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Standardization in UniProtKB/Swiss-Prot

Serenella Ferro Rojas¹, Anne Morgat¹ & UniProt Consortium¹

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1. Swiss-Prot Group, Swiss Institute of Bioinformatics

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Document Type:

Poster

Date:

Received 04 May 2009 09:41 UTC; Posted 08 May 2009

Subjects:

Bioinformatics

Tags:

• Subcellular location
• Controlled Vocabularies
• metabolic pathways
• ontologies
• gene ontology
• UniProtKB
• Swiss-Prot
• annotation
• GO
• biocuration

Abstract:

Within the UniProt consortium, the UniProtKB/Swiss-Prot knowledge base provides the international community with a stable, comprehensive, fully classified, richly and accurately annotated protein sequence database that is fully operable with other databases. Annotation relates to function(s) of the protein (their catalytic activity and the corresponding metabolic pathway(s) in which the protein may be involved), their cellular location, their interactions with other cellular components, etc.

It is challenging to unify the way we annotate proteins, to ensure consistency and to describe data unambiguously. It is also highly valuable both for querying the database and for analyzing high-throughput data (expression data for instance).

Because it is of fundamental importance to use standardized nomenclatures, annotations in UniProtKB/Swiss-Prot are progressively moving towards controlled vocabularies (CVs) and ontologies.

Controlled vocabulary – or terminology – provides a list of concepts and text descriptions of their meaning. Concepts in a CV are often organized in a hierarchy.
Ontology provides a formal representation of knowledge with definitions of concepts, their attributes and relations between them.

As an illustration, we will describe the processes used to produce SUBCELLULAR and PATHWAY annotation sections in UniProtKB/Swiss-Prot. The CVs used in these two sections are based on in-house resources, UniProt subcell¹ and UniPathway² respectively. The links between these resources and other existing resources will be presented too, with a specific focus on Gene Ontology³ as we envisage using it extensively in order to describe protein functions or other biological processes.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Ferro Rojas, Serenella, Morgat, Anne, and Consortium, UniProt. Standardization in UniProtKB/Swiss-Prot. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3214.1> (2009)

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