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Creative: Implement "What gene's activity or abundance is increased by a particular chemical?" #81

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cbizon opened this issue Dec 7, 2022 · 0 comments

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@cbizon
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cbizon commented Dec 7, 2022

ARAs should respond to the following creative mode TRAPI query that looks for genes whose activity or abundance will be increased by the input chemical:

{
    "message": {
        "query_graph": {
            "nodes": {
                "gene": {
                    "categories": [
                        "biolink:Gene"
                    ]
                },
                "chemical": {
                    "categories": [
                        "biolink:ChemicalEntity"
                    ],
                    "ids": [
                        "$INPUTID"
                    ]
                }
            },
            "edges": {
                "t_edge": {
                    "object": "gene",
                    "subject": "chemical",
                    "predicates": [
                        "biolink:affects"
                    ],
                    "knowledge_type": "inferred",
                    "qualifier_constraints": [
                        {
                            "qualifier_set": [
                                {
                                    "qualifier_type_id": "biolink:object_aspect_qualifier",
                                    "qualifier_value": "activity_or_abundance"
                                },
                                {
                                    "qualifier_type_id": "biolink:object_direction_qualifier",
                                    "qualifier_value": "increased"
                                }
                            ]
                        }
                    ]
                }
            }
        }
    }
}

In an actual query $INPUTID will be replaced with a CURIE denoting the input chemical

Some chemicals that can be used for testing include:

Amphetamine	PUBCHEM.COMPOUND:3007
Dextroamphetamine	PUBCHEM.COMPOUND:5826
Methylphenidate	PUBCHEM.COMPOUND:44246724
Metformin	PUBCHEM.COMPOUND:4091
Atorvastatin	PUBCHEM.COMPOUND:60823
Valproic Acid	PUBCHEM.COMPOUND:88111
Vitamin A	PUBCHEM.COMPOUND:445354
Vitamin C	PUBCHEM.COMPOUND:54670067
Vitamin D	PUBCHEM.COMPOUND:5280795
Glucose	PUBCHEM.COMPOUND:79025
Magnesium	PUBCHEM.COMPOUND:888
DHEA	PUBCHEM.COMPOUND:5881
Testosterone	PUBCHEM.COMPOUND:6013
Estrogen	PUBCHEM.COMPOUND:5991
Somatostatin	PUBCHEM.COMPOUND:16129681
Amitriptyline	PUBCHEM.COMPOUND:2160
Gabapentin	PUBCHEM.COMPOUND:3446
Propranolol	PUBCHEM.COMPOUND:4946
Sumatriptan	PUBCHEM.COMPOUND:5358
Palmitic acid	PUBCHEM.COMPOUND:12358543
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