diff --git a/test_assets/Asset_670.json b/test_assets/Asset_670.json new file mode 100644 index 00000000..e115ee70 --- /dev/null +++ b/test_assets/Asset_670.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_670", + "name": "TopAnswer: Dalfampridine treats multiple sclerosis", + "description": "TopAnswer: Dalfampridine treats multiple sclerosis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005301", + "input_name": "multiple sclerosis", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:34385", + "output_name": "Dalfampridine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "1", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_671.json b/test_assets/Asset_671.json new file mode 100644 index 00000000..fc9e277c --- /dev/null +++ b/test_assets/Asset_671.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_671", + "name": "TopAnswer: Apomorphine treats Parkinson disease", + "description": "TopAnswer: Apomorphine treats Parkinson disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005180", + "input_name": "Parkinson disease", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:48538", + "output_name": "Apomorphine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "2", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_672.json b/test_assets/Asset_672.json new file mode 100644 index 00000000..24b02b62 --- /dev/null +++ b/test_assets/Asset_672.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_672", + "name": "TopAnswer: Clonidine treats hypertension", + "description": "TopAnswer: Clonidine treats hypertension. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005044", + "input_name": "hypertension", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:3757", + "output_name": "Clonidine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "3", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_673.json b/test_assets/Asset_673.json new file mode 100644 index 00000000..68298be6 --- /dev/null +++ b/test_assets/Asset_673.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_673", + "name": "TopAnswer: Levodopa treats Parkinson disease", + "description": "TopAnswer: Levodopa treats Parkinson disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005180", + "input_name": "Parkinson disease", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:15765", + "output_name": "Levodopa", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "4", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_674.json b/test_assets/Asset_674.json new file mode 100644 index 00000000..7947e2df --- /dev/null +++ b/test_assets/Asset_674.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_674", + "name": "TopAnswer: Methylprednisolone treats rheumatoid arthritis", + "description": "TopAnswer: Methylprednisolone treats rheumatoid arthritis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0008383", + "input_name": "rheumatoid arthritis", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:6888", + "output_name": "Methylprednisolone", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "5", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_675.json b/test_assets/Asset_675.json new file mode 100644 index 00000000..5f71dbb9 --- /dev/null +++ b/test_assets/Asset_675.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_675", + "name": "TopAnswer: Fenofibrate treats Hypercholesterolemia", + "description": "TopAnswer: Fenofibrate treats Hypercholesterolemia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "HP:0003124", + "input_name": "Hypercholesterolemia", + "input_category": "biolink:PhenotypicFeature", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:5001", + "output_name": "Fenofibrate", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "6", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_676.json b/test_assets/Asset_676.json new file mode 100644 index 00000000..6eed8d00 --- /dev/null +++ b/test_assets/Asset_676.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_676", + "name": "TopAnswer: Pyridostigmine treats myasthenia gravis", + "description": "TopAnswer: Pyridostigmine treats myasthenia gravis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0009688", + "input_name": "myasthenia gravis", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:8665", + "output_name": "Pyridostigmine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "7", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_677.json b/test_assets/Asset_677.json new file mode 100644 index 00000000..72306ae0 --- /dev/null +++ b/test_assets/Asset_677.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_677", + "name": "TopAnswer: Selegiline treats Parkinson disease", + "description": "TopAnswer: Selegiline treats Parkinson disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005180", + "input_name": "Parkinson disease", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:9086", + "output_name": "Selegiline", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "8", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_678.json b/test_assets/Asset_678.json new file mode 100644 index 00000000..0feebc1c --- /dev/null +++ b/test_assets/Asset_678.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_678", + "name": "TopAnswer: Haloperidol treats schizophrenia", + "description": "TopAnswer: Haloperidol treats schizophrenia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005090", + "input_name": "schizophrenia", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:5613", + "output_name": "Haloperidol", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "9", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_679.json b/test_assets/Asset_679.json new file mode 100644 index 00000000..1637a5df --- /dev/null +++ b/test_assets/Asset_679.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_679", + "name": "TopAnswer: Quinapril treats hypertension", + "description": "TopAnswer: Quinapril treats hypertension. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005044", + "input_name": "hypertension", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:8713", + "output_name": "Quinapril", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "10", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_680.json b/test_assets/Asset_680.json new file mode 100644 index 00000000..45cde094 --- /dev/null +++ b/test_assets/Asset_680.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_680", + "name": "TopAnswer: Simvastatin treats Hypercholesterolemia", + "description": "TopAnswer: Simvastatin treats Hypercholesterolemia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "HP:0003124", + "input_name": "Hypercholesterolemia", + "input_category": "biolink:PhenotypicFeature", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:9150", + "output_name": "Simvastatin", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "11", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_69.json b/test_assets/Asset_681.json similarity index 55% rename from test_assets/Asset_69.json rename to test_assets/Asset_681.json index fff8c74a..5491a815 100644 --- a/test_assets/Asset_69.json +++ b/test_assets/Asset_681.json @@ -1,19 +1,21 @@ { - "id": "Asset_69", - "name": "Acceptable: Soot treats Obstructive Sleep Apnea", - "description": "Acceptable: Soot treats Obstructive Sleep Apnea", - "tags": [], + "id": "Asset_681", + "name": "TopAnswer: Sumatriptan treats migraine", + "description": "TopAnswer: Sumatriptan treats migraine. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0007147", - "input_name": "Obstructive Sleep Apnea", + "input_id": "MONDO:0005277", + "input_name": "migraine", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "MESH:D053260", - "output_name": "Soot", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:10650", + "output_name": "Sumatriptan", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -29,20 +31,22 @@ "value": "" } ], - "expected_output": "Acceptable", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "12", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } diff --git a/test_assets/Asset_70.json b/test_assets/Asset_682.json similarity index 58% rename from test_assets/Asset_70.json rename to test_assets/Asset_682.json index f882c4ab..8f8c29a5 100644 --- a/test_assets/Asset_70.json +++ b/test_assets/Asset_682.json @@ -1,19 +1,21 @@ { - "id": "Asset_70", - "name": "TopAnswer: Miglustat treats Niemann-Pick type C", - "description": "TopAnswer: Miglustat treats Niemann-Pick type C", - "tags": [], + "id": "Asset_682", + "name": "TopAnswer: Phenytoin treats epilepsy", + "description": "TopAnswer: Phenytoin treats epilepsy. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0018982", - "input_name": "Niemann-Pick type C", + "input_id": "MONDO:0005027", + "input_name": "epilepsy", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:51634", - "output_name": "Miglustat", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:8107", + "output_name": "Phenytoin", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -33,16 +35,18 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "13", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } diff --git a/test_assets/Asset_683.json b/test_assets/Asset_683.json new file mode 100644 index 00000000..51ba3c0d --- /dev/null +++ b/test_assets/Asset_683.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_683", + "name": "TopAnswer: Iloperidone treats schizophrenia", + "description": "TopAnswer: Iloperidone treats schizophrenia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005090", + "input_name": "schizophrenia", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:65173", + "output_name": "Iloperidone", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "14", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_684.json b/test_assets/Asset_684.json new file mode 100644 index 00000000..2eed05a1 --- /dev/null +++ b/test_assets/Asset_684.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_684", + "name": "TopAnswer: Telmisartan treats hypertension", + "description": "TopAnswer: Telmisartan treats hypertension. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005044", + "input_name": "hypertension", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:9434", + "output_name": "Telmisartan", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "15", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_685.json b/test_assets/Asset_685.json new file mode 100644 index 00000000..05483cef --- /dev/null +++ b/test_assets/Asset_685.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_685", + "name": "TopAnswer: Tamsulosin treats benign prostatic hyperplasia", + "description": "TopAnswer: Tamsulosin treats benign prostatic hyperplasia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0010811", + "input_name": "benign prostatic hyperplasia", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:9398", + "output_name": "Tamsulosin", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "16", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_686.json b/test_assets/Asset_686.json new file mode 100644 index 00000000..401718d7 --- /dev/null +++ b/test_assets/Asset_686.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_686", + "name": "TopAnswer: Quetiapine treats schizophrenia", + "description": "TopAnswer: Quetiapine treats schizophrenia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005090", + "input_name": "schizophrenia", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:8707", + "output_name": "Quetiapine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "17", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_687.json b/test_assets/Asset_687.json new file mode 100644 index 00000000..26377f29 --- /dev/null +++ b/test_assets/Asset_687.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_687", + "name": "TopAnswer: Zolmitriptan treats migraine", + "description": "TopAnswer: Zolmitriptan treats migraine. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005277", + "input_name": "migraine", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:10124", + "output_name": "Zolmitriptan", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "18", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_688.json b/test_assets/Asset_688.json new file mode 100644 index 00000000..0d3fada8 --- /dev/null +++ b/test_assets/Asset_688.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_688", + "name": "TopAnswer: Celecoxib treats rheumatoid arthritis", + "description": "TopAnswer: Celecoxib treats rheumatoid arthritis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0008383", + "input_name": "rheumatoid arthritis", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:41423", + "output_name": "Celecoxib", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "19", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_689.json b/test_assets/Asset_689.json new file mode 100644 index 00000000..53481474 --- /dev/null +++ b/test_assets/Asset_689.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_689", + "name": "TopAnswer: Pyrimethamine treats malaria", + "description": "TopAnswer: Pyrimethamine treats malaria. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005136", + "input_name": "malaria", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:8673", + "output_name": "Pyrimethamine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "20", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_71.json b/test_assets/Asset_690.json similarity index 58% rename from test_assets/Asset_71.json rename to test_assets/Asset_690.json index 8aee4742..5cfab2c7 100644 --- a/test_assets/Asset_71.json +++ b/test_assets/Asset_690.json @@ -1,19 +1,21 @@ { - "id": "Asset_71", - "name": "TopAnswer: Rosuvastatin treats Homozygous Familial Hypercholesterolemia", - "description": "TopAnswer: Rosuvastatin treats Homozygous Familial Hypercholesterolemia", - "tags": [], + "id": "Asset_690", + "name": "TopAnswer: Loperamide treats diarrhea", + "description": "TopAnswer: Loperamide treats diarrhea. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0018328", - "input_name": "Homozygous Familial Hypercholesterolemia", + "input_id": "MONDO:0001673", + "input_name": "diarrhea", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:446157", - "output_name": "Rosuvastatin", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:6532", + "output_name": "Loperamide", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -33,16 +35,18 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "21", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } diff --git a/test_assets/Asset_691.json b/test_assets/Asset_691.json new file mode 100644 index 00000000..702f3b3a --- /dev/null +++ b/test_assets/Asset_691.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_691", + "name": "TopAnswer: Mesalazine treats ulcerative colitis", + "description": "TopAnswer: Mesalazine treats ulcerative colitis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005101", + "input_name": "ulcerative colitis", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:6775", + "output_name": "Mesalazine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "22", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_692.json b/test_assets/Asset_692.json new file mode 100644 index 00000000..ab4cafc9 --- /dev/null +++ b/test_assets/Asset_692.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_692", + "name": "TopAnswer: Riluzole treats amyotrophic lateral sclerosis", + "description": "TopAnswer: Riluzole treats amyotrophic lateral sclerosis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0004976", + "input_name": "amyotrophic lateral sclerosis", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:8863", + "output_name": "Riluzole", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "23", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_68.json b/test_assets/Asset_693.json similarity index 55% rename from test_assets/Asset_68.json rename to test_assets/Asset_693.json index 2686dbf5..514ab6d4 100644 --- a/test_assets/Asset_68.json +++ b/test_assets/Asset_693.json @@ -1,19 +1,21 @@ { - "id": "Asset_68", - "name": "NeverShow: Soot treats Obstructive Sleep Apnea", - "description": "NeverShow: Soot treats Obstructive Sleep Apnea", - "tags": [], + "id": "Asset_693", + "name": "TopAnswer: Lamotrigine treats epilepsy", + "description": "TopAnswer: Lamotrigine treats epilepsy. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0007147", - "input_name": "Obstructive Sleep Apnea", + "input_id": "MONDO:0005027", + "input_name": "epilepsy", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "MESH:D053260", - "output_name": "Soot", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:6367", + "output_name": "Lamotrigine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -29,20 +31,22 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "24", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } diff --git a/test_assets/Asset_694.json b/test_assets/Asset_694.json new file mode 100644 index 00000000..15252277 --- /dev/null +++ b/test_assets/Asset_694.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_694", + "name": "TopAnswer: Rizatriptan treats migraine", + "description": "TopAnswer: Rizatriptan treats migraine. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005277", + "input_name": "migraine", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:48273", + "output_name": "Rizatriptan", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "25", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_695.json b/test_assets/Asset_695.json new file mode 100644 index 00000000..72fe4edd --- /dev/null +++ b/test_assets/Asset_695.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_695", + "name": "TopAnswer: Rivastigmine treats Alzheimer disease", + "description": "TopAnswer: Rivastigmine treats Alzheimer disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0004975", + "input_name": "Alzheimer disease", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:8874", + "output_name": "Rivastigmine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "26", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_696.json b/test_assets/Asset_696.json new file mode 100644 index 00000000..41356fb6 --- /dev/null +++ b/test_assets/Asset_696.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_696", + "name": "TopAnswer: Rosuvastatin treats Hypercholesterolemia", + "description": "TopAnswer: Rosuvastatin treats Hypercholesterolemia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "HP:0003124", + "input_name": "Hypercholesterolemia", + "input_category": "biolink:PhenotypicFeature", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:38545", + "output_name": "Rosuvastatin", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "27", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_697.json b/test_assets/Asset_697.json new file mode 100644 index 00000000..3b23d819 --- /dev/null +++ b/test_assets/Asset_697.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_697", + "name": "TopAnswer: Bortezomib treats plasma cell myeloma", + "description": "TopAnswer: Bortezomib treats plasma cell myeloma. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0009693", + "input_name": "plasma cell myeloma", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:52717", + "output_name": "Bortezomib", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "28", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_698.json b/test_assets/Asset_698.json new file mode 100644 index 00000000..90b7f02e --- /dev/null +++ b/test_assets/Asset_698.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_698", + "name": "TopAnswer: Olaparib treats ovarian cancer", + "description": "TopAnswer: Olaparib treats ovarian cancer. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0008170", + "input_name": "ovarian cancer", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:83766", + "output_name": "Olaparib", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "29", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_699.json b/test_assets/Asset_699.json new file mode 100644 index 00000000..4684167b --- /dev/null +++ b/test_assets/Asset_699.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_699", + "name": "TopAnswer: Aclidinium treats chronic obstructive pulmonary disease", + "description": "TopAnswer: Aclidinium treats chronic obstructive pulmonary disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005002", + "input_name": "chronic obstructive pulmonary disease", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:65346", + "output_name": "Aclidinium", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "30", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_700.json b/test_assets/Asset_700.json new file mode 100644 index 00000000..b1b05ced --- /dev/null +++ b/test_assets/Asset_700.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_700", + "name": "Acceptable: Adenosine affects ADORA2B", + "description": "Acceptable: Adenosine affects ADORA2B. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:136", + "input_name": "ADORA2B", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:16335", + "output_name": "Adenosine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "increased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "31", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_701.json b/test_assets/Asset_701.json new file mode 100644 index 00000000..fcfbec7e --- /dev/null +++ b/test_assets/Asset_701.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_701", + "name": "Acceptable: Aspirin affects PTGS2", + "description": "Acceptable: Aspirin affects PTGS2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:5743", + "input_name": "PTGS2", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:15365", + "output_name": "Aspirin", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "32", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_702.json b/test_assets/Asset_702.json new file mode 100644 index 00000000..250d43df --- /dev/null +++ b/test_assets/Asset_702.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_702", + "name": "Acceptable: Buspirone affects HTR1A", + "description": "Acceptable: Buspirone affects HTR1A. