{"id":"https://openalex.org/W2013571328","doi":"https://doi.org/10.1371/journal.pcbi.1002191","title":"War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?","display_name":"War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?","publication_year":2011,"publication_date":"2011-09-29","ids":{"openalex":"https://openalex.org/W2013571328","doi":"https://doi.org/10.1371/journal.pcbi.1002191","mag":"2013571328"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002191","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002191","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002191&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":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002191&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004739989","display_name":"Andrey Rzhetsky","orcid":"https://orcid.org/0000-0001-6959-7405"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrey Rzhetsky","raw_affiliation_strings":["Computation Institute, University of Chicago, Chicago, Illinois, United States of America","Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America","Department of Medicine, University of Chicago, Chicago, Illinois, United States of America","Institute of Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America"],"affiliations":[{"raw_affiliation_string":"Computation Institute, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Medicine, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Institute of Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076633756","display_name":"James A. Evans","orcid":"https://orcid.org/0000-0001-9838-0707"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James A. Evans","raw_affiliation_strings":["Computation Institute, University of Chicago, Chicago, Illinois, United States of America","Department of Sociology, University of Chicago, Chicago, Illinois, United States of America"],"affiliations":[{"raw_affiliation_string":"Computation Institute, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Sociology, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5004739989"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.55904771,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.63799085,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"7","issue":"9","first_page":"e1002191","last_page":"e1002191"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9947999715805054,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9686999917030334,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.8080546259880066},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6918538808822632},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5502632856369019},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.5195513367652893},{"id":"https://openalex.org/keywords/ontology-language","display_name":"Ontology language","score":0.5127226114273071},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.5025968551635742},{"id":"https://openalex.org/keywords/knowledge-representation-and-reasoning","display_name":"Knowledge representation and reasoning","score":0.4760681986808777},{"id":"https://openalex.org/keywords/ontology-components","display_name":"Ontology components","score":0.4458494782447815},{"id":"https://openalex.org/keywords/process-ontology","display_name":"Process ontology","score":0.4293050765991211},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4152890145778656},{"id":"https://openalex.org/keywords/suggested-upper-merged-ontology","display_name":"Suggested Upper Merged Ontology","score":0.3942752182483673},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35360977053642273},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.29823803901672363},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.26250308752059937},{"id":"https://openalex.org/keywords/conceptualization","display_name":"Conceptualization","score":0.24742728471755981},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.21235275268554688},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.17869412899017334}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.8080546259880066},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6918538808822632},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5502632856369019},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.5195513367652893},{"id":"https://openalex.org/C61673122","wikidata":"https://www.wikidata.org/wiki/Q7095059","display_name":"Ontology language","level":3,"score":0.5127226114273071},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.5025968551635742},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.4760681986808777},{"id":"https://openalex.org/C154210476","wikidata":"https://www.wikidata.org/wiki/Q7095057","display_name":"Ontology components","level":5,"score":0.4458494782447815},{"id":"https://openalex.org/C137003198","wikidata":"https://www.wikidata.org/wiki/Q7247296","display_name":"Process ontology","level":3,"score":0.4293050765991211},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4152890145778656},{"id":"https://openalex.org/C50971890","wikidata":"https://www.wikidata.org/wiki/Q7635093","display_name":"Suggested Upper Merged