test_queries.http

# Switch to local, dev or prod environment
# local: localhost:3000
# dev: dev.api.bte.ncats.io
# prod: api.bte.ncats.io

###
GET {{base_url}}/metakg
###

GET {{base_url}}/v1/predicates

####

GET {{base_url}}/v1/meta_knowledge_graph

####

GET {{base_url}}/v1/team/Textmining%20Provider/meta_knowledge_graph
###

GET {{base_url}}/v1/smartapi/<smartapi_id>/meta_knowledge_graph


# note: CX uses the dev ARS instance, since it seems the most reliable. Queries can be submitted to https://ars-dev.transltr.io/ars/api/submit
# there is also a CI ARS instance.
#registered BTE API endpoint in ARS
https://ars.ci.transltr.io/ara-bte/api/

###
# all registered Actors in ARS
https://ars.ci.transltr.io/ars/api/actors


###
# Explain with two-intermediate nodes
# One of the "results" (a complete path) should have these nodes:
#   - n0 (started with the ID): SmallMolecule is CHEBI:41423 (aka celecoxib aka PUBCHEM.COMPOUND:2662)
#   - n1: Disease is MONDO:0002974 (aka cervical cancer)
#   - n2: Pathway is REACT:R-HSA-109704 (aka PI3K Cascade)
#   - n3 (started with the ID): Gene is NCBIGene:117145 (aka THEM4 aka HGNC:17947)

POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids":["PUBCHEM.COMPOUND:2662"],
                    "categories":["biolink:SmallMolecule"]
                },
                "n1": {
                    "categories":["biolink:Disease"]
               },
               "n2": {
                    "categories":["biolink:Pathway"]
               },
                "n3": {
                    "categories":["biolink:Gene"],
                       "ids":["HGNC:17947"]
               }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1"
                },
                "e1": {
                    "subject": "n1",
                    "object": "n2"
                },
                "e2": {
                    "subject": "n2",
                    "object": "n3"
                }
            }
        }
    }
}

###
# Predict one-hop with predicate filtering
# One of the "results" (a complete path) should have these nodes:
#   - n00 (started with the ID): SmallMolecule is CHEBI:8863 (aka RILUZOLE aka CHEMBL.COMPOUND:CHEMBL744)
#   - n01: Gene is NCBIGene:5670 (aka PSG2)

POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "edges": {
                "e00": {
                    "object": "n01",
                    "subject": "n00",
                    "predicates": ["biolink:physically_interacts_with"]
                }
            },
            "nodes": {
                "n00": {
                    "categories": ["biolink:SmallMolecule"],
                    "ids": ["CHEMBL.COMPOUND:CHEMBL744"]
                },
                "n01": {
                    "categories": ["biolink:Gene"]
                }
            }
        }
    }
}

###
# Predict one-hop with node semantic type expansion
# This query takes > 20 seconds to run...
# One of the "results" (a complete path) should have these nodes:
#   - n0 (started with the ID): Disease is MONDO:0005015 (aka diabetes mellitus (disease))
#   - n3: Disease is MONDO:0009874 (aka Rabson-Mendenhall syndrome)

POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "categories": ["biolink:DiseaseOrPhenotypicFeature"],
                    "ids": ["MONDO:0005015"]
                },
                "n3": {
                    "categories": ["biolink:DiseaseOrPhenotypicFeature"]
                }
            },
            "edges": {
                "e03": {
                    "subject": "n0",
                    "object": "n3"
                }
            }
        }
    }
}

####
# Predict one-hop BUT NO semantic category for the ID AND predicate filtering
# BTE should correctly figure out that the ID corresponds to the Gene semantic type
# note that "name" field on query nodes should be ignored
# DEFUNCT: this used to return answers, but it now doesn't - this is related to Automat and Biolink v2.1
#   1. the data was under ChemicalSubstance but BTE has moved to Biolink v2.1 (no more ChemicalSubstance).
#      Now it's not clear if using SmallMolecule will retrieve the same data.
#   2. Automat is only retrieving data when queried in specific directions (related to "canonical predicate directions")

POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "categories": ["biolink:SmallMolecule"],
                    "name": "some chemical"
                },
                "n1": {
                    "name": "EGFR",
                    "ids": ["NCBIGene:1956"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": [
                        "biolink:decreases_abundance_of",
                        "biolink:decreases_activity_of",
                        "biolink:decreases_expression_of",
                        "biolink:decreases_synthesis_of",
                        "biolink:increases_degradation_of",
                        "biolink:disrupts",
                        "biolink:entity_negatively_regulates_entity"
                    ]
                }
            }
        }
    }
}

