cyREST Examples for Node.js
This is a repository of a basic sample script to automate a Cytoscape workflow using cyRest and node.js.
- Latest version of cyREST
- Cytoscpae 3.1.1 and later
Basic Workflow: Build a Network from NCBI Gene Database Search Result
This is a simple workflow to do the following:
- Send query to [NCBI Gene] database by bionode-ncbi module.
- From the result, extract Entrez gene ID.
- Send the list of genes to BioGIRD via BioJS PSICQUIC client.
- Convert the list of interactions into Cytoscape.js compatible JSON.
- Send it to Cytoscape via cyREST
- Apply layout, edge bundling, and Visual Style.
The following is the result by sending this query to NCBI Gene:
"Homo sapiens"[Organism] AND proteasome[Gene Ontology] AND alive[property]
You can play with some other queries. Note that if the returned list of the genes is too big, BioGRID may return empty result.