SPARQL Queries for WikiPathways

Example SPARQL queries for the WikiPathways Snorql UI. These queries are loaded automatically to help users explore WikiPathways RDF data and build novel queries.

Adding a new query

1. Pick the right directory. Queries are organized by topic in lettered directories (A-J). Place your .rq file in the matching directory.

2. Add a header. Every .rq file must start with these required header fields:

   # title: Genes of a Pathway
   # category: General
   # description: Lists all gene products in a given pathway, returning the pathway
   #   identifier and gene product labels.
   
   SELECT ...

   • title -- short, descriptive name
   • category -- must match an entry in categories.json
   • description -- what the query does (wrap long lines with # continuation indent)

   See HEADER_CONVENTIONS.md for full details, including optional fields like keywords and param.

3. Alternative: TTL format. You can also write a .ttl (Turtle/RDF) file using the SHACL sh:SPARQLExecutable pattern. The CI pipeline will auto-generate the corresponding .rq file on merge to master. If a .ttl source exists, do not edit the .rq file directly.

License

GPLv3