Reactome from a WikiPathways Perspective

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.

Reactome与WikiPathways是当前最受欢迎的两款免费生物通路数据库。Reactome通路采用集中式人工注释模式，定期吸纳精选领域专家的反馈进行更新。WikiPathways则是基于社区的开放平台，任何感兴趣的人员均可参与通路的创建与持续注释维护。WikiPathways与Reactome的初步合作，印证了整合两种不同开发模式所能带来的双向增益。本研究开发了一款格式转换工具，可将Reactome通路转换为WikiPathways所采用的GPML格式。此外，本研究还为PathVisio开发了ComplexViz插件（ComplexViz plugin），可简化复合物组分的查询操作；该插件还可基于用户自定义的评分标准，对通路中的复合物进行打分，并借助插件提供的可视化选项将评分结果展示在复合物节点上。通过整合经人工注释与格式转换的Reactome通路集合，本研究针对此前已公开的多囊卵巢综合征基因表达数据集开展分析，结果显示该整合通路集可提升相关生物过程的通路覆盖度。此外，通过该格式转换工具，研究人员可借助PathVisio的高级数据可视化功能，在Reactome通路上展示自身的实验数据。WikiPathways可从Reactome转换内容的专属聚焦方向，以及丰富的互作语义信息中获得增益；而Reactome则可借助WikiPathways上持续开展的社区注释工作实现获益。广大科研界也将受益于可在PathVisio与Cytoscape中使用的更大规模通路分析资源。当使用更大规模的候选通路集开展分析时，PathVisio所输出的通路统计结果将具备更优异的性能表现。该格式转换方案可为整合采用不同开发模式的多类通路资源提供通用范式。