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PathwayCommons / cpath2

Biological pathway data integration and access platform (Pathway Commons)
http://www.pathwaycommons.org/pc2/
MIT License
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Add sifgraph (xSIF, graph queries) endpoint. #302

Open IgorRodchenkov opened 5 years ago

IgorRodchenkov commented 5 years ago

Let's add a sifgraph dependency and implement new REST controller here.

Having sifgraph-server code here in cpath2 could help extending PC web services in the future, adding new output data formats and options, such as generate input data in JSON format for Cytoscape web apps that visualize biological networks.

IgorRodchenkov commented 5 years ago

I think, unlike sifgraph-server, this feature here should internally use a Pathway Commons TXT (extended SIF) file based of entity URIs rather than (being expanded/mapped to) HGNC Symbols; so, a ..All.uri.txt.gz archive should be then also generated as part of the PC release.

This way would allow future PC2 graph/sifgraph queries (when SIF or TXT format is requested) to accept several type of ID or URIs as input and return (optionally) requested ID types in the SIF/TXT result. Custom JSON output format would be also much easier to generate; see #303.