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As an application scenario, ComPath was used to generate mapping files across pathway databases in order to establish the multiple relationships between equivalent or related pathways in three of the major pathway databases (KEGG, Reactome, and WikiPathways). The protocol established for the mapping is described below.
A total of 3 mapping files were curated, one for each pairwise comparison:
For each pairwise pathway database comparison (resource 1 vs resource 2), they will be a unique template containing the following columns:
We have chosen to use the top of most similar pathways instead of presenting the curator with the full list due to the vast amount of overlapping pathways. If we present the curator with 100 pathways to analyze against one, the curator would need huge amount of time. Instead, the curator is presented with overlapping pathways, order by similarity and top 5 pathways with the most similar name based on string similarity. While the ranked pathway list based on similarity provides insight on pathways sharing genetic similarity, the other one gives suggestion on possible pathways based on the name. Furthermore, hyperlinks to the description were attached so that the curator can confirm that the focus and context of the pathways remain the same, even if the both have high similarity and name.
The final step of the curation process is to agree on the proposed mappings. Therefore, all three curators examined together one by one the mapping files and compare the differences, and subsequently agreeing on the final mappings.
ComPath curation interface allows for two types of mappings: equivalentTo and isPartOf.