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:3350", + "input_name": "HTR1A", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:3223", + "output_name": "Buspirone", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "increased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "33", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_703.json b/test_assets/Asset_703.json new file mode 100644 index 00000000..3fa06005 --- /dev/null +++ b/test_assets/Asset_703.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_703", + "name": "Acceptable: Fluoxetine affects SLC6A4", + "description": "Acceptable: Fluoxetine affects SLC6A4. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:6532", + "input_name": "SLC6A4", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:5118", + "output_name": "Fluoxetine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "34", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_704.json b/test_assets/Asset_704.json new file mode 100644 index 00000000..c461dc1a --- /dev/null +++ b/test_assets/Asset_704.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_704", + "name": "Acceptable: Indomethacin affects PTGS2", + "description": "Acceptable: Indomethacin affects PTGS2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:5743", + "input_name": "PTGS2", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:49662", + "output_name": "Indomethacin", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "35", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_705.json b/test_assets/Asset_705.json new file mode 100644 index 00000000..525ad543 --- /dev/null +++ b/test_assets/Asset_705.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_705", + "name": "Acceptable: Lovastatin affects HMGCR", + "description": "Acceptable: Lovastatin affects HMGCR. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:3156", + "input_name": "HMGCR", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:40303", + "output_name": "Lovastatin", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "36", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_706.json b/test_assets/Asset_706.json new file mode 100644 index 00000000..a528301b --- /dev/null +++ b/test_assets/Asset_706.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_706", + "name": "Acceptable: Ramipril affects ACE", + "description": "Acceptable: Ramipril affects ACE. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:1636", + "input_name": "ACE", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:8774", + "output_name": "Ramipril", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "37", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_707.json b/test_assets/Asset_707.json new file mode 100644 index 00000000..5263675f --- /dev/null +++ b/test_assets/Asset_707.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_707", + "name": "Acceptable: Simvastatin affects HMGCR", + "description": "Acceptable: Simvastatin affects HMGCR. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:3156", + "input_name": "HMGCR", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:9150", + "output_name": "Simvastatin", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "38", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_708.json b/test_assets/Asset_708.json new file mode 100644 index 00000000..5f05039a --- /dev/null +++ b/test_assets/Asset_708.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_708", + "name": "Acceptable: Tolcapone affects COMT", + "description": "Acceptable: Tolcapone affects COMT. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:1312", + "input_name": "COMT", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:63630", + "output_name": "Tolcapone", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "39", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_709.json b/test_assets/Asset_709.json new file mode 100644 index 00000000..49ae1f11 --- /dev/null +++ b/test_assets/Asset_709.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_709", + "name": "Acceptable: Erlotinib affects EGFR", + "description": "Acceptable: Erlotinib affects EGFR. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:1956", + "input_name": "EGFR", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:114785", + "output_name": "Erlotinib", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "40", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_710.json b/test_assets/Asset_710.json new file mode 100644 index 00000000..63dba647 --- /dev/null +++ b/test_assets/Asset_710.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_710", + "name": "Acceptable: Canagliflozin affects SLC5A2", + "description": "Acceptable: Canagliflozin affects SLC5A2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:6524", + "input_name": "SLC5A2", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:73274", + "output_name": "Canagliflozin", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "41", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_711.json b/test_assets/Asset_711.json new file mode 100644 index 00000000..ea97e207 --- /dev/null +++ b/test_assets/Asset_711.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_711", + "name": "Acceptable: Dabrafenib affects BRAF", + "description": "Acceptable: Dabrafenib affects BRAF. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:673", + "input_name": "BRAF", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:75045", + "output_name": "Dabrafenib", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "42", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_712.json b/test_assets/Asset_712.json new file mode 100644 index 00000000..b0f301e1 --- /dev/null +++ b/test_assets/Asset_712.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_712", + "name": "Acceptable: Ibrutinib affects BTK", + "description": "Acceptable: Ibrutinib affects BTK. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:695", + "input_name": "BTK", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:76612", + "output_name": "Ibrutinib", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "43", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_713.json b/test_assets/Asset_713.json new file mode 100644 index 00000000..bf879320 --- /dev/null +++ b/test_assets/Asset_713.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_713", + "name": "Acceptable: Sonidegib affects SMO", + "description": "Acceptable: Sonidegib affects SMO. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:6608", + "input_name": "SMO", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:90863", + "output_name": "Sonidegib", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "44", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_714.json b/test_assets/Asset_714.json new file mode 100644 index 00000000..888abf68 --- /dev/null +++ b/test_assets/Asset_714.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_714", + "name": "Acceptable: Venetoclax affects BCL2", + "description": "Acceptable: Venetoclax affects BCL2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:596", + "input_name": "BCL2", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:133021", + "output_name": "Venetoclax", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "45", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_715.json b/test_assets/Asset_715.json new file mode 100644 index 00000000..019256e2 --- /dev/null +++ b/test_assets/Asset_715.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_715", + "name": "Acceptable: Adenosine affects ADORA2A", + "description": "Acceptable: Adenosine affects ADORA2A. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:135", + "input_name": "ADORA2A", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:16335", + "output_name": "Adenosine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "increased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "46", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_716.json b/test_assets/Asset_716.json new file mode 100644 index 00000000..c61f235d --- /dev/null +++ b/test_assets/Asset_716.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_716", + "name": "Acceptable: Bumetanide affects SLC12A1", + "description": "Acceptable: Bumetanide affects SLC12A1. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:6557", + "input_name": "SLC12A1", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:3213", + "output_name": "Bumetanide", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "47", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_717.json b/test_assets/Asset_717.json new file mode 100644 index 00000000..aca8929b --- /dev/null +++ b/test_assets/Asset_717.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_717", + "name": "Acceptable: Citalopram affects SLC6A4", + "description": "Acceptable: Citalopram affects SLC6A4. SemMedDB replacement test - also covered by: chembl, dgidb, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:6532", + "input_name": "SLC6A4", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:3723", + "output_name": "Citalopram", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "48", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_718.json b/test_assets/Asset_718.json new file mode 100644 index 00000000..31497cb4 --- /dev/null +++ b/test_assets/Asset_718.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_718", + "name": "Acceptable: Clozapine affects HTR2A", + "description": "Acceptable: Clozapine affects HTR2A. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:3356", + "input_name": "HTR2A", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:3766", + "output_name": "Clozapine", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "decreased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "49", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_assets/Asset_719.json b/test_assets/Asset_719.json new file mode 100644 index 00000000..7e3e26bf --- /dev/null +++ b/test_assets/Asset_719.json @@ -0,0 +1,53 @@ +{ + "id": "Asset_719", + "name": "Acceptable: Dinoprostone affects PTGER2", + "description": "Acceptable: Dinoprostone affects PTGER2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "NCBIGene:5732", + "input_name": "PTGER2", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:15551", + "output_name": "Dinoprostone", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:causes" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "activity" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "increased" + } + ], + "expected_output": "Acceptable", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": false, + "test_reference": null, + "test_metadata": { + "id": "50", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } +} \ No newline at end of file diff --git a/test_cases/TestCase_0.json b/test_cases/TestCase_0.json index a1a71c01..237575aa 100644 --- a/test_cases/TestCase_0.json +++ b/test_cases/TestCase_0.json @@ -1,7 +1,7 @@ { "id": "TestCase_0", - "name": "what treats MONDO:0011426", - "description": "NeverShow: Iron (PUBCHEM) treats Aceruloplasminemia; NeverShow: organic group treats Aceruloplasminemia; NeverShow: iron treats Aceruloplasminemia; BadButForgivable: Iron (PUBCHEM) treats Aceruloplasminemia; NeverShow: Organic Chemicals treats Aceruloplasminemia; NeverShow: molecular entity treats Aceruloplasminemia; NeverShow: molecule treats Aceruloplasminemia; NeverShow: oxygen molecular entity treats Aceruloplasminemia; NeverShow: polyatomic entity treats Aceruloplasminemia; NeverShow: carbon group molecular entity treats Aceruloplasminemia; NeverShow: inorganic chemicals treats Aceruloplasminemia; NeverShow: heteroorganic entity treats Aceruloplasminemia; NeverShow: main group molecular entity treats Aceruloplasminemia; NeverShow: heteroatomic molecular entity treats Aceruloplasminemia; NeverShow: cyclic compound treats Aceruloplasminemia; NeverShow: heterocyclic compounds treats Aceruloplasminemia; NeverShow: inorganic oxide treats Aceruloplasminemia; NeverShow: chemical entity treats Aceruloplasminemia; NeverShow: cell nucleus treats Aceruloplasminemia; NeverShow: Rotenone treats Aceruloplasminemia; TopAnswer: deferipone treats Aceruloplasminemia; TopAnswer: deferasirox treats Aceruloplasminemia; TopAnswer: Deferoxamine treats Aceruloplasminemia", + "name": "what treats MONDO:0005301", + "description": "TopAnswer: Dalfampridine treats multiple sclerosis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,1050 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_1", - "name": "NeverShow: Iron (PUBCHEM) treats Aceruloplasminemia", - "description": "NeverShow: Iron (PUBCHEM) treats Aceruloplasminemia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0011426", - "input_name": "Aceruloplasminemia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:23925", - "output_name": "Iron (PUBCHEM)", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/506", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_2", - "name": "NeverShow: organic group treats Aceruloplasminemia", - "description": "NeverShow: organic group treats Aceruloplasminemia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0011426", - "input_name": "Aceruloplasminemia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:33247", - "output_name": "organic group", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - 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"test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_56", - "name": "NeverShow: cell nucleus treats Aceruloplasminemia", - "description": "NeverShow: cell nucleus treats Aceruloplasminemia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0011426", - "input_name": "Aceruloplasminemia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D002467", - "output_name": "cell nucleus", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/597", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_62", - "name": "NeverShow: Rotenone treats Aceruloplasminemia", - "description": "NeverShow: Rotenone treats Aceruloplasminemia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0011426", - "input_name": "Aceruloplasminemia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:6758", - "output_name": "Rotenone", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/505", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_303", - "name": "TopAnswer: deferipone treats Aceruloplasminemia", - "description": "TopAnswer: deferipone treats Aceruloplasminemia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0011426", - "input_name": "Aceruloplasminemia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:2972", - "output_name": "deferipone", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_304", - "name": "TopAnswer: deferasirox treats Aceruloplasminemia", - "description": "TopAnswer: deferasirox treats Aceruloplasminemia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0011426", - "input_name": "Aceruloplasminemia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:49005", - "output_name": "deferasirox", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_670", + "name": "TopAnswer: Dalfampridine treats multiple sclerosis", + "description": "TopAnswer: Dalfampridine treats multiple sclerosis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_305", - "name": "TopAnswer: Deferoxamine treats Aceruloplasminemia", - "description": "TopAnswer: Deferoxamine treats Aceruloplasminemia", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0011426", - "input_name": "Aceruloplasminemia", + "input_id": "MONDO:0005301", + "input_name": "multiple sclerosis", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:2973", - "output_name": "Deferoxamine", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:34385", + "output_name": "Dalfampridine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -1072,15 +45,17 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { "id": "1", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -1093,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0011426", + "test_case_input_id": "MONDO:0005301", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -1109,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_1.json b/test_cases/TestCase_1.json index e3ba2a49..44d33ff2 100644 --- a/test_cases/TestCase_1.json +++ b/test_cases/TestCase_1.json @@ -1,7 +1,7 @@ { "id": "TestCase_1", - "name": "what treats MONDO:0010794", - "description": "NeverShow: Valproic Acid treats NARP Syndrome; NeverShow: Barbiturates treats NARP Syndrome", + "name": "what treats MONDO:0005180", + "description": "TopAnswer: Apomorphine treats Parkinson disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Levodopa treats Parkinson disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Selegiline treats Parkinson disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,21 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_3", - "name": "NeverShow: Valproic Acid treats NARP Syndrome", - "description": "NeverShow: Valproic Acid treats NARP Syndrome", - "tags": [], + "id": "Asset_671", + "name": "TopAnswer: Apomorphine treats Parkinson disease", + "description": "TopAnswer: Apomorphine treats Parkinson disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0010794", - "input_name": "NARP Syndrome", + "input_id": "MONDO:0005180", + "input_name": "Parkinson disease", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "DRUGBANK:DB00313", - "output_name": "Valproic Acid", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:48538", + "output_name": "Apomorphine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -39,40 +41,97 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "2", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/147", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_4", - "name": "NeverShow: Barbiturates treats NARP Syndrome", - "description": "NeverShow: Barbiturates treats NARP Syndrome", - "tags": [], + "id": "Asset_673", + "name": "TopAnswer: Levodopa treats Parkinson disease", + "description": "TopAnswer: Levodopa treats Parkinson disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005180", + "input_name": "Parkinson disease", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:15765", + "output_name": "Levodopa", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "4", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } + }, + { + "id": "Asset_677", + "name": "TopAnswer: Selegiline treats Parkinson disease", + "description": "TopAnswer: Selegiline treats Parkinson disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0010794", - "input_name": "NARP Syndrome", + "input_id": "MONDO:0005180", + "input_name": "Parkinson disease", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "MESH:D001463", - "output_name": "Barbiturates", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:9086", + "output_name": "Selegiline", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -88,20 +147,22 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "8", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/147", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -113,7 +174,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0010794", + "test_case_input_id": "MONDO:0005180", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -129,7 +190,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_10.json b/test_cases/TestCase_10.json index e5b8fe2d..5e05ae52 100644 --- a/test_cases/TestCase_10.json +++ b/test_cases/TestCase_10.json @@ -1,7 +1,7 @@ { "id": "TestCase_10", - "name": "what treats MONDO:0005799", - "description": "TopAnswer: Mebendazole treats Hookworm Infectious Disease; TopAnswer: Pyrantel treats Hookworm Infectious Disease; TopAnswer: Thiabendazole treats Hookworm Infectious Disease; BadButForgivable: Dichlorophen treats Hookworm Infectious Disease", + "name": "what treats MONDO:0005136", + "description": "TopAnswer: Pyrimethamine treats malaria. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,70 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_52", - "name": "TopAnswer: Mebendazole treats Hookworm Infectious Disease", - "description": "TopAnswer: Mebendazole treats Hookworm Infectious Disease", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005799", - "input_name": "Hookworm Infectious Disease", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:4030", - "output_name": "Mebendazole", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_689", + "name": "TopAnswer: Pyrimethamine treats malaria", + "description": "TopAnswer: Pyrimethamine treats malaria. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/483", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_53", - "name": "TopAnswer: Pyrantel treats Hookworm Infectious Disease", - "description": "TopAnswer: Pyrantel treats Hookworm Infectious Disease", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0005799", - "input_name": "Hookworm Infectious Disease", + "input_id": "MONDO:0005136", + "input_name": "malaria", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:708857", - "output_name": "Pyrantel", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:8673", + "output_name": "Pyrimethamine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -92,114 +45,18 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/483", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_54", - "name": "TopAnswer: Thiabendazole treats Hookworm Infectious Disease", - "description": "TopAnswer: Thiabendazole treats Hookworm Infectious Disease", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005799", - "input_name": "Hookworm Infectious Disease", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5430", - "output_name": "Thiabendazole", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/483", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_55", - "name": "BadButForgivable: Dichlorophen treats Hookworm Infectious Disease", - "description": "BadButForgivable: Dichlorophen treats Hookworm Infectious Disease", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005799", - "input_name": "Hookworm Infectious Disease", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:3037", - "output_name": "Dichlorophen", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "BadButForgivable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "20", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/483", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -211,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0005799", + "test_case_input_id": "MONDO:0005136", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -227,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_11.json b/test_cases/TestCase_11.json index 5ec4769f..1ee54b58 100644 --- a/test_cases/TestCase_11.json +++ b/test_cases/TestCase_11.json @@ -1,7 +1,7 @@ { "id": "TestCase_11", - "name": "what treats MONDO:0004975", - "description": "NeverShow: Pharmaceutical preparations treats Alzheimer Disease", + "name": "what treats MONDO:0001673", + "description": "TopAnswer: Loperamide treats diarrhea. