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MarkDWilliams edited this page Dec 2, 2020 · 9 revisions

Use cases gathered from the September 2020 Translator Relay More details can be found here: https://drive.google.com/drive/folders/1nn2RzNTMo72BcWA9VdcNOFR0JGjCm8la?usp=sharing

Asthma Loop Short - Ranking Agent - Aragorn

{ "edges": [ { "id": "asthma_geneA", "source_id": "asthma", "target_id": "geneA", "type": "associated" }, { "id": "asthma_drugA", "source_id": "asthma", "target_id": "drugA", "type": "association" }, { "id": "geneA_drugA", "source_id": "drugA", "target_id": "geneA", "type": "related_to" } ], "nodes": [ { "id": "asthma", "type": "disease", "curie": "MONDO:0004979" }, { "id": "geneA", "type": "gene" }, { "id": "drugA", "type": "chemical_substance" } ] }

Asthma Loop Long - Ranking Agent - Aragorn

{ "edges": [ { "id": "asthma_geneA", "source_id": "asthma", "target_id": "geneA", "type": "associated" }, { "id": "asthma_drugA", "source_id": "asthma", "target_id": "drugA", "type": "association" }, { "id": "geneA_drugA", "source_id": "drugA", "target_id": "geneA", "type": "related_to" }, { "id": "geneA_geneB", "source_id": "geneA", "target_id": "geneB", "type": "directly_interacts_with" }, { "id": "geneB_drugB", "source_id": "geneB", "target_id": "drugB", "type": "affected_by" } ], "nodes": [ { "id": "asthma", "type": "disease", "curie": "MONDO:0004979" }, { "id": "geneA", "type": "gene" }, { "id": "drugA", "type": "chemical_substance" }, { "id": "geneB", "type": "gene" }, { "id": "drugB", "type": "chemical_substance" } ] }

What genes are associated with disease X? - Explanatory Agent

Explanatory-genes-disease

Compound-Disease-Disease - (im)Proving Agent

{ "query_message": { "query_graph": { "nodes": [ { "node_id": "n0", "curie": "", "type": "biolink:ChemicalSubstance" }, { "node_id": "n1", "curie": "DOID:7148", "type": "biolink:Disease" }, { "node_id": "n2", "curie": "", "type": "biolink:Disease" }, { "node_id": "n3", "curie": "", "type": "biolink:Gene" } ], "edges": [ { "edge_id": "e0", "source_id": "n0", "target_id": "n1" }, { "edge_id": "e1", "source_id": "n1", "target_id": "n2" }, { "edge_id": "e2", "source_id": "n2", "target_id": "n3" } ] }, "query_options": { "psev-context": "DOID:7148", "query_kps": "true" } } }

Symptom-Disease-Drug-Protein - (im)Proving Agent

{ "query_message": { "query_graph": { "nodes": [ { "node_id": "n0", "curie": "", "type": "biolink:PhenotypicFeature" }, { "node_id": "n1", "curie": "DOID:3393", "type": "biolink:Disease" }, { "node_id": "n2", "curie": "", "type": "biolink:ChemicalSubstance" }, { "node_id": "n3", "curie": "", "type": "biolink:Protein" } ], "edges": [ { "edge_id": "e0", "source_id": "n0", "target_id": "n1" }, { "edge_id": "e1", "source_id": "n1", "target_id": "n2" }, { "edge_id": "e2", "source_id": "n2", "target_id": "n3" } ] }, "query_options": { "psev-context": "DOID:3393", "query_kps": "true" } } }

Symptom-Disease-Gene-Gene - (im)Proving Agent

{ "query_message": { "query_graph": { "nodes": [ { "node_id": "n0", "curie": "", "type": "biolink:PhenotypicFeature" }, { "node_id": "n1", "curie": "DOID:3393", "type": "biolink:Disease" }, { "node_id": "n2", "curie": "", "type": "biolink:Gene" }, { "node_id": "n3", "curie": "", "type": "biolink:Gene" } ], "edges": [ { "edge_id": "e0", "source_id": "n0", "target_id": "n1" }, { "edge_id": "e1", "source_id": "n1", "target_id": "n2" }, { "edge_id": "e2", "source_id": "n2", "target_id": "n3" } ] }, "query_options": { "psev-context": "DOID:3393", "query_kps": "true" } } }

