{"id":"https://openalex.org/W2118035767","doi":"https://doi.org/10.1093/bioinformatics/bts029","title":"CODEX: exploration of semantic changes between ontology versions","display_name":"CODEX: exploration of semantic changes between ontology versions","publication_year":2012,"publication_date":"2012-01-16","ids":{"openalex":"https://openalex.org/W2118035767","doi":"https://doi.org/10.1093/bioinformatics/bts029","mag":"2118035767","pmid":"https://pubmed.ncbi.nlm.nih.gov/22253292"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts029","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts029","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/895/48880467/bioinformatics_28_6_895.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/895/48880467/bioinformatics_28_6_895.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102879929","display_name":"Michael Hartung","orcid":"https://orcid.org/0000-0002-3992-0125"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Michael Hartung","raw_affiliation_strings":["1 Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany and 2Department of Computer Science, University of Leipzig, Leipzig, Germany"],"affiliations":[{"raw_affiliation_string":"1 Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany and 2Department of Computer Science, University of Leipzig, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004046987","display_name":"Anika Gro\u00df","orcid":"https://orcid.org/0000-0002-2684-8427"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Anika Gross","raw_affiliation_strings":["1 Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany and 2Department of Computer Science, University of Leipzig, Leipzig, Germany"],"affiliations":[{"raw_affiliation_string":"1 Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany and 2Department of Computer Science, University of Leipzig, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075756237","display_name":"Erhard Rahm","orcid":"https://orcid.org/0000-0002-2665-1114"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Erhard Rahm","raw_affiliation_strings":["1 Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany and 2Department of Computer Science, University of Leipzig, Leipzig, Germany"],"affiliations":[{"raw_affiliation_string":"1 Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany and 2Department of Computer Science, University of Leipzig, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5102879929"],"corresponding_institution_ids":["https://openalex.org/I926574661"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.4447,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.81230278,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"28","issue":"6","first_page":"895","last_page":"896"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9944999814033508,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9797999858856201,"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":0.8340626955032349},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8140482902526855},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.624819278717041},{"id":"https://openalex.org/keywords/owl-s","display_name":"OWL-S","score":0.5912759304046631},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5827438235282898},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.5736429691314697},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5475873947143555},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5379112362861633},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5250232815742493},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.44990500807762146},{"id":"https://openalex.org/keywords/semantic-web-stack","display_name":"Semantic Web Stack","score":0.3317135274410248},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2080886960029602},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.057108521461486816}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.8340626955032349},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8140482902526855},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.624819278717041},{"id":"https://openalex.org/C50382505","wikidata":"https://www.wikidata.org/wiki/Q2553356","display_name":"OWL-S","level":4,"score":0.5912759304046631},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5827438235282898},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.5736429691314697},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5475873947143555},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5379112362861633},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5250232815742493},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.44990500807762146},{"id":"https://openalex.org/C167379230","wikidata":"https://www.wikidata.org/wiki/Q1026884","display_name":"Semantic Web Stack","level":3,"score":0.3317135274410248},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2080886960029602},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.057108521461486816},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bts029","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts029","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/895/48880467/bioinformatics_28_6_895.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22253292","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22253292","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts029","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts029","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/895/48880467/bioinformatics_28_6_895.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2118035767.pdf","grobid_xml":"https://content.openalex.org/works/W2118035767.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1480700989","https://openalex.org/W1527927437","https://openalex.org/W2096704019","https://openalex.org/W2113142309","https://openalex.org/W2122733285","https://openalex.org/W2123171788"],"related_works":["https://openalex.org/W1596824673","https://openalex.org/W2360961025","https://openalex.org/W2366430559","https://openalex.org/W2370680756","https://openalex.org/W2349698472","https://openalex.org/W4241207218","https://openalex.org/W2362529750","https://openalex.org/W2367015831","https://openalex.org/W13789069","https://openalex.org/W2209613360"],"abstract_inverted_index":{"Life":[0],"science":[1],"ontologies":[2],"substantially":[3],"change":[4],"over":[5],"time":[6],"to":[7,15,26],"meet":[8],"the":[9,17],"requirements":[10],"of":[11,35,69],"their":[12],"users":[13,73],"and":[14,48],"include":[16],"newest":[18],"domain":[19],"knowledge.":[20],"Thus,":[21],"an":[22,36,70],"important":[23],"task":[24],"is":[25],"know":[27],"what":[28],"has":[29],"been":[30],"modified":[31],"between":[32,66],"two":[33,67],"versions":[34,68],"ontology":[37],"(diff).":[38],"This":[39],"diff":[40],"should":[41],"contain":[42],"all":[43],"performed":[44],"changes":[45,65],"as":[46,50],"compact":[47],"understandable":[49],"possible.":[51],"We":[52],"present":[53],"CODEX":[54],"(Complex":[55],"Ontology":[56],"Diff":[57],"Explorer),":[58],"a":[59],"tool":[60],"that":[61],"allows":[62],"determining":[63],"semantic":[64],"ontology,":[71],"which":[72],"can":[74],"interactively":[75],"analyze":[76],"in":[77],"multiple":[78],"ways.":[79]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}