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MarkDWilliams edited this page Feb 4, 2021 · 2 revisions

Use cases gathered from the February 2021 Translator Relay Fix It Sessions More details can be found here: https://docs.google.com/document/d/17Pzg88AlMC0mli-z132pq-sCoaPrd6OAFK6mKM6lznk/edit

Subclasses of Viral Hemorrhagic Hantavirus

{ "message": { "query_graph": { "nodes": { "n00": { "id": "MONDO:0005784", "category": "biolink:Disease" }, "n01": { "category": "biolink:Disease" } }, "edges": { "e00": { "subject": "n00", "object": "n01", "predicate":"biolink:subclass_of" } } } } }

Drugs that treat Cytomegalovirus but are contraindicated for pregnancy

{ "message": { "query_graph": { "nodes": { "n0": { "id": "MONDO:0005132", "category":"biolink:Disease" }, "n1": { "category": "biolink:ChemicalSubstance" }, "n2": { "id": "UMLS:C0032961", "category":"biolink:Disease" } }, "edges": { "e01": { "subject": "n1", "object": "n0", "predicate":"biolink:treats" }, "e02": { "subject": "n1", "object": "n2", "predicate": "biolink:contraindicated_for" } } } } }

Genes Associated with Atrial Fib

{ "message": { "query_graph": { "edges": { "e00": { "subject": "n00", "object": "n01", "predicate": "biolink:condition_associated_with_gene" } }, "nodes": { "n00": { "id": "MONDO:0004981", "category": "biolink:Disease" }, "n01": { "category": "biolink:Gene" } } } } } Results: https://ars.transltr.io/ars/api/messages/29f446ab-4479-4626-9f58-6dfa9ba3e183?trace=y

Aragorn Mult-hop

{ "message": { "query_graph": { "nodes": { "n00": { "id": "MONDO:0002715" }, "n01": { "category": "biolink:ChemicalSubstance" }, "n02": { "category": "biolink:Gene" } }, "edges": { "e00": { "predicate": "biolink:correlated_with", "subject": "n00", "object": "n01" }, "e01": { "predicate": "biolink:related_to", "subject": "n01", "object": "n02" } } } } }

Condition Associated With Gene Breast Cancer

{ "message": { "query_graph": { "edges": { "e00": { "subject": "n00", "object": "n01", "predicate": "biolink:condition_associated_with_gene" } }, "nodes": { "n00": { "id": "MONDO:0007254", "category": "biolink:Disease" }, "n01": { "category": "biolink:Gene" } } } } } Results: https://ars.transltr.io/ars/api/messages/9a697020-686b-4ac5-bac7-8bc3cd66f942?trace=y

Gene Associated with Condition (Breast Cancer)

{ "message": { "query_graph": { "edges": { "e0": { "predicate": "biolink:gene_associated_with_condition", "subject": "n0", "object": "n1" } }, "nodes": { "n0": { "category": "biolink:Gene" }, "n1": { "category": "biolink:Disease", "id": "MONDO:0007254" } } } } } Results: https://ars.transltr.io/ars/api/messages/5b883c4c-342c-4237-bb88-3f613fac91fe?trace=y

Drugs to treat Alzheimer's

{ "message": { "query_graph": { "edges": { "e00": { "subject": "n01", "object": "n00", "predicate": "biolink:treats" } }, "nodes": { "n00": { "id": "MONDO:0004975", "category": "biolink:Disease" }, "n01": { "category": "biolink:ChemicalSubstance" } } } } } Results https://ars.transltr.io/ars/api/messages/b79d9200-e394-4a96-81ba-c5ee1a62709d?trace=y

Chemicals connected with Dementia

{ "message": { "query_graph": { "edges": { "e00": { "subject": "n00", "object": "n01" } }, "nodes": { "n00": { "id": "MONDO:0001627", "category": "biolink:Disease" }, "n01": { "category": "biolink:ChemicalSubstance" } } } } } Results (fail due to timeout in ARS) https://ars.transltr.io/ars/api/messages/5c09cd57-6135-4c0a-a819-46c8493b46dd?trace=y

Edges Between Bupivacaine and LRP15

{ "message": { "query_graph": { "nodes": { "n0": { "category": "biolink:ChemicalSubstance", "id": "CHEBI:3215" }, "n3": { "id": "PR:000031567", "category": "biolink:GeneOrGeneProduct" } }, "edges": { "e03": { "subject": "n0", "object": "n3" } } } } } Results: https://ars.transltr.io/ars/api/messages/7c4dbc36-88c2-40a0-a3e3-28c89f66fd0d?trace=y

Drugs Associated with Decreased Risk for Atrial Fib

{ "message": { "query_graph": { "edges": { "e00": { "subject": "n00", "object": "n01", "predicate": "biolink:associated_with_decreased_risk_for" } }, "nodes": { "n00": { "category": "biolink:Drug" }, "n01": { "category": "biolink:Disease", "id": "MONDO:0004981" } } } } }

Results: https://ars.transltr.io/ars/api/messages/7c4dbc36-88c2-40a0-a3e3-28c89f66fd0d?trace=y

Drugs that treat OCD and its Phenotypes (Triangular Query)

