A Translator Knowledge Provider for Systems Chemical Biology

系统化学生物学翻译知识提供者

基本信息

  • 批准号:
    10548044
  • 负责人:
  • 金额:
    $ 71.13万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2020
  • 资助国家:
    美国
  • 起止时间:
    2020-01-23 至 2022-11-30
  • 项目状态:
    已结题

项目摘要

Chemical biology and systems biology operate at different scales of molecular or cellular organization, requiring translation between the disciplines (e.g., terminology, existing evidence, new findings) to allow each to inform the other (1, 2). We propose a Biomedical Data Translator Knowledge Provider for Systems Chemical Biology to address this need. Centrally, the promise of systems chemical biology (SCB) is discovering novel therapeutics and re-purposing opportunities, avoiding toxicity and other side effects, and understanding how small molecules function (i.e., mechanism-of-action studies). Many evidence types used to solve such problems can also be used to understand functions of alterations at similar molecular scales, such as post-translational modification and protein-coding genetic variants. Currently, researchers in the field face major data access and interpretation challenges. For example, to support mechanism-of-action (MoA) studies, many experimental methods produce relevant data (gene-expression, protein-protein interactions, diverse bioactivities against pure proteins and cells, etc.) that are too numerous and heterogeneous to query for most researchers. Many web-based tools exist to share such data, but they are scattered, not always easy to find, and generally lack any communication between each other. As the field matures and increasingly embraces high-throughput experiments, these problems will only get worse (3). Our proposed SCB Knowledge Provider will mitigate these challenges by: • integrating and reconciling core molecular data (structure, name, annotated target) from multiple existing resources; • integrating and analyzing biological activity data for small molecules across multiple biological scales (binding, cellular activity, disease indication) (4); and • providing context for activities of small molecules and their targets informed by systems biology (complexes, pathways, processes). Our proposed SCB Knowledge Provider will enable answering questions such as: • what is the mechanism of action of a small molecule identified from a phenotypic screen? • which compounds are available to modulate my target of interest, and which other candidate targets might influence the activity of my target in a particular cellular context? • given my interest in a disease process or pathway, which candidate targets should I consider in relevant models, and which compounds are known to modulate those targets? We anticipate addressing gaps in data by scouting for inclusion additional sources of small-molecule bioactivity and contextual information about protein target function (see Data Milestones). We will implement existing and develop new methods to surface inconsistencies and prioritize returned results (see Methods Milestones). Finally, we propose an Advisory Committee to help prioritize content most relevant to researchers, overcome development obstacles, and keep abreast of emerging data and methods (see Outreach Milestones). We have core expertise needed to realize this SCB vision via 15+ years of experience with small-molecule bioactivity databases and portals (5-7), plus expertise in phenotypic screening, small-molecule profiling, and MoA studies (8-10), which demand integrated understanding of diverse data for hypothesis-driven science. We also made key contributions to Translator feasibility, including a workflow-centric view of data exploration by subject-matter experts, identifying and providing key datasets and methods for production of TIDBITS, and prototyping set-based (e.g., gene-list) analyses in workflows. These experiences ideally position us to realize a Systems Chemical Biology Knowledge Provider for Translator.
化学生物学和系统生物学在不同的分子或细胞尺度上运作

项目成果

期刊论文数量(0)
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PAUL ANDREW CLEMONS其他文献

PAUL ANDREW CLEMONS的其他文献

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{{ truncateString('PAUL ANDREW CLEMONS', 18)}}的其他基金

Translating novel cancer targets and mechanisms from the CTD^2 Network using molecular glues
使用分子胶从 CTD^2 网络转化新的癌症靶点和机制
  • 批准号:
    10704124
  • 财政年份:
    2022
  • 资助金额:
    $ 71.13万
  • 项目类别:
Translating novel cancer targets and mechanisms from the CTD^2 Network using molecular glues
使用分子胶从 CTD^2 网络转化新的癌症靶点和机制
  • 批准号:
    10505307
  • 财政年份:
    2022
  • 资助金额:
    $ 71.13万
  • 项目类别:
A Translator Knowledge Provider for Systems Chemical Biology
系统化学生物学翻译知识提供者
  • 批准号:
    10332543
  • 财政年份:
    2020
  • 资助金额:
    $ 71.13万
  • 项目类别:
Biomedical Data Translator Technical Feasibility Assessment and Architecture Design
生物医学数据转换器技术可行性评估和架构设计
  • 批准号:
    9540181
  • 财政年份:
    2016
  • 资助金额:
    $ 71.13万
  • 项目类别:
Informing synthetic decision making using cheminformatic and bioinformatic profil
使用化学信息学和生物信息学分析为综合决策提供信息
  • 批准号:
    7696771
  • 财政年份:
    2008
  • 资助金额:
    $ 71.13万
  • 项目类别:
General data-analysis tools:cCemical Diversity (RMI)
通用数据分析工具:cChemical Diversity (RMI)
  • 批准号:
    7032046
  • 财政年份:
    2005
  • 资助金额:
    $ 71.13万
  • 项目类别:
General data-analysis tools to relate chemical diversity
关联化学多样性的通用数据分析工具
  • 批准号:
    7476648
  • 财政年份:
    2005
  • 资助金额:
    $ 71.13万
  • 项目类别:
General data-analysis tools to relate chemical diversity
关联化学多样性的通用数据分析工具
  • 批准号:
    7125582
  • 财政年份:
    2005
  • 资助金额:
    $ 71.13万
  • 项目类别:
Small-molecule fluorophores: screening for specific protein or RNA binding
小分子荧光团:筛选特定蛋白质或 RNA 结合
  • 批准号:
    6941848
  • 财政年份:
    2004
  • 资助金额:
    $ 71.13万
  • 项目类别:
Informing synthetic decision making using cheminformatic and bioinformatic profil
使用化学信息学和生物信息学分析为综合决策提供信息
  • 批准号:
    8331513
  • 财政年份:
  • 资助金额:
    $ 71.13万
  • 项目类别:

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