Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Creative: Implement "What gene's activity or abundance is decreased by a particular chemical?" #82

Open
cbizon opened this issue Dec 7, 2022 · 0 comments

Comments

@cbizon
Copy link
Collaborator

cbizon commented Dec 7, 2022

ARAs should respond to a creative query asking for genes whose activity or abundance is decreased by an input chemical. TRAPI:

{
    "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": "decreased"
                                }
                            ]
                        }
                    ]
                }
            }
        }
    }
}

$INPUTID will be the CURIE of 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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant