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UniProt release 2011_08

Published July 27, 2011


UniProt collaboration with IMEx for the annotation of protein interactions to MIMIx standard

UniProt is committed to the development and application of workflows and standards in the curation of biological data, its dissemination and exchange, and works with other consortia and data providers to achieve this. An example of this ongoing effort is the collaboration between UniProt and the International Molecular Exchange (IMEx) consortium.

The IMEx consortium is an international collaboration between a group of major public interaction data providers who share curation effort, and work to common curation rules using common standards. Our collaboration with IMEx will increase the flow of curated interaction data into IMEx, and will allow UniProt to leverage existing standards for the curation of protein interaction data and to contribute to the future development of such standards.

The standard we have chosen to adopt for the curation of protein interaction data in UniProt is the “minimum information required for reporting a molecular interaction experiment” standard, or MIMIx. MIMIx provides a useful compromise between free-text descriptions of protein interactions (which are difficult to parse) and the very detailed curation performed within IMEx (which aims to capture most experimental parameters). MIMIx-level annotation requires the accession numbers of the interacting proteins as well as a number of key experimental annotations made using terms from the Proteomics Standards Initiative (PSI) molecular interaction (MI) vocabulary. These annotations cover the type of interaction, the methods used to detect the interaction and identify the participants, the experimental roles of the participants, and the host organism in which the interaction was observed. MIMIx provides information that should be sufficient to allow a trained biologist to evaluate the biological relevance of an experimentally observed interaction.

UniProt curators have begun to curate protein interaction data to MIMIx standards as part of their normal workflow. Interactions are curated directly within the IntAct database, which forms the contact point between UniProt and the wider IMEx consortium. These curated interactions form a small part of the larger IntAct dataset which can be accessed from the IntAct website. A subset of presumably reliable interactions is extracted from the IntAct dataset and made available within the ‘Binary interactions’ section of UniProtKB entries (see for example entry Q13426). From UniProt release 2011_09, export from IntAct to UniProt will be determined using a simple scoring system developed by IntAct, coupled to a score threshold that has been deliberately chosen to exclude interactions supported by only one experimental observation. Further details of how interactions are scored can be found at the IntAct website. This simple score-based filter will be used in combination with a set of defined rules that excludes certain types of data, such as interactions that have been inferred but not experimentally proven.

We anticipate that these developments will enhance the availability and usability of high quality protein interaction data within UniProtKB, and promote the use of the MIMIx in reporting such data. We welcome feedback on this development and other curation standards.

UniProtKB News

Changes concerning the controlled vocabulary for PTMs

New terms for the feature key ‘Cross-link’ (‘CROSSLNK’ in the flat file):
  • (2-aminosuccinimidyl)acetic acid (Asn-Gly)
  • N,N-(cysteine-1,S-diyl)phenylalanine (Cys-Phe)
New term for the feature key ‘Modified residue’ (‘MOD_RES’ in the flat file):
  • S-bacillithiol cysteine disulfide
Modified terms for the feature key ‘Modified residue’ (‘MOD_RES’ in the flat file):
  • 4-amino-3-isothiazolidinone serine (Cys-Ser) > N,N(cysteine-1,S-diyl)serine (Cys-Ser)