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Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, Touré V, Zobolas J, Licata L. CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinformatics 2020; 35:3779-3785. [PMID: 30793173 DOI: 10.1093/bioinformatics/btz132] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/01/2019] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
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 formalization 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, organizing 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 standardization 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 AND IMPLEMENTATION PSI-MITAB 2.8 format and the new reference implementation of PSICQUIC are available online (https://psicquic.github.io/ and https://psicquic.github.io/MITAB28Format.html). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- L Perfetto
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - M L Acencio
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - G Bradley
- Computational Biology and Statistics, Target Sciences, GSK, UK
| | - G Cesareni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.,IRCCS, Fondazione Santa Lucia, Rome, Italy
| | - N Del Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - D Fazekas
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary.,Earlham Institute, Norwich, UK
| | - H Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.,State Key Laboratory of Proteomics, Beijing Institute of Life Omics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, China
| | - T Korcsmaros
- Earlham Institute, Norwich, UK.,Quadram Institute, Norwich, UK
| | - M Kuiper
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - A Lægreid
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - P Lo Surdo
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - R C Lovering
- Department of Preclinical and Fundamental Science, Institute of Cardiovascular Science, University College London, UK
| | - S Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - P Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - P D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - V Touré
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - J Zobolas
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - L Licata
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
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