{ "message": { "query_graph": { "nodes": { "n0": { "id": "MONDO:0008114", "category": "biolink:Disease" }, "n1": { "category": "biolink:PhenotypicFeature" }, "n2": { "category": "biolink:ChemicalSubstance" } }, "edges": { "e01": { "subject": "n0", "object": "n1", "predicate": "biolink:has_phenotype" }, "e02": { "subject": "n2", "object": "n1", "predicate": "biolink:treats" }, "e03": { "subject": "n2", "object": "n0", "predicate": "biolink:treats" } } } } }

Batch Query

{ "message": { "query_graph": { "nodes": { "n0": { "category": "biolink:ChemicalSubstance" }, "n1": { "id": [ "DOID:0060060", "DOID:0060224" ], "category": "biolink:Disease" } }, "edges": { "e00": { "subject": "n0", "object": "n1" } } } } }

Drugs for the Phenotypic Features of Subtypes of Hepatitis

{ "message": { "query_graph": { "nodes": { "n00": { "id": "MONDO:0002251", "category": "biolink:Disease" }, "n01": { "category": "biolink:Disease" }, "n02": { "category": "biolink:PhenotypicFeature" } }, "edges": { "e00": { "subject": "n01", "object": "n00", "predicate":"biolink:subclass_of" }, "e01": { "subject": "n01", "object": "n02", "predicate":"biolink:has_phenotype" } } } } }

Drugs that treat Primary malignant neoplasm of perihilar bile duct

{ “message”: { “query_graph”: { “nodes”: { “n00": { “category”: “biolink:Disease” “id”: “SCTID:86049000" }, “n01”: { “category”: “biolink:Drug”, “id”: “chembl:192976” } }, “edges”: { “e00”: { “predicate”: “biolink:treats”, “subject”: “n00”, “object”: “n01” } } } } }

Disease Modifying Drugs for Rheumatoid Arthritis

{ "message": { "query_graph": { "nodes": { "n0": { "id": "MONDO:0008383", "category": "biolink:Disease" }, "n1": { "category": "biolink:PhenotypicFeature" }, "n2": { "category": "biolink:ChemicalSubstance" } }, "edges": { "e01": { "subject": "n0", "object": "n1", "predicate": "biolink:has_phenotype" }, "e02": { "subject": "n2", "object": "n1", "predicate": "biolink:treats" }, "e03": { "subject": "n2", "object": "n0", "predicate": "biolink:treats" } } } } }

Gene's that Morphine Physically Interacts with (proxy for targets)

{ "message": { "query_graph": { "nodes": { "n00": { "id": "CHEBI:17303", "category": "biolink:ChemicalSubstance" }, "n01": { "category": "biolink:Gene" } }, "edges": { "e00": { "subject": "n00", "object": "n01", "predicate":"biolink:physically_interacts_with" } } } } } Results: https://ars.transltr.io/ars/api/messages/f8036886-1449-4468-932c-1750cace99fc?trace=y

Relationship between Pendred and Hearing Loss

{ "message": { "query_graph": { "nodes": { "n00": { "id": "MONDO:0010134", "category": "biolink:Disease" }, "n01": { "id": "MONDO:0005365", "category": "biolink:Disease" } }, "edges": { "e00": { "subject": "n00", "object": "n01" } } } } } Results: https://ars.transltr.io/ars/api/messages/593caf54-6808-4012-b49f-8e8a7336ca40?trace=y

Proteins that are part of the lipid droplet

{ "message": { "query_graph": { "nodes": { "n0": { "category": "biolink:Protein" }, "n1": { "category": "biolink:AnatomicalEntity", "id": "GO:0005811" } }, "edges": { "e0": { "subject": "n0", "object": "n1", "predicate": "biolink:part_of" } } } } }

Gene Members of the RAS Family

{ "message": { "query_graph": { "nodes": { "n0": { "id":"UMLS:C0034678", }, "n1": { "category": "biolink:Gene" } }, "edges": { "e0": { "subject": "n1", "object": "n0", "predicate": "biolink:subclass_of" } } } } } Results: https://ars.transltr.io/ars/api/messages/79d4e3f9-2e49-4593-acf0-97c82cfc37c2?trace=y

Gene Members of RAS GeneFamily (switched direction)

{ "message": { "query_graph": { "nodes": { "n0": { "id":"UMLS:C0034678", "category":"biolink:GeneFamily" }, "n1": { "category": "biolink:Gene" } }, "edges": { "e0": { "subject": "n0", "object": "n1", "predicate": "biolink:subclass_of" } } } } }

Results: https://ars.transltr.io/ars/api/messages/f9f611fd-9ad1-4b33-99cb-6f772749d083?trace=y

Genes Part of RAS Gene Family

{ "message": { "query_graph": { "nodes": { "n0": { "id":"UMLS:C0034678", "category":"biolink:GeneFamily" }, "n1": { "category": "biolink:Gene" } }, "edges": { "e0": { "subject": "n1", "object": "n0", "predicate": "biolink:part_of" } } } } } Results: https://ars.transltr.io/ars/api/messages/ec4b84bd-722c-428c-8964-7d3d5291b024?trace=y

EGFR Ligands

{ "message": { "query_graph": { "nodes": { "n0": { "id": "UMLS:C1414313" }, "n1": { "category": "biolink:MolecularEntity" } }, "edges": { "e0": { "predicate": "biolink:directly_interacts_with", "subject": "n0", "object": "n1" } } } } }

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