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Creative: Implement "What Chemical decreases a particular gene's activity or abundance" #80

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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 takes in a particular gene and returns chemicals that are inferred to decrease that gene's abundance or activiy:

{
    "message": {
        "query_graph": {
            "nodes": {
                "gene": {
                    "categories": [
                        "biolink:Gene"
                    ],
                    "ids": [
                        "$INPUTID$"
                    ]
                },
                "chemical": {
                    "categories": [
                        "biolink:ChemicalEntity"
                    ]
                }
            },
            "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": "decreased"
                                }
                            ]
                        }
                    ]
                }
            }
        }
    }
}

$INPUTID will be replaced with a CURIE denoting the input gene. Some genes that can be used for testing:

MAPK8IP3	NCBIGene:23162
TP53	NCBIGene:7157
P450	NCBIGene:1594
XIST	NCBIGene:7503
TSIX	NCBIGene:9383
ADNP	NCBIGene:23394
BORCS8-MEF2B	
MMP9	NCBIGene:4318
MEF2C	NCBIGene:4208
MALAT1	NCBIGene:378938
DYRK1A	NCBIGene:1859
PCSK1N	NCBIGene:27344
TTR	NCBIGene:7276
GNAS	NCBIGene:2778
FAU	NCBIGene:2197
IAPP	NCBIGene:3375
SCG5	NCBIGene:6447
B2M	NCBIGene:567
GAPDH	NCBIGene:2597
Cytochrome oxidase	NCBIGene:4512
Cutochrome B	
RBP4	NCBIGene:5950
NGLY1	NCBIGene:55768
RHOBTB2	NCBIGene:23221
WDFY3	NCBIGene:23001
PPP3CA	NCBIGene:5530
KCNT1	NCBIGene:57582
NALCN	NCBIGene:259232
CACNA1A	NCBIGene:773
DHX30	NCBIGene:22907
SAMD9L	NCBIGene:219285
BICD2	NCBIGene:23299
FHL1	NCBIGene:3075
ATF3	NCBIGene:467
SETBP1	NCBIGene:26040
Engase	NCBIGene:64772
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