Goal

Release PC2 v9 BioPAX database and web service using the latest improved cPath2 and Paxtools versions; update docs and RDF (SPARQL) endpoint; collect and analyze logs with Elasticsearch tools.

Details

• Remove the web app for searching pathways by keywords and displaying pathway summary pages (i.e., the /view#pw; the "pathways" app is now being developed separately);
• Improve pathway data merging (perhaps, add TREMBL data to the warehouse);
• Improve ID coverage (ChEBI, HGNC Symbol and UniProt Xrefs), which should improve our exporting to SIF;
• Improve the full-text index, should boost graph queries' performance (by excluding intermediate id-mapping step);
• Extend the Web service API: add a parameter to track/log clients (optional with reasonable default value, such as 'cpath-client' or 'cytoscape'); a parameter to include/exclude SIF types; etc.
• Implement graph queries based on pre-built "All" SIF graph/model; also extend the web api to optionally run these queries instead of biopax model based ones.