integrate new AGR API for gene-disease relationships into BTE

[colleenXu]

Involves:

• writing SmartAPI yaml with x-bte operations (for gene <-> disease associations)
• registering the yaml with SmartAPI Registry
• changing the list of APIs BTE ingests to include this new API

[mnarayan1]

I can start working on this issue.

[colleenXu]

Current situation

• AGR yaml is written and registered in SmartAPI registry
• However, I haven't successfully tested >50% of the operations (ones that have DOID or MGI input), due to bugs. So I haven't made a PR to add this API to BTE's config list yet.
• Related infores stuff is ready:
  • updated infores page for agrkb (primary knowledge source)
  • EDIT: new infores catalog entry for biothings-agr in this PR but this may not be important (UI doesn't show because it's not the primary knowledge source?)
  • created placeholder infores page for biothings-agr

Note for the future: It may be useful to update the BioThings AGR data/parser? It looks like the last updates may be from 2021, based on the /metadata endpoint + source code. And new data like Xenbase was added in 2022 (https://www.alliancegenome.org/about-us), which would involve checking/probably-adding x-bte annotation.

---

Notes on writing the SmartAPI yaml

• lots of prior discussion in the original PR AGR API Yaml NCATS-Tangerine/translator-api-registry#127
• my latest edits were direct commits: NCATS-Tangerine/translator-api-registry@e067feb to NCATS-Tangerine/translator-api-registry@5bdd73b
• I didn't end up using qualifiers:
  • unclear how to handle for the "via orthology" data: is the species context from another field like with_orthologs?
  • not necessary for direct data? (the gene node/ids/symbols is species-specific)
• Madhumita noted in the yaml comments that there were Xenbase and GO _id values, but I didn't see any. I only found 7 species in the data, as noted in the yaml comments (no Xenopus from Xenbase). I used this query in my search.

[colleenXu]

Because of the bug fix, I was able to test the x-bte annotation locally and confirm that it all worked.

Test query: start with MGI

Start with Gene MGI:109384 (Atf3), based on this operation's example

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["MGI:109384"],
                    "categories": ["biolink:Gene"]
                },
                "n1": {
                    "categories": ["biolink:Disease"]
                }
            },
            "edges": {
                "e01": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": ["biolink:biomarker_for"]
                }
            }
        }
    }
}

Should retrieve this edge linked to prostate cancer (DOID:10283 in original API, MONDO:0008315 in TRAPI)

                "543f7cb2ec69057e885f3a90b50f1705": {
                    "predicate": "biolink:biomarker_for",
                    "subject": "NCBIGene:11910",
                    "object": "MONDO:0008315",
                    "attributes": [],
                    "sources": [
                        {
                            "resource_id": "infores:agrkb",
                            "resource_role": "primary_knowledge_source"
                        },
                        {
                            "resource_id": "infores:biothings-agr",
                            "resource_role": "aggregator_knowledge_source",
                            "upstream_resource_ids": [
                                "infores:agrkb"
                            ]
                        },
                        {
                            "resource_id": "infores:service-provider-trapi",
                            "resource_role": "aggregator_knowledge_source",
                            "upstream_resource_ids": [
                                "infores:biothings-agr"
                            ]
                        }
                    ]
                },

Test query: start with DOID

Start with Disease DOID:10629 (microphthalmia), based on this operation's example

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["DOID:10629"],
                    "categories": ["biolink:Disease"]
                },
                "n1": {
                    "categories": ["biolink:Gene"]
                }
            },
            "edges": {
                "e01": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": ["biolink:condition_associated_with_gene"]
                }
            }
        }
    }
}

Should retrieve this edge linked to CYC3 (SGD:S000000037 in original API, NCBIGene:851192 in TRAPI)

                "37b3244f58abee6b388df2686e2f4571": {
                    "predicate": "biolink:condition_associated_with_gene",
                    "subject": "MONDO:0021129",
                    "object": "NCBIGene:851192",
                    "attributes": [],
                    "sources": [
                        {
                            "resource_id": "infores:agrkb",
                            "resource_role": "primary_knowledge_source"
                        },
                        {
                            "resource_id": "infores:biothings-agr",
                            "resource_role": "aggregator_knowledge_source",
                            "upstream_resource_ids": [
                                "infores:agrkb"
                            ]
                        },
                        {
                            "resource_id": "infores:service-provider-trapi",
                            "resource_role": "aggregator_knowledge_source",
                            "upstream_resource_ids": [
                                "infores:biothings-agr"
                            ]
                        }
                    ]
                },

So I made a PR to add it to BTE's regular use. biothings/bte-server#3

[colleenXu]

Closing this issue since the changes have been deployed to Prod with the Feb 2024 release.

I've confirmed that I can query BioThings AGR through BTE prod https://bte.transltr.io/v1/team/Service Provider/query with the examples in #260 (comment) and get the expected response.