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feat: add trapi kps to config for BTE's use #43

Merged
merged 3 commits into from
Sep 27, 2024
Merged

feat: add trapi kps to config for BTE's use #43

merged 3 commits into from
Sep 27, 2024

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colleenXu
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@colleenXu colleenXu commented Sep 25, 2024

Related to biothings/biothings_explorer#865

@tokebe, Andrew and I were wondering what automated testing could be done/set up to see if there are any issues using this KPs. Questions I have:

  • Can BTE successfully use these KPs to retrieve edges?
  • Do the retrieved edges make sense (match the QGraph, aren't weird like SmallMolecule-treats-SmallMolecule)?
  • Do the retrieved edges pass TRAPI validation?

I did some manual testing and could retrieve edges from these KPs. Here's my example queries:

Automat robokop

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["NCBIGene:672"],
                    "categories": ["biolink:Gene"]
                },
                "n1": {
                    "categories": [
                        "biolink:GrossAnatomicalStructure"
                    ]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": ["biolink:expressed_in"]
                }
            }
        }
    }
}

MolePro

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["CHEBI:52717"],
                    "categories": ["biolink:SmallMolecule"]
                },
                "n1": {
                    "categories": ["biolink:SmallMolecule"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": ["biolink:correlated_with"]
                }
            }
        }
    }
}

Multiomics-Microbiome

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids":["GO:0009106"],
                    "categories":["biolink:BiologicalProcess"]
                },
                "n1": {
                    "categories": ["biolink:SmallMolecule"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": ["biolink:correlated_with"]
                }
            }
        }
    }
}

Multiomics-multiomics

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids":["UniProtKB:Q8NET8"],
                    "categories":["biolink:Protein"]
                },
                "n1": {
                    "categories": ["biolink:Disease"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": ["biolink:associated_with"]
                }
            }
        }
    }
}

@tokebe tokebe merged commit 741b825 into main Sep 27, 2024
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2 participants