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cPathSquaredArchitecture
Reengineer cPath (cPath1) software and PC portal based on it to support BioPAX Level 3 and beyond, advanced graph-theoretic queries and other enhancements, such as incremental updates of pathway data.
To see the phases that describe the development process and where we are in the process.
cPath2 will be built on a Paxtools/Hibernate core and use Spring Framework (Core IOC, MVC, AOP, etc.). In addition, Maven2 will be used to manage software library dependencies, builds and releases. cPath2 will be comprised of the following sub-projects or modules:
- accessing a persisted biopax model using the Paxtools API
- persisting and retrieving various types of data and metadata into the warehouse
- pre-merge pipeline: fetching, converting, cleaning, normalizing (also miriam access and id-mapping), validating, merging of pathway data
- merger: for saving the pre-processed pathway, molecules (warehouse) and ontology data into the main PC database (global model)
- admin console, which allows various processes to be kicked off via cron, such as fetching or merging of data
- web service (see: designing cPath2 Web API)
- command line service (shell, scripting service)
We suggest that for some period of time there will exist two Pathway Commons web resources, the old (BioPAX L2, cPath) and new (BioPAX L3, cPath2), at the same time, but only the latter will be actively developed and data there updated. Eventually, the former will become obsolete (when exactly depends on users's feedback and vote).