discuss":[151],"barriers":[152],"integration":[154],"make":[159],"recommendations":[160],"developing":[162],"an":[163],"operationally":[164],"useful,":[165],"semantically":[166],"interoperable":[167],"ecosystem.":[170]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
