{"id":"https://openalex.org/W2110078328","doi":"https://doi.org/10.1093/bioinformatics/btg1024","title":"Predicting phenotype from patterns of annotation","display_name":"Predicting phenotype from patterns of annotation","publication_year":2003,"publication_date":"2003-07-03","ids":{"openalex":"https://openalex.org/W2110078328","doi":"https://doi.org/10.1093/bioinformatics/btg1024","mag":"2110078328","pmid":"https://pubmed.ncbi.nlm.nih.gov/12855456"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg1024","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg1024","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/A5085529697","display_name":"Oliver D. King","orcid":"https://orcid.org/0000-0002-9460-4491"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oliver D. King","raw_affiliation_strings":["Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, Massachusetts, 02115, USA","Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, Massachusetts 02115 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, Massachusetts, 02115, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, Massachusetts 02115 USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056604051","display_name":"Jeffrey C. Lee","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jeffrey C. Lee","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078669073","display_name":"Aim\u00e9e M. Dudley","orcid":"https://orcid.org/0000-0003-3644-0625"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Aim\u00e9e M. Dudley","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017396678","display_name":"Daniel M. Janse","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniel M. Janse","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103076360","display_name":"George M. Church","orcid":"https://orcid.org/0000-0003-3535-2076"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"George M. Church","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5090936599","display_name":"Frederick P. Roth","orcid":"https://orcid.org/0000-0002-6628-649X"},"institutions":[{"id":"https://openalex.org/I2801851002","display_name":"Harvard University Press","ror":"https://ror.org/006v7bf86","country_code":"US","type":"other","lineage":["https://openalex.org/I136199984","https://openalex.org/I2801851002"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Frederick P. Roth","raw_affiliation_strings":["Harvard University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Harvard University","institution_ids":["https://openalex.org/I2801851002"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.833,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.84823535,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"19","issue":"suppl_1","first_page":"i183","last_page":"i189"},"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":0.9976000189781189,"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":0.9897000193595886,"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/phenotype","display_name":"Phenotype","score":0.805662989616394},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.674157977104187},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.6123992800712585},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5958802700042725},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5585758090019226},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5167438387870789},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.493191659450531},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.42413920164108276},{"id":"https://openalex.org/keywords/strain","display_name":"Strain (injury)","score":0.4101915955543518}],"concepts":[{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.805662989616394},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.674157977104187},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.6123992800712585},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5958802700042725},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5585758090019226},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5167438387870789},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.493191659450531},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.42413920164108276},{"id":"https://openalex.org/C2778022156","wikidata":"https://www.wikidata.org/wiki/Q576145","display_name":"Strain (injury)","level":2,"score":0.4101915955543518},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004718","descriptor_name":"Saccharomycetales","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","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":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","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":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","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":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btg1024","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg1024","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:12855456","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12855456","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":null,"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"}],"awards":[{"id":"https://openalex.org/G6543117397","display_name":null,"funder_award_id":"F32 HG002552","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W153647241","https://openalex.org/W1504694836","https://openalex.org/W1594031697","https://openalex.org/W1601258312","https://openalex.org/W1602727746","https://openalex.org/W1698663318","https://openalex.org/W2020011509","https://openalex.org/W2057778600","https://openalex.org/W2081995991","https://openalex.org/W2082607144","https://openalex.org/W2099111195","https://openalex.org/W2107817133","https://openalex.org/W2110325612","https://openalex.org/W2118892942","https://openalex.org/W2125055259","https://openalex.org/W2137786672","https://openalex.org/W2140948740","https://openalex.org/W2142437744","https://openalex.org/W2162891889","https://openalex.org/W2168175751","https://openalex.org/W3085162807","https://openalex.org/W3142026388"],"related_works":["https://openalex.org/W2143066563","https://openalex.org/W2114217399","https://openalex.org/W2902341958","https://openalex.org/W2157166663","https://openalex.org/W2102678326","https://openalex.org/W2094069166","https://openalex.org/W3179054707","https://openalex.org/W2011544219","https://openalex.org/W1968595539","https://openalex.org/W138964897"],"abstract_inverted_index":{"Abstract":[0],"Motivation:Predicting":[1],"the":[2,9,21,51,60,70,75,85,95,106,122],"outcome":[3],"of":[4,11,35,53,121,137,157],"specific":[5],"experiments":[6,30],"(such":[7],"as":[8],"growth":[10,163],"a":[12,17,117],"particular":[13,18],"mutant":[14],"strain":[15],"in":[16,87,99,130,153],"medium)":[19],"has":[20],"potential":[22],"to":[23,26,29,42,144],"allow":[24],"researchers":[25],"devote":[27],"resources":[28],"with":[31,46],"higher":[32],"expected":[33,167],"numbers":[34],"\u2018hits\u2019.":[36],"Results:":[37],"We":[38,83],"use":[39,92,141],"decision":[40,181],"trees":[41],"predict":[43],"phenotypes":[44],"associated":[45],"Saccharomyces":[47,61],"cerevisiae":[48],"genes":[49],"on":[50,94],"basis":[52],"Gene":[54],"Ontology":[55],"(GO)":[56],"functional":[57],"annotations":[58,68,97],"from":[59,69],"Genome":[62],"Database":[63],"(SGD)":[64],"and":[65,101,111,132],"other":[66],"phenotypic":[67,96],"Yeast":[71],"Phenotype":[72],"Catalog":[73],"at":[74,178],"Munich":[76],"Information":[77],"Center":[78],"for":[79,119,135],"Protein":[80],"Sequences":[81],"(MIPS).":[82],"assess":[84,146],"methodology":[86],"three":[88],"ways:":[89],"(1)":[90],"we":[91,115,140],"cross-validation":[93],"listed":[98,129,152],"MIPS,":[100,131],"show":[102,161],"ROC":[103],"curves":[104],"indicating":[105],"tradeoff":[107],"between":[108],"true-positive":[109],"rate":[110],"false-positive":[112],"rate;":[113],"(2)":[114],"do":[116],"literature-search":[118],"100":[120],"predicted":[123,148],"gene-phenotype":[124,149],"associations":[125,150],"that":[126],"are":[127,176],"not":[128,151],"find":[133],"evidence":[134],"43":[136],"them;":[138],"(3)":[139],"deletion":[142,159],"strains":[143,160],"experimentally":[145],"61":[147],"MIPS;":[154],"significantly":[155],"more":[156],"these":[158],"abnormal":[162],"than":[164],"would":[165],"be":[166,190],"by":[168],"chance.":[169],"Contact:":[170],"fritz_roth@hms.harvard.edu":[171],"Supplementary":[172],"Information:":[173],"Complete":[174],"results":[175],"available":[177],"http://llama.med.harvard.edu/~king/pheno.html":[179],"Keywords:":[180],"trees;":[182],"phenotype;":[183],"gene":[184],"function":[185],"*To":[186],"whom":[187],"correspondence":[188],"should":[189],"addressed.":[191]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
