Abstract
BackgroundSystems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes.ResultsThe Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal.ConclusionsPSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.
Highlights
Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level
The capture and curation of published interaction data has been the work of interaction databases for many years, and many of these resources have collaborated through the Molecular Interaction workgroup of the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to create and maintain community data formats and standards [1]
Because the data required to describe cooperative interactions rarely comes from a single experiment, or may even need to be assembled from many distinct publications, they are treated as abstract interactions and in PSI-Molecular Interactions (MI) XML3.0, captured using the abstractInteraction element
Summary
All data resources using the IntAct database as their data storage repository, i.e., members of the IMEx Consortium [17] including IntAct, IID, InnateDB, MINT, DIP, MatrixDB, HPIDB routinely make their data available in PSI-MI XML3.0 in addition to the existing PSIMI XML2.5 and MITAB 2.7 formats. Curated protein complexes from the Complex Portal are made available in PSI-MI XML3.0. The PSI-MI maker software (https://github.com/MICommunity/psimi-maker-flattener), a desktop application that helps users to create PSI-MI XML documents and extract data from them, has been updated to support PSI-MI XML3.0. The new features included in PSI-MI XML 3.0 are currently being used to extend an existing tool suite, the MI Bundle, that integrates molecular, structural and genomics data and that already relies on the PSI-MI standard [18]
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