connecting to ICEES Asthma

[colleenXu]

This is an issue to collect issues related to ingesting ICEES Asthma and COVID APIs. At the moment, issues are not expected for BTE's ingestion....instead there are issues regarding the other team's APIs.

At the moment:

• The ICEES Asthma API query endpoint seems to not be working. I get "500 Internal Server Error" when I try to POST a query to https://icees.renci.org:16339/query.
• The ICEES COVID API query endpoint (not for Jan 2021) seems to be live and return results. However, I see issues with IDs used (for example, PUBCHEM should be PUCHEM.COMPOUND, CHEMBL should be CHEMBL.COMPOUND). The example query I did that returned results was SmallMolecule NCIT:C152185 (Remdesivir) -> Disease
• The SmartAPI registration for the ICEES COVID Jan 2021 API does not point to the correct server url (probably https://covid.icees.renci.org/jan2021/apidocs#/). Instead it points to the same server url as the other instance above. These two should have different datasets/cohorts and should therefore be two separate APIs...

[colleenXu]

@karafecho Here are some issues known for BTE connecting to the other ICEES APIs.

I've closed the other issue here, noting what was going on regarding the ICEES DILI instance

[colleenXu]

on-hold because it depends on fixes from another team

[colleenXu]

TDLR: the server url issues seem to be fixed. However, there are still other issues with the APIs...

For example, I've noticed the following issues with the ICEES COVID API (https://covid.icees.renci.org/query):

• The provenance edge attribute says "icees-asthma", which seems incorrect
• There seems to be outdated terms like ChemicalSubstance (semantic type), PUBCHEM (should be PUBCHEM.COMPOUND), UMLSCUI (should be UMLS)

--

This is a query that should get results back from ICEES Asthma (sometimes there are timeouts for the sub-queries sent to the API). It seems to be working as-expected...

Asthma query

{
    "message": {
        "query_graph": {
            "edges": {
                "e00": {
                    "subject": "n00",
                    "object": "n01",
                    "predicates": ["biolink:has_real_world_evidence_of_association_with"]
                }
            },
            "nodes": {
                "n00": {
                    "ids": ["MONDO:0004766"],
                    "categories": ["biolink:Disease"]
                },
                "n01": {
                    "categories": ["biolink:Disease"]
                }
            }
        }
    }
}

This is a query that should get results back from ICEES COVID (not the Jan 2021 instance)

uses COPD as starting point query

{
    "message": {
        "query_graph": {
            "edges": {
                "e00": {
                    "subject": "n00",
                    "object": "n01",
                    "predicates": ["biolink:has_real_world_evidence_of_association_with"]
                }
            },
            "nodes": {
                "n00": {
                    "ids": ["MONDO:0011751"],
                    "categories": ["biolink:Disease"]
                },
                "n01": {
                    "categories": ["biolink:ChemicalEntity"]
                }
            }
        }
    }
}

[colleenXu]

I've received news that we are not expected to connect to the ICEES COVID APIs, and that they are not actively funded right now and may break.

Since ICEES Asthma and ICEES DILI now seem to be incorporated into BTE, we can close this issue...