Introducing CI/CD Technologies to Optimize Software Development in Reactome

Ontario Institute For Cancer Research, Toronto ON

Investigators

Linked publications, trials & patents

Abstract

Project Summary/Abstract We seek supplemental support to the core operating funding for the Reactome Knowledgebase of human biological pathways and processes. Reactome is a curated knowledgebase available online as an open access resource that can be freely used and redistributed by all members of the biological and biomedical research communities. It is used by clinicians, genomics researchers, and molecular biologists to interpret the results of high- throughput experimental studies, by bioinformaticians seeking to develop novel algorithms for mining knowledge from genomic studies, and by systems biologists building predictive models of normal and disease variant pathways. Our curators, Ph.D.-level scientists, work closely with independent investigators within the community to assemble machine-readable descriptions of human biological pathways. Pathways are checked and peer-reviewed prior to publication to ensure its factual accuracy and compliance with the data model. A system of evidence tracking ensures that the primary literature supports all assertions. Reactome uses community-standard controlled vocabularies and ontologies to increase interoperability across resources. Pathways are reviewed and updated regularly. Reactome pathways are available on our website for browsing, downloading, and are accessible to in-house and third-party analysis tools. The project is highly cited in the literature, has been used repeatedly to make significant biological and clinical discoveries, and is incorporated into many high-impact informatics tools and resources. Over the past two decades, Reactome has developed a sophisticated software ecosystem. This ecosystem comprises various components for curation, quality assurance/quality control, data analysis and visualization, release, and export. Our primary focus in the parent Reactome grant is to upgrade the old GWT-based web application to a modern Angular-based app, port the standalone Java-based curator tool to the web, and migrate our internal curator database from MySQL to Neo4j. With the backing of this supplemental grant, we aim to introduce modern Continuous Integration/Continuous Deployment (CI/CD) technologies into our software development process. This will allow us to update existing components more efficiently and integrate new ones seamlessly. We also plan to adopt LinkML, a modern tool for editing knowledge graph schemas, to manage our data model. We will replace the outdated multi-step data model update protocol, which relies on Perl and Protege and requires tedious manual editing across multiple components. With the help of this supplemental grant, we will make our software development more streamlined and efficient.