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,21 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_57", - "name": "NeverShow: Pharmaceutical preparations treats Alzheimer Disease", - "description": "NeverShow: Pharmaceutical preparations treats Alzheimer Disease", - "tags": [], + "id": "Asset_690", + "name": "TopAnswer: Loperamide treats diarrhea", + "description": "TopAnswer: Loperamide treats diarrhea. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0004975", - "input_name": "Alzheimer Disease", + "input_id": "MONDO:0001673", + "input_name": "diarrhea", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "UMLS:C0013227", - "output_name": "Pharmaceutical preparations", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:6532", + "output_name": "Loperamide", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -39,19 +41,21 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "21", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -64,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0004975", + "test_case_input_id": "MONDO:0001673", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -80,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_12.json b/test_cases/TestCase_12.json index 9270d5fa..4c24c8dd 100644 --- a/test_cases/TestCase_12.json +++ b/test_cases/TestCase_12.json @@ -1,7 +1,7 @@ { "id": "TestCase_12", - "name": "what treats MONDO:0009265", - "description": "TopAnswer: Eliglustat treats Gaucher Disease type1; TopAnswer: Imiglucerase treats Gaucher Disease type1; TopAnswer: Taliglucerase alfa treats Gaucher Disease type1; TopAnswer: Velaglucerase-alfa treats Gaucher Disease type1; TopAnswer: Miglustat treats Gaucher Disease type1", + "name": "what treats MONDO:0005101", + "description": "TopAnswer: Mesalazine treats ulcerative colitis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,217 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_63", - "name": "TopAnswer: Eliglustat treats Gaucher Disease type1", - "description": "TopAnswer: Eliglustat treats Gaucher Disease type1", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0009265", - "input_name": "Gaucher Disease type1", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:82752", - "output_name": "Eliglustat", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_64", - "name": "TopAnswer: Imiglucerase treats Gaucher Disease type1", - "description": "TopAnswer: Imiglucerase treats Gaucher Disease type1", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_691", + "name": "TopAnswer: Mesalazine treats ulcerative colitis", + "description": "TopAnswer: Mesalazine treats ulcerative colitis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0009265", - "input_name": "Gaucher Disease type1", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UNII:Q6U6J48BWY", - "output_name": "Imiglucerase", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_65", - "name": "TopAnswer: Taliglucerase alfa treats Gaucher Disease type1", - "description": "TopAnswer: Taliglucerase alfa treats Gaucher Disease type1", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0009265", - "input_name": "Gaucher Disease type1", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UNII:0R4NLX88O4", - "output_name": "Taliglucerase alfa", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_66", - "name": "TopAnswer: Velaglucerase-alfa treats Gaucher Disease type1", - "description": "TopAnswer: Velaglucerase-alfa treats Gaucher Disease type1", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0009265", - "input_name": "Gaucher Disease type1", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEMBL.COMPOUND:CHEMBL1201865", - "output_name": "Velaglucerase-alfa", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_67", - "name": "TopAnswer: Miglustat treats Gaucher Disease type1", - "description": "TopAnswer: Miglustat treats Gaucher Disease type1", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0009265", - "input_name": "Gaucher Disease type1", + "input_id": "MONDO:0005101", + "input_name": "ulcerative colitis", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:51634", - "output_name": "Miglustat", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:6775", + "output_name": "Mesalazine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -239,16 +45,18 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "22", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -260,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0009265", + "test_case_input_id": "MONDO:0005101", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -276,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_13.json b/test_cases/TestCase_13.json index ed5851a3..d7880fec 100644 --- a/test_cases/TestCase_13.json +++ b/test_cases/TestCase_13.json @@ -1,7 +1,7 @@ { "id": "TestCase_13", - "name": "what treats MONDO:0007147", - "description": "NeverShow: Soot treats Obstructive Sleep Apnea; Acceptable: Soot treats Obstructive Sleep Apnea", + "name": "what treats MONDO:0004976", + "description": "TopAnswer: Riluzole treats amyotrophic lateral sclerosis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,70 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_68", - "name": "NeverShow: Soot treats Obstructive Sleep Apnea", - "description": "NeverShow: Soot treats Obstructive Sleep Apnea", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_692", + "name": "TopAnswer: Riluzole treats amyotrophic lateral sclerosis", + "description": "TopAnswer: Riluzole treats amyotrophic lateral sclerosis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0007147", - "input_name": "Obstructive Sleep Apnea", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D053260", - "output_name": "Soot", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_69", - "name": "Acceptable: Soot treats Obstructive Sleep Apnea", - "description": "Acceptable: Soot treats Obstructive Sleep Apnea", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0007147", - "input_name": "Obstructive Sleep Apnea", + "input_id": "MONDO:0004976", + "input_name": "amyotrophic lateral sclerosis", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "MESH:D053260", - "output_name": "Soot", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:8863", + "output_name": "Riluzole", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -88,20 +41,22 @@ "value": "" } ], - "expected_output": "Acceptable", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "23", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -113,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0007147", + "test_case_input_id": "MONDO:0004976", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -129,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_14.json b/test_cases/TestCase_14.json index 97f0801b..28d8989e 100644 --- a/test_cases/TestCase_14.json +++ b/test_cases/TestCase_14.json @@ -1,7 +1,7 @@ { "id": "TestCase_14", - "name": "what treats MONDO:0018982", - "description": "TopAnswer: Miglustat treats Niemann-Pick type C", + "name": "what treats MONDO:0004975", + "description": "TopAnswer: Rivastigmine treats Alzheimer disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,21 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_70", - "name": "TopAnswer: Miglustat treats Niemann-Pick type C", - "description": "TopAnswer: Miglustat treats Niemann-Pick type C", - "tags": [], + "id": "Asset_695", + "name": "TopAnswer: Rivastigmine treats Alzheimer disease", + "description": "TopAnswer: Rivastigmine treats Alzheimer disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0018982", - "input_name": "Niemann-Pick type C", + "input_id": "MONDO:0004975", + "input_name": "Alzheimer disease", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:51634", - "output_name": "Miglustat", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:8874", + "output_name": "Rivastigmine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -43,16 +45,18 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "26", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -64,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0018982", + "test_case_input_id": "MONDO:0004975", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -80,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_15.json b/test_cases/TestCase_15.json index 9277eaa0..e38590a7 100644 --- a/test_cases/TestCase_15.json +++ b/test_cases/TestCase_15.json @@ -1,7 +1,7 @@ { "id": "TestCase_15", - "name": "what treats MONDO:0018328", - "description": "TopAnswer: Rosuvastatin treats Homozygous Familial Hypercholesterolemia; TopAnswer: Lomitapide treats Homozygous Familial Hypercholesterolemia; TopAnswer: Mipomersen treats Homozygous Familial Hypercholesterolemia; TopAnswer: Evolocumab treats Homozygous Familial Hypercholesterolemia", + "name": "what treats MONDO:0009693", + "description": "TopAnswer: Bortezomib treats plasma cell myeloma. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,168 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_71", - "name": "TopAnswer: Rosuvastatin treats Homozygous Familial Hypercholesterolemia", - "description": "TopAnswer: Rosuvastatin treats Homozygous Familial Hypercholesterolemia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018328", - "input_name": "Homozygous Familial Hypercholesterolemia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:446157", - "output_name": "Rosuvastatin", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_72", - "name": "TopAnswer: Lomitapide treats Homozygous Familial Hypercholesterolemia", - "description": "TopAnswer: Lomitapide treats Homozygous Familial Hypercholesterolemia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018328", - "input_name": "Homozygous Familial Hypercholesterolemia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:9853053", - "output_name": "Lomitapide", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_73", - "name": "TopAnswer: Mipomersen treats Homozygous Familial Hypercholesterolemia", - "description": "TopAnswer: Mipomersen treats Homozygous Familial Hypercholesterolemia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018328", - "input_name": "Homozygous Familial Hypercholesterolemia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UNII:9GJ8S4GU0M", - "output_name": "Mipomersen", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_697", + "name": "TopAnswer: Bortezomib treats plasma cell myeloma", + "description": "TopAnswer: Bortezomib treats plasma cell myeloma. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_74", - "name": "TopAnswer: Evolocumab treats Homozygous Familial Hypercholesterolemia", - "description": "TopAnswer: Evolocumab treats Homozygous Familial Hypercholesterolemia", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0018328", - "input_name": "Homozygous Familial Hypercholesterolemia", + "input_id": "MONDO:0009693", + "input_name": "plasma cell myeloma", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "UNII:LKC0U3A8NJ", - "output_name": "Evolocumab", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:52717", + "output_name": "Bortezomib", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -190,16 +45,18 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "28", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/494", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -211,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0018328", + "test_case_input_id": "MONDO:0009693", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -227,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_16.json b/test_cases/TestCase_16.json index 3da86ed6..4b434e43 100644 --- a/test_cases/TestCase_16.json +++ b/test_cases/TestCase_16.json @@ -1,7 +1,7 @@ { "id": "TestCase_16", - "name": "what treats MONDO:0043233", - "description": "NeverShow: Imatinib treats Exfoliative Dermatitis; NeverShow: Sorafenib treats Exfoliative Dermatitis; NeverShow: Toluene treats Exfoliative Dermatitis; NeverShow: Isoxaflutole treats Exfoliative Dermatitis; NeverShow: Clofenotane treats Exfoliative Dermatitis", + "name": "what treats MONDO:0008170", + "description": "TopAnswer: Olaparib treats ovarian cancer. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,217 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_80", - "name": "NeverShow: Imatinib treats Exfoliative Dermatitis", - "description": "NeverShow: Imatinib treats Exfoliative Dermatitis", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_698", + "name": "TopAnswer: Olaparib treats ovarian cancer", + "description": "TopAnswer: Olaparib treats ovarian cancer. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0043233", - "input_name": "Exfoliative Dermatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5291", - "output_name": "Imatinib", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/486", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_81", - "name": "NeverShow: Sorafenib treats Exfoliative Dermatitis", - "description": "NeverShow: Sorafenib treats Exfoliative Dermatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0043233", - "input_name": "Exfoliative Dermatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:216239", - "output_name": "Sorafenib", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/486", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_82", - "name": "NeverShow: Toluene treats Exfoliative Dermatitis", - "description": "NeverShow: Toluene treats Exfoliative Dermatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0043233", - "input_name": "Exfoliative Dermatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:1140", - "output_name": "Toluene", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_83", - "name": "NeverShow: Isoxaflutole treats Exfoliative Dermatitis", - "description": "NeverShow: Isoxaflutole treats Exfoliative Dermatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0043233", - "input_name": "Exfoliative Dermatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:84098", - "output_name": "Isoxaflutole", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_84", - "name": "NeverShow: Clofenotane treats Exfoliative Dermatitis", - "description": "NeverShow: Clofenotane treats Exfoliative Dermatitis", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0043233", - "input_name": "Exfoliative Dermatitis", + "input_id": "MONDO:0008170", + "input_name": "ovarian cancer", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:3036", - "output_name": "Clofenotane", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:83766", + "output_name": "Olaparib", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -235,19 +41,21 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "29", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -260,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0043233", + "test_case_input_id": "MONDO:0008170", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -276,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_17.json b/test_cases/TestCase_17.json index aaa01994..fe1da8e7 100644 --- a/test_cases/TestCase_17.json +++ b/test_cases/TestCase_17.json @@ -1,7 +1,7 @@ { "id": "TestCase_17", - "name": "what treats MONDO:0005267", - "description": "NeverShow: fibrinogen treats Heart Disorder", + "name": "what treats MONDO:0005002", + "description": "TopAnswer: Aclidinium treats chronic obstructive pulmonary disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,21 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_90", - "name": "NeverShow: fibrinogen treats Heart Disorder", - "description": "NeverShow: fibrinogen treats Heart Disorder", - "tags": [], + "id": "Asset_699", + "name": "TopAnswer: Aclidinium treats chronic obstructive pulmonary disease", + "description": "TopAnswer: Aclidinium treats chronic obstructive pulmonary disease. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0005267", - "input_name": "Heart Disorder", + "input_id": "MONDO:0005002", + "input_name": "chronic obstructive pulmonary disease", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "CHEBI:80160", - "output_name": "fibrinogen", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:65346", + "output_name": "Aclidinium", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -39,20 +41,22 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "30", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/477", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -64,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0005267", + "test_case_input_id": "MONDO:0005002", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -80,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_18.json b/test_cases/TestCase_18.json index 2419b652..bb569453 100644 --- a/test_cases/TestCase_18.json +++ b/test_cases/TestCase_18.json @@ -1,7 +1,7 @@ { "id": "TestCase_18", - "name": "what treats MONDO:0008251", - "description": "BadButForgivable: retinol treats familial pityriasis rubra pilaris; NeverShow: Alcohols treats familial pityriasis rubra pilaris", + "name": "what affects NCBIGene:136", + "description": "Acceptable: Adenosine affects ADORA2B. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,98 +9,53 @@ "query_type": null, "test_assets": [ { - "id": "Asset_92", - "name": "BadButForgivable: retinol treats familial pityriasis rubra pilaris", - "description": "BadButForgivable: retinol treats familial pityriasis rubra pilaris", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0008251", - "input_name": "familial pityriasis rubra pilaris", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:445354", - "output_name": "retinol", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_700", + "name": "Acceptable: Adenosine affects ADORA2B", + "description": "Acceptable: Adenosine affects ADORA2B. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "BadButForgivable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/473", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_95", - "name": "NeverShow: Alcohols treats familial pityriasis rubra pilaris", - "description": "NeverShow: Alcohols treats familial pityriasis rubra pilaris", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0008251", - "input_name": "familial pityriasis rubra pilaris", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D000438", - "output_name": "Alcohols", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:136", + "input_name": "ADORA2B", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:16335", + "output_name": "Adenosine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "increased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "31", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -111,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0008251", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:136", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "increased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_19.json b/test_cases/TestCase_19.json index f1e009f0..f39dbb06 100644 --- a/test_cases/TestCase_19.json +++ b/test_cases/TestCase_19.json @@ -1,7 +1,7 @@ { "id": "TestCase_19", - "name": "what treats MONDO:0019173", - "description": "NeverShow: methionine treats Rabies; NeverShow: cefaclor treats Rabies", + "name": "what affects NCBIGene:5743", + "description": "Acceptable: Aspirin affects PTGS2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd; Acceptable: Indomethacin affects PTGS2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,99 +9,107 @@ "query_type": null, "test_assets": [ { - "id": "Asset_93", - "name": "NeverShow: methionine treats Rabies", - "description": "NeverShow: methionine treats Rabies", - "tags": [], + "id": "Asset_701", + "name": "Acceptable: Aspirin affects PTGS2", + "description": "Acceptable: Aspirin affects PTGS2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0019173", - "input_name": "Rabies", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:16811", - "output_name": "methionine", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:5743", + "input_name": "PTGS2", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:15365", + "output_name": "Aspirin", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "32", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/463", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_94", - "name": "NeverShow: cefaclor treats Rabies", - "description": "NeverShow: cefaclor treats Rabies", - "tags": [], + "id": "Asset_704", + "name": "Acceptable: Indomethacin affects PTGS2", + "description": "Acceptable: Indomethacin affects PTGS2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0019173", - "input_name": "Rabies", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:3478", - "output_name": "cefaclor", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:5743", + "input_name": "PTGS2", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:49662", + "output_name": "Indomethacin", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "35", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/463", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -111,25 +119,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0019173", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:5743", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_2.json b/test_cases/TestCase_2.json index 5b7c34b5..19141201 100644 --- a/test_cases/TestCase_2.json +++ b/test_cases/TestCase_2.json @@ -1,7 +1,7 @@ { "id": "TestCase_2", - "name": "what treats MONDO:0001119", - "description": "NeverShow: hexadrin treats Premature Menopause; NeverShow: busulfan treats Premature Menopause; NeverShow: basis treats Premature Menopause; NeverShow: lasofoxifene treats Premature Menopause; NeverShow: busulfan treats Premature Menopause; TopAnswer: estradiol treats Premature Menopause; TopAnswer: progestin treats Premature Menopause", + "name": "what treats MONDO:0005044", + "description": "TopAnswer: Clonidine treats hypertension. