Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large pub...

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Autores principales:	Alexandra M Schnoes, Shoshana D Brown, Igor Dodevski, Patricia C Babbitt
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/d399fec6c83b4f6a983821429be3ec92
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spelling	oai:doaj.org-article:d399fec6c83b4f6a983821429be3ec922021-11-25T05:42:47ZAnnotation error in public databases: misannotation of molecular function in enzyme superfamilies.1553-734X1553-735810.1371/journal.pcbi.1000605https://doaj.org/article/d399fec6c83b4f6a983821429be3ec922009-12-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20011109/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families); the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%-63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with "overprediction" of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation.Alexandra M SchnoesShoshana D BrownIgor DodevskiPatricia C BabbittPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 5, Iss 12, p e1000605 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Alexandra M Schnoes Shoshana D Brown Igor Dodevski Patricia C Babbitt Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
description	Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families); the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%-63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with "overprediction" of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation.
format	article
author	Alexandra M Schnoes Shoshana D Brown Igor Dodevski Patricia C Babbitt
author_facet	Alexandra M Schnoes Shoshana D Brown Igor Dodevski Patricia C Babbitt
author_sort	Alexandra M Schnoes
title	Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
title_short	Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
title_full	Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
title_fullStr	Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
title_full_unstemmed	Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
title_sort	annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/d399fec6c83b4f6a983821429be3ec92
work_keys_str_mv	AT alexandramschnoes annotationerrorinpublicdatabasesmisannotationofmolecularfunctioninenzymesuperfamilies AT shoshanadbrown annotationerrorinpublicdatabasesmisannotationofmolecularfunctioninenzymesuperfamilies AT igordodevski annotationerrorinpublicdatabasesmisannotationofmolecularfunctioninenzymesuperfamilies AT patriciacbabbitt annotationerrorinpublicdatabasesmisannotationofmolecularfunctioninenzymesuperfamilies
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Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

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