Ontology","level":4,"score":0.3942752182483673},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35360977053642273},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.29823803901672363},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26250308752059937},{"id":"https://openalex.org/C90734943","wikidata":"https://www.wikidata.org/wiki/Q17008777","display_name":"Conceptualization","level":2,"score":0.24742728471755981},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.21235275268554688},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.17869412899017334},{"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},{"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}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1002191","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002191","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002191&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":"pmh:oai:uchicago.tind.io:8568","is_oa":true,"landing_page_url":"http://knowledge.uchicago.edu/record/8568","pdf_url":null,"source":{"id":"https://openalex.org/S4306402460","display_name":"Knowledge@UChicago (University of Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40347166","host_organization_name":"University of Chicago","host_organization_lineage":["https://openalex.org/I40347166"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://knowledge.uchicago.edu/record/8568","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:afe1a4b02c834df2b688e0c23ffa3a9b","is_oa":true,"landing_page_url":"https://doaj.org/article/afe1a4b02c834df2b688e0c23ffa3a9b","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 7, Iss 9, p e1002191 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2192355","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3182873","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1002191","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002191","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002191&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":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.7400000095367432}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2013571328.pdf","grobid_xml":"https://content.openalex.org/works/W2013571328.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W163465660","https://openalex.org/W173647602","https://openalex.org/W1605850762","https://openalex.org/W1981747532","https://openalex.org/W1983068008","https://openalex.org/W1989255885","https://openalex.org/W2002607603","https://openalex.org/W2018737226","https://openalex.org/W2020718817","https://openalex.org/W2034792128","https://openalex.org/W2036361902","https://openalex.org/W2062475609","https://openalex.org/W2118877284","https://openalex.org/W2122410182","https://openalex.org/W2122747165","https://openalex.org/W2128601422","https://openalex.org/W2137079713","https://openalex.org/W2163670493","https://openalex.org/W2169155903","https://openalex.org/W2469338873","https://openalex.org/W2616328948","https://openalex.org/W2623293810","https://openalex.org/W4230392683","https://openalex.org/W4242753540","https://openalex.org/W4254835207","https://openalex.org/W4301961341","https://openalex.org/W6645522605","https://openalex.org/W6666194717","https://openalex.org/W6678016177","https://openalex.org/W6678087030"],"related_works":["https://openalex.org/W2726617685","https://openalex.org/W2732632690","https://openalex.org/W72173000","https://openalex.org/W1506177826","https://openalex.org/W2012420033","https://openalex.org/W1794266373","https://openalex.org/W2127299687","https://openalex.org/W4206428734","https://openalex.org/W2156480584","https://openalex.org/W1838034317"],"abstract_inverted_index":{"The":[0],"use":[1],"of":[2,13,73,81,152,160],"structured":[3],"knowledge":[4,127],"representations-ontologies":[5],"and":[6,21,35,57,68,71,78,93,106,129,147],"terminologies-has":[7],"become":[8],"standard":[9],"in":[10,145],"biomedicine.":[11],"Definitions":[12],"ontologies":[14,97],"vary":[15],"widely,":[16],"as":[17,53,60,87,120],"do":[18],"the":[19,63,79,108,157],"values":[20],"philosophies":[22],"that":[23,50,112],"underlie":[24],"them.":[25],"In":[26],"seeking":[27],"to":[28,98],"make":[29],"these":[30,139],"views":[31,44,140],"explicit,":[32],"we":[33,51],"conducted":[34],"summarized":[36],"interviews":[37],"with":[38,142],"a":[39,150],"dozen":[40],"leading":[41],"ontologists.":[42],"Their":[43],"clustered":[45],"into":[46],"three":[47],"broad":[48],"perspectives":[49],"summarize":[52],"mathematics,":[54],"computer":[55,88,102],"code,":[56],"Esperanto.":[58],"Ontology":[59,86,119],"mathematics":[61],"puts":[62],"ultimate":[64],"premium":[65],"on":[66,91,123],"rigor":[67],"logic,":[69],"symmetry":[70],"consistency":[72],"representation":[74],"across":[75,131],"scientific":[76],"subfields,":[77],"inclusion":[80],"only":[82],"established,":[83],"non-contradictory":[84],"knowledge.":[85],"code":[89,109],"focuses":[90,122],"utility":[92],"cultivates":[94],"diversity,":[95],"fitting":[96],"their":[99,153],"purpose.":[100],"Like":[101],"languages":[103],"C++,":[104],"Prolog,":[105],"HTML,":[107],"perspective":[110],"holds":[111],"diverse":[113,134],"applications":[114],"warrant":[115],"custom":[116],"designed":[117],"ontologies.":[118,162],"Esperanto":[121],"facilitating":[124],"cross-disciplinary":[125],"communication,":[126],"cross-referencing,":[128],"computation":[130],"datasets":[132],"from":[133],"communities.":[135],"We":[136],"show":[137],"how":[138,149],"align":[141],"classical":[143],"divides":[144],"science":[146],"suggest":[148],"synthesis":[151],"concerns":[154],"could":[155],"strengthen":[156],"next":[158],"generation":[159],"biomedical":[161]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}
