Reactome: new services and widgets to ease third-party integration
Year: 2016
Type: other
Abstract: Reactome (http://www.reactome.org) is a free, open-source, curated and peer-reviewed knowledge base of biomolecular pathways. It aims to provide intuitive bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education. Thus, the mainstays of its software development are usability and responsiveness from the user’s point of view, likewise modularity and reusability from the developer’s side. Reactome offers web services and widgets (http://goo.gl/koRvhp) to facilitate integration in third-party software. One service provides database access while the other performs overrepresentation and expression analysis as well as species comparison. Widgets for the Pathways Overview and Pathway Diagrams are provided for JavaScript and GWT. Both widgets overlay the results of the Analysis Service. Protein-protein or protein-chemical interactions can be used to extend pathways beyond Reactome’s curated content. IntAct is the default resource but all other PSICQUIC databases can be selected and in addition, users can submit custom interactions. Interaction data from IntAct are also included in the Reactome main search and the Analysis Service, helping users identify pathways of interest. In summary, Reactome has facilitated data integration by providing easy-to-use services and reusable widgets. Several resources such as OpenTargets (https://www.targetvalidation.org/), ChEBI (https://www.ebi.ac.uk/chebi/), BluePrint (http://dcc.blueprint-epigenome.eu/), PRIDE (http://www.ebi.ac.uk/pride/archive/), PINT (http://sealion.scripps.edu/pint/) and IP2 (http://goldfish.scripps.edu) have already integrated these services and widgets.
Institution: European Bioinformatics Institute
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W2618108099