WikiPathways and BioPlanet

[karafecho]

The QotM surfaced a desire for Translator to draw from WikiPathways and BioPlanet. These are considered ‘trusted’ by toxicologists, but are not Translator knowledge sources. Note that BioPlanet is an NCATS resource.

[andrewsu]

Both WikiPathways and BioPlanet are available in Translator through BTE. For example, this query retrieves pathways associated with NCBIGene:1017 (CDK2):

{
    "message": {
      "query_graph": {
        "nodes": {
          "n0": {
            "ids": ["NCBIGene:1017"]
          },
          "n1": {
            "categories": ["biolink:Pathway"]
          }
        },
        "edges": {
          "e01": {
            "subject": "n0",
            "object": "n1"
          }
        }
      }
    }
  }

Example results: https://arax.ncats.io/?r=3571f4ec-6214-4d4d-83bc-0f383f415e71 (Wikipathways is imported through CPDB)

See BTE results 92-160 to see them in the ARAX UI.

This does point out that we should do more to get human-readable names there. We will investigate a little and create a new ticket that links to this one...

[sierra-moxon]

@andrewsu @karafecho - since we already have this data available to Translator, does it makes sense to close this ticket (will still be available to reference in your new ticket @andrewsu)? I'll close, but please reopen if I got this wrong. :)

[marcdubybroad]

@karafecho we also have wikipathways data with genetics associations to disease edges (p-values). I did notice that our curie format for them differ from BTE, so I'll fix that. We downloaded are gene sets from https://www.gsea-msigdb.org/gsea/msigdb/ (the C2 and C5) library; I don't remember seeing the bioplanet datasets there. I'm more than happy to incorporate those in our computational workflow if someone points me to the where I can download the data.

[karafecho]

@andrewsu : Perhaps you can point Marc to the correct URL for accessing the BioPlanet data?

[karafecho]

Reopening, as issue is active.

[sierra-moxon]

for @sierra-moxon - please add 'wikipathways' as an id_prefix for the correct class, with the correct prefix to Biolink. edit: Marc found WIKIPATHWAYS in Biolink already and has what he needs to implement.

[andrewsu]

@andrewsu : Perhaps you can point Marc to the correct URL for accessing the BioPlanet data?

Looks like the bioplanet website is down at the moment... https://tripod.nih.gov/bioplanet/

[sstemann]

@andrewsu : Perhaps you can point Marc to the correct URL for accessing the BioPlanet data?

Looks like the bioplanet website is down at the moment... https://tripod.nih.gov/bioplanet/

looks like its back up

[andrewsu]

I think @marcdubybroad and team should import BioPlanet into their system if they like, but I'd suggest that for the purposes of Translator, the objective of providing BioPlanet and Wikipathways data as KPs has already been achieved and this issue should be closed. My two cents!