Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
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Date
2018-04-11
Authors
Sivade Dumousseau, M
Alonso-Lopez, Diego
Ammari, Mais
Bradley, Glyn
Campbell, Nancy H
Ceol, Arnaud
Cesareni, Gianni
Combe, Colin W
De Las Rivas, Javier
Del-Toro, Noemi
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Rights
© The Author(s). 2018
Rights Holder
The Author(s).
Abstract
Abstract
Background
Systems 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.
Results
The 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.
Conclusions
PSI-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.
Description
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Keywords
Molecular interactions, Protein-protein interaction, Protein complexes, Data standards, XML, HUPO-PSI, PSI-MI
Citation
Sivade, M., Alonso-López, D., Ammari, M., Bradley, G., Campbell, N. H., Ceol, A., … Orchard, S. (2018). Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics, 19(1). https://doi.org/10.1186/s12859-018-2118-1