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

Bioinformatics
Livia PerfettoLuana Licata

Abstract

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. 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...Continue Reading

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Citations

Oct 11, 2019·Nucleic Acids Research·Marta IannuccelliGianni Cesareni
Nov 23, 2019·International Journal of Molecular Sciences·Dániel KovácsJános Barna
Oct 31, 2019·Nucleic Acids Research·Luana LicataGianni Cesareni
Jul 9, 2020·Bioinformatics·Vasundra TouréMartin Kuiper
Dec 3, 2020·Nature Communications·Pablo PorrasSandra Orchard
Aug 16, 2019·Emerging Topics in Life Sciences·J Harry Caufield, Peipei Ping
Feb 7, 2021·Database : the Journal of Biological Databases and Curation·Vasundra TouréSteven Vercruysse
Mar 8, 2021·Nucleic Acids Research·Birgit H M MeldalPablo Porras
Jun 29, 2021·Frontiers in Genetics·Gianni CesareniLivia Perfetto
Oct 12, 2021·Nucleic Acids Research·Luca CsabaiTamás Korcsmáros

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