Yasmin Alam-Faruque

English

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Email: help@uniprot.org
URL: www.uniprot.org
     www.ebi.ac.uk/intact
European Bioinformatics Institute (EMBL-EBI)
Swiss Institute of Bioinformatics (SIB)
Protein Information Resource (PIR)
THE RELATIONSHIP BETWEEN THE UNIPROT 
KNOWLEDGEBASE (UNIPROTKB) AND INTACT 
MOLECULAR INTERACTION DATABASES.
Yasmin Alam-Faruque (PhD)1 , The IntAct Team1, and UniProt Consortium1,2,3
1European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
2Swiss Institute of Bioinformatics, Geneva, Switzerland
3Protein Information Resource, Georgetown University, Washington DC, USA
UniProtKB, IntAct and their relationship.
UniProt (Universal Protein Resource) provides a central resource on 
protein sequences and functional annotation [1].
UniProt Knowledgebase (UniProtKB) contains reviewed, high quality 
manually annotated, non-redundant protein sequence records in the 
UniProtKB/Swiss-Prot section,  and the unreviewed, automatically 
annotated  protein sequence records in the UniProtKB/TrEMBL section. 
Within a UniProtKB/SwissProt entry, information from literature is added 
by the curator (via the CRISP editor) to a referenced general annotation 
section (providing information such as function, tissue specificity, 
developmental-specific expression, subunit structure, subcellular 
location, disease, isoforms, binary interactions), a feature table (FT) 
(showing domains/sites of interest with illustrations) and extensive 
cross-linking to other databases (e.g. IntAct, GO, EMBL, Ensembl, 
HGNC, OMIM, PDB, InterPro, ArrayExpress, PRIDE, KEGG, GeneID).
Interaction information from the literature is added to the SUBUNIT 
comment, the Reference citation/ Reference position (RP) of the 
relevant publication and within the FT sections within the UniProtKB 
entry. There may also be a single INTERACTION comment present 
within an entry which conveys information relevant to binary protein-
protein interactions. This is automatically derived from the IntAct 
database, along with the database cross-reference DR line and is 
updated on a tri-weekly basis.
Statistics: Release 57.0 (of 24-Mar-09) of UniProtKB/Swiss-Prot contains 428650 sequence entries. 
IntAct provides a freely available, open source database system and 
analysis tools for protein-protein interaction data [2] . 
All interactions are derived from literature curation or direct submissions 
and all experimental information relating to binary protein-protein 
interactions is entered into the IntAct database by curators, via a web-
based editor for Experiment, Interaction, Biosource, Protein, Small 
molecule, Nucleic acid and controlled vocabularies.
Interactions can be derived by any appropriate experimental method as 
described by the HUPO PSI-MI controlled vocabularies, in order to be 
successfully exported to the UniProtKB database.
UniProtKB export is based on the method used to detect interaction. 
Methods deemed to demonstrate high quality binary interactions are 
exported to the general annotation section. Complementation assays 
require validation by a second method before export. For 
INTERACTION comment and DR line export, all proteins with 
interactions obeying the above criteria are exported. In addition, 
interactions judged by the curators to be high confidence are also 
exported. 
You can perform a search within the IntAct database using: 
Gene name: DMD;  UniProtKB AC: P11532;  UniProtKB ID: 
DMD_HUMAN or PubMed ID: 16000376.
There are links from the IntAct database to several other databases 
including UniProtKB, GO and InterPro.
Statistics: The IntAct Database (March-09) contains: 189082 binary interactions, comprising 56985 
proteins and 10192 experiments.
Acknowledgements
UniProt is supported by grants from the National Institutes of Health, European Commission, Swiss Federal Government and PATRIC BRC.
IntAct is funded by the European Commission under FELICS, contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme.
European Bioinformatics Institute
References:
[1] The Universal Protein Resource (UniProt) 2009 The UniProt Consortium Nucleic Acids Res. Jan 2009 37: D169-74   PMID: 18836194. 
[2] IntAct – Open Source Resource for Molecular Interaction Data S Kerrien, Y Alam-Faruque et al. Nucleic Acids Res. Jan 2007 35: D561-565  PMID:17145710.
Features within a UniProtKB/SwissProt entry leading to connection with the IntAct database:
In addition to a ‘Subunit structure’ annotation comment within a 
UniProtKB/SwissProt entry, there may be an ‘Interaction’ /  ‘Binary 
interactions’ section which contains a link to IntAct that provides detailed 
information for the experimental support. 
A graphical representation of the interactions can also be viewed:
There is also a ‘Protein-protein interaction 
database’ / ‘DR’ cross-reference section within 
the entry which directs the user to additional 
interaction data for that molecule within IntAct.
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The Relationship between the UniProt Knowledgebase (UniProtKB) and the IntAct Molecular Interaction Databases

http://precedings.nature.com/documents/3936/version/1/files/npre20093936-1.pdf

The Relationship between the UniProt Knowledgebase (UniProtKB) and the IntAct Molecular Interaction Databases

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