####
# Explain with no intermediate nodes
# DEFUNCT: This query returns empty knowledge_graph, results. This is expected because
#   1. querying Disease OMIM:606703 -> Gene only gets a different gene (NCBIGene:111)
#   2. querying Gene NCBIGene:1956 -> Disease gets a bunch of Disease IDs, but "OMIM:606703" isn't in the response json

POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["OMIM:606703"],
                    "categories": ["biolink:Disease"]
                },
                "n1": {
                    "categories": ["biolink:Gene"],
                    "ids": ["NCBIGene:1956"]
                }
            },
            "edges": {
                "e01": {
                    "subject": "n0",
                    "object": "n1"
                }
            }
        }
    }
}


####
###
# Predict one-hop
# One of the "results" (a complete path) should have these nodes connected with an edge with the predicate "homologous_to"
#   - n0 (started with the ID): Gene is NCBIGene:1017 (aka CDK2)
#   - n1: Gene is MGI:104772

POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["NCBIGene:1017"],
                    "categories": ["biolink:Gene"]
                },
                "n1": {
                    "categories": ["biolink:Gene"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": [
                        "biolink:homologous_to",
                        "biolink:orthologous_to"
                    ]
                }
            }
        }
    }
}



####
# Predict one-hop (depends on Automat APIs)
# One of the "results" (a complete path) should have these nodes:
#   - n0 (started with the ID): Gene is NCBIGene:6658 (aka SOX3)
#   - n1: GeneFamily is HGNC.FAMILY:757

POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["NCBIGene:6658"],
                    "categories": ["biolink:Gene"]
                },
                "n1": {
		             "categories":["biolink:GeneFamily"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1"
                }
            }
        }
    }
}

###
# https://github.com/NCATSTranslator/minihackathons/issues/160
####
# Predict one-hop BUT NO semantic category for the ID AND predicate filtering
# BTE should correctly figure out that the ID corresponds to the Protein semantic category
# note that "name" field on query nodes should be ignored
# this query should use the "Text Mining Targeted Association API" since it currently has PR IDs (Protein semantic type)
# One of the "results" (a complete path) should have these nodes:
#   - n0 (started with the ID): Protein is PR:000006933 (no ID resolution, so no name or equivalent IDs in node attributes)
#   - n1: SmallMolecule is CHEBI:28748 (aka DOXORUBICIN)


POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
    "query_graph": {
      "edges": {
        "e0": {
          "object": "n1",
          "predicates": [
            "biolink:negatively_regulates_entity_to_entity",
            "biolink:entity_negatively_regulates_entity"
          ],
          "subject": "n0"
        }
      },
      "nodes": {
        "n0": {
          "categories": ["biolink:SmallMolecule"],
          "name": "some chemical"
        },
        "n1": {
          "ids": ["PR:000006933"],
          "name": "EGFR"
        }
      }
    }
    }
}


###
# https://github.com/NCATSTranslator/minihackathons/issues/157
# DON'T USE THIS QUERY for most tests, since it will take a long time to run AND BTE has some bugs related to this:
# Predict one-hop BUT have multiple starting nodes/IDs, with predicate filtering, node semantic type expansion
# Designed to retrieve information from "clinical KPs"
# The issues / bugs:
#   - querying with MONDO:0005359 AND/OR MESH:D056487 AND/OR NCIT:C26991 in n0 leads to an empty knowledge_graph/results.
#     This is because there are no associations/edges with those predicates
#   - querying with only SNOMEDCT:197358007 in n0 leads to some associations/edges from Columbia Open Health Data (COHD).
#     However, BTE incorrectly identifies the node with SNOMEDCT:197358007 as a Drug.
#     it's actually a Disease; the ID has the label "Toxic liver disease with acute hepatitis"

POST  {{base_url}}/v1/query
Content-Type: application/json

{
"message": {
    "query_graph": {
  "edges": {
    "e1": {
      "object": "n1",
      "predicates": [
        "biolink:has_normalized_google_distance_with",
        "biolink:correlated_with"
      ],
      "subject": "n0"
    }
  },
  "nodes": {
    "n0": {
      "ids": [
        "MONDO:0005359",
        "SNOMEDCT:197358007",
        "MESH:D056487",
        "NCIT:C26991"
      ]
    },
    "n1": {
      "categories": ["biolink:DiseaseOrPhenotypicFeature"]
    }
  }
    }
  }
}