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Quinapril treats hypertension. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Telmisartan treats hypertension. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,70 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_5", - "name": "NeverShow: hexadrin treats Premature Menopause", - "description": "NeverShow: hexadrin treats Premature Menopause", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_672", + "name": "TopAnswer: Clonidine treats hypertension", + "description": "TopAnswer: Clonidine treats hypertension. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0001119", - "input_name": "Premature Menopause", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:12358480", - "output_name": "hexadrin", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/490", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_6", - "name": "NeverShow: busulfan treats Premature Menopause", - "description": "NeverShow: busulfan treats Premature Menopause", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0001119", - "input_name": "Premature Menopause", + "input_id": "MONDO:0005044", + "input_name": "hypertension", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:2478", - "output_name": "busulfan", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:3757", + "output_name": "Clonidine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -88,187 +41,44 @@ "value": "" } ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/490", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_48", - "name": "NeverShow: basis treats Premature Menopause", - "description": "NeverShow: basis treats Premature Menopause", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001119", - "input_name": "Premature Menopause", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C1874451", - "output_name": "basis", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/567", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_76", - "name": "NeverShow: lasofoxifene treats Premature Menopause", - "description": "NeverShow: lasofoxifene treats Premature Menopause", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001119", - "input_name": "Premature Menopause", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:216416", - "output_name": "lasofoxifene", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "3", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/489", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_77", - "name": "NeverShow: busulfan treats Premature Menopause", - "description": "NeverShow: busulfan treats Premature Menopause", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001119", - "input_name": "Premature Menopause", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:2478", - "output_name": "busulfan", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_679", + "name": "TopAnswer: Quinapril treats hypertension", + "description": "TopAnswer: Quinapril treats hypertension. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/608", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_78", - "name": "TopAnswer: estradiol treats Premature Menopause", - "description": "TopAnswer: estradiol treats Premature Menopause", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0001119", - "input_name": "Premature Menopause", + "input_id": "MONDO:0005044", + "input_name": "hypertension", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5757", - "output_name": "estradiol", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:8713", + "output_name": "Quinapril", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -288,36 +98,40 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "10", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_79", - "name": "TopAnswer: progestin treats Premature Menopause", - "description": "TopAnswer: progestin treats Premature Menopause", - "tags": [], + "id": "Asset_684", + "name": "TopAnswer: Telmisartan treats hypertension", + "description": "TopAnswer: Telmisartan treats hypertension. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0001119", - "input_name": "Premature Menopause", + "input_id": "MONDO:0005044", + "input_name": "hypertension", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "MESH:D011372", - "output_name": "progestin", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:9434", + "output_name": "Telmisartan", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -337,15 +151,17 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "15", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -358,7 +174,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0001119", + "test_case_input_id": "MONDO:0005044", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -374,7 +190,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_20.json b/test_cases/TestCase_20.json index 05af2b2d..6152ca34 100644 --- a/test_cases/TestCase_20.json +++ b/test_cases/TestCase_20.json @@ -1,7 +1,7 @@ { "id": "TestCase_20", - "name": "what treats MONDO:0019600", - "description": "NeverShow: cadmium treats Xeroderma Pigmentosum; NeverShow: mercury treats Xeroderma Pigmentosum", + "name": "what affects NCBIGene:3350", + "description": "Acceptable: Buspirone affects HTR1A. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,99 +9,54 @@ "query_type": null, "test_assets": [ { - "id": "Asset_96", - "name": "NeverShow: cadmium treats Xeroderma Pigmentosum", - "description": "NeverShow: cadmium treats Xeroderma Pigmentosum", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0019600", - "input_name": "Xeroderma Pigmentosum", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:22977", - "output_name": "cadmium", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_702", + "name": "Acceptable: Buspirone affects HTR1A", + "description": "Acceptable: Buspirone affects HTR1A. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/465", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_97", - "name": "NeverShow: mercury treats Xeroderma Pigmentosum", - "description": "NeverShow: mercury treats Xeroderma Pigmentosum", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0019600", - "input_name": "Xeroderma Pigmentosum", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:25195", - "output_name": "mercury", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:3350", + "input_name": "HTR1A", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:3223", + "output_name": "Buspirone", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "increased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "33", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/465", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -111,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0019600", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:3350", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "increased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_21.json b/test_cases/TestCase_21.json index 93b7e254..22c7d78c 100644 --- a/test_cases/TestCase_21.json +++ b/test_cases/TestCase_21.json @@ -1,7 +1,7 @@ { "id": "TestCase_21", - "name": "what treats MONDO:0018911", - "description": "NeverShow: Receptor, insulin treats Maturity-onset Diabetes Of The Young; NeverShow: Autoantibodies treats Maturity-onset Diabetes Of The Young; NeverShow: Thyroid hormones treats Maturity-onset Diabetes Of The Young; NeverShow: Enzymes treats Maturity-onset Diabetes Of The Young; NeverShow: Receptor, IGF Type 1 treats Maturity-onset Diabetes Of The Young; NeverShow: Complement system proteins treats Maturity-onset Diabetes Of The Young; NeverShow: bisphenol A treats Maturity-onset Diabetes Of The Young", + "name": "what affects NCBIGene:6532", + "description": "Acceptable: Fluoxetine affects SLC6A4. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd; Acceptable: Citalopram affects SLC6A4. SemMedDB replacement test - also covered by: chembl, dgidb, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,372 +9,135 @@ "query_type": null, "test_assets": [ { - "id": "Asset_124", - "name": "NeverShow: Receptor, insulin treats Maturity-onset Diabetes Of The Young", - "description": "NeverShow: Receptor, insulin treats Maturity-onset Diabetes Of The Young", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_703", + "name": "Acceptable: Fluoxetine affects SLC6A4", + "description": "Acceptable: Fluoxetine affects SLC6A4. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0018911", - "input_name": "Maturity-onset Diabetes Of The Young", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D011972", - "output_name": "Receptor, insulin", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/613", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_125", - "name": "NeverShow: Autoantibodies treats Maturity-onset Diabetes Of The Young", - "description": "NeverShow: Autoantibodies treats Maturity-onset Diabetes Of The Young", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0018911", - "input_name": "Maturity-onset Diabetes Of The Young", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D001323", - "output_name": "Autoantibodies", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:6532", + "input_name": "SLC6A4", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:5118", + "output_name": "Fluoxetine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "34", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_126", - "name": "NeverShow: Thyroid hormones treats Maturity-onset Diabetes Of The Young", - "description": "NeverShow: Thyroid hormones treats Maturity-onset Diabetes Of The Young", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_717", + "name": "Acceptable: Citalopram affects SLC6A4", + "description": "Acceptable: Citalopram affects SLC6A4. SemMedDB replacement test - also covered by: chembl, dgidb, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0018911", - "input_name": "Maturity-onset Diabetes Of The Young", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:53462828", - "output_name": "Thyroid hormones", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_127", - "name": "NeverShow: Enzymes treats Maturity-onset Diabetes Of The Young", - "description": "NeverShow: Enzymes treats Maturity-onset Diabetes Of The Young", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0018911", - "input_name": "Maturity-onset Diabetes Of The Young", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D004798", - "output_name": "Enzymes", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:6532", + "input_name": "SLC6A4", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:3723", + "output_name": "Citalopram", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "48", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } - }, - { - "id": "Asset_128", - "name": "NeverShow: Receptor, IGF Type 1 treats Maturity-onset Diabetes Of The Young", - "description": "NeverShow: Receptor, IGF Type 1 treats Maturity-onset Diabetes Of The Young", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018911", - "input_name": "Maturity-onset Diabetes Of The Young", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D017526", - "output_name": "Receptor, IGF Type 1", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_129", - "name": "NeverShow: Complement system proteins treats Maturity-onset Diabetes Of The Young", - "description": "NeverShow: Complement system proteins treats Maturity-onset Diabetes Of The Young", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018911", - "input_name": "Maturity-onset Diabetes Of The Young", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D003165", - "output_name": "Complement system proteins", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/615", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_130", - "name": "NeverShow: bisphenol A treats Maturity-onset Diabetes Of The Young", - "description": "NeverShow: bisphenol A treats Maturity-onset Diabetes Of The Young", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018911", - "input_name": "Maturity-onset Diabetes Of The Young", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:6623", - "output_name": "bisphenol A", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/444", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } } ], "preconditions": [], "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0018911", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:6532", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_22.json b/test_cases/TestCase_22.json index 54fd7315..7bba1f15 100644 --- a/test_cases/TestCase_22.json +++ b/test_cases/TestCase_22.json @@ -1,7 +1,7 @@ { "id": "TestCase_22", - "name": "what treats MONDO:0015364", - "description": "NeverShow: Immunoglobulins, intravenous treats Hereditary Sensory And Autonomic Neuropathy Type; NeverShow: Isoxaflutole treats Hereditary Sensory And Autonomic Neuropathy Type; NeverShow: Erythromelalgia treats Hereditary Sensory And Autonomic Neuropathy; NeverShow: Riley-day Syndrome treats Hereditary Sensory And Autonomic Neuropathy", + "name": "what affects NCBIGene:3156", + "description": "Acceptable: Lovastatin affects HMGCR. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd; Acceptable: Simvastatin affects HMGCR. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,197 +9,107 @@ "query_type": null, "test_assets": [ { - "id": "Asset_131", - "name": "NeverShow: Immunoglobulins, intravenous treats Hereditary Sensory And Autonomic Neuropathy Type", - "description": "NeverShow: Immunoglobulins, intravenous treats Hereditary Sensory And Autonomic Neuropathy Type", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_705", + "name": "Acceptable: Lovastatin affects HMGCR", + "description": "Acceptable: Lovastatin affects HMGCR. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0015364", - "input_name": "Hereditary Sensory And Autonomic Neuropathy Type", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D016756", - "output_name": "Immunoglobulins, intravenous", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_132", - "name": "NeverShow: Isoxaflutole treats Hereditary Sensory And Autonomic Neuropathy Type", - "description": "NeverShow: Isoxaflutole treats Hereditary Sensory And Autonomic Neuropathy Type", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0015364", - "input_name": "Hereditary Sensory And Autonomic Neuropathy Type", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:84098", - "output_name": "Isoxaflutole", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:3156", + "input_name": "HMGCR", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:40303", + "output_name": "Lovastatin", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "36", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_182", - "name": "NeverShow: Erythromelalgia treats Hereditary Sensory And Autonomic Neuropathy", - "description": "NeverShow: Erythromelalgia treats Hereditary Sensory And Autonomic Neuropathy", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_707", + "name": "Acceptable: Simvastatin affects HMGCR", + "description": "Acceptable: Simvastatin affects HMGCR. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0015364", - "input_name": "Hereditary Sensory And Autonomic Neuropathy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MONDO:0016028", - "output_name": "Erythromelalgia", - "output_category": "biolink:Disease", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/632", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_183", - "name": "NeverShow: Riley-day Syndrome treats Hereditary Sensory And Autonomic Neuropathy", - "description": "NeverShow: Riley-day Syndrome treats Hereditary Sensory And Autonomic Neuropathy", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0015364", - "input_name": "Hereditary Sensory And Autonomic Neuropathy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MONDO:0009131", - "output_name": "Riley-day Syndrome", - "output_category": "biolink:Disease", + "input_id": "NCBIGene:3156", + "input_name": "HMGCR", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:9150", + "output_name": "Simvastatin", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "38", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/633", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -209,25 +119,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0015364", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:3156", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:Disease", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_23.json b/test_cases/TestCase_23.json index 8d16b9e6..25f4169a 100644 --- a/test_cases/TestCase_23.json +++ b/test_cases/TestCase_23.json @@ -1,7 +1,7 @@ { "id": "TestCase_23", - "name": "what treats MONDO:0009746", - "description": "NeverShow: Carbon treats Hereditary sensory and autonomic neuropathy type 4; NeverShow: Botulinum toxin type a treats Hereditary sensory and autonomic neuropathy type 4; NeverShow: Methamidophos treats Hereditary sensory and autonomic neuropathy type 4", + "name": "what affects NCBIGene:1636", + "description": "Acceptable: Ramipril affects ACE. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,147 +9,53 @@ "query_type": null, "test_assets": [ { - "id": "Asset_133", - "name": "NeverShow: Carbon treats Hereditary sensory and autonomic neuropathy type 4", - "description": "NeverShow: Carbon treats Hereditary sensory and autonomic neuropathy type 4", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_706", + "name": "Acceptable: Ramipril affects ACE", + "description": "Acceptable: Ramipril affects ACE. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0009746", - "input_name": "Hereditary sensory and autonomic neuropathy type 4", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5462310", - "output_name": "Carbon", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/404", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_134", - "name": "NeverShow: Botulinum toxin type a treats Hereditary sensory and autonomic neuropathy type 4", - "description": "NeverShow: Botulinum toxin type a treats Hereditary sensory and autonomic neuropathy type 4", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0009746", - "input_name": "Hereditary sensory and autonomic neuropathy type 4", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UNII:E211KPY694", - "output_name": "Botulinum toxin type a", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/405", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_137", - "name": "NeverShow: Methamidophos treats Hereditary sensory and autonomic neuropathy type 4", - "description": "NeverShow: Methamidophos treats Hereditary sensory and autonomic neuropathy type 4", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0009746", - "input_name": "Hereditary sensory and autonomic neuropathy type 4", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:4096", - "output_name": "Methamidophos", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:1636", + "input_name": "ACE", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:8774", + "output_name": "Ramipril", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "37", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -160,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0009746", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:1636", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_24.json b/test_cases/TestCase_24.json index e5d723c7..20965fff 100644 --- a/test_cases/TestCase_24.json +++ b/test_cases/TestCase_24.json @@ -1,7 +1,7 @@ { "id": "TestCase_24", - "name": "what affects NCBIGene:8653", - "description": "NeverShow: dna double stranded decreases activity or abundance of DDX3Y; NeverShow: Small molecule decreases activity or abundance of DDX3Y", + "name": "what affects NCBIGene:1312", + "description": "Acceptable: Tolcapone affects COMT. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,70 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_135", - "name": "NeverShow: dna double stranded decreases activity or abundance of DDX3Y", - "description": "NeverShow: dna double stranded decreases activity or abundance of DDX3Y", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_708", + "name": "Acceptable: Tolcapone affects COMT", + "description": "Acceptable: Tolcapone affects COMT. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "NCBIGene:8653", - "input_name": "DDX3Y", - "input_category": "biolink:Gene", - "predicate_id": "biolink:affects", - "predicate_name": "affects", - "output_id": "UMLS:C0311474", - "output_name": "dna double stranded", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:causes" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "activity_or_abundance" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "decreased" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/384", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_136", - "name": "NeverShow: Small molecule decreases activity or abundance of DDX3Y", - "description": "NeverShow: Small molecule decreases activity or abundance of DDX3Y", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "NCBIGene:8653", - "input_name": "DDX3Y", + "input_id": "NCBIGene:1312", + "input_name": "COMT", "input_category": "biolink:Gene", "predicate_id": "biolink:affects", "predicate_name": "affects", - "output_id": "UMLS:C1328819", - "output_name": "Small molecule", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:63630", + "output_name": "Tolcapone", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -81,27 +34,29 @@ }, { "parameter": "biolink_object_aspect_qualifier", - "value": "activity_or_abundance" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "39", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/384", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -113,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "affects", "test_case_predicate_id": "biolink:affects", - "test_case_input_id": "NCBIGene:8653", + "test_case_input_id": "NCBIGene:1312", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -121,7 +76,7 @@ }, { "parameter": "biolink_object_aspect_qualifier", - "value": "activity_or_abundance" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", @@ -129,7 +84,7 @@ } ], "input_category": "biolink:Gene", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_25.json b/test_cases/TestCase_25.json index f68d7149..0e063070 100644 --- a/test_cases/TestCase_25.json +++ b/test_cases/TestCase_25.json @@ -1,7 +1,7 @@ { "id": "TestCase_25", - "name": "what treats MONDO:0018493", - "description": "NeverShow: Halothane treats Malignant Hyperthermia Of Anesthesia; NeverShow: isoflurane treats Malignant Hyperthermia Of Anesthesia; NeverShow: Pharmaceutical preparations treats Malignant Hyperthermia Of Anesthesia; NeverShow: Carbon treats Malignant Hyperthermia Of Anesthesia; NeverShow: Anesthetics, local treats Malignant Hyperthermia Of Anesthesia; NeverShow: 4-aminopyridine treats Malignant Hyperthermia Of Anesthesia; NeverShow: Anesthetics treats Malignant Hyperthermia Of Anesthesia; NeverShow: Antibiotics treats Malignant Hyperthermia Of Anesthesia; NeverShow: basis treats Malignant Hyperthermia Of Anesthesia", + "name": "what affects NCBIGene:1956", + "description": "Acceptable: Erlotinib affects EGFR. