Expand query graph predicates based on Biolink Model hierarchy

[andrewsu]

In #102, we extended BTE so that it would expand general Biolink node types (e.g., biolink:NamedThing) into all of its subclasses (e.g., biolink:Disease, biolink:Gene). Along similar lines this issue proposes to expand query graph predicates in a similar manner. For example, this query uses the predicate biolink:causes (https://biolink.github.io/biolink-model/docs/causes.html), which in turn has antecedants for biolink:contributes_to (https://biolink.github.io/biolink-model/docs/contributes_to.html) and biolink:related_to (https://biolink.github.io/biolink-model/docs/related_to.html).

In the example query above, if I replace the predicate biolink:causes with biolink:related_to, I expect that the BTE response for the latter will be a superset of the former, but that is not currently the case.

[newgene]

Implemented and merged here: biothings/bte_trapi_query_graph_handler#10

[colleenXu]

It's hard to tell if the predicate expansion is working properly or not, since now the predicate in the query seems to be ignored (#185). This happens even when only 1 predicate is specified.

My tentative guess is that the "predicate expansion" work or some other work on the query-making module may have broken the predicate restriction/filtering ability that BTE previously did have.

I recall that the "predicate restriction/filtering" used to work - like February, or a month or two ago.

• I could run a query with MolecularActivity GO:0032451 -(subclass_of)-> MolecularActivity, and expect only edges back that had subclass_of in the predicate. I remember doing queries like this, since I was checking every operation in x-bte for whether BTE could correctly execute the sub-queries to other APIs at the time.
• Back then, BTE wasn't doing predicate expansion. So querying with related_to would ONLY give you results with related_to in it.
• Unfortunately I don't think I saved any of the responses from BTE TRAPI from that time
• I don't remember if BTE TRAPI only queried other APIs with the exact predicate, or whether it queried everything (based on ID namespaces and semantic types) and then filtered out non-matching predicates from the edges/results. This would have been visible in the logs

[andrewsu]

Great, let's put this issue on hold pending resolution of #185

[andrewsu]

Now that #185 is closed but this issue was not magically fixed, reassigning this to @marcodarko to look into more.

[colleenXu]

This is still not working.

For example, the following query should return answers where the edge's predicates are children of the related_to - aka any predicate is fine. Instead, the only answers returned are ones where the edge's predicate is EXACTLY related_to.

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "categories": [
                        "biolink:ChemicalSubstance"
                    ],
                    "name": "Chemical Substance"
                },
                "n1": {
                    "name": "EGFR",
                    "ids": [
                        "NCBIGene:1956"
                    ],
		    "categories":["biolink:Gene"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": [
                        "biolink:related_to"
                    ]
                }
            }
        }
    }
}

[marcodarko]

I think we can use the existing expand predicates functionality of the edge class to include children in the filters, I will try it and see how it goes.

[marcodarko]

@colleenXu given the query above, do these results look like what you would expect? Instead I used the expanded predicates of "biolink:related_to" as the post query filters. Sorry about the lengthy response... *EDIT see below for correct query, I made a mistake, the nodes are a little different.

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004979-biolink:positively_correlated_with-CHEBI:23012"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:25195"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:25195"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:16130"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:16130"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:16136"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:16136"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:23003"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:23003"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:27928"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:27928"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:34594"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:34594"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:28793"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:28793"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"MESH:D006533"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-MESH:D006533"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"MESH:D014028"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-MESH:D014028"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:24527"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:24527"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:39106"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:39106"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:34682"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:34682"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:28854"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:28854"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:16480"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:16480"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:25944"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:25944"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:2555"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:2555"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:17245"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:17245"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"MESH:D026023"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-MESH:D026023"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"PUBCHEM.COMPOUND:18594026"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-PUBCHEM.COMPOUND:18594026"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:33101"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:33101"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:37734"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:positively_correlated_with-CHEBI:37734"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:38069"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:negatively_correlated_with-CHEBI:38069"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:34846"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:negatively_correlated_with-CHEBI:34846"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:27744"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:negatively_correlated_with-CHEBI:27744"}]}},{"node_bindings":{"n0":[{"id":"MONDO:0004979"}],"n1":[{"id":"CHEBI:34905"}]},"edge_bindings":{"e01":[{"id":"MONDO:0004979-biolink:negatively_correlated_with-CHEBI:34905"}]}}]

[colleenXu]

@marcodarko I can't tell where this is from, so I'm not sure how to answer. It looks like a Disease MONDO:0004979 -> ChemicalSubstance query, but I just ran that and didn't find those CHEBI IDs.

It looks right in that the predicates are descendants of related_to, so I do want those returned.

[marcodarko]

@colleenXu my bad, it is Disease MONDO:0004979 > ChemicalSubstance with predicate "correlated_with", sorry! but that's the query I'm running to test this expansion.
So basically the expanded predicates for this query give me:
["positively_correlated_with","negatively_correlated_with","coexpressed_with","has_biomarker","biomarker_for","correlated_with"]
And I'm taking those into consideration when filtering the final results.

*EDIT will work further on this, this might not be the results I'm looking for

[colleenXu]

@marcodarko That kind of expansion looks correct.

However, I would try using some different queries for your testing, because that one seems to depend on clinical risk kp api (which doesn't have positively_correlated_with right now and also has some other issues that I'm dealing with).

You could use the query that I gave above (#167 (comment)), or I can give you some other queries that involve predicate expansion...

[colleenXu]

This looks resolved now.

This query (predicate restriction to "interacts_with" and its children) correctly returns edges with "interacts_with" AND child predicates like "physically_interacts_with" and "directly_interacts_with".

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["HGNC:6284"],
                    "categories":["biolink:Gene"]
                },
                "n1":{
                    "categories": ["biolink:ChemicalSubstance"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": ["biolink:interacts_with"]
                }
            }
        }
    }
}