reciprocal queries not matching

[andrewsu]

I execute this query to find any NamedThing related to xylitol (UMLS:C0043369):

{
   "message": {
       "query_graph": {
           "edges": {
               "e01": {
                   "subject": "n0",
                   "object": "n1"
               }
           },
           "nodes": {
               "n0": {
                   "ids": ["UMLS:C0043369"],
                   "categories": ["biolink:SmallMolecule"]
               },
               "n1": {
                   "categories": ["biolink:NamedThing"]
               }
           }
       }
   }
}

one of the results is Aldehyde Reductase (UMLS:C0002003)

                "UMLS:C0002003": {
                    "categories": [
                        "biolink:Protein"
                    ],
                    "name": "Aldehyde Reductase",

                "e4adf01204f21097e082a304b13da4f2": {
                    "predicate": "biolink:physically_interacts_with",
                    "subject": "UMLS:C0043369",
                    "object": "UMLS:C0002003",
                    "attributes": [
                        ...
                        {
                            "attribute_type_id": "biolink:aggregator_knowledge_source",
                            "value": [
                                "infores:biothings-semmeddb-chemical"
                            ],
                            "value_type_id": "biolink:InformationResource"
                        },
                        {
                            "attribute_type_id": "publications",
                            "value": [
                                "PMID:26264136",
                                "PMID:28188449"
                            ]
                        }
                    ]

But when I query for NamedThings related to Aldehyde Reductase (UMLS:C0002003), I get no results:

{
   "message": {
       "query_graph": {
           "edges": {
               "e01": {
                   "subject": "n0",
                   "object": "n1"
               }
           },
           "nodes": {
               "n0": {
                   "ids": ["UMLS:C0002003"],
                   "categories": ["biolink:Protein"]
               },
               "n1": {
                   "categories": ["biolink:NamedThing"]
               }
           }
       }
   }
}

        "knowledge_graph": {
            "nodes": {},
            "edges": {}
        },
        "results": []

[colleenXu]

This is related to #227 and was going to be addressed with x-bte annotations of the new SEMMEDDB API

[colleenXu]

The records involved in the new semmeddb api are here

However, BTE did not ingest these two records based on the notebook because:

• Currently there isn't a good way to express negation in Translator, although a PR was recently proposed to handle that
• the SEMMED semantic type for xylitol is carb (carbohydrate). However, records with this semantic type are currently filtered out (see the heading "Remove semantic types in data but not in SRDEF" here).

However, reverse operations do exist for all operations generated by the semmeddb notebook for the new semmeddb api...

I therefore propose closing this issue... Andrew and I discussed on 12/6.....making the change after the demo to "not remove semantic types that are in the data but not in SRDEF" and working from there...

[colleenXu]

Yao noticed that the data file used "old SEMMED semantic types" from 2013AA, and these semantic types didn't exist in the latest SRDEF file (2018AA).

In response, Andrew said to keep this data

[colleenXu]

Should be addressed by NCATS-Tangerine/translator-api-registry@aa681a2

[colleenXu]

The query that is the same direction compared to the data now successfully finds this triple, as well as the query in the "reverse" direction. POST to https://api.bte.ncats.io/v1/smartapi/1d288b3a3caf75d541ffaae3aab386c8/query

forward-direction query

{
   "message": {
       "query_graph": {
           "edges": {
               "e01": {
                   "subject": "n0",
                   "object": "n1",
                   "predicates": ["biolink:produces"]
               }
           },
           "nodes": {
               "n0": {
                   "ids": ["UMLS:C0002003"],
                   "categories": ["biolink:Polypeptide"]
               },
               "n1": {
                   "categories": ["biolink:SmallMolecule"]
               }
           }
       }
   }
}

response

                "50c72726686ae3b85be43be067ca39e3": {
                    "predicate": "biolink:produces",
                    "subject": "UMLS:C0002003",
                    "object": "UMLS:C0043369",
                    "attributes": [
                        {
                            "attribute_type_id": "biolink:aggregator_knowledge_source",
                            "value": [
                                "infores:biothings-explorer"
                            ],
                            "value_type_id": "biolink:InformationResource"
                        },
                        {
                            "attribute_type_id": "biolink:primary_knowledge_source",
                            "value": [
                                "infores:semmeddb"
                            ],
                            "value_type_id": "biolink:InformationResource"
                        },
                        {
                            "attribute_type_id": "biolink:aggregator_knowledge_source",
                            "value": [
                                "infores:biothings-semmeddb"
                            ],
                            "value_type_id": "biolink:InformationResource"
                        },
                        {
                            "attribute_type_id": "biolink:publications",
                            "value": [
                                "PMID:28188449"
                            ]
                        },
                        {
                            "attribute_type_id": "biolink:original_object",
                            "value": "C0043369"
                        },
                        {
                            "attribute_type_id": "biolink:original_predicate",
                            "value": "PRODUCES"
                        },
                        {
                            "attribute_type_id": "biolink:original_subject",
                            "value": "C0002003"
                        },
                        {
                            "attribute_type_id": "original_object_name",
                            "value": "Xylitol"
                        },
                        {
                            "attribute_type_id": "original_subject_name",
                            "value": "Aldehyde Reductase"
                        }
                    ]
                },

---

reverse direction query

{
   "message": {
       "query_graph": {
           "edges": {
               "e01": {
                   "subject": "n1",
                   "object": "n0",
                   "predicates": ["biolink:produced_by"]
               }
           },
           "nodes": {
               "n0": {
                   "ids": ["UMLS:C0002003"],
                   "categories": ["biolink:Polypeptide"]
               },
               "n1": {
                   "categories": ["biolink:SmallMolecule"]
               }
           }
       }
   }
}

response

                "2004c79c178267eb6face02282a9f573": {
                    "predicate": "biolink:produced_by",
                    "subject": "UMLS:C0043369",
                    "object": "UMLS:C0002003",
                    "attributes": [
                        {
                            "attribute_type_id": "biolink:aggregator_knowledge_source",
                            "value": [
                                "infores:biothings-explorer"
                            ],
                            "value_type_id": "biolink:InformationResource"
                        },
                        {
                            "attribute_type_id": "biolink:primary_knowledge_source",
                            "value": [
                                "infores:semmeddb"
                            ],
                            "value_type_id": "biolink:InformationResource"
                        },
                        {
                            "attribute_type_id": "biolink:aggregator_knowledge_source",
                            "value": [
                                "infores:biothings-semmeddb"
                            ],
                            "value_type_id": "biolink:InformationResource"
                        },
                        {
                            "attribute_type_id": "biolink:publications",
                            "value": [
                                "PMID:28188449"
                            ]
                        },
                        {
                            "attribute_type_id": "biolink:original_object",
                            "value": "C0043369"
                        },
                        {
                            "attribute_type_id": "biolink:original_predicate",
                            "value": "PRODUCES"
                        },
                        {
                            "attribute_type_id": "biolink:original_subject",
                            "value": "C0002003"
                        },
                        {
                            "attribute_type_id": "original_object_name",
                            "value": "Xylitol"
                        },
                        {
                            "attribute_type_id": "original_subject_name",
                            "value": "Aldehyde Reductase"
                        }
                    ]
                },