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,441 +9,53 @@ "query_type": null, "test_assets": [ { - "id": "Asset_138", - "name": "NeverShow: Halothane treats Malignant Hyperthermia Of Anesthesia", - "description": "NeverShow: Halothane treats Malignant Hyperthermia Of Anesthesia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018493", - "input_name": "Malignant Hyperthermia Of Anesthesia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:3562", - "output_name": "Halothane", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/362", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_139", - "name": "NeverShow: isoflurane treats Malignant Hyperthermia Of Anesthesia", - "description": "NeverShow: isoflurane treats Malignant Hyperthermia Of Anesthesia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018493", - "input_name": "Malignant Hyperthermia Of Anesthesia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:3763", - "output_name": "isoflurane", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/362", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_142", - "name": "NeverShow: Pharmaceutical preparations treats Malignant Hyperthermia Of Anesthesia", - "description": "NeverShow: Pharmaceutical preparations treats Malignant Hyperthermia Of Anesthesia", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_709", + "name": "Acceptable: Erlotinib affects EGFR", + "description": "Acceptable: Erlotinib affects EGFR. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0018493", - "input_name": "Malignant Hyperthermia Of Anesthesia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0013227", - "output_name": "Pharmaceutical preparations", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_143", - "name": "NeverShow: Carbon treats Malignant Hyperthermia Of Anesthesia", - "description": "NeverShow: Carbon treats Malignant Hyperthermia Of Anesthesia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018493", - "input_name": "Malignant Hyperthermia Of Anesthesia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5462310", - "output_name": "Carbon", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_144", - "name": "NeverShow: Anesthetics, local treats Malignant Hyperthermia Of Anesthesia", - "description": "NeverShow: Anesthetics, local treats Malignant Hyperthermia Of Anesthesia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018493", - "input_name": "Malignant Hyperthermia Of Anesthesia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D000779", - "output_name": "Anesthetics, local", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_145", - "name": "NeverShow: 4-aminopyridine treats Malignant Hyperthermia Of Anesthesia", - "description": "NeverShow: 4-aminopyridine treats Malignant Hyperthermia Of Anesthesia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018493", - "input_name": "Malignant Hyperthermia Of Anesthesia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:1727", - "output_name": "4-aminopyridine", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_146", - "name": "NeverShow: Anesthetics treats Malignant Hyperthermia Of Anesthesia", - "description": "NeverShow: Anesthetics treats Malignant Hyperthermia Of Anesthesia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018493", - "input_name": "Malignant Hyperthermia Of Anesthesia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0002932", - "output_name": "Anesthetics", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_147", - "name": "NeverShow: Antibiotics treats Malignant Hyperthermia Of Anesthesia", - "description": "NeverShow: Antibiotics treats Malignant Hyperthermia Of Anesthesia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018493", - "input_name": "Malignant Hyperthermia Of Anesthesia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0003232", - "output_name": "Antibiotics", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_148", - "name": "NeverShow: basis treats Malignant Hyperthermia Of Anesthesia", - "description": "NeverShow: basis treats Malignant Hyperthermia Of Anesthesia", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0018493", - "input_name": "Malignant Hyperthermia Of Anesthesia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C1874451", - "output_name": "basis", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:1956", + "input_name": "EGFR", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:114785", + "output_name": "Erlotinib", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "40", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -454,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0018493", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:1956", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_26.json b/test_cases/TestCase_26.json index 11316290..763cfcf3 100644 --- a/test_cases/TestCase_26.json +++ b/test_cases/TestCase_26.json @@ -1,7 +1,7 @@ { "id": "TestCase_26", - "name": "what treats MONDO:0004758", - "description": "NeverShow: prednisone treats scotoma; NeverShow: vigabatrin treats scotoma", + "name": "what affects NCBIGene:6524", + "description": "Acceptable: Canagliflozin affects SLC5A2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,99 +9,54 @@ "query_type": null, "test_assets": [ { - "id": "Asset_140", - "name": "NeverShow: prednisone treats scotoma", - "description": "NeverShow: prednisone treats scotoma", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004758", - "input_name": "scotoma", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5865", - "output_name": "prednisone", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_710", + "name": "Acceptable: Canagliflozin affects SLC5A2", + "description": "Acceptable: Canagliflozin affects SLC5A2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/362", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_141", - "name": "NeverShow: vigabatrin treats scotoma", - "description": "NeverShow: vigabatrin treats scotoma", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0004758", - "input_name": "scotoma", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5665", - "output_name": "vigabatrin", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:6524", + "input_name": "SLC5A2", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:73274", + "output_name": "Canagliflozin", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "41", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/362", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -111,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0004758", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:6524", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_27.json b/test_cases/TestCase_27.json index 15fb779b..68787ae4 100644 --- a/test_cases/TestCase_27.json +++ b/test_cases/TestCase_27.json @@ -1,7 +1,7 @@ { "id": "TestCase_27", - "name": "what treats MONDO:0010808", - "description": "NeverShow: Atom treats Fatal familial insomnia; NeverShow: Cell nucleus treats Fatal familial insomnia; NeverShow: salts treats Fatal familial insomnia; NeverShow: Water treats Fatal familial insomnia; NeverShow: Hydrogen(.) treats Fatal familial insomnia; NeverShow: Electrons treats Fatal familial insomnia; NeverShow: Anions treats Fatal familial insomnia; NeverShow: Oxygen treats Fatal familial insomnia; NeverShow: Cations treats Fatal familial insomnia; NeverShow: Halogen molecular entity treats Fatal familial insomnia; NeverShow: Nitrogen molecular entity treats Fatal familial insomnia; NeverShow: Alcohols treats Fatal familial insomnia; NeverShow: Molecule treats Fatal familial insomnia; NeverShow: Organic salt treats Fatal familial insomnia; NeverShow: Organic chemicals treats Fatal familial insomnia; NeverShow: Organic chloride salt treats Fatal familial insomnia; NeverShow: Oxygen treats Fatal familial insomnia; NeverShow: Analgesics treats Fatal familial insomnia; NeverShow: Volatile organic compound treats Fatal familial insomnia", + "name": "what affects NCBIGene:673", + "description": "Acceptable: Dabrafenib affects BRAF. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,931 +9,53 @@ "query_type": null, "test_assets": [ { - "id": "Asset_149", - "name": "NeverShow: Atom treats Fatal familial insomnia", - "description": "NeverShow: Atom treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:33250", - "output_name": "Atom", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_150", - "name": "NeverShow: Cell nucleus treats Fatal familial insomnia", - "description": "NeverShow: Cell nucleus treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D002467", - "output_name": "Cell nucleus", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_151", - "name": "NeverShow: salts treats Fatal familial insomnia", - "description": "NeverShow: salts treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D012492", - "output_name": "salts", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_152", - "name": "NeverShow: Water treats Fatal familial insomnia", - "description": "NeverShow: Water treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:962", - "output_name": "Water", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_153", - "name": "NeverShow: Hydrogen(.) treats Fatal familial insomnia", - "description": "NeverShow: Hydrogen(.) treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:962", - "output_name": "Hydrogen(.)", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_154", - "name": "NeverShow: Electrons treats Fatal familial insomnia", - "description": "NeverShow: Electrons treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D004583", - "output_name": "Electrons", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_155", - "name": "NeverShow: Anions treats Fatal familial insomnia", - "description": "NeverShow: Anions treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D000838", - "output_name": "Anions", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_156", - "name": "NeverShow: Oxygen treats Fatal familial insomnia", - "description": "NeverShow: Oxygen treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:977", - "output_name": "Oxygen", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_157", - "name": "NeverShow: Cations treats Fatal familial insomnia", - "description": "NeverShow: Cations treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D002412", - "output_name": "Cations", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_158", - "name": "NeverShow: Halogen molecular entity treats Fatal familial insomnia", - "description": "NeverShow: Halogen molecular entity treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:24471", - "output_name": "Halogen molecular entity", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_159", - "name": "NeverShow: Nitrogen molecular entity treats Fatal familial insomnia", - "description": "NeverShow: Nitrogen molecular entity treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:51143", - "output_name": "Nitrogen molecular entity", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_160", - "name": "NeverShow: Alcohols treats Fatal familial insomnia", - "description": "NeverShow: Alcohols treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D000438", - "output_name": "Alcohols", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_161", - "name": "NeverShow: Molecule treats Fatal familial insomnia", - "description": "NeverShow: Molecule treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:25367", - "output_name": "Molecule", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_162", - "name": "NeverShow: Organic salt treats Fatal familial insomnia", - "description": "NeverShow: Organic salt treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:24868", - "output_name": "Organic salt", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_163", - "name": "NeverShow: Organic chemicals treats Fatal familial insomnia", - "description": "NeverShow: Organic chemicals treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D009930", - "output_name": "Organic chemicals", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_164", - "name": "NeverShow: Organic chloride salt treats Fatal familial insomnia", - "description": "NeverShow: Organic chloride salt treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:36094", - "output_name": "Organic chloride salt", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_165", - "name": "NeverShow: Oxygen treats Fatal familial insomnia", - "description": "NeverShow: Oxygen treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0030054", - "output_name": "Oxygen", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_166", - "name": "NeverShow: Analgesics treats Fatal familial insomnia", - "description": "NeverShow: Analgesics treats Fatal familial insomnia", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D000700", - "output_name": "Analgesics", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_711", + "name": "Acceptable: Dabrafenib affects BRAF", + "description": "Acceptable: Dabrafenib affects BRAF. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_167", - "name": "NeverShow: Volatile organic compound treats Fatal familial insomnia", - "description": "NeverShow: Volatile organic compound treats Fatal familial insomnia", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0010808", - "input_name": "Fatal familial insomnia", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:134179", - "output_name": "Volatile organic compound", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:673", + "input_name": "BRAF", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:75045", + "output_name": "Dabrafenib", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "42", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -944,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0010808", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:673", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_28.json b/test_cases/TestCase_28.json index 34640200..c84895c6 100644 --- a/test_cases/TestCase_28.json +++ b/test_cases/TestCase_28.json @@ -1,7 +1,7 @@ { "id": "TestCase_28", - "name": "what treats MONDO:0006497", - "description": "NeverShow: Antibiotics treats Cerebral palsy; NeverShow: Pharmaceutical preparations treats Cerebral palsy; BadButForgivable: Ibuprofen treats Cerebral palsy; Acceptable: Baclofen treats Cerebral palsy; Acceptable: Botulinum toxin type b treats Cerebral palsy; Acceptable: Carbamazepine treats Cerebral palsy; NeverShow: Air treats Cerebral Palsy; BadButForgivable: Air treats Cerebral Palsy; Acceptable: Air treats Cerebral Palsy; NeverShow: Aerosols treats Cerebral Palsy; NeverShow: Pharmaceutical Preparations treats Cerebral Palsy; Acceptable: Hyperbaric oxygen therapy treats Cerebral Palsy", + "name": "what affects NCBIGene:695", + "description": "Acceptable: Ibrutinib affects BTK. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,279 +9,36 @@ "query_type": null, "test_assets": [ { - "id": "Asset_168", - "name": "NeverShow: Antibiotics treats Cerebral palsy", - "description": "NeverShow: Antibiotics treats Cerebral palsy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0003232", - "output_name": "Antibiotics", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_169", - "name": "NeverShow: Pharmaceutical preparations treats Cerebral palsy", - "description": "NeverShow: Pharmaceutical preparations treats Cerebral palsy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0013227", - "output_name": "Pharmaceutical preparations", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_170", - "name": "BadButForgivable: Ibuprofen treats Cerebral palsy", - "description": "BadButForgivable: Ibuprofen treats Cerebral palsy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:3672", - "output_name": "Ibuprofen", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "BadButForgivable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_171", - "name": "Acceptable: Baclofen treats Cerebral palsy", - "description": "Acceptable: Baclofen treats Cerebral palsy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:2284", - "output_name": "Baclofen", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "Acceptable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_172", - "name": "Acceptable: Botulinum toxin type b treats Cerebral palsy", - "description": "Acceptable: Botulinum toxin type b treats Cerebral palsy", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_712", + "name": "Acceptable: Ibrutinib affects BTK", + "description": "Acceptable: Ibrutinib affects BTK. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEMBL.COMPOUND:CHEMBL1201569", - "output_name": "Botulinum toxin type b", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "Acceptable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_173", - "name": "Acceptable: Carbamazepine treats Cerebral palsy", - "description": "Acceptable: Carbamazepine treats Cerebral palsy", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:2554", - "output_name": "Carbamazepine", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:695", + "input_name": "BTK", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:76612", + "output_name": "Ibrutinib", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], "expected_output": "Acceptable", @@ -291,335 +48,43 @@ "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "43", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } - }, - { - "id": "Asset_188", - "name": "NeverShow: Air treats Cerebral Palsy", - "description": "NeverShow: Air treats Cerebral Palsy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral Palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C3536832", - "output_name": "Air", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/624", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_189", - "name": "BadButForgivable: Air treats Cerebral Palsy", - "description": "BadButForgivable: Air treats Cerebral Palsy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral Palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C3536832", - "output_name": "Air", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "BadButForgivable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/624", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_190", - "name": "Acceptable: Air treats Cerebral Palsy", - "description": "Acceptable: Air treats Cerebral Palsy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral Palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C3536832", - "output_name": "Air", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "Acceptable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/624", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_192", - "name": "NeverShow: Aerosols treats Cerebral Palsy", - "description": "NeverShow: Aerosols treats Cerebral Palsy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral Palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D000336", - "output_name": "Aerosols", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/624", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_193", - "name": "NeverShow: Pharmaceutical Preparations treats Cerebral Palsy", - "description": "NeverShow: Pharmaceutical Preparations treats Cerebral Palsy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral Palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0013227", - "output_name": "Pharmaceutical Preparations", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/624", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_194", - "name": "Acceptable: Hyperbaric oxygen therapy treats Cerebral Palsy", - "description": "Acceptable: Hyperbaric oxygen therapy treats Cerebral Palsy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0006497", - "input_name": "Cerebral Palsy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "NCIT:C38065", - "output_name": "Hyperbaric oxygen therapy", - "output_category": null, - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "Acceptable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/624", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } } ], "preconditions": [], "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0006497", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:695", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": null, + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_29.json b/test_cases/TestCase_29.json index a37e1ebb..3e6d622e 100644 --- a/test_cases/TestCase_29.json +++ b/test_cases/TestCase_29.json @@ -1,7 +1,7 @@ { "id": "TestCase_29", - "name": "what treats MONDO:0018958", - "description": "Acceptable: Tyrosine treats Nemaline myopathy; Acceptable: Melphalan treats Nemaline myopathy; NeverShow: 2,3,7,8-tetrachlorodibenzo-p-dioxin treats Nemaline myopathy; Acceptable: Thalidimide treats Nemaline myopathy", + "name": "what affects NCBIGene:6608", + "description": "Acceptable: Sonidegib affects SMO. