Knowledge Management Center for Illuminating the Druggable Genome

阐明可药物基因组的知识管理中心

• 批准号: 10598542
• 负责人: Jeremy S Edwards
• 金额: $ 94.01万
• 依托单位: UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-01-03 至 2024-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10598542
• 关键词: Acceleration; Address; Adoption; Age; Alleles; Archives; Articulation; Basic Science; Biological Sciences; Biology; Biomedical Research; Chemistry; Code; Communities; Community Outreach; Computer software; Coupled; Data; Data Analytics; Data Element; Data Set; Databases; Dependence; Disease; Documentation; FAIR principles; Family; Feedback; Funding; Future; Generations; Genes; Genome; Genome Components; Genotype; Goals; Grant; Healthcare; Human; Informatics; International; Internet; Knowledge; Knowledge Management; Knowledge Management Center; Life; Link; Machine Learning; Manuals; Maps; Medicine; Metadata; Methods; Modeling; Mutation; Non-Human Protein; Ontology; Pathway interactions; Performance; Phase; Phenotype; Process; Protein Isoforms; Proteins; Proteome; Public Domains; Publications; Reagent; Research Domain Criteria; Resources; Scientist; Series; Services; Source; Structure; System; Translational Research; Trees; United States National Institutes of Health; Update; Work; analytical method; base; computer science; data ecosystem; data integration; data resource; design; disease classification; experience; gender difference; genome resource; health data; improved; interest; knowledge base; knowledge graph; knowledgebase; member; novel; online community; outreach; programs; public repository; repository; therapeutic protein; tool; web site

The main goal of the Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) program is to aggregate, update and articulate protein-centric data, information and knowledge for the entire human proteome with emphasis on understudied proteins from the 3 families that are the focus of the IDG (“IDG List”). The long-term objective of the KMC is to encourage and support biomedical research aimed at understudied proteins by providing an extensive resource of data, information, knowledge, methods and reagents for the entire human proteome, and to support the growing online community focused on understudied proteins. With focus on the IDG List and human proteins, the KMC will enable support for expanded coverage for non-human proteins of therapeutic interest and other associated human health data, in order to catalyze novel biomedical discoveries. To support the overall IDG objective, and to maintain, update and improve these integrated resources, the KMC draws upon expertise from multiple knowledge domains, specifically biology, chemistry and medicine, as well as computer science, graphic design and web programming. Specifically, for the Phase 2 of the IDG KMC we propose 4 Aims:1. Create an automated workflow that captures relevant public data for the entire proteome and manual annotations for the IDG list. The KMC knowledge management system will be built around knowledge graphs, focused on five major branches of the target knowledge tree, tkt: Genotype, Phenotype, Expression, Structure & Function, and Interactions & Pathways, respectively. Aim 2: Design, develop and implement a protein knowledgebase with Data Analytics support. Our protein-centric biomedical knowledge base, TCKB (Target Central Knowledgebase) will be comprised of the data, knowledge and information container, together with its codebase and software pipelines. TCKB will be the repository for experimental, processed and computed data and reagents originating from the IDG DRGCs (Data and Resource Generation Centers). We will provide informatics and modeling support for DRGC activities. Aim 3: We will expand, improve and maintain Pharos. Particularly “knowledge packages,” support automated data summaries for Protein Dossiers, and actively seek feedback from our community. Aim 4. Outreach to scientific community. We will support a series of activities that will leverage TCKB, Pharos and other IDG resources to increase adoption of IDG work, while observing FAIR (findable, accessible, interoperable, reusable) principles for our knowledgebase, portal and pipelines. The KMC will engage in community outreach by leading tutorials and feedback sessions and dissemination of the Pharos system. To meet its goals, the KMC will coordinate all core activities in close coordination with the IDG Steering Committee and IDG Project Scientists (PS), and include members of the IDG Consortium (IDG- C), other NIH Common Fund programs, NIH Commons, as well as other initiatives.

