{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T15:27:42Z","timestamp":1773242862463,"version":"3.50.1"},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2003,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In addition, a performance evaluation of automated systems that attempt to tackle sequence analyses rapidly and reproducibly is generally missing. In order to quantify the accuracy and reproducibility of function assignments on a genome-wide scale, we have re-annotated the entire genome sequence of Chlamydia trachomatis (serovar D), in a collaborative manner.<\/jats:p>\n               <jats:p>Results: We have encoded all annotations in a structured format to allow further comparison and data exchange and have used a scale that records the different levels of potential annotation errors according to their propensity to propagate in the database due to transitive function assignments. We conclude that genome annotation may entail a considerable amount of errors, ranging from simple typographical errors to complex sequence analysis problems. The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences.<\/jats:p>\n               <jats:p>Availability and supplementary information: http:\/\/www.ebi.ac.uk\/research\/cgg\/annotation\/cteval\/<\/jats:p>\n               <jats:p>Contact: ouzounis@ebi.ac.uk<\/jats:p>\n               <jats:p>* To whom correspondence should be addressed.<\/jats:p>\n               <jats:p>\u2020 INA-EKETA, GR-57001 Thessaloniki, Greece<\/jats:p>\n               <jats:p>\u2021 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA<\/jats:p>\n               <jats:p>\u00a7 Aetion Technologies LLC, Worthington, OH 43085, USA<\/jats:p>\n               <jats:p>\u00b6 Institut Curie, F-75248 Paris, France<\/jats:p>\n               <jats:p>\u2225 CNRS, UMR6543, F-06108 Nice, France<\/jats:p>\n               <jats:p>** Alma Bioinformatics, E-28760 Madrid, Spain<\/jats:p>\n               <jats:p>\u2020\u2020 Cap Gemini Ernst &amp; Young, London SW1X 7LX, UK<\/jats:p>\n               <jats:p>\u2021\u2021 Univ. of Rome \u2018La Sapienza\u2019, I-00185 Rome, Italy<\/jats:p>\n               <jats:p>\u00a7\u00a7 MWG-Biotech AG, Ebersberg, D-85560 Berlin, Germany<\/jats:p>\n               <jats:p>\u00b6\u00b6 Wellcome Trust Biocentre, Univ. of Dundee, Dundee DD1 5HN, UK<\/jats:p>","DOI":"10.1093\/bioinformatics\/btg077","type":"journal-article","created":{"date-parts":[[2003,4,11]],"date-time":"2003-04-11T18:03:47Z","timestamp":1050084227000},"page":"717-726","source":"Crossref","is-referenced-by-count":54,"title":["Evaluation of annotation strategies using an entire genome sequence"],"prefix":"10.1093","volume":"19","author":[{"given":"Ioannis","family":"Iliopoulos","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sophia","family":"Tsoka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miguel A.","family":"Andrade","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anton J.","family":"Enright","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Carroll","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Poullet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vassilis","family":"Promponas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Theodore","family":"Liakopoulos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giorgos","family":"Palaios","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claude","family":"Pasquier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stavros","family":"Hamodrakas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javier","family":"Tamames","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Asutosh T.","family":"Yagnik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Tramontano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damien","family":"Devos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Blaschke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Brett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Martin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe","family":"Leroy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isidore","family":"Rigoutsos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Sander","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christos A.","family":"Ouzounis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2003,4,12]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/19\/6\/717\/48903886\/bioinformatics_19_6_717.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/19\/6\/717\/48903886\/bioinformatics_19_6_717.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T16:02:50Z","timestamp":1674662570000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/6\/717\/234576"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,4,12]]},"references-count":0,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2003,4,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btg077","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2003,4,12]]},"published":{"date-parts":[[2003,4,12]]}}}