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,181 +9,36 @@ "query_type": null, "test_assets": [ { - "id": "Asset_174", - "name": "Acceptable: Tyrosine treats Nemaline myopathy", - "description": "Acceptable: Tyrosine treats Nemaline myopathy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018958", - "input_name": "Nemaline myopathy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:6057", - "output_name": "Tyrosine", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "Acceptable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_175", - "name": "Acceptable: Melphalan treats Nemaline myopathy", - "description": "Acceptable: Melphalan treats Nemaline myopathy", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_713", + "name": "Acceptable: Sonidegib affects SMO", + "description": "Acceptable: Sonidegib affects SMO. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0018958", - "input_name": "Nemaline myopathy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:460612", - "output_name": "Melphalan", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "Acceptable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_176", - "name": "NeverShow: 2,3,7,8-tetrachlorodibenzo-p-dioxin treats Nemaline myopathy", - "description": "NeverShow: 2,3,7,8-tetrachlorodibenzo-p-dioxin treats Nemaline myopathy", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0018958", - "input_name": "Nemaline myopathy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:15625", - "output_name": "2,3,7,8-tetrachlorodibenzo-p-dioxin", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_177", - "name": "Acceptable: Thalidimide treats Nemaline myopathy", - "description": "Acceptable: Thalidimide treats Nemaline myopathy", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0018958", - "input_name": "Nemaline myopathy", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5426", - "output_name": "Thalidimide", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:6608", + "input_name": "SMO", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:90863", + "output_name": "Sonidegib", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], "expected_output": "Acceptable", @@ -193,12 +48,14 @@ "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "44", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -209,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0018958", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:6608", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_3.json b/test_cases/TestCase_3.json index 028e53d9..884a44ce 100644 --- a/test_cases/TestCase_3.json +++ b/test_cases/TestCase_3.json @@ -1,7 +1,7 @@ { "id": "TestCase_3", - "name": "what treats MONDO:0015564", - "description": "NeverShow: Vehicle Emissions treats Castleman Disease; TopAnswer: sirolimus treats Castleman Disease; TopAnswer: rituximab treats Castleman Disease; TopAnswer: anakinra treats Castleman Disease; TopAnswer: interferon-beta 1a treats Castleman Disease; TopAnswer: interferon-beta 1b treats Castleman Disease", + "name": "what treats MONDO:0008383", + "description": "TopAnswer: Methylprednisolone treats rheumatoid arthritis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Celecoxib treats rheumatoid arthritis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,168 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_7", - "name": "NeverShow: Vehicle Emissions treats Castleman Disease", - "description": "NeverShow: Vehicle Emissions treats Castleman Disease", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0015564", - "input_name": "Castleman Disease", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D001335", - "output_name": "Vehicle Emissions", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/480", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_11", - "name": "TopAnswer: sirolimus treats Castleman Disease", - "description": "TopAnswer: sirolimus treats Castleman Disease", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0015564", - "input_name": "Castleman Disease", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5284616", - "output_name": "sirolimus", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_12", - "name": "TopAnswer: rituximab treats Castleman Disease", - "description": "TopAnswer: rituximab treats Castleman Disease", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_674", + "name": "TopAnswer: Methylprednisolone treats rheumatoid arthritis", + "description": "TopAnswer: Methylprednisolone treats rheumatoid arthritis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0015564", - "input_name": "Castleman Disease", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UNII:4F4X42SYQ6", - "output_name": "rituximab", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_13", - "name": "TopAnswer: anakinra treats Castleman Disease", - "description": "TopAnswer: anakinra treats Castleman Disease", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0015564", - "input_name": "Castleman Disease", + "input_id": "MONDO:0008383", + "input_name": "rheumatoid arthritis", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "UNII:9013DUQ28K", - "output_name": "anakinra", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:6888", + "output_name": "Methylprednisolone", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -190,85 +45,40 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "5", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_14", - "name": "TopAnswer: interferon-beta 1a treats Castleman Disease", - "description": "TopAnswer: interferon-beta 1a treats Castleman Disease", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_688", + "name": "TopAnswer: Celecoxib treats rheumatoid arthritis", + "description": "TopAnswer: Celecoxib treats rheumatoid arthritis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0015564", - "input_name": "Castleman Disease", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEMBL.COMPOUND:CHEMBL1201562", - "output_name": "interferon-beta 1a", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_306", - "name": "TopAnswer: interferon-beta 1b treats Castleman Disease", - "description": "TopAnswer: interferon-beta 1b treats Castleman Disease", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0015564", - "input_name": "Castleman Disease", + "input_id": "MONDO:0008383", + "input_name": "rheumatoid arthritis", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "CHEMBL.COMPOUND:CHEMBL1201563", - "output_name": "interferon-beta 1b", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:41423", + "output_name": "Celecoxib", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -288,15 +98,17 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "19", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -309,7 +121,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0015564", + "test_case_input_id": "MONDO:0008383", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -325,7 +137,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_30.json b/test_cases/TestCase_30.json index 08df419c..36ba8656 100644 --- a/test_cases/TestCase_30.json +++ b/test_cases/TestCase_30.json @@ -1,7 +1,7 @@ { "id": "TestCase_30", - "name": "what treats MONDO:0007743", - "description": "NeverShow: Cocaine treats ADHD; Acceptable: Methylphenidate treats ADHD", + "name": "what affects NCBIGene:596", + "description": "Acceptable: Venetoclax affects BCL2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,83 +9,36 @@ "query_type": null, "test_assets": [ { - "id": "Asset_178", - "name": "NeverShow: Cocaine treats ADHD", - "description": "NeverShow: Cocaine treats ADHD", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_714", + "name": "Acceptable: Venetoclax affects BCL2", + "description": "Acceptable: Venetoclax affects BCL2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0007743", - "input_name": "ADHD", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:446220", - "output_name": "Cocaine", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_179", - "name": "Acceptable: Methylphenidate treats ADHD", - "description": "Acceptable: Methylphenidate treats ADHD", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0007743", - "input_name": "ADHD", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:4158", - "output_name": "Methylphenidate", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:596", + "input_name": "BCL2", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:133021", + "output_name": "Venetoclax", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], "expected_output": "Acceptable", @@ -95,12 +48,14 @@ "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "45", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -111,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0007743", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:596", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_31.json b/test_cases/TestCase_31.json index 41035293..1395cf28 100644 --- a/test_cases/TestCase_31.json +++ b/test_cases/TestCase_31.json @@ -1,7 +1,7 @@ { "id": "TestCase_31", - "name": "what treats MONDO:0005393", - "description": "Acceptable: Pegloticase treats Gout; Acceptable: Prednisone treats Gout", + "name": "what affects NCBIGene:135", + "description": "Acceptable: Adenosine affects ADORA2A. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp", "tags": [], "test_runner_settings": [ "inferred" @@ -9,83 +9,36 @@ "query_type": null, "test_assets": [ { - "id": "Asset_180", - "name": "Acceptable: Pegloticase treats Gout", - "description": "Acceptable: Pegloticase treats Gout", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_715", + "name": "Acceptable: Adenosine affects ADORA2A", + "description": "Acceptable: Adenosine affects ADORA2A. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0005393", - "input_name": "Gout", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UNNI:R581OT55EA", - "output_name": "Pegloticase", - "output_category": null, - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "Acceptable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_181", - "name": "Acceptable: Prednisone treats Gout", - "description": "Acceptable: Prednisone treats Gout", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0005393", - "input_name": "Gout", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5865", - "output_name": "Prednisone", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:135", + "input_name": "ADORA2A", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:16335", + "output_name": "Adenosine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "increased" } ], "expected_output": "Acceptable", @@ -95,12 +48,14 @@ "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "46", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -111,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0005393", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:135", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "increased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_32.json b/test_cases/TestCase_32.json index 50b49936..573ab9cd 100644 --- a/test_cases/TestCase_32.json +++ b/test_cases/TestCase_32.json @@ -1,7 +1,7 @@ { "id": "TestCase_32", - "name": "what treats MONDO:0005015", - "description": "OverlyGeneric: Pharmaceutical preparations treats Diabetes Mellitus; TopAnswer: Metformin treats Diabetes Mellitus; TopAnswer: Insulin human treats Diabetes Mellitus; TopAnswer: Insulin detremir treats Diabetes Mellitus", + "name": "what affects NCBIGene:6557", + "description": "Acceptable: Bumetanide affects SLC12A1. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,147 +9,53 @@ "query_type": null, "test_assets": [ { - "id": "Asset_184", - "name": "OverlyGeneric: Pharmaceutical preparations treats Diabetes Mellitus", - "description": "OverlyGeneric: Pharmaceutical preparations treats Diabetes Mellitus", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_716", + "name": "Acceptable: Bumetanide affects SLC12A1", + "description": "Acceptable: Bumetanide affects SLC12A1. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0005015", - "input_name": "Diabetes Mellitus", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0013227", - "output_name": "Pharmaceutical preparations", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "OverlyGeneric", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_185", - "name": "TopAnswer: Metformin treats Diabetes Mellitus", - "description": "TopAnswer: Metformin treats Diabetes Mellitus", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005015", - "input_name": "Diabetes Mellitus", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:4091", - "output_name": "Metformin", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_187", - "name": "TopAnswer: Insulin detremir treats Diabetes Mellitus", - "description": "TopAnswer: Insulin detremir treats Diabetes Mellitus", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0005015", - "input_name": "Diabetes Mellitus", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:16137271", - "output_name": "Insulin detremir", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:6557", + "input_name": "SLC12A1", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:3213", + "output_name": "Bumetanide", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "expected_output": "TopAnswer", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "47", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -160,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0005015", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:6557", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_33.json b/test_cases/TestCase_33.json index 8481abbe..543a34ee 100644 --- a/test_cases/TestCase_33.json +++ b/test_cases/TestCase_33.json @@ -1,7 +1,7 @@ { "id": "TestCase_33", - "name": "what treats MONDO:0001505", - "description": "NeverShow: Ethanol treats alcoholic hepatitis; Acceptable: Ethanol treats alcoholic hepatitis; NeverShow: Fenthion treats alcoholic hepatitis; NeverShow: Isoxaflutole treats alcoholic hepatitis; NeverShow: Rotenone treats alcoholic hepatitis; NeverShow: Lindane treats alcoholic hepatitis; NeverShow: Pharmaceutical preparations treats alcoholic hepatitis; BadButForgivable: Acetaminophen treats alcoholic hepatitis; NeverShow: Nanotubes, carbon treats alcoholic hepatitis; NeverShow: Bisphenol a treats alcoholic hepatitis; NeverShow: Water treats alcoholic hepatitis; NeverShow: Ketorolac treats alcoholic hepatitis; NeverShow: Ouabain treats alcoholic hepatitis; NeverShow: Formaldehyde treats alcoholic hepatitis; NeverShow: Cocaine treats alcoholic hepatitis; NeverShow: Coumarin treats alcoholic hepatitis; NeverShow: Mineral oil treats alcoholic hepatitis; NeverShow: Methamphetamine treats alcoholic hepatitis", + "name": "what affects NCBIGene:3356", + "description": "Acceptable: Clozapine affects HTR2A. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp", "tags": [], "test_runner_settings": [ "inferred" @@ -9,83 +9,36 @@ "query_type": null, "test_assets": [ { - "id": "Asset_195", - "name": "NeverShow: Ethanol treats alcoholic hepatitis", - "description": "NeverShow: Ethanol treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:702", - "output_name": "Ethanol", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_718", + "name": "Acceptable: Clozapine affects HTR2A", + "description": "Acceptable: Clozapine affects HTR2A. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, drugcentral, signor, tmkp", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/638", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_196", - "name": "Acceptable: Ethanol treats alcoholic hepatitis", - "description": "Acceptable: Ethanol treats alcoholic hepatitis", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:702", - "output_name": "Ethanol", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:3356", + "input_name": "HTR2A", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:3766", + "output_name": "Clozapine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], "expected_output": "Acceptable", @@ -95,796 +48,14 @@ "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/638", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_197", - "name": "NeverShow: Fenthion treats alcoholic hepatitis", - "description": "NeverShow: Fenthion treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:3346", - "output_name": "Fenthion", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_198", - "name": "NeverShow: Isoxaflutole treats alcoholic hepatitis", - "description": "NeverShow: Isoxaflutole treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:84098", - "output_name": "Isoxaflutole", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_199", - "name": "NeverShow: Rotenone treats alcoholic hepatitis", - "description": "NeverShow: Rotenone treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:6758", - "output_name": "Rotenone", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_200", - "name": "NeverShow: Lindane treats alcoholic hepatitis", - "description": "NeverShow: Lindane treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UNII:59NEE7PCAB", - "output_name": "Lindane", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_201", - "name": "NeverShow: Pharmaceutical preparations treats alcoholic hepatitis", - "description": "NeverShow: Pharmaceutical preparations treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0013227", - "output_name": "Pharmaceutical preparations", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_202", - "name": "BadButForgivable: Acetaminophen treats alcoholic hepatitis", - "description": "BadButForgivable: Acetaminophen treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:1983", - "output_name": "Acetaminophen", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "BadButForgivable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_203", - "name": "NeverShow: Nanotubes, carbon treats alcoholic hepatitis", - "description": "NeverShow: Nanotubes, carbon treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D037742", - "output_name": "Nanotubes, carbon", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_204", - "name": "NeverShow: Bisphenol a treats alcoholic hepatitis", - "description": "NeverShow: Bisphenol a treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:6623", - "output_name": "Bisphenol a", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_205", - "name": "NeverShow: Water treats alcoholic hepatitis", - "description": "NeverShow: Water treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:962", - "output_name": "Water", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_206", - "name": "NeverShow: Ketorolac treats alcoholic hepatitis", - "description": "NeverShow: Ketorolac treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:3826", - "output_name": "Ketorolac", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_207", - "name": "NeverShow: Ouabain treats alcoholic hepatitis", - "description": "NeverShow: Ouabain treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:439501", - "output_name": "Ouabain", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_208", - "name": "NeverShow: Formaldehyde treats alcoholic hepatitis", - "description": "NeverShow: Formaldehyde treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:712", - "output_name": "Formaldehyde", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_209", - "name": "NeverShow: Cocaine treats alcoholic hepatitis", - "description": "NeverShow: Cocaine treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:446220", - "output_name": "Cocaine", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_210", - "name": "NeverShow: Coumarin treats alcoholic hepatitis", - "description": "NeverShow: Coumarin treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:323", - "output_name": "Coumarin", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_211", - "name": "NeverShow: Mineral oil treats alcoholic hepatitis", - "description": "NeverShow: Mineral oil treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEMBL.COMPOUND:CHEMBL2109152", - "output_name": "Mineral oil", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_212", - "name": "NeverShow: Methamphetamine treats alcoholic hepatitis", - "description": "NeverShow: Methamphetamine treats alcoholic hepatitis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0001505", - "input_name": "alcoholic hepatitis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:10836", - "output_name": "Methamphetamine", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", + "id": "49", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -895,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0001505", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:3356", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "decreased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_34.json b/test_cases/TestCase_34.json index 95beb02e..1a054c62 100644 --- a/test_cases/TestCase_34.json +++ b/test_cases/TestCase_34.json @@ -1,7 +1,7 @@ { "id": "TestCase_34", - "name": "what treats MONDO:0004260", - "description": "NeverShow: Methylprednisolone treats Peptic Ulcer Perforation; NeverShow: Prednisone treats Peptic Ulcer Perforation; NeverShow: Hydrocortisone treats Peptic Ulcer Perforation; NeverShow: Dexamethasone treats Peptic Ulcer Perforation; NeverShow: Triamcinolone treats Peptic Ulcer Perforation; NeverShow: Tobacco smoke pollution treats Peptic Ulcer Perforation; NeverShow: Cholera Toxin treats Peptic Ulcer Perforation; NeverShow: Pertussis toxin treats Peptic Ulcer Perforation; NeverShow: Cocain-chlorhydrat treats Peptic Ulcer Perforation; NeverShow: Cations treats Peptic Ulcer Perforation; NeverShow: Sodium arsenite treats Peptic Ulcer Perforation; NeverShow: Anions treats Peptic Ulcer Perforation; NeverShow: Cadmium treats Peptic Ulcer Perforation; BadButForgivable: Azoles treats Peptic Ulcer Perforation; BadButForgivable: Cyanides treats Peptic Ulcer