知识管理中心（KMC）的主要目标是照亮可药用基因组（IDG） 该计划的目的是为整个人类聚集、更新和表达以蛋白质为中心的数据、信息和知识。 人类蛋白质组，重点是来自IDG重点关注的3个家族的未充分研究的蛋白质 （“IDG名单”）。KMC的长期目标是鼓励和支持生物医学研究， 通过提供广泛的数据，信息，知识，方法和 整个人类蛋白质组的试剂，并支持不断增长的在线社区， 研究不足的蛋白质。KMC将重点关注IDG清单和人类蛋白质， 扩大了具有治疗意义的非人类蛋白质和其他相关人类健康数据的覆盖范围， 以促进新的生物医学发现。支持IDG的总体目标，并维护、更新 并改善这些综合资源，KMC利用来自多个知识领域的专业知识， 特别是生物学、化学和医学，以及计算机科学、平面设计和网络 编程.具体来说，对于IDG KMC的第二阶段，我们提出了4个目标：1。创建一个自动化 工作流程，捕获整个蛋白质组的相关公共数据和IDG列表的手动注释。 KMC知识管理系统将围绕知识图谱构建，重点关注五个主要方面。 目标知识树的分支，tkt：基因型、表型、表达、结构和功能，以及 互动和路径，分别。目标2：设计、开发和实现蛋白质知识库， 数据分析支持。我们以蛋白质为中心的生物医学知识库，TCKB（目标中心 知识库）将由数据、知识和信息容器及其 代码库和软件管道。TCKB将是实验、处理和计算数据的储存库 以及源自IDG DRGCs（数据和资源生成中心）的试剂。我们将提供 为DRGC活动提供信息学和建模支持。目标3：我们将扩大，改善和维护灯塔。 特别是“知识包”，支持蛋白质档案的自动数据汇总，并积极寻求 来自我们社区的反馈。目标4。与科学界的联系。我们将支持一系列活动 这将利用TCKB、Pharos和其他IDG资源来提高IDG工作的采用率，同时观察 我们的知识库、门户和管道的公平（可查找、可访问、可互操作、可重用）原则。 KMC将通过领导教程和反馈会议以及传播 灯塔系统为了实现其目标，KMC将与联合国密切协调所有核心活动。 IDG指导委员会和IDG项目科学家（PS），并包括IDG联盟（IDG- C），其他NIH共同基金计划，NIH共享，以及其他举措。

项目成果

Molecular Complexity: You Know It When You See It.

分子复杂性：当你看到它时你就知道它。

• DOI: 10.1021/acs.jmedchem.3c01507
• 发表时间: 2023
• 期刊: Journal of medicinal chemistry
• 影响因子: 7.3
• 作者: Oprea,TudorI;Bologa,Cristian
• 通讯作者: Bologa,Cristian

DrugCentral 2021 supports drug discovery and repositioning.

• DOI: 10.1093/nar/gkaa997
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Avram S;Bologa CG;Holmes J;Bocci G;Wilson TB;Nguyen DT;Curpan R;Halip L;Bora A;Yang JJ;Knockel J;Sirimulla S;Ursu O;Oprea TI
• 通讯作者: Oprea TI

AlphaFold illuminates half of the dark human proteins.

• DOI: 10.1016/j.sbi.2022.102372
• 发表时间: 2022-06
• 期刊: CURRENT OPINION IN STRUCTURAL BIOLOGY
• 影响因子: 6.8
• 作者: Binder, Jessica L.;Berendzen, Joel;Stevens, Amy O.;He, Yi;Wang, Jian;Dokholyan, Nikolay, V;Oprea, Tudor, I
• 通讯作者: Oprea, Tudor, I

DrugCentral 2023 extends human clinical data and integrates veterinary drugs.

• DOI: 10.1093/nar/gkac1085
• 发表时间: 2023-01-06
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Avram, Sorin;Wilson, Thomas B.;Curpan, Ramona;Halip, Liliana;Borota, Ana;Bora, Alina;Bologa, Cristian G.;Holmes, Jayme;Knockel, Jeffrey;Yang, Jeremy J.;Oprea, Tudor, I
• 通讯作者: Oprea, Tudor, I

Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19.

• DOI: 10.1021/acsptsci.0c00131
• 发表时间: 2020-12-11
• 期刊: ACS pharmacology & translational science
• 作者: Bocci G;Bradfute SB;Ye C;Garcia MJ;Parvathareddy J;Reichard W;Surendranathan S;Bansal S;Bologa CG;Perkins DJ;Jonsson CB;Sklar LA;Oprea TI
• 通讯作者: Oprea TI