{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T20:40:03Z","timestamp":1765485603120},"reference-count":32,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2012,5,31]],"date-time":"2012-05-31T00:00:00Z","timestamp":1338422400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002533","type":"journal-article","created":{"date-parts":[[2012,5,31]],"date-time":"2012-05-31T21:04:05Z","timestamp":1338498245000},"page":"e1002533","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":98,"title":["Quality of Computationally Inferred Gene Ontology Annotations"],"prefix":"10.1371","volume":"8","author":[{"given":"Nives","family":"\u0160kunca","sequence":"first","affiliation":[]},{"given":"Adrian","family":"Altenhoff","sequence":"additional","affiliation":[]},{"given":"Christophe","family":"Dessimoz","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2012,5,31]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"D331","DOI":"10.1093\/nar\/gkp1018","article-title":"The Gene Ontology in 2010: extensions and refinements.","volume":"38","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1093\/bib\/bbr002","article-title":"The what, where, how and why of gene ontology\u2013a primer for bioinformaticians.","volume":"12","author":"L du Plessis","year":"2011","journal-title":"Brief Bioinform"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"i136","DOI":"10.1093\/bioinformatics\/bti1019","article-title":"A procedure for assessing GO annotation consistency.","volume":"21","author":"ME Dolan","year":"2005","journal-title":"Bioinformatics"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1186\/1471-2105-8-170","article-title":"Estimating the annotation error rate of curated GO database sequence annotations.","volume":"8","author":"CE Jones","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/1471-2105-9-50","article-title":"Defining functional distances over Gene Ontology.","volume":"9","author":"A del Pozo","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"e12","DOI":"10.1093\/nar\/gkm1167","article-title":"Gene Ontology annotation quality analysis in model eukaryotes.","volume":"36","author":"TJ Buza","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1186\/1471-2105-11-588","article-title":"IntelliGO: a new vector-based semantic similarity measure including annotation origin.","volume":"11","author":"S Benabderrahmane","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"S17","DOI":"10.1186\/1471-2105-6-S1-S17","article-title":"An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.","volume":"6","author":"EB Camon","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"D396","DOI":"10.1093\/nar\/gkn803","article-title":"The GOA database in 2009\u2013an integrated Gene Ontology Annotation resource.","volume":"37","author":"D Barrell","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e1000431","DOI":"10.1371\/journal.pcbi.1000431","article-title":"The Gene Ontology&apos;s Reference Genome Project: A Unified Framework for Functional Annotation across Species.","volume":"5","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"S16","DOI":"10.1186\/1471-2105-6-S1-S16","article-title":"Evaluation of BioCreAtIvE assessment of task 2.","volume":"6","author":"C Blaschke","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2445","DOI":"10.1093\/bioinformatics\/btq449","article-title":"Identifying informative subsets of the Gene Ontology with information bottleneck methods.","volume":"26","author":"B Jin","year":"2010","journal-title":"Bioinformatics"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1007\/s10969-011-9105-3","article-title":"A new approach to assess and predict the functional roles of proteins across all known structures.","volume":"12","author":"ES Julfayev","year":"2011","journal-title":"J Struct Funct Genomics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1093\/bib\/bbr042","article-title":"Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.","volume":"12","author":"P Gaudet","year":"2011","journal-title":"Brief Bioinform"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"e1000867","DOI":"10.1371\/journal.pcbi.1000867","article-title":"More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology.","volume":"6","author":"W-C Wong","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1006\/geno.2001.6513","article-title":"Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics.","volume":"74","author":"DP Hill","year":"2001","journal-title":"Genomics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"262D","DOI":"10.1093\/nar\/gkh021","article-title":"The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.","volume":"32","author":"E Camon","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"i41","DOI":"10.1093\/bioinformatics\/btm229","article-title":"Manual curation is not sufficient for annotation of genomic databases.","volume":"23","author":"WA Baumgartner","year":"2007","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.tibtech.2009.01.002","article-title":"Protein function prediction\u2013the power of multiplicity.","volume":"27","author":"R Rentzsch","year":"2009","journal-title":"Trends Biotechnol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1186\/1471-2180-9-S1-S8","article-title":"Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae.","volume":"9","author":"S Meng","year":"2009","journal-title":"BMC Microbiol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1093\/bioinformatics\/19.2.241","article-title":"Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).","volume":"19","author":"I Yeh","year":"2003","journal-title":"Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1186\/1471-2105-12-325","article-title":"How the Gene Ontology Evolves.","volume":"12","author":"S Leonelli","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"D142","DOI":"10.1093\/nar\/gkp846","article-title":"The Universal Protein Resource (UniProt) in 2010.","volume":"38","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1093\/nar\/28.1.304","article-title":"The ENZYME database in 2000.","volume":"28","author":"A Bairoch","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"D211","DOI":"10.1093\/nar\/gkn785","article-title":"InterPro: the integrative protein signature database.","volume":"37","author":"S Hunter","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"D471","DOI":"10.1093\/nar\/gkn661","article-title":"HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB\/Swiss-Prot.","volume":"37","author":"T Lima","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1101\/gr.073585.107","article-title":"EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.","volume":"19","author":"AJ Vilella","year":"2009","journal-title":"Genome Res"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"D322","DOI":"10.1093\/nar\/gkl799","article-title":"GO PaD: the Gene Ontology Partition Database.","volume":"35","author":"G Alterovitz","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1007\/s11517-007-0274-y","article-title":"Tissue-specific functions based on information content of gene ontology using cap analysis gene expression.","volume":"45","author":"S Maekawa","year":"2007","journal-title":"Med Bio Eng Comput"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v040.i01","article-title":"The Split-Apply-Combine Strategy for Data Analysis.","volume":"40","author":"H Wickham","year":"2011","journal-title":"J Stat Softw"},{"key":"ref31","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-98141-3","article-title":"ggplot2: Elegant Graphics for Data Analysis.","author":"H Wickham","year":"2009"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"e21800","DOI":"10.1371\/journal.pone.0021800","article-title":"REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms.","volume":"6","author":"F Supek","year":"2011","journal-title":"PLoS ONE"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002533","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,19]],"date-time":"2018-10-19T19:06:17Z","timestamp":1539975977000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002533"}},"subtitle":[],"editor":[{"given":"Lars Juhl","family":"Jensen","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2012,5,31]]},"references-count":32,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2012,5,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002533","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,5,31]]}}}