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

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.

HSF1Base: A Comprehensive Database of HSF1 (Heat Shock Factor 1) Target Genes

“…In addition, relevant high throughput transcriptomic and chromatin immunoprecipitation data were analyzed to support the biological relevance of predicted HSF1 targets. The format of the HSF1base is PSI-MITAB 2.8, an extended version of the PSI-MI tab-delimited format [24]. This uses standardized expression data denoted with a well-defined ID, thereby facilitating the accurate use of the database for systems biology.…”

VSM-box: General-purpose Interface for Biocuration and Knowledge Representation

“…(C) A vsm-box user-interface element that holds a template; plus functionality descriptions. For a vsm-box application, see CausalBuilder, which also produces MI2CAST and PSI-MITAB2.8 compliant data (Touré et al, 2020a(Touré et al, , 2020bPerfetto et al, 2019). taxon).…”

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

“…Yet since most physical interactions are known to be involved in regulatory processes, several knowledge base resources started to collect causal interactions by incorporating directionality information as well [4][5][6]. Therefore, the PSI-MI standard has been extended to also represent the causality of interactions through a direction and sign (up-or down-regulation) [7]. The extraction and annotation of causal interactions are predominantly performed via detailed manual curation of scientific publications [4]; but as techniques to infer causality through natural language processing [8] or 'omics data using prior knowledge [9][10][11] are also maturing, their results should also be supplied with the essential context details.…”

“…The extraction and annotation of causal interactions are predominantly performed via detailed manual curation of scientific publications [4]; but as techniques to infer causality through natural language processing [8] or 'omics data using prior knowledge [9][10][11] are also maturing, their results should also be supplied with the essential context details. Current formats of causal statements range from the simplest, with only two entities and the causal regulatory effect (e.g., the Simple Interaction Format (SIF) with "A activates B" or "A -> B"), to more complex statements including contextual description (e.g., BEL (Biological Expression Language, https://bel.bio/) [12], GO-CAM [13], and PSI-MITAB2.8 [7]). At present, various resources host molecular causal relationships (e.g., IntAct [14], SIGNOR [4,15], Causal Biological Network [16], SignaLink [5], TRRUST [17], TFacTS [18], DoRothEA [19]), each adhering to some of the formats mentioned above and annotated with specific controlled vocabularies (CVs) or ontologies (PSI-MI CV, Gene Ontology [20]).…”

“…In response to the "reproducibility crisis" in science [21], novel projects focus on setting up formal structures for data management with collaborations between domain experts [22][23][24]. For instance, the description of molecular interactions has been formalized by the Human Proteome Organization (HUPO) PSI-MI community [25], leading to standard guidelines (MIMIx [26]), exchange formats (PSI-MI TAB [7], PSI-MI XML [27]), and CVs (PSI-MI CV [28]). These standards are adopted by biological databases (e.g., IntAct [14], the IMEx Consortium [29], SIGNOR [4,15], Reactome [30]), and researchers are called upon to describe their data following these standards.…”