###
# https://github.com/NCATSTranslator/testing/issues/91
# Predict one-hop with node semantic expansion (the same node has the ID...)
# One of the "results" (a complete path) should have these nodes:
#   - n0 (started with the ID): Disease is UMLS:C0042963 (aka HP:0002013 aka Vomiting)
#   - n1: SmallMolecule is CHEBI:94848 (aka DIMENHYDRINATE)
#   - e0: the edge should have the predicate treated_by and be from MyChem.info

POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": [
                        "HP:0002013"
                    ],
                    "categories": [
                        "biolink:DiseaseOrPhenotypicFeature"
                    ]
                },
                "n1": {
		             "categories":[
                         "biolink:SmallMolecule"
                        ]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates":["biolink:related_to"]

                }
            }
        }
    }
}

###
# Predict one-hop
# DEFUNCT: This query is not working because of how this API's x-bte operations are set up (clinical risk kp api)
#   - There is a lack of clarity around how the data is represented (and therefore how to query it)
#   - this has to do with the predicate directionality, and what counts as the SUBJECT and OBJECT
#   - see https://ncatstranslator.slack.com/archives/C022EL8D3AB/p1624480395075900 for the thread on this issue

# Ryan: https://ncatstranslator.slack.com/archives/C022EL8D3AB/p1627338809084200
POST  {{base_url}}/v1/smartapi/d86a24f6027ffe778f84ba10a7a1861a/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "edges": {
                "e00": {
                    "subject": "n00",
                    "object": "n01",
                    "predicates": ["biolink:related_to"]
                }
            },
            "nodes": {
                "n00": {
                    "categories": ["biolink:SmallMolecule"]
                },
                "n01": {
                    "categories": ["biolink:Disease"],
                    "ids": ["MONDO:0005301"]
                }
            }
        }
    }
}


###
# Predict one-hop
# DEFUNCT: This query is not working because the less-constrained node n1 has no ID or category.

# https://github.com/NCATSTranslator/minihackathons/issues/139
# POST  {{base_url}}/v1/query
POST https://ars.transltr.io/ars/api/submit
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "edges": {
                "e01": {
                "object": "n0",
                "predicates": [
                    "biolink:entity_negatively_regulates_entity",
                    "biolink:negatively_regulates_entity_to_entity"
                ],
                "subject": "n1"
                }
            },
            "nodes": {
                "n0": {
                "categories": ["biolink:Gene"],
                "ids": ["NCBIGene:23221"]
                },
                "n1": {}
            }
        }
    }
}


###
# Predict one-hop
# DEFUNCT: This query is not working because the less-constrained node n1 has no ID or category.

# https://github.com/NCATSTranslator/minihackathons/issues/142
POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "edges": {
                "e01": {
                "object": "n0",
                "subject": "n1"
                }
            },
            "nodes": {
                "n0": {
                "categories": ["biolink:Gene"],
                "ids": ["NCBIGene:23221"]
                },
                "n1": {}
            }
        }
    }
}


###
# https://github.com/NCATSTranslator/minihackathons/issues/142
####
# Predict one-hop BUT NO semantic category for the ID AND predicate filtering AND node semantic expansion
# DEFUNCT: this query has never returned answers with BTE
#   - it's designed to use the Clinical Risk KP API (which BTE does query),
#     but that KP API doesn't have records with this MONDO ID

POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "edges": {
                "e0": {
                    "object": "n1",
                    "predicates": [
                        "biolink:correlated_with"
                    ],
                    "subject": "n0"
                }
            },
            "nodes": {
                "n0": {
                    "ids": ["MONDO:0005359"],
                    "name": "drug-induced liver injury"
                },
                "n1": {
                    "categories": ["biolink:DiseaseOrPhenotypicFeature"],
                    "name": "Disease Or Phenotypic Feature"
                }
            }
        }
    }
}


###
POST  {{base_url}}/v1/query
Content-Type: application/json

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["WIKIPATHWAYS:WP195"],
                    "categories": ["biolink:Pathway"]
                },
                "n1": {
                    "ids": ["NCBIGene:3556"],
                    "categories": ["biolink:Gene"]
                },
                "n2": {
                    "categories": ["biolink:SmallMolecule"]
                }
            },
            "edges": {
                "e01": {
                    "subject": "n0",
                    "object": "n1"
                },
                "e02": {
                    "subject": "n1",
                    "object": "n2"
                }
            }
        }
    }
}