[bug] missing Automat publications (and other attributes)

[colleenXu]

Summary

Bug: Automat services are returning publications + other attributes in their edge properties, which we aren't picking up.

Expected behavior: For TRAPI APIs, we should ingest and keep their edge attributes (a caveat is what if those edge attributes aren't TRAPI/biolink compliant? but this shouldn't be much of a concern. They should be since they're TRAPI APIs...).

---

Example:

EDIT: use different forks/branch code to run these queries:

• Eric's bte-trapi/BioThings Explorer code (Eric's fork here, my branch with copied files here) so BTE uses the latest smartapi specs
• CX's biomedical id resolver branch code so BTE can query Automat correctly

BTE has edge attributes like this from Automat Pharos API, in response to the query below. (This is from the edge between PUBCHEM.COMPOUND:2662-biolink:activity_decreased_by-NCBIGene:763)

                    "attributes": [
                        {
                            "attribute_type_id": "provided_by",
                            "value": [],
                            "value_type_id": "biolink:provided_by"
                        },
                        {
                            "attribute_type_id": "api",
                            "value": [
                                "Automat Pharos (trapi v-1.1.0)"
                            ],
                            "value_type_id": "bts:api"
                        },
                        {
                            "attribute_type_id": "publications",
                            "value": [],
                            "value_type_id": "biolink:publication"
                        }
                    ]

Compare to the corresponding edge, directly from Automat Pharos (this is edge 4386b8d7bf0ac020588859df59f811c9 that has the object NCBIGene:763). Notice that there are values in the publications attribute that BTE did not ingest properly above.

                    "attributes": [
                        {
                            "attribute_type_id": "biolink:Attribute",
                            "original_attribute_name": "affinity_parameter",
                            "value": "Ki",
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "attribute_type_id": "biolink:knowledge_source",
                            "original_attribute_name": "knowledge_source",
                            "value": [
                                "PHAROS_1_norm_edges.jsonl"
                            ],
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "attribute_type_id": "biolink:aggregator_knowledge_source",
                            "original_attribute_name": "biolink:aggregator_knowledge_source",
                            "value": [
                                "infores:pharos",
                                "infores:pharos"
                            ],
                            "value_type_id": "biolink:InformationResource"
                        },
                        {
                            "attribute_type_id": "biolink:Attribute",
                            "original_attribute_name": "affinity",
                            "value": 6.1,
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "attribute_type_id": "biolink:publications",
                            "original_attribute_name": "publications",
                            "value": [
                                "PMID:20605094",
                                "PMID:23067387"
                            ],
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "attribute_type_id": "biolink:relation",
                            "original_attribute_name": "relation",
                            "value": "GAMMA:ki",
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "attribute_type_id": "biolink:aggregator_knowledge_source",
                            "value": "infores:automat.pharos",
                            "value_type_id": "biolink:InformationResource",
                            "original_attribute_name": "biolink:aggregator_knowledge_source"
                        }
                    ],

---

The query

this can be POST request to BTE or to Automat Pharos: https://automat.renci.org/pharos/query

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids":["PUBCHEM.COMPOUND:2662"],
                    "categories":["biolink:SmallMolecule"]
                },
                "n1": {
                    "categories":["biolink:Gene"]
               }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": ["biolink:activity_decreased_by"]
                }
            }
        }
    }
}

[colleenXu]

Why was this issue closed? My understanding is that this is still being worked on...

[newgene]

It was closed by Github automatically after merging @ericz1803 's PR above. Reopen it...