Perforation; BadButForgivable: Imidazoles treats Peptic Ulcer Perforation; NeverShow: Inorganic chemicals treats Peptic Ulcer Perforation; NeverShow: Chemical entity treats Peptic Ulcer Perforation; NeverShow: Molecular entity treats Peptic Ulcer Perforation; NeverShow: Nitrogen molecular entity treats Peptic Ulcer Perforation; NeverShow: Organic molecular entity treats Peptic Ulcer Perforation; NeverShow: Carbon group molecular entity treats Peptic Ulcer Perforation; NeverShow: Cell nucleus treats Peptic Ulcer Perforation; NeverShow: Organic oxo compound treats Peptic Ulcer Perforation; NeverShow: Atom treats Peptic Ulcer Perforation; NeverShow: Ions treats Peptic Ulcer Perforation; NeverShow: Group treats Peptic Ulcer Perforation; NeverShow: Cocaine treats Peptic Ulcer Perforation; BadButForgivable: Hydrogen peroxide treats Peptic Ulcer Perforation; NeverShow: Nitrogen 99.9 % treats Peptic Ulcer Perforation; NeverShow: Oxygen molecular entity treats Peptic Ulcer Perforation; NeverShow: Halogens treats Peptic Ulcer Perforation; NeverShow: Carbonyl compound treats Peptic Ulcer Perforation; NeverShow: Nitrogen 99.7 % treats Peptic Ulcer Perforation; NeverShow: Monoanion treats Peptic Ulcer Perforation; NeverShow: Organic cyclic compound treats Peptic Ulcer Perforation; NeverShow: Organic heterocyclic compound treats Peptic Ulcer Perforation", + "name": "what affects NCBIGene:5732", + "description": "Acceptable: Dinoprostone affects PTGER2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, signor, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,1813 +9,53 @@ "query_type": null, "test_assets": [ { - "id": "Asset_213", - "name": "NeverShow: Methylprednisolone treats Peptic Ulcer Perforation", - "description": "NeverShow: Methylprednisolone treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:6741", - "output_name": "Methylprednisolone", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/636", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_214", - "name": "NeverShow: Prednisone treats Peptic Ulcer Perforation", - "description": "NeverShow: Prednisone treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5865", - "output_name": "Prednisone", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/636", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_215", - "name": "NeverShow: Hydrocortisone treats Peptic Ulcer Perforation", - "description": "NeverShow: Hydrocortisone treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5754", - "output_name": "Hydrocortisone", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/636", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_216", - "name": "NeverShow: Dexamethasone treats Peptic Ulcer Perforation", - "description": "NeverShow: Dexamethasone treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5743", - "output_name": "Dexamethasone", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/636", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_217", - "name": "NeverShow: Triamcinolone treats Peptic Ulcer Perforation", - "description": "NeverShow: Triamcinolone treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:31307", - "output_name": "Triamcinolone", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/636", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_218", - "name": "NeverShow: Tobacco smoke pollution treats Peptic Ulcer Perforation", - "description": "NeverShow: Tobacco smoke pollution treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D014028", - "output_name": "Tobacco smoke pollution", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_219", - "name": "NeverShow: Cholera Toxin treats Peptic Ulcer Perforation", - "description": "NeverShow: Cholera Toxin treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D002772", - "output_name": "Cholera Toxin", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_220", - "name": "NeverShow: Pertussis toxin treats Peptic Ulcer Perforation", - "description": "NeverShow: Pertussis toxin treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D037342", - "output_name": "Pertussis toxin", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_221", - "name": "NeverShow: Cocain-chlorhydrat treats Peptic Ulcer Perforation", - "description": "NeverShow: Cocain-chlorhydrat treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:11302220", - "output_name": "Cocain-chlorhydrat", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_222", - "name": "NeverShow: Cations treats Peptic Ulcer Perforation", - "description": "NeverShow: Cations treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D002412", - "output_name": "Cations", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - 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"qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_225", - "name": "NeverShow: Cadmium treats Peptic Ulcer Perforation", - "description": "NeverShow: Cadmium treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - 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"test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:", - "output_name": "Azoles", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "BadButForgivable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - 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}, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_247", - "name": "NeverShow: Monoanion treats Peptic Ulcer Perforation", - "description": "NeverShow: Monoanion treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:36830", - "output_name": "Monoanion", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_248", - "name": "NeverShow: Organic cyclic compound treats Peptic Ulcer Perforation", - "description": "NeverShow: Organic cyclic compound treats Peptic Ulcer Perforation", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:33832", - "output_name": "Organic cyclic compound", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_719", + "name": "Acceptable: Dinoprostone affects PTGER2", + "description": "Acceptable: Dinoprostone affects PTGER2. SemMedDB replacement test - also covered by: chembl, dgidb, drug_rep_hub, signor, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_249", - "name": "NeverShow: Organic heterocyclic compound treats Peptic Ulcer Perforation", - "description": "NeverShow: Organic heterocyclic compound treats Peptic Ulcer Perforation", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0004260", - "input_name": "Peptic Ulcer Perforation", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:24532", - "output_name": "Organic heterocyclic compound", - "output_category": "biolink:ChemicalEntity", + "input_id": "NCBIGene:5732", + "input_name": "PTGER2", + "input_category": "biolink:Gene", + "predicate_id": "biolink:affects", + "predicate_name": "affects", + "output_id": "CHEBI:15551", + "output_name": "Dinoprostone", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "increased" } ], - "expected_output": "NeverShow", + "expected_output": "Acceptable", "test_issue": null, "semantic_severity": null, "in_v1": null, "well_known": false, "test_reference": null, "test_metadata": { - "id": "1", + "id": "50", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -1826,25 +66,25 @@ "trapi_template": null, "test_case_objective": "AcceptanceTest", "test_case_source": null, - "test_case_predicate_name": "treats", - "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0004260", + "test_case_predicate_name": "affects", + "test_case_predicate_id": "biolink:affects", + "test_case_input_id": "NCBIGene:5732", "qualifiers": [ { "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" + "value": "biolink:causes" }, { "parameter": "biolink_object_aspect_qualifier", - "value": "" + "value": "activity" }, { "parameter": "biolink_object_direction_qualifier", - "value": "" + "value": "increased" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:Gene", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_4.json b/test_cases/TestCase_4.json index 1f92108c..932c99ae 100644 --- a/test_cases/TestCase_4.json +++ b/test_cases/TestCase_4.json @@ -1,7 +1,7 @@ { "id": "TestCase_4", - "name": "what treats MONDO:0005301", - "description": "TopAnswer: fingolimod treats Multiple Sclerosis; TopAnswer: natalizumab treats Multiple Sclerosis; NeverShow: lead treats Multiple Sclerosis; NeverShow: vaccines treats Multiple Sclerosis; NeverShow: Covid-19 vaccines treats Multiple Sclerosis; NeverShow: Influenza vaccines treats Multiple Sclerosis; NeverShow: Vaccines, peptide treats Multiple Sclerosis; NeverShow: Metric treats Multiple Sclerosis; NeverShow: Agonists treats Multiple Sclerosis; NeverShow: Therapeutic agent treats Multiple Sclerosis; NeverShow: Vitamin supplementation treats Multiple Sclerosis; NeverShow: Anti-inflammatory agents treats Multiple Sclerosis; NeverShow: Adjuvants, immunologic treats Multiple Sclerosis; NeverShow: Antibodies treats Multiple Sclerosis; NeverShow: Anti-anxiety agents treats Multiple Sclerosis; NeverShow: Antibodies, monoclonal treats Multiple Sclerosis; NeverShow: Biological products treats Multiple Sclerosis; BadButForgivable: Neuroprotective agents treats Multiple Sclerosis; NeverShow: Antibiotics treats Multiple Sclerosis; NeverShow: basis treats Multiple Sclerosis; Acceptable: Anticholinergic agents treats Multiple Sclerosis; NeverShow: Analgesics treats Multiple Sclerosis; NeverShow: Mercury treats Multiple Sclerosis; NeverShow: Fatty acids treats Multiple Sclerosis; NeverShow: Plant extracts treats Multiple Sclerosis; NeverShow: Drugs, chinese herbal treats Multiple Sclerosis; NeverShow: Carbon treats Multiple Sclerosis; NeverShow: Water treats Multiple Sclerosis", + "name": "what treats HP:0003124", + "description": "TopAnswer: Fenofibrate treats Hypercholesterolemia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Simvastatin treats Hypercholesterolemia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Rosuvastatin treats Hypercholesterolemia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,70 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_8", - "name": "TopAnswer: fingolimod treats Multiple Sclerosis", - "description": "TopAnswer: fingolimod treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:107970", - "output_name": "fingolimod", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_675", + "name": "TopAnswer: Fenofibrate treats Hypercholesterolemia", + "description": "TopAnswer: Fenofibrate treats Hypercholesterolemia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "TopAnswer", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_9", - "name": "TopAnswer: natalizumab treats Multiple Sclerosis", - "description": "TopAnswer: natalizumab treats Multiple Sclerosis", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", + "input_id": "HP:0003124", + "input_name": "Hypercholesterolemia", + "input_category": "biolink:PhenotypicFeature", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "MESH:D000069442", - "output_name": "natalizumab", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:5001", + "output_name": "Fenofibrate", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -92,281 +45,40 @@ "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_10", - "name": "NeverShow: lead treats Multiple Sclerosis", - "description": "NeverShow: lead treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5352425", - "output_name": "lead", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_98", - "name": "NeverShow: vaccines treats Multiple Sclerosis", - "description": "NeverShow: vaccines treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D014612", - "output_name": "vaccines", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/431", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_100", - "name": "NeverShow: Covid-19 vaccines treats Multiple Sclerosis", - "description": "NeverShow: Covid-19 vaccines treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C5387588", - "output_name": "Covid-19 vaccines", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_101", - "name": "NeverShow: Influenza vaccines treats Multiple Sclerosis", - "description": "NeverShow: Influenza vaccines treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEMBL:2109042", - "output_name": "Influenza vaccines", - "output_category": null, - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "6", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_102", - "name": "NeverShow: Vaccines, peptide treats Multiple Sclerosis", - "description": "NeverShow: Vaccines, peptide treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0599934", - "output_name": "Vaccines, peptide", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_680", + "name": "TopAnswer: Simvastatin treats Hypercholesterolemia", + "description": "TopAnswer: Simvastatin treats Hypercholesterolemia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_103", - "name": "NeverShow: Metric treats Multiple Sclerosis", - "description": "NeverShow: Metric treats Multiple Sclerosis", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", + "input_id": "HP:0003124", + "input_name": "Hypercholesterolemia", + "input_category": "biolink:PhenotypicFeature", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "UMLS:C0699680", - "output_name": "Metric", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:9150", + "output_name": "Simvastatin", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -382,89 +94,44 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "11", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_104", - "name": "NeverShow: Agonists treats Multiple Sclerosis", - "description": "NeverShow: Agonists treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0243192", - "output_name": "Agonists", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_696", + "name": "TopAnswer: Rosuvastatin treats Hypercholesterolemia", + "description": "TopAnswer: Rosuvastatin treats Hypercholesterolemia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_105", - "name": "NeverShow: Therapeutic agent treats Multiple Sclerosis", - "description": "NeverShow: Therapeutic agent treats Multiple Sclerosis", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", + "input_id": "HP:0003124", + "input_name": "Hypercholesterolemia", + "input_category": "biolink:PhenotypicFeature", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "UMLS:C1611640", - "output_name": "Therapeutic agent", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:38545", + "output_name": "Rosuvastatin", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -480,901 +147,21 @@ "value": "" } ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_106", - "name": "NeverShow: Vitamin supplementation treats Multiple Sclerosis", - "description": "NeverShow: Vitamin supplementation treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0302837", - "output_name": "Vitamin supplementation", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_107", - "name": "NeverShow: Anti-inflammatory agents treats Multiple Sclerosis", - "description": "NeverShow: Anti-inflammatory agents treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0003209", - "output_name": "Anti-inflammatory agents", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_108", - "name": "NeverShow: Adjuvants, immunologic treats Multiple Sclerosis", - "description": "NeverShow: Adjuvants, immunologic treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D000276", - "output_name": "Adjuvants, immunologic", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_109", - "name": "NeverShow: Antibodies treats Multiple Sclerosis", - "description": "NeverShow: Antibodies treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D000906", - "output_name": "Antibodies", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_110", - "name": "NeverShow: Anti-anxiety agents treats Multiple Sclerosis", - "description": "NeverShow: Anti-anxiety agents treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0040616", - "output_name": "Anti-anxiety agents", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_111", - "name": "NeverShow: Antibodies, monoclonal treats Multiple Sclerosis", - "description": "NeverShow: Antibodies, monoclonal treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D000911", - "output_name": "Antibodies, monoclonal", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_112", - "name": "NeverShow: Biological products treats Multiple Sclerosis", - "description": "NeverShow: Biological products treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0005522", - "output_name": "Biological products", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_113", - "name": "BadButForgivable: Neuroprotective agents treats Multiple Sclerosis", - "description": "BadButForgivable: Neuroprotective agents treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0242912", - "output_name": "Neuroprotective agents", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "BadButForgivable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_114", - "name": "NeverShow: Antibiotics treats Multiple Sclerosis", - "description": "NeverShow: Antibiotics treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0003232", - "output_name": "Antibiotics", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_115", - "name": "NeverShow: basis treats Multiple Sclerosis", - "description": "NeverShow: basis treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C1874451", - "output_name": "basis", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_116", - "name": "Acceptable: Anticholinergic agents treats Multiple Sclerosis", - "description": "Acceptable: Anticholinergic agents treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UMLS:C0242896", - "output_name": "Anticholinergic agents", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "Acceptable", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_117", - "name": "NeverShow: Analgesics treats Multiple Sclerosis", - "description": "NeverShow: Analgesics treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D000700", - "output_name": "Analgesics", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_118", - "name": "NeverShow: Mercury treats Multiple Sclerosis", - "description": "NeverShow: Mercury treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:23931", - "output_name": "Mercury", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_119", - "name": "NeverShow: Fatty acids treats Multiple Sclerosis", - "description": "NeverShow: Fatty acids treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D005227", - "output_name": "Fatty acids", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_120", - "name": "NeverShow: Plant extracts treats Multiple Sclerosis", - "description": "NeverShow: Plant extracts treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D010936", - "output_name": "Plant extracts", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_121", - "name": "NeverShow: Drugs, chinese herbal treats Multiple Sclerosis", - "description": "NeverShow: Drugs, chinese herbal treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D004365", - "output_name": "Drugs, chinese herbal", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_122", - "name": "NeverShow: Carbon treats Multiple Sclerosis", - "description": "NeverShow: Carbon treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5462310", - "output_name": "Carbon", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_123", - "name": "NeverShow: Water treats Multiple Sclerosis", - "description": "NeverShow: Water treats Multiple Sclerosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0005301", - "input_name": "Multiple Sclerosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:962", - "output_name": "Water", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "27", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -1387,7 +174,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0005301", + "test_case_input_id": "HP:0003124", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -1402,8 +189,8 @@ "value": "" } ], - "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "input_category": "biolink:PhenotypicFeature", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_5.json b/test_cases/TestCase_5.json index 8471eb5a..f282da1a 100644 --- a/test_cases/TestCase_5.json +++ b/test_cases/TestCase_5.json @@ -1,7 +1,7 @@ { "id": "TestCase_5", - "name": "what treats MONDO:0100345", - "description": "TopAnswer: Lactase treats Lactose intolerance; NeverShow: beta-Lactose treats Lactose intolerance; NeverShow: Plant extracts treats Lactose intolerance; NeverShow: Plant preparations treats Lactose intolerance; NeverShow: alpha-Lactose treats Lactose intolerance; NeverShow: Ergocalciferol treats Lactose intolerance; NeverShow: Mebendazole treats Lactose intolerance; NeverShow: Bithionol treats Lactose intolerance; NeverShow: Thiabendazole treats Lactose intolerance; NeverShow: Levamisole treats Lactose intolerance; NeverShow: Methamidophos treats Lactose intolerance; NeverShow: Potassium bicarbonate treats Lactose intolerance; NeverShow: Triclosan treats Lactose intolerance; NeverShow: Tacrolimus treats Lactose intolerance", + "name": "what treats MONDO:0009688", + "description": "TopAnswer: Pyridostigmine treats myasthenia gravis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,21 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_32", - "name": "TopAnswer: Lactase treats Lactose intolerance", - "description": "TopAnswer: Lactase treats Lactose intolerance", - "tags": [], + "id": "Asset_676", + "name": "TopAnswer: Pyridostigmine treats myasthenia gravis", + "description": "TopAnswer: Pyridostigmine treats myasthenia gravis. