Wednesday – October 27, 2010
Amphimax, room 414
Dr. Ursula Hinz
Swiss-Prot group, Swiss Institute of Bioinformatics
The UniProt/Swiss-Prot Knowledgebase: a hub for information about proteins
The UniProt Knowledgebase (UniProtKB, http://www.uniprot.org) is a source of valuable information about proteins, due to high-quality manual and automated annotation, and provides cross-references to over 120 databases, including wwPDB member sites and the Protein Model Portal. Within UniProtKB, UniProtKB/Swiss-Prot contains entries that are manually annotated, while UniProtKB/TrEMBL contains entries that are automatically annotated. UniProtKB/Swiss-Prot entries combine the manually verified sequence with experimental evidence derived from biochemical and genetic analyses, 3D-structures, mutagenesis experiments, information about protein interactions and post-translational modifications, and the corresponding source citations from the literature. Each UniProtKB/Swiss-Prot entry also includes both the official nomenclature and the synonyms found in the literature, and thereby facilitates finding relevant information, or selecting targets for new experiments.
The UniProt Knowledgebase avoids duplicating the efforts of other resources and aims to function as a hub that actively promotes collaborations and exchanges with other databases and resources. No single institution can keep up with all the available information. Hence, reciprocal links between specialized databases and resources are essential to provide the scientific community with easy access to a plethora of related and complementary knowledge.
UniProtKB/Swiss-Prot prioritizes the curation of proteins from model organisms and proteins with 3D-structures. UniProt curators extract information from scientific publications and combine it with information derived from protein 3D-structures including the positions of enzyme active sites, post-translational modifications, and binding sites for physiologically relevant ligands such as metal ions, cofactors, substrates and effectors. The combined results are displayed in dedicated line types, using many controlled vocabularies, to facilitate queries and information retrieval.