Pathway Commons: Research Resource for Biological Pathways

Pathway Commons：生物途径研究资源

• 批准号: 9357629
• 负责人: CHRIS SANDER
• 金额: $ 91.24万
• 依托单位: HARVARD MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-22 至 2019-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9357629
• 关键词: Automobile Driving; Behavior; Big Data; Biological; Biological Process; Biology; Cells; Collaborations; Communication; Communities; Community Healthcare; Computer software; Data; Data Aggregation; Data Analyses; Data Science; Data Set; Databases; Development; Diagnosis; Ecosystem; Elements; Explosion; Feeds; Funding; Genetic Predisposition to Disease; Genetic Variation; Genomic medicine; Health; Human Genetics; Human Genome; Incentives; Internet; Knowledge; Language; Link; Maps; Modeling; Molecular; National Human Genome Research Institute; Pathway Analysis; Pathway interactions; Patients; Process; Provider; Research; Research Infrastructure; Research Personnel; Resource Informatics; Resources; Scheme; Science; Services; Software Tools; Source; Speed; System; Technology; Time; Training; Translating; United States National Institutes of Health; Vision; Work; annotation system; base; biological systems; computerized tools; cost effective; data exchange; design; experimental study; feeding; flexibility; genome-wide; healthcare community; improved; indexing; next generation; novel; open source; predictive modeling; public health relevance; synergism; tool; web services

 DESCRIPTION (provided by applicant): Biological pathways represent knowledge about molecules, processes and their interactions. Maps of such pathways are used to design and analyze experiments, and for predicting the behavior of biological systems. Pathway information is extremely difficult for biologists to use in its current fragmented and incomplete state, involving a large amount of time and effort to wade through, piece together and analyze. The Pathway Commons research resource is being developed to overcome this roadblock by providing researchers with a convenient single point of access to diverse biological pathway information translated to a common data language. This project is an important step towards the development of a complete and integrated computable map of the cell across all species and developmental stages. Pathway Commons promotes and supports convergence, by the community, to a truly integrated computable and searchable representation of cellular biological processes. Pathway Commons does not compete with or duplicate efforts of pathway databases or software tool providers. Existing database groups provide pathway curation, while Pathway Commons provides mechanism and technology for adding value, disseminating, and reducing duplication of effort. Collaboration with user and database groups is a central component, driven by the desire for maximum synergy and efficiency. The Pathway Commons resource will aggregate datasets from multiple major pathway databases; translate, store, validate, index, integrate, hyperlink and maintain the information for maximum quality access; freely deliver pathway information to the scientific public, both academic and commercial, using advanced internet technology; and, provide open-source end user software for pathway browsing and analysis. User support and training for Pathway Commons and related resources will be freely available to the scientific community.

 描述（由申请人提供）：生物学途径代表有关分子、过程及其相互作用的知识。这些路径的地图用于设计和分析实验，并用于预测生物系统的行为。对于生物学家来说，在目前支离破碎和不完整的状态下使用途径信息是非常困难的，需要花费大量的时间和精力来进行研究，拼凑和分析。正在开发的Pathway Commons研究资源，通过为研究人员提供一个方便的单一访问点，将各种生物途径信息翻译成一种通用的数据语言，以克服这一障碍。该项目是朝着开发跨所有物种和发育阶段的细胞的完整和综合可计算地图迈出的重要一步。Pathway Commons促进和支持社区的融合，以真正整合细胞生物学过程的可计算和可搜索的表示。Pathway Commons不与Pathway数据库或软件工具提供商竞争或重复努力。现有的数据库组提供路径管理，而Pathway Commons提供了增加价值、传播和减少重复工作的机制和技术。与用户和数据库组的协作是一个核心组成部分，其驱动因素是对最大协同作用和效率的期望。Pathway Commons资源将汇集来自多个主要途径数据库的数据集;翻译、存储、验证、索引、整合、超链接和维护信息，以获得最高质量的访问;使用先进的互联网技术向学术和商业科学公众免费提供途径信息;并提供用于途径浏览和分析的开源最终用户软件。Pathway Commons和相关资源的用户支持和培训将免费提供给科学界。

项目成果

Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites.

• DOI: 10.1016/j.jmb.2014.11.001
• 发表时间: 2015-01-30
• 期刊: JOURNAL OF MOLECULAR BIOLOGY
• 影响因子: 5.6
• 作者: Nishi, Hafumi;Demir, Emek;Panchenko, Anna R.
• 通讯作者: Panchenko, Anna R.

Communicating Structure and Function in Synthetic Biology Diagrams.

• DOI: 10.1021/acssynbio.9b00139
• 发表时间: 2019-08-16
• 期刊: ACS synthetic biology
• 影响因子: 4.7
• 作者: Beal J;Nguyen T;Gorochowski TE;Goñi-Moreno A;Scott-Brown J;McLaughlin JA;Madsen C;Aleritsch B;Bartley B;Bhakta S;Bissell M;Castillo Hair S;Clancy K;Luna A;Le Novère N;Palchick Z;Pocock M;Sauro H;Sexton JT;Tabor JJ;Voigt CA;Zundel Z;Myers C;Wipat A
• 通讯作者: Wipat A

Using biological pathway data with paxtools.

• DOI: 10.1371/journal.pcbi.1003194
• 发表时间: 2013
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Demir E;Babur O;Rodchenkov I;Aksoy BA;Fukuda KI;Gross B;Sümer OS;Bader GD;Sander C
• 通讯作者: Sander C