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", + "input_id": "MONDO:0009688", + "input_name": "myasthenia gravis", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "CHEMBL.COMPOUND:CHEMBL2108505", - "output_name": "Lactase", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:8665", + "output_name": "Pyridostigmine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -46,653 +48,18 @@ "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/427", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_33", - "name": "NeverShow: beta-Lactose treats Lactose intolerance", - "description": "NeverShow: beta-Lactose treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:6134", - "output_name": "beta-Lactose", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", + "id": "7", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/427", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_34", - "name": "NeverShow: Plant extracts treats Lactose intolerance", - "description": "NeverShow: Plant extracts treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D010936", - "output_name": "Plant extracts", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } - }, - { - "id": "Asset_35", - "name": "NeverShow: Plant preparations treats Lactose intolerance", - "description": "NeverShow: Plant preparations treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "MESH:D028321", - "output_name": "Plant preparations", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": null, - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_36", - "name": "NeverShow: alpha-Lactose treats Lactose intolerance", - "description": "NeverShow: alpha-Lactose treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:6134", - "output_name": "alpha-Lactose", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/427", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_37", - "name": "NeverShow: Ergocalciferol treats Lactose intolerance", - "description": "NeverShow: Ergocalciferol treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5280793", - "output_name": "Ergocalciferol", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/601", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_38", - "name": "NeverShow: Mebendazole treats Lactose intolerance", - "description": "NeverShow: Mebendazole treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:4030", - "output_name": "Mebendazole", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/601", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_39", - "name": "NeverShow: Bithionol treats Lactose intolerance", - "description": "NeverShow: Bithionol treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:2406", - "output_name": "Bithionol", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/601", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_40", - "name": "NeverShow: Thiabendazole treats Lactose intolerance", - "description": "NeverShow: Thiabendazole treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5430", - "output_name": "Thiabendazole", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/601", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_41", - "name": "NeverShow: Levamisole treats Lactose intolerance", - "description": "NeverShow: Levamisole treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:26879", - "output_name": "Levamisole", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/601", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_42", - "name": "NeverShow: Methamidophos treats Lactose intolerance", - "description": "NeverShow: Methamidophos treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:4096", - "output_name": "Methamidophos", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/601", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_43", - "name": "NeverShow: Potassium bicarbonate treats Lactose intolerance", - "description": "NeverShow: Potassium bicarbonate treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:516893", - "output_name": "Potassium bicarbonate", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/601", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_44", - "name": "NeverShow: Triclosan treats Lactose intolerance", - "description": "NeverShow: Triclosan treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5564", - "output_name": "Triclosan", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/601", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_45", - "name": "NeverShow: Tacrolimus treats Lactose intolerance", - "description": "NeverShow: Tacrolimus treats Lactose intolerance", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0100345", - "input_name": "Lactose intolerance", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:445643", - "output_name": "Tacrolimus", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/601", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } } ], "preconditions": [], @@ -701,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0100345", + "test_case_input_id": "MONDO:0009688", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -717,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_6.json b/test_cases/TestCase_6.json index cac245b2..56ba1293 100644 --- a/test_cases/TestCase_6.json +++ b/test_cases/TestCase_6.json @@ -1,7 +1,7 @@ { "id": "TestCase_6", - "name": "what treats MONDO:0005260", - "description": "NeverShow: Valproic acid treats Autism; NeverShow: Pesticides treats Autism", + "name": "what treats MONDO:0005090", + "description": "TopAnswer: Haloperidol treats schizophrenia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Iloperidone treats schizophrenia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Quetiapine treats schizophrenia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,21 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_46", - "name": "NeverShow: Valproic acid treats Autism", - "description": "NeverShow: Valproic acid treats Autism", - "tags": [], + "id": "Asset_678", + "name": "TopAnswer: Haloperidol treats schizophrenia", + "description": "TopAnswer: Haloperidol treats schizophrenia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0005260", - "input_name": "Autism", + "input_id": "MONDO:0005090", + "input_name": "schizophrenia", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:3121", - "output_name": "Valproic acid", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:5613", + "output_name": "Haloperidol", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -39,40 +41,97 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "9", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/577", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_47", - "name": "NeverShow: Pesticides treats Autism", - "description": "NeverShow: Pesticides treats Autism", - "tags": [], + "id": "Asset_683", + "name": "TopAnswer: Iloperidone treats schizophrenia", + "description": "TopAnswer: Iloperidone treats schizophrenia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005090", + "input_name": "schizophrenia", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:65173", + "output_name": "Iloperidone", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "14", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } + }, + { + "id": "Asset_686", + "name": "TopAnswer: Quetiapine treats schizophrenia", + "description": "TopAnswer: Quetiapine treats schizophrenia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0005260", - "input_name": "Autism", + "input_id": "MONDO:0005090", + "input_name": "schizophrenia", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "MESH:D010575", - "output_name": "Pesticides", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:8707", + "output_name": "Quetiapine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -88,20 +147,22 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "17", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/575", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -113,7 +174,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0005260", + "test_case_input_id": "MONDO:0005090", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -129,7 +190,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_7.json b/test_cases/TestCase_7.json index 801a3c44..9bae05ba 100644 --- a/test_cases/TestCase_7.json +++ b/test_cases/TestCase_7.json @@ -1,7 +1,7 @@ { "id": "TestCase_7", - "name": "what treats MONDO:0017314", - "description": "NeverShow: methylphenidate treats Ehlers-Danlos Syndrome; NeverShow: Omniscan treats Ehlers-Danlos Syndrome; NeverShow: Gadobutrol treats Ehlers-Danlos Syndrome; NeverShow: Gadopentetate dimeglumine treats Ehlers-Danlos Syndrome; NeverShow: alendronic acid treats Ehlers-Danlos Syndrome", + "name": "what treats MONDO:0005277", + "description": "TopAnswer: Sumatriptan treats migraine. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Zolmitriptan treats migraine. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Rizatriptan treats migraine. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,70 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_49", - "name": "NeverShow: methylphenidate treats Ehlers-Danlos Syndrome", - "description": "NeverShow: methylphenidate treats Ehlers-Danlos Syndrome", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0017314", - "input_name": "Ehlers-Danlos Syndrome", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:4158", - "output_name": "methylphenidate", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } + "id": "Asset_681", + "name": "TopAnswer: Sumatriptan treats migraine", + "description": "TopAnswer: Sumatriptan treats migraine. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/562", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_58", - "name": "NeverShow: Omniscan treats Ehlers-Danlos Syndrome", - "description": "NeverShow: Omniscan treats Ehlers-Danlos Syndrome", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0017314", - "input_name": "Ehlers-Danlos Syndrome", + "input_id": "MONDO:0005277", + "input_name": "migraine", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:24847884", - "output_name": "Omniscan", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:10650", + "output_name": "Sumatriptan", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -88,89 +41,44 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "12", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/546", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_59", - "name": "NeverShow: Gadobutrol treats Ehlers-Danlos Syndrome", - "description": "NeverShow: Gadobutrol treats Ehlers-Danlos Syndrome", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_687", + "name": "TopAnswer: Zolmitriptan treats migraine", + "description": "TopAnswer: Zolmitriptan treats migraine. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0017314", - "input_name": "Ehlers-Danlos Syndrome", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "UNII:1BJ477IO2L", - "output_name": "Gadobutrol", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/546", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_60", - "name": "NeverShow: Gadopentetate dimeglumine treats Ehlers-Danlos Syndrome", - "description": "NeverShow: Gadopentetate dimeglumine treats Ehlers-Danlos Syndrome", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0017314", - "input_name": "Ehlers-Danlos Syndrome", + "input_id": "MONDO:0005277", + "input_name": "migraine", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:73415823", - "output_name": "Gadopentetate dimeglumine", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:10124", + "output_name": "Zolmitriptan", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -186,40 +94,44 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "18", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/546", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } }, { - "id": "Asset_99", - "name": "NeverShow: alendronic acid treats Ehlers-Danlos Syndrome", - "description": "NeverShow: alendronic acid treats Ehlers-Danlos Syndrome", - "tags": [], + "id": "Asset_694", + "name": "TopAnswer: Rizatriptan treats migraine", + "description": "TopAnswer: Rizatriptan treats migraine. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0017314", - "input_name": "Ehlers-Danlos Syndrome", + "input_id": "MONDO:0005277", + "input_name": "migraine", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "CHEBI:2567", - "output_name": "alendronic acid", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:48273", + "output_name": "Rizatriptan", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -235,20 +147,22 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "25", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/428", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -260,7 +174,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0017314", + "test_case_input_id": "MONDO:0005277", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -276,7 +190,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_8.json b/test_cases/TestCase_8.json index abdbc5e4..4cdd6aa7 100644 --- a/test_cases/TestCase_8.json +++ b/test_cases/TestCase_8.json @@ -1,7 +1,7 @@ { "id": "TestCase_8", - "name": "what treats MONDO:0004784", - "description": "NeverShow: particulate matter treats Allergic Asthma", + "name": "what treats MONDO:0005027", + "description": "TopAnswer: Phenytoin treats epilepsy. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd; TopAnswer: Lamotrigine treats epilepsy. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,21 +9,76 @@ "query_type": null, "test_assets": [ { - "id": "Asset_50", - "name": "NeverShow: particulate matter treats Allergic Asthma", - "description": "NeverShow: particulate matter treats Allergic Asthma", - "tags": [], + "id": "Asset_682", + "name": "TopAnswer: Phenytoin treats epilepsy", + "description": "TopAnswer: Phenytoin treats epilepsy. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [ + "inferred" + ], + "input_id": "MONDO:0005027", + "input_name": "epilepsy", + "input_category": "biolink:Disease", + "predicate_id": "biolink:treats", + "predicate_name": "treats", + "output_id": "CHEBI:8107", + "output_name": "Phenytoin", + "output_category": "biolink:Drug", + "association": null, + "qualifiers": [ + { + "parameter": "biolink_qualified_predicate", + "value": "biolink:treats" + }, + { + "parameter": "biolink_object_aspect_qualifier", + "value": "" + }, + { + "parameter": "biolink_object_direction_qualifier", + "value": "" + } + ], + "expected_output": "TopAnswer", + "test_issue": null, + "semantic_severity": null, + "in_v1": null, + "well_known": true, + "test_reference": null, + "test_metadata": { + "id": "13", + "name": null, + "description": null, + "tags": [ + "semmeddb_replacement" + ], + "test_runner_settings": [], + "test_source": "TranslatorTeam", + "test_reference": null, + "test_objective": "AcceptanceTest", + "test_annotations": [] + } + }, + { + "id": "Asset_693", + "name": "TopAnswer: Lamotrigine treats epilepsy", + "description": "TopAnswer: Lamotrigine treats epilepsy. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0004784", - "input_name": "Allergic Asthma", + "input_id": "MONDO:0005027", + "input_name": "epilepsy", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "MESH:D052638", - "output_name": "particulate matter", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:6367", + "output_name": "Lamotrigine", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -39,20 +94,22 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "24", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/561", + "test_source": "TranslatorTeam", + "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] } @@ -64,7 +121,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0004784", + "test_case_input_id": "MONDO:0005027", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -80,7 +137,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ], diff --git a/test_cases/TestCase_9.json b/test_cases/TestCase_9.json index 17e03c0d..ed2b14cb 100644 --- a/test_cases/TestCase_9.json +++ b/test_cases/TestCase_9.json @@ -1,7 +1,7 @@ { "id": "TestCase_9", - "name": "what treats MONDO:0020333", - "description": "NeverShow: Histamine treats Aggressive Systemic Mastocytosis; NeverShow: ibuprofen treats Aggressive Systemic Mastocytosis; NeverShow: botulinum toxin treats Aggressive Systemic Mastocytosis; NeverShow: dinoprostone treats Aggressive Systemic Mastocytosis; NeverShow: calcitriol treats Aggressive Systemic Mastocytosis; NeverShow: ergocalciferol treats Aggressive Systemic Mastocytosis; NeverShow: 4-Aminopyridine treats Aggressive Systemic Mastocytosis", + "name": "what treats MONDO:0010811", + "description": "TopAnswer: Tamsulosin treats benign prostatic hyperplasia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", "tags": [], "test_runner_settings": [ "inferred" @@ -9,315 +9,23 @@ "query_type": null, "test_assets": [ { - "id": "Asset_51", - "name": "NeverShow: Histamine treats Aggressive Systemic Mastocytosis", - "description": "NeverShow: Histamine treats Aggressive Systemic Mastocytosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0020333", - "input_name": "Aggressive Systemic Mastocytosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:774", - "output_name": "Histamine", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/488", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_85", - "name": "NeverShow: ibuprofen treats Aggressive Systemic Mastocytosis", - "description": "NeverShow: ibuprofen treats Aggressive Systemic Mastocytosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0020333", - "input_name": "Aggressive Systemic Mastocytosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:3672", - "output_name": "ibuprofen", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/479", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_86", - "name": "NeverShow: botulinum toxin treats Aggressive Systemic Mastocytosis", - "description": "NeverShow: botulinum toxin treats Aggressive Systemic Mastocytosis", - "tags": [], - "test_runner_settings": [ - "inferred" + "id": "Asset_685", + "name": "TopAnswer: Tamsulosin treats benign prostatic hyperplasia", + "description": "TopAnswer: Tamsulosin treats benign prostatic hyperplasia. SemMedDB replacement test - also covered by: ctkp, dakp, drug_rep_hub, drugcentral, tmkp, ttd", + "tags": [ + "semmeddb_replacement" ], - "input_id": "MONDO:0020333", - "input_name": "Aggressive Systemic Mastocytosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "NCIT:C163032", - "output_name": "botulinum toxin", - "output_category": null, - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/479", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_87", - "name": "NeverShow: dinoprostone treats Aggressive Systemic Mastocytosis", - "description": "NeverShow: dinoprostone treats Aggressive Systemic Mastocytosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0020333", - "input_name": "Aggressive Systemic Mastocytosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "NCIT:C61727", - "output_name": "dinoprostone", - "output_category": null, - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/479", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_88", - "name": "NeverShow: calcitriol treats Aggressive Systemic Mastocytosis", - "description": "NeverShow: calcitriol treats Aggressive Systemic Mastocytosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0020333", - "input_name": "Aggressive Systemic Mastocytosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "CHEBI:17823", - "output_name": "calcitriol", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/479", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_89", - "name": "NeverShow: ergocalciferol treats Aggressive Systemic Mastocytosis", - "description": "NeverShow: ergocalciferol treats Aggressive Systemic Mastocytosis", - "tags": [], - "test_runner_settings": [ - "inferred" - ], - "input_id": "MONDO:0020333", - "input_name": "Aggressive Systemic Mastocytosis", - "input_category": "biolink:Disease", - "predicate_id": "biolink:treats", - "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:5280793", - "output_name": "ergocalciferol", - "output_category": "biolink:ChemicalEntity", - "association": null, - "qualifiers": [ - { - "parameter": "biolink_qualified_predicate", - "value": "biolink:treats" - }, - { - "parameter": "biolink_object_aspect_qualifier", - "value": "" - }, - { - "parameter": "biolink_object_direction_qualifier", - "value": "" - } - ], - "expected_output": "NeverShow", - "test_issue": null, - "semantic_severity": null, - "in_v1": null, - "well_known": false, - "test_reference": null, - "test_metadata": { - "id": "1", - "name": null, - "description": null, - "tags": [], - "test_runner_settings": [], - "test_source": "SMURF", - "test_reference": "https://github.com/NCATSTranslator/Feedback/issues/479", - "test_objective": "AcceptanceTest", - "test_annotations": [] - } - }, - { - "id": "Asset_91", - "name": "NeverShow: 4-Aminopyridine treats Aggressive Systemic Mastocytosis", - "description": "NeverShow: 4-Aminopyridine treats Aggressive Systemic Mastocytosis", - "tags": [], "test_runner_settings": [ "inferred" ], - "input_id": "MONDO:0020333", - "input_name": "Aggressive Systemic Mastocytosis", + "input_id": "MONDO:0010811", + "input_name": "benign prostatic hyperplasia", "input_category": "biolink:Disease", "predicate_id": "biolink:treats", "predicate_name": "treats", - "output_id": "PUBCHEM.COMPOUND:1727", - "output_name": "4-Aminopyridine", - "output_category": "biolink:ChemicalEntity", + "output_id": "CHEBI:9398", + "output_name": "Tamsulosin", + "output_category": "biolink:Drug", "association": null, "qualifiers": [ { @@ -333,19 +41,21 @@ "value": "" } ], - "expected_output": "NeverShow", + "expected_output": "TopAnswer", "test_issue": null, "semantic_severity": null, "in_v1": null, - "well_known": false, + "well_known": true, "test_reference": null, "test_metadata": { - "id": "1", + "id": "16", "name": null, "description": null, - "tags": [], + "tags": [ + "semmeddb_replacement" + ], "test_runner_settings": [], - "test_source": "SMURF", + "test_source": "TranslatorTeam", "test_reference": null, "test_objective": "AcceptanceTest", "test_annotations": [] @@ -358,7 +68,7 @@ "test_case_source": null, "test_case_predicate_name": "treats", "test_case_predicate_id": "biolink:treats", - "test_case_input_id": "MONDO:0020333", + "test_case_input_id": "MONDO:0010811", "qualifiers": [ { "parameter": "biolink_qualified_predicate", @@ -374,7 +84,7 @@ } ], "input_category": "biolink:Disease", - "output_category": "biolink:ChemicalEntity", + "output_category": "biolink:Drug", "components": [ "ars" ],