Proteomics databases made available
The study of the proteome, the entire set of proteins produced by an organism in its complexity, is the subject of proteomics. To understand the biology of a single protein within the cellular environment, it is necessary to know the molecules with which it interacts. Protein interaction data is generated by many different methods. Collating this information is the work of the many interaction databases in existence today. The 'International Molecular Exchange' consortium (IMEx) optimised the services that these databases provide to the community. It introduced managed curation, to produce a single, non-redundant dataset, consistently annotated to a uniformly high standard. Recently the EU-funded PSIMEX (Proteomics standards international molecular exchange - systematic capture of published molecular interaction data) project took the next step, transitioning the IMEx from exploratory to full production mode. PSIMEX developed a portal for access to aggregated data on protein interactions stored in databases across Europe. By the end of August 2013, IMEx included ten databases, serving 284 402 interactions available from 8 067 publications. The IMEx Central database assigned unique identifiers to each publication. A sophisticated web-based tool to manage data so it is fit for reuse and preservation (curation) allows new resources to perform IMEx-level curation directly in IntAct, an open source molecular interaction database used by PSIMEX. All data can be accessed either at a central website or locally, at the member database websites. All data and software are freely available to the scientific community for use under the 'Creative Commons' attribution license. PSIMEX also supported a series of workshops to teach attendees how to use the data in large-scale network analysis. Online teaching modules, tutorials and instructions for new users provide the necessary instruction. The enhanced accessibility of proteomics data through PSIMEX will benefit public health and European agriculture by facilitating the development of new pharmaceuticals, bioceuticals and pesticides.
Keywords
Proteomics, database, molecular, curation, publication
