Sample Queries

[cbizon]

Kara / Chris / Alex will produce some sample graph queries. These will be JSON TRAPI query graphs. Each will also have a name and a text description.

We'd like those to show up on the query builder - Somewhere on the query graph page, there could be simply a list of links/buttons with the query names. When you click one, the json query graph is loaded into the UI.

So the UI at that point will look like somebody hand-added the query and you can just hit quick submit.

[cbizon]

Example Query 1: Name: Chemicals that ameliorate Huntington Disease

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "categories": [
            "biolink:ChemicalEntity"
          ],
          "name": "Chemical Entity"
        },
        "n1": {
          "name": "Huntington disease",
          "categories": [
            "biolink:Disease"
          ],
          "ids": [
            "MONDO:0007739"
          ]
        }
      },
      "edges": {
        "e0": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:ameliorates"
          ]
        }
      }
    }
  }
}

[cbizon]

Name: Diseases that share a genetic association with Ebola

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "categories": [
            "biolink:Gene"
          ],
          "name": "Gene"
        },
        "n1": {
          "name": "Ebola hemorrhagic fever",
          "categories": [
            "biolink:DiseaseOrPhenotypicFeature",
            "biolink:BiologicalEntity",
            "biolink:NamedThing",
            "biolink:Entity",
            "biolink:ThingWithTaxon",
            "biolink:Disease"
          ],
          "ids": [
            "MONDO:0005737"
          ]
        },
        "n2": {
          "categories": [
            "biolink:Disease"
          ],
          "name": "Disease"
        }
      },
      "edges": {
        "e0": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:related_to"
          ]
        },
        "e1": {
          "subject": "n0",
          "object": "n2",
          "predicates": [
            "biolink:related_to"
          ]
        }
      }
    }
  }
}

[cbizon]

Example query 3 Name: Genes involved in Histone H3 Deaceytlation

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "name": "histone H3 deacetylation",
          "categories": [
            "biolink:BiologicalProcessOrActivity",
            "biolink:BiologicalEntity",
            "biolink:NamedThing",
            "biolink:Entity",
            "biolink:Occurrent",
            "biolink:OntologyClass",
            "biolink:ThingWithTaxon",
            "biolink:PhysicalEssenceOrOccurrent",
            "biolink:BiologicalProcess"
          ],
          "ids": [
            "GO:0070932"
          ]
        },
        "n1": {
          "categories": [
            "biolink:Gene"
          ],
          "name": "Gene"
        }
      },
      "edges": {
        "e0": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:related_to"
          ]
        }
      }
    }
  }
}

[cbizon]

Example Query 4: Name: Genes and chemicals related to GLUT 1 deficiency, and to each other.

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "categories": [
            "biolink:ChemicalEntity"
          ],
          "name": "Chemical Entity"
        },
        "n1": {
          "categories": [
            "biolink:Gene"
          ],
          "name": "Gene"
        },
        "n2": {
          "name": "GLUT1 deficiency syndrome",
          "categories": [
            "biolink:DiseaseOrPhenotypicFeature",
            "biolink:BiologicalEntity",
            "biolink:NamedThing",
            "biolink:Entity",
            "biolink:ThingWithTaxon",
            "biolink:Disease"
          ],
          "ids": [
            "MONDO:0000188"
          ]
        }
      },
      "edges": {
        "e0": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:related_to"
          ]
        },
        "e1": {
          "subject": "n1",
          "object": "n2",
          "predicates": [
            "biolink:related_to"
          ]
        },
        "e2": {
          "subject": "n2",
          "object": "n0",
          "predicates": [
            "biolink:related_to"
          ]
        }
      }
    }
  }
}

[karafecho]

Example Query 0: Name: Diseases associated with 2,3,7,8-tetrochlorodibenzo-p-dioxin

{
  "message": {
    "query_graph": {
      "nodes": {
        "n0": {
          "name": "2,3,7,8-Tetrachlorodibenzo-P-dioxin",
          "categories": [
            "biolink:MolecularEntity",
            "biolink:ChemicalEntity",
            "biolink:NamedThing",
            "biolink:Entity",
            "biolink:PhysicalEssence",
            "biolink:ChemicalOrDrugOrTreatment",
            "biolink:ChemicalEntityOrGeneOrGeneProduct",
            "biolink:ChemicalEntityOrProteinOrPolypeptide",
            "biolink:PhysicalEssenceOrOccurrent",
            "biolink:SmallMolecule"
          ],
          "ids": [
            "PUBCHEM.COMPOUND:15625"
          ]
        },
        "n1": {
          "categories": [
            "biolink:Disease"
          ],
          "name": "Disease"
        }
      },
      "edges": {
        "e0": {
          "subject": "n0",
          "object": "n1",
          "predicates": [
            "biolink:associated_with"
          ]
        }
      }
    }
  }
}

`

[Woozl]

https://user-images.githubusercontent.com/16181779/232581085-d70da1b0-6364-494b-b97d-9a7165cce69f.mov

[Woozl]

All sample queries tested and working