Application of text-mining for updating protein post-translational modification annotation in UniProtKB.

Détails

Ressource 1Télécharger: BIB_D000C70905CF.P001.pdf (944.61 [Ko])
Etat: Public
Version: de l'auteur
ID Serval
serval:BIB_D000C70905CF
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Application of text-mining for updating protein post-translational modification annotation in UniProtKB.
Périodique
BMC Bioinformatics
Auteur(s)
Veuthey A.L., Bridge A., Gobeill J., Ruch P., McEntyre J.R., Bougueleret L., Xenarios I.
ISSN
1471-2105 (Electronic)
ISSN-L
1471-2105
Statut éditorial
Publié
Date de publication
2013
Volume
14
Pages
104
Langue
anglais
Résumé
BACKGROUND: The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have developed a system which extracts information from the scientific literature for the most frequently annotated PTMs in UniProtKB.
RESULTS: The procedure uses a pattern-matching and rule-based approach to extract sentences with information on the type and site of modification. A ranked list of protein candidates for the modification is also provided. For PTM extraction, precision varies from 57% to 94%, and recall from 75% to 95%, according to the type of modification. The procedure was used to track new publications on PTMs and to recover potential supporting evidence for phosphorylation sites annotated based on the results of large scale proteomics experiments.
CONCLUSIONS: The information retrieval and extraction method we have developed in this study forms the basis of a simple tool for the manual curation of protein post-translational modifications in UniProtKB/Swiss-Prot. Our work demonstrates that even simple text-mining tools can be effectively adapted for database curation tasks, providing that a thorough understanding of the working process and requirements are first obtained. This system can be accessed at http://eagl.unige.ch/PTM/.
Mots-clé
Data Mining/methods, Databases, Protein, Humans, Knowledge Bases, Molecular Sequence Annotation, Protein Processing, Post-Translational, Proteomics
Pubmed
Web of science
Open Access
Oui
Création de la notice
12/02/2014 17:35
Dernière modification de la notice
20/08/2019 15:50
Données d'usage