Current Phase 3+ Approved Treatments for Alzheimer’s Disease - Unsecret Agent

[Drug] ----> Alzheimer’s Disease

{ "message": { "query_graph": { "nodes": [ { "id": "n1", "type": "biolink:Drug" }, { "id": "n2", "curie": "UMLS:C0002395" } ], "edges": [ { "id": "e1", "type": "clinically_tested_approved_unknown_phase", "source_id": "n1", "target_id": "n2" } ] } } }

Finding Alzheimer’s Associated Genes - Unsecret Agent

[Gene/Gene-Product] ----> Alzheimer’s Disease

{ "message": { "query_graph": { "nodes": [ { "id": "n1", "type": ["biolink:Gene", "biolink:GeneGrouping", "biolink:GeneProduct", "biolink:Protein"] }, { "id": "n2", "curie": "DOID:10652" } ], "edges": [ { "id": "e1", "type": ["gene_mapped_to_disease", "gene_involved_in_pathogenesis_of_disease", "gene_associated_with_disease", "associated_with_disease", "INVERTED:disease_has_basis_in_dysfunction_of"], "source_id": "n1", "target_id": "n2" } ] } } }

Proposing New Potential Alzheimer’s Disease Therapies - Unsecret Agent

[Phase 3 FDA Approved Drug for non-Alzhiemer’s Disease Treatment ] --targets--> [Gene/Gene-Product] --associated-with--> Alzheimer’s Disease

{ "message": { "query_graph": { "nodes": [ { "id": "n0", "type":"biolink:Drug" }, { "id": "n1", "type": ["biolink:Gene", "biolink:GeneGrouping", "biolink:GeneProduct", "biolink:Protein"] }, { "id": "n2", "curie": "DOID:10652" }, { "id": "n3", "type": "disease" } ], "edges": [ { "id": "e0", "type" : "target", "source_id": "n0", "target_id": "n1" }, { "id": "e1", "type": ["gene_mapped_to_disease", "gene_involved_in_pathogenesis_of_disease", "gene_associated_with_disease", "associated_with_disease", "INVERTED:disease_has_basis_in_dysfunction_of"], "source_id": "n1", "target_id": "n2" }, { "id": "e2", "type": "clinically_tested_approved_unknown_phase", "source_id": "n0", "target_id": "n3" } ] } } }

For a patient with disease X, what are some factors (such as genetic features, comorbidities, etc) that could cause sensitivity or resistance to drug Y?

  • Exploring Agent { "message": { "query_graph": { "edges": [ { "id": "e00", "source_id": "n00", "target_id": "n01", "filter": { "ngd": { "<": 0.6 } } }, { "id": "e01", "source_id": "n00", "target_id": "n02" }, { "id": "e02", "source_id": "n01", "target_id": "n03", "relation": "gene_has_variant_that_contributes_to_drug_response_association", "filter": { "disease_context": { "=": "MONDO:0006256" } } }, { "id": "e03", "source_id": "n02", "target_id": "n03" } ], "nodes": [ { "curie": "MONDO:0007254", "id": "n00", "type": "disease" }, { "id": "n01", "type": "gene" }, { "id": "n02", "type": "sequence_variant" }, { "id": "n03", "type": "chemical_substance" } ] } } }

What drugs can be repurposed to treat disease X? - Expander Agent

{ "edges": [ { "id": "qg3", "negated": null, "relation": null, "source_id": "qg1", "target_id": "qg2", "type": "molecularly_interacts_with" }, { "id": "qg4", "negated": null, "relation": null, "source_id": "qg2", "target_id": "qg0", "type": null } ], "nodes": [ { "id": "qg0", "is_set": null, "name": "neutropenia", "curie": "MONDO:0001475", "type": "disease" }, { "id": "qg1", "is_set": null, "name": null, "desc": "Generic chemical_substance", "curie": null, "type": "chemical_substance" }, { "id": "qg2", "is_set": "true", "name": null, "desc": "Generic protein", "curie": null, "type": "protein" } ] }

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