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Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
M Sivade Dumousseau1, D Alonso-López2, M Ammari3
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
BMC Bioinformatics
|April 13, 2018
Summary
The PSI-MI XML 3.0 format now supports complex molecular interaction data, expanding beyond basic experimental information. This updated standard, developed with community input, enhances systems biology research by accommodating new data types and use cases.
Area of Science:
- Systems Biology
- Molecular Interaction Data
- Bioinformatics Data Standards
Background:
- Systems biologists require high-quality molecular interaction datasets in standard formats for analyzing cellular behavior.
- The existing PSI-XML 2.5 standard accommodates basic experimental data but struggles with new use cases like allosteric interactions, protein complexes, and dynamic data.
- Advanced analysis requires linking kinetic and affinity data to specific mutations, which current formats do not fully support.
Purpose of the Study:
- To extend the PSI-MI XML interchange format to meet emerging use cases and capture new data types in molecular interactions.
- To develop an updated standard that accommodates complex data beyond simple experimental readouts.
- To ensure continued support and development of tools compatible with the new format.
Main Methods:
- Community consultation involving data producers, users, and tool developers within the HUPO-PSI Molecular Interaction workgroup.
- Extension of the existing PSI-MI XML standard to incorporate new data types and functionalities.
- Development and implementation of a compatible tool suite to support the updated format.
Main Results:
- The development and release of PSI-MI XML 3.0, an enhanced version of the molecular interaction data interchange format.
- PSI-MI XML 3.0 expands capabilities beyond simple experimental data to include complex interactions and data types.
- Key data producers, including the International Molecular Exchange (IMEx) Consortium and Complex Portal, have adopted the new format.
Conclusions:
- PSI-MI XML 3.0 has been developed collaboratively by stakeholders in the molecular interaction data ecosystem.
- The PSI-MI workgroup actively supports PSI-MI XML 2.5 for experimental data, PSI-MI XML 3.0 for complex data, and MITAB formats for rapid data exchange.
- The new format addresses limitations of previous versions, enabling more comprehensive analysis in systems biology.
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