Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

摘要

Author Summary WikiPathways is a crowd-sourced online platform for biological pathways. It is based on the same underlying platform as Wikipedia. Pathways are saved as graphical images embedded in a set of meta data elements (i.e. references, list of pathways elements, and context annotations). Pathways are used as proxies of biological knowledge in their role as descriptors of processes. Yet integrating these hubs of biological knowledge with other biological data resources remains challenging due to a cacophony of file formats, identifier systems, and hidden content. We show the application of the semantic web to enable a straightforward integration of heterogeneous biological data sources. We have taken high-quality pathways from a curated set from WikiPathways and converted the content into a data format native to the semantic web. Here, data is expressed as a set of statements where the statements are built upon a set of web addresses. Given the results, we successfully integrated external resources (e.g., EBI Expression Atlas) and pathway content with a single query.