title: Annotation of post-translational modifications in the Swiss-Prot knowledge base.
abstract: High-throughput proteomic studies produce a wealth of new information regarding post-translational modifications (PTMs). The Swiss-Prot knowledge base is faced with the challenge of including this information in a consistent and structured way, in order to facilitate easy retrieval and promote understanding by biologist expert users as well as computer programs. We are therefore standardizing the annotation of PTM features represented in Swiss-Prot. Indeed, a controlled vocabulary has been associated with every described PTM. In this paper, we present the major update of the feature annotation, and, by showing a few examples, explain how the annotation is implemented and what it means. Mod-Prot, a future companion database of Swiss-Prot, devoted to the biological aspects of PTMs (i.e., general description of the process, identity of the modification enzyme(s), taxonomic range, mass modification) is briefly described. Finally we encourage once again the scientific community (i.e., both individual researchers and database maintainers) to interact with us, so that we can continuously enhance the quality and swiftness of our services.
authors.affiliation: Swiss Institute of Bioinformatics, Centre Médical Universitaire, Geneva, Switzerland. nathalie.farriol-mathis@isb-sib.ch
authors.forename: Nathalie
authors.initials: N
authors.lastname: Farriol-Mathis
authors.forename: John S
authors.initials: JS
authors.lastname: Garavelli
authors.forename: Brigitte
authors.initials: B
authors.lastname: Boeckmann
authors.forename: Séverine
authors.initials: S
authors.lastname: Duvaud
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Gasteiger
authors.forename: Alain
authors.initials: A
authors.lastname: Gateau
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Veuthey
authors.forename: Amos
authors.initials: A
authors.lastname: Bairoch
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein / Q000592:standards; D005544:Forecasting; D007256:Information Systems; D011499:Protein Processing, Post-Translational; D020539:Sequence Analysis, Protein; D018511:Systems Integration