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. PanniP. Porras, S. Ricard-Blum, B. Roechert, L. Salwinski, A. Shrivastava, J. Sullivan, N. Thierry-Mieg, Y. Yehudi, K. Van Roey, S. Orchard

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35 Citations (Scopus)

Abstract

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.
Original languageEnglish
JournalBMC Bioinformatics
Volume19
Issue number1
DOIs
Publication statusPublished or Issued - 2018

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