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Tracker for Plant Reactome issues in Production, whether internally or externally reported.
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is the BAR PSICQUIC Interactor service returning correct results? #25

Closed preecej closed 6 years ago

preecej commented 7 years ago

My local Reactome environment hosts its own web ContentService/. That service calls PSICQUIC to get a URL registry of available interaction data services, including BAR. Using the resulting provider URL, the local service makes another call to retrieve data for given accession ids at given resources.

This entire process returns results for IntAct, but not for BAR, but I can't quite see all of the data interactions. BAR gives good results directly via HTTP, so I'm not sure what is going on.

Circadian rhythm example for AT1G22770: http://plantreactomedev.oicr.on.ca/PathwayBrowser/#/R-ATH-8933811&SEL=R-ATH-8933813&DTAB=MT

Local calls:

http://plantreactomedev.oicr.on.ca/ContentService/interactors/psicquic/resources

curl -X POST --header 'Content-Type: text/plain' --header 'Accept: application/json' -d 'AT1G22770' 'http://plantreactomedev.oicr.on.ca/ContentService/interactors/psicquic/molecules/IntAct/details'
    {
      "resource": "IntAct",
      "entities": [
        {
          "acc": "AT1G22770",
          "count": 1,
          "interactors": [
            {
              "acc": "Q9SQI2",
              "alias": "GIGAN ARATH",
              "id": 1,
              "evidences": 10,
              "score": 0.74,
              "accURL": "http://www.uniprot.org/uniprot/Q9SQI2",
              "evidencesURL": "http://www.ebi.ac.uk/intact/pages/interactions/interactions.xhtml?query=EBI-1387694%20OR%20EBI-1387906%20OR%20EBI-1387950%20OR%20EBI-1535787%20OR%20EBI-1535826%20OR%20EBI-1535871%20OR%20EBI-1535893%20OR%20EBI-1535921%20OR%20EBI-1535944%20OR%20EBI-1536000"
            }
          ]
        }
      ]
    }
curl -X POST --header 'Content-Type: text/plain' --header 'Accept: application/json' -d 'AT1G22770' 'http://plantreactomedev.oicr.on.ca/ContentService/interactors/psicquic/molecules/BAR/details'
    {
      "resource": "BAR",
      "entities": []
    }

Remote, direct calls (both return several results):

http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/AT1G22770
http://bar.utoronto.ca:9090/psicquic/webservices/current/search/query/AT1G22770

I can't figure out how to see inside the local calls to know if the remote, wrappered BAR calls are incorrectly formatted, even with browser tracing.

preecej commented 7 years ago

In the interim, I will be removing the BAR service option from the interface.

preecej commented 6 years ago

BAR changed the format of their service-delivered data to send UniProt IDs. We are now able to digest their data via the IntAct PSICQUIC registry.