Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

Abstract

Background: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions.

Protein Interactome and Its Application to Protein Function Prediction

“…On the other hand, some of proteins form stable complexes where the participants in the complexes permanently interact with each other. Various PPI types are defined in standard and annotated across many PPI databases (Cote et al, 2010;Kerrien et al, 2007).…”

Complex Portal - A Unifying Protein Complex Database

“…PDB IDs) and species IDs and names can be used as query terms. Data is available via our web service or our ftp site in the new MI-JSON format, in the standard interaction formats [3], PSI-MI XML 2.5 & 3.0, and in a bespoke, tab-delimited format, ComplexTAB. Other formats can be made available on request.…”

The MINTAct Archive for Mutations Influencing Molecular Interactions

“…In light of that need, we have also adapted the PSI-MI standard format [2] to its 3.0 version 1 , enabling new fields that can capture the sequence changes in a consistent manner. Our effort has resulted in what to our knowledge represents the biggest dataset of its type: a high-quality, experimentally derived and manually curated list featuring mutations affecting interactions.…”