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Reactome 通路知识库。

The reactome pathway knowledgebase.

机构信息

Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.

NYU School of Medicine, New York, NY 10016, USA.

出版信息

Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031.


DOI:10.1093/nar/gkz1031
PMID:31691815
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7145712/
Abstract

The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data model, an extended version of a classic metabolic map. Reactome functions both as an archive of biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. To extend our ability to annotate human disease processes, we have implemented a new drug class and have used it initially to annotate drugs relevant to cardiovascular disease. Our annotation model depends on external domain experts to identify new areas for annotation and to review new content. New web pages facilitate recruitment of community experts and allow those who have contributed to Reactome to identify their contributions and link them to their ORCID records. To improve visualization of our content, we have implemented a new tool to automatically lay out the components of individual reactions with multiple options for downloading the reaction diagrams and associated data, and a new display of our event hierarchy that will facilitate visual interpretation of pathway analysis results.

摘要

Reactome 知识库(https://reactome.org)提供了信号转导、运输、DNA 复制、代谢和其他细胞过程的分子细节,作为一个分子转化的有序网络,在一个单一的一致数据模型中,这是经典代谢图的扩展版本。Reactome 既是生物过程的档案,也是发现基因表达谱或肿瘤细胞体细胞突变目录等数据中功能关系的工具。为了扩展我们注释人类疾病过程的能力,我们实现了一个新的药物类别,并最初使用它来注释与心血管疾病相关的药物。我们的注释模型依赖于外部领域专家来识别新的注释领域,并审查新的内容。新的网页方便了社区专家的招募,并允许那些对 Reactome 有贡献的人识别他们的贡献,并将其链接到他们的 ORCID 记录。为了改善我们内容的可视化,我们实现了一个新的工具,用于自动布局单个反应的组件,提供了多种下载反应图和相关数据的选项,以及我们事件层次结构的新显示,这将有助于视觉解释通路分析结果。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/d13b2e22cd59/gkz1031fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/d432b67ad06d/gkz1031fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/3553e527adf9/gkz1031fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/37c3ee86525b/gkz1031fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/f548059d325d/gkz1031fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/d13b2e22cd59/gkz1031fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/d432b67ad06d/gkz1031fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/3553e527adf9/gkz1031fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/37c3ee86525b/gkz1031fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/f548059d325d/gkz1031fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76db/7145712/d13b2e22cd59/gkz1031fig5.jpg

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本文引用的文献

[1]
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.

Nucleic Acids Res. 2019-1-8

[2]
The Gene Ontology Resource: 20 years and still GOing strong.

Nucleic Acids Res. 2019-1-8

[3]
New approach for understanding genome variations in KEGG.

Nucleic Acids Res. 2019-1-8

[4]
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Nucleic Acids Res. 2019-1-8

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Nucleic Acids Res. 2018-1-4

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Nucleic Acids Res. 2018-1-4

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Nucleic Acids Res. 2018-1-4

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Nucleic Acids Res. 2016-1-4

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Nucleic Acids Res. 2016-1-4

[10]
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

Nucleic Acids Res. 2015-1

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