BMC Bioinformatics (Apr 2018)

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

  • M. Sivade (Dumousseau),
  • D. Alonso-López,
  • M. Ammari,
  • G. Bradley,
  • N. H. Campbell,
  • A. Ceol,
  • G. Cesareni,
  • C. Combe,
  • J. De Las Rivas,
  • N. del-Toro,
  • J. Heimbach,
  • H. Hermjakob,
  • I. Jurisica,
  • M. Koch,
  • L. Licata,
  • R. C. Lovering,
  • D. J. Lynn,
  • B. H. M. Meldal,
  • G. Micklem,
  • S. Panni,
  • P. Porras,
  • S. Ricard-Blum,
  • B. Roechert,
  • L. Salwinski,
  • A. Shrivastava,
  • J. Sullivan,
  • N. Thierry-Mieg,
  • Y. Yehudi,
  • K. Van Roey,
  • S. Orchard

DOI
https://doi.org/10.1186/s12859-018-2118-1
Journal volume & issue
Vol. 19, no. 1
pp. 1 – 8

Abstract

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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.

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