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Introducing CI/CD Technologies to Optimize Software Development in Reactome

引入 CI/CD 技术优化 Reactome 软件开发

基本信息

批准号：
10839036
负责人：
PETER G DEUSTACHIO
金额：
$ 9.37万
依托单位：
ONTARIO INSTITUTE FOR CANCER RESEARCH
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-08-18 至 2027-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10839036
关键词：
Adopted Algorithms Basic Science Biological Biomedical Research Clinical Code Communities Computer software Controlled Vocabulary Data Analyses Databases Disease Doctor of Philosophy Ecosystem Ensure Feedback Funding Genomics Grant Human Internet Java Knowledge Literature Maintenance Manuals Mining Modeling Modernization Molecular Morphologic artifacts Ontology Parents Pathway interactions Peer Review Process Production Protocols documentation Publications Quality Control Readability Research Personnel Resources Running Scientist Services Staging Students System Technology Translational Research Update Variant Work aged base biological research cost data modeling data visualization experimental study graph database informatics tool interoperability knowledge graph knowledgebase member migration novel predictive modeling quality assurance relational database research study software development software infrastructure tool web app web site

项目摘要

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.

项目概要/摘要我们寻求对 Reactome 核心运营资金的补充支持人类生物途径和过程的知识库。 Reactome 是一个精心策划的知识库作为开放获取资源在线提供，可以免费使用和由生物和生物医学研究界的所有成员重新分发。它被用来由临床医生、基因组学研究人员和分子生物学家解释高生物信息学家寻求开发新算法的吞吐量实验研究从基因组研究中挖掘知识，并由系统生物学家构建预测模型正常和疾病变异途径。我们的策展人、博士级科学家与我们密切合作社区内的独立调查员收集机器可读的描述人类的生物学途径。在发布之前对途径进行检查和同行评审确保其事实准确性并符合数据模型。证据追踪系统确保主要文献支持所有主张。 Reactome 使用社区标准受控词汇和本体以提高跨资源的互操作性。途径定期审查和更新。反应组途径可在我们的网站上找到浏览、下载，并可使用内部和第三方分析工具。这该项目在文献中被高度引用，已被反复使用以产生重大的生物和临床发现，并被纳入许多高影响力的信息学工具和资源。在过去的二十年里，Reactome 开发了一套复杂的软件生态系统。该生态系统由各种组件组成，用于管理、质量保证/质量控制、数据分析和可视化、发布和导出。我们的小学父 Reactome 资助的重点是将旧的基于 GWT 的 Web 应用程序升级为现代基于 Angular 的应用程序，将独立的基于 Java 的 curator 工具移植到网络上，以及将我们的内部策展人数据库从 MySQL 迁移到 Neo4j。有了这个的支持补充补助金，我们的目标是引入现代持续集成/持续将 (CI/CD) 技术部署到我们的软件开发流程中。这将使我们能够更有效地更新现有组件并无缝集成新组件。我们还计划采用 LinkML（一种用于编辑知识图模式的现代工具）来管理我们的数据模型。我们将替换过时的多步数据模型更新协议，该协议依赖于 Perl 和 Protege，并且需要跨多个组件进行繁琐的手动编辑。在以下人员的帮助下这笔补充赠款，我们将使我们的软件开发更加精简和高效。