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:
- 金额:$ 9.37万
- 依托单位:
- 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:
- 关键词:AdoptedAlgorithmsBasic ScienceBiologicalBiomedical ResearchClinicalCodeCommunitiesComputer softwareControlled VocabularyData AnalysesDatabasesDiseaseDoctor of PhilosophyEcosystemEnsureFeedbackFundingGenomicsGrantHumanInternetJavaKnowledgeLiteratureMaintenanceManualsMiningModelingModernizationMolecularMorphologic artifactsOntologyParentsPathway interactionsPeer ReviewProcessProductionProtocols documentationPublicationsQuality ControlReadabilityResearch PersonnelResourcesRunningScientistServicesStagingStudentsSystemTechnologyTranslational ResearchUpdateVariantWorkagedbasebiological researchcostdata modelingdata visualizationexperimental studygraph databaseinformatics toolinteroperabilityknowledge graphknowledgebasemembermigrationnovelpredictive modelingquality assurancerelational databaseresearch studysoftware developmentsoftware infrastructuretoolweb appweb 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.
项目总结/文摘
项目成果
期刊论文数量(1)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis.
- DOI:10.1093/nar/gkad1052
- 发表时间:2024-01-05
- 期刊:
- 影响因子:14.9
- 作者:
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PETER G DEUSTACHIO其他文献
PETER G DEUSTACHIO的其他文献
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{{ truncateString('PETER G DEUSTACHIO', 18)}}的其他基金
Reactome: An Open Knowledgebase of Human Pathways.
Reactome:人类通路的开放知识库。
- 批准号:
10341517 - 财政年份:2022
- 资助金额:
$ 9.37万 - 项目类别:
Reactome: An Open Knowledgebase of Human Pathways.
Reactome:人类通路的开放知识库。
- 批准号:
10685940 - 财政年份:2022
- 资助金额:
$ 9.37万 - 项目类别:
Reactome and the Gene Ontology: Digital pathway convergence for core data resources
Reactome 和基因本体:核心数据资源的数字路径融合
- 批准号:
10657749 - 财政年份:2021
- 资助金额:
$ 9.37万 - 项目类别:
Reactome and the Gene Ontology: Digital pathway convergence for core data resources
Reactome 和基因本体:核心数据资源的数字路径融合
- 批准号:
10270593 - 财政年份:2021
- 资助金额:
$ 9.37万 - 项目类别:
Reactome and the Gene Ontology: Digital pathway convergence for core data resources
Reactome 和基因本体:核心数据资源的数字路径融合
- 批准号:
10494099 - 财政年份:2021
- 资助金额:
$ 9.37万 - 项目类别:
Reactome IDG portal: Pathway-based analysis and visualization of understudied human proteins
Reactome IDG 门户:对正在研究的人类蛋白质进行基于通路的分析和可视化
- 批准号:
9904593 - 财政年份:2019
- 资助金额:
$ 9.37万 - 项目类别:
Reactome IDG portal: Pathway-based analysis and visualization of understudied human proteins
Reactome IDG 门户:对正在研究的人类蛋白质进行基于通路的分析和可视化
- 批准号:
10348828 - 财政年份:2019
- 资助金额:
$ 9.37万 - 项目类别:
Rapid and Precise Molecular Pathway Modelling of the SARS-CoV-1 and SARS-CoV-2 Infection Cycle with Human Host Protein and Therapeutic Interactions
SARS-CoV-1 和 SARS-CoV-2 与人类宿主蛋白的感染周期和治疗相互作用的快速、精确的分子途径建模
- 批准号:
10165320 - 财政年份:2007
- 资助金额:
$ 9.37万 - 项目类别:
Reactome: An Open Knowledgebase of Human Pathways
Reactome:人类通路的开放知识库
- 批准号:
9451318 - 财政年份:2007
- 资助金额:
$ 9.37万 - 项目类别:
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