MVP2 Qualified: What chemicals [qualified] affect (decreases/downregulates) a given protein/gene (COX2)?

[sstemann]

Query: cox2qualified.json PK: 3da8a00b-2890-4768-8dd5-6575745249fb

This was run on ARS-Dev looking for KPs and ARAs that have updated their dev environments to support qualifiers

[sstemann]

It seems there are some predicates in the results that do not match the qualification in the query. we didn't look through them all but ARAGORN result #1 Oxygen uses "entity positively regulates entity" and ARAX #10 HYDROCORTISONE PHOSPHORIC ACID uses "increases expression of". so just tagging you here @cbizon @dkoslicki

[colleenXu]

@sstemann @MarkDWilliams

EDIT: looks like ARS-dev is using BTE's ITRB instance (http://bte.transltr.io/v1/, based on the TRAPI logs)

Is ARS-dev correctly querying the BTE dev instance (https://api.bte.ncats.io/v1/query or https://api.bte.ncats.io/v1/asyncquery)? It looks like it's querying a different instance.

When I POST the TRAPI query to https://api.bte.ncats.io/v1/query, I get 1108 results. You can paste the contents of the text file into ARAX (import -> response) to view what I got. cox2.txt

[khanspers]

Here's the updated PK from Mark: https://arax.ncats.io/?r=7350a9a4-748c-4ae3-87dd-edbd526e9fb7

For BTE, it is working as intended and using qualifiers.

[saramsey]

Hi Sarah,

Thank you for bringing this issue to the attention of Team Expander Agent. I have noted this issue in the overall tracking issue for achieving Biolink 3.0 compatibility in ARAX (RTXteam/RTX issue 1937).

We are well on our way toward having some support for qualified triples/predicates in an ITRB-deployed ARAX service, but we currently need to do some integration testing in a controlled & controllable setting (i.e., where we can log in and examine logfiles and, if necessary, insert debugging code into the code on the server; I'll call that "Stage 1 integration testing") before rolling the new ARAX out to an ITRB-deployed test-environment ARAX system (where we find that debugging is harder). Until recently, our team's SOP was to do such work on arax.ncats.io, where we have a bunch of installed ARAX areas set up for different branches, developers, and tasks. With the recent change in security policy for arax.ncats.io, we currently can't ssh in to do that work. So, we are planning to set up an AWS instance (arax-backup.rtx.ai) for hosting ARAX where we have ssh access and where can do the required controlled integration testing; but to set it up, we need some files fromarax.ncats.io. The work to set up the integration test server and it's ARAX environment will go more rapidly if we can clone the Docker container from arax.ncats.io; my understanding is that we are hoping to get ssh access so that we can copy files off of arax.ncats.io, soon. So, we are in a bit of a wait-state at the moment, but once we have an integration-test environment where we have direct access, the test/debug/fix/retest cycle time should be much shorter and thus we'll probably reach the end-goal faster than if we tried to debug using the ITRB (kubernetes)-deployed ARAX without first doing Stage 1 integration testing.

[saramsey]

Hi Sarah, OK, our team has now got ssh access to arax.ncats.io and work to deploy a Biolink-3.0 version of RTX-KG2 into ARAX is proceeding. We expect to roll out a development version to arax.ncats.io this week. For details, see the Translator Progress Tracker and ARAX GitHub issue 1937.

[sstemann]

@brettasmi @webyrd this is still an issue for standard mode queries for Improve and Unsecret in TEST

https://arax.ncats.io/beta/?r=84fa29cd-febd-4411-9586-1a421b49d3d4

{
    "message": {
        "query_graph": {
            "nodes": {
                "gene": {
                    "categories": [
                        "biolink:Gene"
                    ],
                    "ids": [
                        "NCBIGene:4513"
                    ]
                },
                "chemical": {
                    "categories": [
                        "biolink:ChemicalEntity"
                    ]
                }
            },
            "edges": {
                "t_edge": {
                    "object": "gene",
                    "subject": "chemical",
                    "predicates": [
                        "biolink:affects"
                    ],
                    "qualifier_constraints": [
                        {
                            "qualifier_set": [
                                {
                                    "qualifier_type_id": "biolink:object_aspect_qualifier",
                                    "qualifier_value": "activity_or_abundance"
                                },
                                {
                                    "qualifier_type_id": "biolink:object_direction_qualifier",
                                    "qualifier_value": "decreased"
                                }
                            ]
                        }
                    ]
                }
            }
        }
    }
}