The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

Abstract

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

An integrated map of corticotropin‐releasing hormone signaling pathway

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Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancer

“…With the rapidly expanding pool of proteomic data, there is a need for standards for exchanging data [60,61]. This is similar to the situation in cDNA microarray data [62].…”

“…The hope is to avoid repetition and to allow for better comparisons between studies for more definitive answers. Recent initiatives by HUPO have addressed this issue [60,61].…”

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