UniProt Knowledgebase: a hub of integrated protein data

Abstract

The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialized data collections. UniProtKB also integrates a range of data from other resources. All information is attributed to its original source, allowing users to trace the provenance of all data. The UniProt Consortium is committed to using and promoting common data exchange formats and technologies, and UniProtKB data is made freely available in a range of formats to facilitate integration with other databases. Database URL: http://www.uniprot.org/

Figure 1.

Flow diagram showing an outline of the UniProtKB manual curation process.

Figure 2.

Cross-references in a UniProtKB entry. This figure shows a subset of the cross-references provided in UniProtKB entry O54952.

Figure 3.

Binary protein–protein interactions in UniProtKB entry Q13541 which have been imported from IntAct. Each interaction is displayed on a separate line. The ‘With’ column contains the gene names of the interacting proteins. Accession numbers of interacting proteins are listed in the ‘Entry’ column. The ‘#Exp’ column provides the number of experiments in which an interaction has been observed. The ‘IntAct’ column contains the IntAct database accession numbers of the two interacting proteins. These are hyperlinked to provide users with access to the underlying data in the IntAct database. Specific information regarding the interaction may be present in the ‘Notes’ column.

Figure 4.

Information in a UniProtKB entry is linked to underlying data sources. The source of each data item is indicated and the source information is hyperlinked to allow users to access the original data source directly.

Figure 5.

Using the query builder on the UniProt website to refine a search. An initial query for insulin is further refined using the query builder to include a taxonomic restriction.

Figure 6.

Mapping database identifiers using the identifier mapping tool on the UniProt website. The identifier mapping tool allows mapping of UniProt identifiers to identifiers in a database referenced from UniProt or vice versa. Here, a set of RefSeq identifiers are mapped to the corresponding UniProtKB entries.