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Bioinformatics. 2019 Feb 21. pii: btz132. doi: 10.1093/bioinformatics/btz132. [Epub ahead of print]

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

Author information

1
Department of Biology, University of Rome Tor Vergata, Rome, Italy.
2
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.
3
Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
4
Computational Biology and Statistics, Target Sciences, GSK, UK.
5
IRCCS, Fondazione Santa Lucia, Rome, Italy.
6
Department of Genetics, Eötvös Loránd University, Budapest, Hungary.
7
Earlham Institute, Norwich, United Kingdom.
8
State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Life Omics, Beijing, China.
9
Quadram Institute, Norwich, United Kingdom.
10
Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
11
Department of Preclinical and Fundamental Science, Institute of Cardiovascular Science, University College London, United Kingdom.
12
Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.

Abstract

MOTIVATION:

Combining multiple layers of information underlying biological complexity into a structured framework represent a challenge in systems biology. A key task is the formalisation of such information in models describing how biological entities interact to mediate the response to external and internal signals. Several databases with signalling information, focus on capturing, organising and displaying signalling interactions by representing them as binary, causal relationships between biological entities. The curation efforts that build these individual databases demand a concerted effort to ensure interoperability among resources.

RESULTS:

Aware of the enormous benefits of standardisation efforts in the molecular interaction research field, representatives of the signalling network community agreed to extend the PSI-MI controlled vocabulary to include additional terms representing aspects of causal interactions.Here, we present a common standard for the representation and dissemination of signalling information: the PSI Causal Interaction tabular format (CausalTAB) which is an extension of the existing PSI-MI tab-delimited format, now designated PSI-MITAB 2.8. We define the new term "causal interaction", and related child terms, which are children of the PSI-MI "molecular interaction" term. The new vocabulary terms in this extended PSI-MI format will enable systems biologists to model large-scale signalling networks more precisely and with higher coverage than before.

AVAILABILITY:

PSI-MITAB 2.8 format and the new reference implementation of PSICQUIC are available on online at https://psicquic.github.io/ and https://psicquic.github.io/MITAB28Format.html.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

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