{"id":"https://openalex.org/W2099889778","doi":"https://doi.org/10.1093/bioinformatics/bth495","title":"OntologyTraverser: an R package for GO analysis","display_name":"OntologyTraverser: an R package for GO analysis","publication_year":2004,"publication_date":"2004-08-27","ids":{"openalex":"https://openalex.org/W2099889778","doi":"https://doi.org/10.1093/bioinformatics/bth495","mag":"2099889778","pmid":"https://pubmed.ncbi.nlm.nih.gov/15333457"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth495","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth495","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101566054","display_name":"Andrew Young","orcid":"https://orcid.org/0000-0002-9751-9241"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A. Young","raw_affiliation_strings":["Baylor College of Medicine, Department of Molecular and Human Genetics Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baylor College of Medicine, Department of Molecular and Human Genetics Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076764763","display_name":"Nathan L. Whitehouse","orcid":null},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"N. Whitehouse","raw_affiliation_strings":["Baylor College of Medicine, Department of Molecular and Human Genetics Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baylor College of Medicine, Department of Molecular and Human Genetics Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018460115","display_name":"Jaechoon Cho","orcid":null},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Cho","raw_affiliation_strings":["Baylor College of Medicine, Department of Molecular and Human Genetics Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baylor College of Medicine, Department of Molecular and Human Genetics Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072387201","display_name":"Chad A. Shaw","orcid":"https://orcid.org/0000-0001-7267-5398"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C. Shaw","raw_affiliation_strings":["Baylor College of Medicine, Department of Molecular and Human Genetics Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baylor College of Medicine, Department of Molecular and Human Genetics Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5101566054"],"corresponding_institution_ids":["https://openalex.org/I181547552"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.6025,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.89773368,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"21","issue":"2","first_page":"275","last_page":"276"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9986000061035156,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9865999817848206,"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/java","display_name":"Java","score":0.7437335252761841},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7358724474906921},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5786439776420593},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5054609775543213},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.45378372073173523},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.45280224084854126},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4314877986907959},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3704349100589752},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.339356005191803},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.32951560616493225},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.29534342885017395},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16539517045021057},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13070708513259888},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08418333530426025}],"concepts":[{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.7437335252761841},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7358724474906921},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5786439776420593},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5054609775543213},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.45378372073173523},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.45280224084854126},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4314877986907959},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3704349100589752},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.339356005191803},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.32951560616493225},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.29534342885017395},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16539517045021057},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13070708513259888},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08418333530426025},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bth495","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth495","pdf_url":null,"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:15333457","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15333457","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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5726791822","display_name":null,"funder_award_id":"U01 DK63588-01","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W92461833","https://openalex.org/W2074857313","https://openalex.org/W2102992354","https://openalex.org/W2110065044","https://openalex.org/W2122683221","https://openalex.org/W2124388496"],"related_works":["https://openalex.org/W4389426664","https://openalex.org/W2566205467","https://openalex.org/W3012616639","https://openalex.org/W3126000805","https://openalex.org/W2010064959","https://openalex.org/W2119742499","https://openalex.org/W1985266044","https://openalex.org/W4220940831","https://openalex.org/W3008797681","https://openalex.org/W4254478096"],"abstract_inverted_index":{"UNLABELLED:":[0],"Gene":[1],"Ontology":[2],"(GO)":[3],"annotations":[4],"have":[5,16],"become":[6],"a":[7,30,74],"major":[8,31],"tool":[9,94],"for":[10,21],"analysis":[11,23],"of":[12,24],"genome-scale":[13],"experiments.":[14],"We":[15],"created":[17],"OntologyTraverser--an":[18],"R":[19,45,63,89],"package":[20,90],"GO":[22,55],"gene":[25],"lists.":[26],"Our":[27,80],"system":[28,39,49,60,69],"is":[29,70,82],"advance":[32],"over":[33],"previous":[34],"work":[35],"because":[36],"(1)":[37],"the":[38,48,54,58,68,88,92],"can":[40],"be":[41],"installed":[42],"as":[43,73],"an":[44],"package,":[46],"(2)":[47],"uses":[50],"Java":[51,65],"to":[52,61],"instantiate":[53],"structure":[56],"and":[57,64,66,91],"SJava":[59],"integrate":[62],"(3)":[67],"also":[71],"deployed":[72],"publicly":[75],"available":[76,84],"web":[77,93],"tool.":[78],"AVAILABILITY:":[79],"software":[81],"academically":[83],"through":[85],"http://franklin.imgen.bcm.tmc.edu/OntologyTraverser/.":[86],"Both":[87],"are":[95],"accessible.":[96],"CONTACT:":[97],"cashaw@bcm.tmc.edu":[98]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2016-06-24T00:00:00"}
