Reactome from a WikiPathways Perspective.
Reactome from a WikiPathways Perspective.
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DOI：
10.1371/journal.pcbi.1004941
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发表时间：
2016-05
影响因子：
4.3
通讯作者：
Evelo CT
中科院分区：
文献类型：
--
作者：
Bohler A;Wu G;Kutmon M;Pradhana LA;Coort SL;Hanspers K;Haw R;Pico AR;Evelo CT
Reactome和WikiPathways是两个最受欢迎的生物学途径免费数据库。Reactome途径由选定的领域专家定期输入。WikiPathways是一个基于社区的平台，任何感兴趣的人都可以在这里创建和持续策划路径。WikiPathways和Reactome之间的新生合作说明了结合这两种方法的共同利益。我们创建了一个格式转换器，将Reactome路径转换为WikiPathways中使用的GPML格式。此外，我们还为Pathplugin开发了ComplexViz插件，它简化了查找复杂组件的过程。该插件还可以根据用户定义的标准对路径上的复合物进行评分。然后可以使用插件提供的可视化选项在复杂节点上可视化该分数。使用合并的精选和转化的Reactome途径集合，我们证明了相关生物过程的途径覆盖范围的改善，用于分析先前描述的多囊卵巢综合征基因表达数据集。此外，这种转换允许研究人员使用Pathworld的高级数据可视化功能可视化他们在Reactome途径上的数据。WikiPathways受益于对从Reactome转换的内容的专注和关注，以及关于交互的丰富语义信息。Reactome反过来又受益于WikiPathways上提供的持续社区策展。整个研究界都受益于Pathodium和Cytoscape中更大的分析途径集。当使用更大的候选途径集进行分析时，从Pathweight获得的途径统计结果明显更好。转换作为一个通用的模式，使用不同的方法开发的多途径资源的整合。生物学途径是描述生物学过程的描述性图表，即基因，蛋白质和代谢物之间的相互作用。因此，路径可以用于整合和可视化不同生物条件下的基因、蛋白质和代谢物的分子测量，例如健康状态与疾病状态。这有助于研究人员研究疾病。例如，某种基因的低表达可能反过来导致某种蛋白质的低丰度，这可能会阻止某种代谢物的分解，这种代谢物的积累有助于疾病的进展。高通量“组学”技术产生大量的生物测量数据。生物学途径为整合这些数据提供了一个直观的基于知识的支架，WikiPathways和Reactome是两个常用的途径数据库。Reactome路径由领域专家定期输入集中策划，而WikiPathways是一个基于社区的平台，任何感兴趣的人都可以创建并持续策划路径。作为Reactome和WikiPathways正在进行的合作的一部分，我们已经将Reactome路径添加到WikiPathways中，并使它们可以从WikiPathways上的Reactome门户网站获得。在这里，我们展示了这样的整合对Reactome和WikiPathways社区以及一般研究社区都是有利的。
Reactome and WikiPathways are two of the most popular freely available databases for biological pathways. Reactome pathways are centrally curated with periodic input from selected domain experts. WikiPathways is a community-based platform where pathways are created and continually curated by any interested party. The nascent collaboration between WikiPathways and Reactome illustrates the mutual benefits of combining these two approaches. We created a format converter that converts Reactome pathways to the GPML format used in WikiPathways. In addition, we developed the ComplexViz plugin for PathVisio which simplifies looking up complex components. The plugin can also score the complexes on a pathway based on a user defined criterion. This score can then be visualized on the complex nodes using the visualization options provided by the plugin. Using the merged collection of curated and converted Reactome pathways, we demonstrate improved pathway coverage of relevant biological processes for the analysis of a previously described polycystic ovary syndrome gene expression dataset. Additionally, this conversion allows researchers to visualize their data on Reactome pathways using PathVisio’s advanced data visualization functionalities. WikiPathways benefits from the dedicated focus and attention provided to the content converted from Reactome and the wealth of semantic information about interactions. Reactome in turn benefits from the continuous community curation available on WikiPathways. The research community at large benefits from the availability of a larger set of pathways for analysis in PathVisio and Cytoscape. The pathway statistics results obtained from PathVisio are significantly better when using a larger set of candidate pathways for analysis. The conversion serves as a general model for integration of multiple pathway resources developed using different approaches. Biological pathways are descriptive diagrams that describe biological processes, i.e. interactions between genes, proteins, and metabolites. Pathways can therefore be used to integrate and visualize molecular measurements of genes, proteins, and metabolites in different biological conditions, e.g. healthy state vs. diseased state. This helps researchers investigate a disease. For instance, the low expression of a certain gene might in turn lead to the low abundance of a certain protein which might prevent the breakdown of a certain metabolite, the accumulation of which contributes to disease progression. High throughput “omics” technologies produce vast quantities of biological measurement data. Biological pathways provide an intuitive knowledge-based scaffold for integrating these data WikiPathways and Reactome are two commonly used pathway databases. Reactome pathways are centrally curated with periodic input by domain experts, while WikiPathways is a community-based platform where pathways are created and continually curated by any interested party. As part of an ongoing collaboration between Reactome and WikiPathways, we have added the Reactome pathways to WikiPathways and made them available from the Reactome portal on WikiPathways. Here, we demonstrate how such an integration is advantageous to both the Reactome and WikiPathways communities and to the general research community at large.