Genes correlated with Gene (NCBIGene:23221)

[rtroper]

The query below gives results when posted directly to the Multiomics Big GIM I KP (containing gene-gene expression correlation relations) TRAPI endpoint: https://api.bte.ncats.io/v1/smartapi/520851943d84a639c23b0a2116e6e83c/query.

When posted to the ARS endpoint (https://ars.transltr.io/ars/api/submit), the following results were returned: https://arax.ncats.io/?source=ARS&id=7dae3cd4-2b6c-400d-8643-b3641142d63f. However, the results from the ARS are very few in comparison to what's returned when querying directly on the Big GIM I endpoint. Also, when I inspected results from the ARS, none of them came from the Big GIM I KP.

Furthermore, when I post the query to the ARS through the ARAX UI (using the {json} tab), I get the following:

{
    "message": {
        "query_graph": {
            "edges": {
                "e00": {
                    "subject": "n00",
                    "object": "n01",
                    "predicates": ["biolink:correlated_with"]
                }
            },
            "nodes": {
                "n00": {
                    "categories": ["biolink:Gene"]
                },
                "n01": {
                    "categories": ["biolink:Gene"],
                    "ids": ["NCBIGene:23221"]
                }
            }
        }
    }
}

[edeutsch]

The ARAX GUI has been submitting to https://ars.ci.transltr.io/ars/api/submit for a few months, and I am under the impression that that is the current recommended one. but it does seems that that server has been down since last week. We could switch the ARAX GUI to go back to the old server https://ars.transltr.io/ars/api/submit which still seems to be functioning.

[rtroper]

Hmm, yeah, it does look like it's down. I just tried submitting to https://ars.ci.transltr.io/ars/api/submit and I got a 504 gateway timeout. As for no results showing up from Big GIM I (when submitting to the old server), I wonder if we need to have ARAs register/add the endpoint. It was added to the SmartAPI registry, but I'm not sure how many ARAs make use of the registry to check for new KPs to add.

[gloriachin]

Thank you Eric for your response, what is the mechanism of update or add an API endpoint in the ARAX or ARS system? Is there a document or standard we could refer to if we would like a new deployed API can be queried in the ARAX or ARS system?

[edeutsch]

For ARAX, you can get API documentation here: https://arax.ncats.io/api/arax/v1.2/ui/ For ARS I don't know.

[gloriachin]

Thanks Eric. For the issue we can query the Multiomics:BigGIM (gene co-expression) from the SmartAPI endpoint ("https://api.bte.ncats.io/v1/smartapi/520851943d84a639c23b0a2116e6e83c/query" ) , but could not get results from ARAX or ARS through the following endpoints: ars_url='https://ars.ci.transltr.io/ars/api/submit' ars_url = "https://ars.transltr.io/ars/api/submit" arax_url='https://arax.ci.transltr.io' Which is the right person we should speak to and get the problem resolved? Maybe Chunlei (@newgene) and Eric(@edeutsch) ?

[amykglen]

Hi @rtroper, @gloriachin - I'm a bit confused about which Multiomics KP this issue relates to. ARAX currently has these four plugged in:

infores:biothings-multiomics-clinical-risk: https://api.bte.ncats.io/v1/smartapi/d86a24f6027ffe778f84ba10a7a1861a infores:biothings-multiomics-wellness: https://api.bte.ncats.io/v1/smartapi/02af7d098ab304e80d6f4806c3527027 infores:biothings-multiomics-drug-response: https://api.bte.ncats.io/v1/smartapi/adf20dd6ff23dfe18e8e012bde686e31 infores:biothings-tcga-mut-freq: https://api.bte.ncats.io/v1/smartapi/5219cefb9d2b8d5df08c3a956fdd20f3

Is this issue about a fifth Multiomics KP?

[gloriachin]

Thank you AMY for your response. Yes, it is about the fifth one:) Multiomics-BigGIM: https://api.bte.ncats.io/v1/smartapi/520851943d84a639c23b0a2116e6e83c/query. Which is current registered in the smartAPI