diff --git a/ImplementationGuidance/DataExamples/causes_predicate_vs_qualifier.json b/ImplementationGuidance/DataExamples/causes_predicate_vs_qualifier.json index 64976a19..50b52275 100644 --- a/ImplementationGuidance/DataExamples/causes_predicate_vs_qualifier.json +++ b/ImplementationGuidance/DataExamples/causes_predicate_vs_qualifier.json @@ -22,24 +22,15 @@ "predicates": [ "biolink:affects" ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - }, - { - "qualifier_type_id": "biolink:object_modifier_qualifier", - "qualifier_value": "increased" - }, - { - "qualifier_type_id": "biolink:qualified_predicate", - "qualifier_value": "biolink:causes" - } - ] - } - ] + "constraints": { + "qualifiers": [ + { + "biolink:object_aspect_qualifier": "activity", + "biolink:object_modifier_qualifier": "increased", + "biolink:qualified_predicate": "biolink:causes" + } + ] + } } } }, @@ -80,30 +71,43 @@ "qualifier_type_id": "biolink:causal_mechanism_qualifier", "qualifier_value": "binding" } - ] + ], + "sources": [ + { + "resource_id": "infores:chembl", + "resource_role": "primary_knowledge_source" + } + ], + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" } }, "results": [ { "node_bindings": { - "n0": [ - { - "id": "PUBCHEM.COMPOUND:6623" - } - ], - "n1": [ - { - "id": "HGNC:3467" - } - ] + "n0": { + "ids": [ + "PUBCHEM.COMPOUND:6623" + ] + }, + "n1": { + "ids": [ + "HGNC:3467" + ] + } }, - "edge_bindings": { - "e01": [ - { - "id": "x17770" + "analyses": [ + { + "resource_id": "infores:arax", + "edge_bindings": { + "e01": { + "ids": [ + "x17770" + ] + } } - ] - } + } + ] } ] } diff --git a/ImplementationGuidance/DataExamples/complex_gocam_qualifiers.json b/ImplementationGuidance/DataExamples/complex_gocam_qualifiers.json index 3b918179..bf1a9b94 100644 --- a/ImplementationGuidance/DataExamples/complex_gocam_qualifiers.json +++ b/ImplementationGuidance/DataExamples/complex_gocam_qualifiers.json @@ -25,36 +25,18 @@ "predicates": [ "biolink:regulates" ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:subject_aspect_qualifier", - "qualifier_value": "GO:0043539" - }, - { - "qualifier_type_id": "biolink:subject_context_qualifier", - "qualifier_value": "GO:0005886" - }, - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "GO:0004708" - }, - { - "qualifier_type_id": "biolink:object_context_qualifier", - "qualifier_value": "GO:0005737" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - }, - { - "qualifier_type_id": "biolink:pathway_context_qualifier", - "qualifier_value": "GO:0038134" - } - ] - } - ] + "constraints": { + "qualifiers": [ + { + "biolink:subject_aspect_qualifier": "GO:0043539", + "biolink:subject_context_qualifier": "GO:0005886", + "biolink:object_aspect_qualifier": "GO:0004708", + "biolink:object_context_qualifier": "GO:0005737", + "biolink:object_direction_qualifier": "increased", + "biolink:pathway_context_qualifier": "GO:0038134" + } + ] + } } } }, @@ -103,31 +85,44 @@ "qualifier_type_id": "biolink:pathway_context_qualifier", "qualifier_value": "GO:0038134" } - ] + ], + "sources": [ + { + "resource_id": "infores:chembl", + "resource_role": "primary_knowledge_source" + } + ], + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" } } }, "results": [ { "node_bindings": { - "n0": [ - { - "id": "FB:FBgn0003205" - } - ], - "n1": [ - { - "id": "FB:FBgn0003079" - } - ] + "n0": { + "ids": [ + "FB:FBgn0003205" + ] + }, + "n1": { + "ids": [ + "FB:FBgn0003079" + ] + } }, - "edge_bindings": { - "e01": [ - { - "id": "x17770" + "analyses": [ + { + "resource_id": "infores:arax", + "edge_bindings": { + "e01": { + "ids": [ + "x17770" + ] + } } - ] - } + } + ] } ] } diff --git a/ImplementationGuidance/DataExamples/localization_or_transport.json b/ImplementationGuidance/DataExamples/localization_or_transport.json index 75c73668..f35780ff 100644 --- a/ImplementationGuidance/DataExamples/localization_or_transport.json +++ b/ImplementationGuidance/DataExamples/localization_or_transport.json @@ -4,7 +4,8 @@ "n0": { "categories": [ "biolink:ChemicalEntity" - ] + ], + "set_interpretation": "COLLATE" }, "n1": { "categories": [ @@ -22,24 +23,16 @@ "predicates": [ "biolink:affects" ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "localization" - } - ] - }, - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "transport" - } - ] - } - ] + "constraints": { + "qualifiers": [ + { + "biolink:object_aspect_qualifier": "localization" + }, + { + "biolink:object_aspect_qualifier": "transport" + } + ] + } } } }, @@ -74,7 +67,15 @@ "qualifier_type_id": "biolink:object_aspect_qualifier", "qualifier_value": "localization" } - ] + ], + "sources": [ + { + "resource_id": "infores:chembl", + "resource_role": "primary_knowledge_source" + } + ], + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" }, "x17771": { "predicate": "biolink:affects", @@ -85,37 +86,46 @@ "qualifier_type_id": "biolink:object_aspect_qualifier", "qualifier_value": "transport" } - ] + ], + "sources": [ + { + "resource_id": "infores:chembl", + "resource_role": "primary_knowledge_source" + } + ], + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" } } }, "results": [ { "node_bindings": { - "n0": [ - { - "id": "PUBCHEM.COMPOUND:6623" - }, - { - "id": "PUBCHEM.COMPOUND:6625" - } - ], - "n1": [ - { - "id": "HGNC:3467" - } - ] + "n0": { + "ids": [ + "PUBCHEM.COMPOUND:6623", + "PUBCHEM.COMPOUND:6625" + ] + }, + "n1": { + "ids": [ + "HGNC:3467" + ] + } }, - "edge_bindings": { - "e01": [ - { - "id": "x17770" - }, - { - "id": "x17771" + "analyses": [ + { + "resource_id": "infores:arax", + "edge_bindings": { + "e01": { + "ids": [ + "x17770", + "x17771" + ] + } } - ] - } + } + ] } ] } diff --git a/ImplementationGuidance/DataExamples/object_qualifiers.json b/ImplementationGuidance/DataExamples/object_qualifiers.json index fa12f3d6..e4eb8c28 100644 --- a/ImplementationGuidance/DataExamples/object_qualifiers.json +++ b/ImplementationGuidance/DataExamples/object_qualifiers.json @@ -22,24 +22,15 @@ "predicates": [ "biolink:affects" ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "degradation" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - }, - { - "qualifier_type_id": "biolink:qualified_predicate", - "qualifier_value": "biolink:causes" - } - ] - } - ] + "constraints": { + "qualifiers": [ + { + "biolink:object_aspect_qualifier": "degradation", + "biolink:object_direction_qualifier": "decreased", + "biolink:qualified_predicate": "biolink:causes" + } + ] + } } } }, @@ -76,31 +67,44 @@ "qualifier_type_id": "biolink:qualified_predicate", "qualifier_value": "biolink:causes" } - ] + ], + "sources": [ + { + "resource_id": "infores:chembl", + "resource_role": "primary_knowledge_source" + } + ], + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" } } }, "results": [ { "node_bindings": { - "n0": [ - { - "id": "PUBCHEM.COMPOUND:6623" - } - ], - "n1": [ - { - "id": "HGNC:3467" - } - ] + "n0": { + "ids": [ + "PUBCHEM.COMPOUND:6623" + ] + }, + "n1": { + "ids": [ + "HGNC:3467" + ] + } }, - "edge_bindings": { - "e01": [ - { - "id": "x17770" + "analyses": [ + { + "resource_id": "infores:arax", + "edge_bindings": { + "e01": { + "ids": [ + "x17770" + ] + } } - ] - } + } + ] } ] } diff --git a/ImplementationGuidance/DataExamples/simple.json b/ImplementationGuidance/DataExamples/simple.json index 26ff2e46..b8be6197 100644 --- a/ImplementationGuidance/DataExamples/simple.json +++ b/ImplementationGuidance/DataExamples/simple.json @@ -35,57 +35,83 @@ "x17770": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "HGNC:17770" + "object": "HGNC:17770", + "sources": [ + { + "resource_id": "infores:chembl", + "resource_role": "primary_knowledge_source" + } + ], + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" }, "x13236": { "predicate": "biolink:related_to", "subject": "MONDO:0005737", - "object": "HGNC:13236" + "object": "HGNC:13236", + "sources": [ + { + "resource_id": "infores:chembl", + "resource_role": "primary_knowledge_source" + } + ], + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" } } }, "results": [ { "node_bindings": { - "n0": [ - { - "id": "MONDO:0005737" - } - ], - "n1": [ - { - "id": "HGNC:17770" - } - ] + "n0": { + "ids": [ + "MONDO:0005737" + ] + }, + "n1": { + "ids": [ + "HGNC:17770" + ] + } }, - "edge_bindings": { - "e01": [ - { - "id": "x17770" + "analyses": [ + { + "resource_id": "infores:arax", + "edge_bindings": { + "e01": { + "ids": [ + "x17770" + ] + } } - ] - } + } + ] }, { "node_bindings": { - "n0": [ - { - "id": "MONDO:0005737" - } - ], - "n1": [ - { - "id": "HGNC:13236" - } - ] + "n0": { + "ids": [ + "MONDO:0005737" + ] + }, + "n1": { + "ids": [ + "HGNC:13236" + ] + } }, - "edge_bindings": { - "e01": [ - { - "id": "x13236" + "analyses": [ + { + "resource_id": "infores:arax", + "edge_bindings": { + "e01": { + "ids": [ + "x13236" + ] + } } - ] - } + } + ] } ] } diff --git a/ImplementationGuidance/DataExamples/single_node_example.json b/ImplementationGuidance/DataExamples/single_node_example.json index c77c7b67..99090155 100644 --- a/ImplementationGuidance/DataExamples/single_node_example.json +++ b/ImplementationGuidance/DataExamples/single_node_example.json @@ -6,7 +6,6 @@ "categories": [ "biolink:Disease" ], - "constraints": [], "ids": [ "MONDO:0004979" ] @@ -26,13 +25,13 @@ "name": "asthma", "attributes": [ { - "attribute_type_id": "biolink:log_odds_ratio_95_ci", + "attribute_type_id": "biolink:log_odds_ratio", "value": 100.0, "value_type_id": "EDAM:data_0006", - "original_attribute_name": "information_content" + "original_attribute_name": "log_odds_ratio" }, { - "attribute_type_id": "biolink:Attribute", + "attribute_type_id": "biolink:information_content", "value": 77.1, "original_attribute_name": "information_content" }, @@ -42,11 +41,6 @@ "value_type_id": "metatype:String", "attribute_source": "infores:rtx-kg2" }, - { - "attribute_type_id": "biolink:Attribute", - "value": true, - "original_attribute_name": "MONDO_SUPERCLASS_disease" - }, { "attribute_type_id": "dct:description", "value": "A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety.", @@ -54,17 +48,7 @@ "original_attribute_name": "description" }, { - "attribute_type_id": "biolink:Attribute", - "value": 77.4, - "original_attribute_name": "information_content" - }, - { - "attribute_type_id": "biolink:Attribute", - "value": true, - "original_attribute_name": "MONDO_SUPERCLASS_lower_respiratory_tract_disorder" - }, - { - "attribute_type_id": "biolink:Attribute", + "attribute_type_id": "biolink:xref", "value": [ "MEDDRA:10003553", "MEDDRA:10037993", @@ -97,49 +81,6 @@ ], "original_attribute_name": "equivalent_identifiers" }, - { - "attribute_type_id": "biolink:description", - "value": "A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety.", - "value_type_id": "dct:description", - "original_attribute_name": "description" - }, - { - "attribute_type_id": "biolink:Attribute", - "value": [ - "MONDO:0004979", - "DOID:2841", - "UMLS:C0004096", - "UMLS:C0085129", - "UMLS:C0340062", - "UMLS:C3714497", - "MESH:D001249", - "MESH:D016535", - "MEDDRA:10003553", - "MEDDRA:10003555", - "MEDDRA:10003560", - "MEDDRA:10003561", - "MEDDRA:10003565", - "MEDDRA:10006450", - "MEDDRA:10037993", - "MEDDRA:10056285", - "MEDDRA:10066091", - "MEDDRA:10066863", - "MEDDRA:10082852", - "NCIT:C28397", - "SNOMEDCT:195967001", - "SNOMEDCT:991000119106", - "ICD10:J45", - "ICD9:493", - "KEGG.DISEASE:05310", - "HP:0002099" - ], - "original_attribute_name": "equivalent_identifiers" - }, - { - "attribute_type_id": "biolink:Attribute", - "value": true, - "original_attribute_name": "MONDO_SUPERCLASS_human_disease" - }, { "attribute_type_id": "biolink:synonym", "value": [ @@ -158,38 +99,6 @@ "value": "http://purl.obolibrary.org/obo/MONDO_0004979", "value_type_id": "metatype:Uri", "attribute_source": "infores:rtx-kg2" - }, - { - "attribute_type_id": "biolink:log_odds_ratio_95_ci", - "value": [ - "MONDO:0004979", - "DOID:2841", - "UMLS:C0004099", - "MESH:D001249", - "MESH:D001250", - "MEDDRA:10003557", - "MEDDRA:10015649", - "MEDDRA:10079895", - "NCIT:C28397", - "SNOMEDCT:31387002", - "medgen:2109", - "ICD10:J45", - "ICD9:493", - "KEGG.DISEASE:05310", - "HP:0012652" - ], - "value_type_id": "EDAM:data_0006", - "original_attribute_name": "equivalent_identifiers" - }, - { - "attribute_type_id": "biolink:Attribute", - "value": true, - "original_attribute_name": "MONDO_SUPERCLASS_respiratory_system_disorder" - }, - { - "attribute_type_id": "biolink:Attribute", - "value": 78.2, - "original_attribute_name": "information_content" } ] } @@ -198,12 +107,11 @@ "results": [ { "node_bindings": { - "n0": [ - { - "id": "MONDO:0004979", - "attributes": [] - } - ] + "n0": { + "ids": [ + "MONDO:0004979" + ] + } } } ] diff --git a/ImplementationGuidance/DataExamples/subject_and_object_qualifiers.json b/ImplementationGuidance/DataExamples/subject_and_object_qualifiers.json index a29429a8..27847b45 100644 --- a/ImplementationGuidance/DataExamples/subject_and_object_qualifiers.json +++ b/ImplementationGuidance/DataExamples/subject_and_object_qualifiers.json @@ -22,32 +22,17 @@ "predicates": [ "biolink:affects" ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:subject_aspect_qualifier", - "qualifier_value": "abundance" - }, - { - "qualifier_type_id": "biolink:subject_direction_qualifier", - "qualifier_value": "decreased" - }, - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "expression" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - }, - { - "qualifier_type_id": "biolink:qualified_predicate", - "qualifier_value": "biolink:causes" - } - ] - } - ] + "constraints": { + "qualifiers": [ + { + "biolink:subject_aspect_qualifier": "abundance", + "biolink:subject_direction_qualifier": "decreased", + "biolink:object_aspect_qualifier": "expression", + "biolink:object_direction_qualifier": "increased", + "biolink:qualified_predicate": "biolink:causes" + } + ] + } } } }, @@ -92,31 +77,44 @@ "qualifier_type_id": "biolink:object_direction_qualifier", "qualifier_value": "increased" } - ] + ], + "sources": [ + { + "resource_id": "infores:chembl", + "resource_role": "primary_knowledge_source" + } + ], + "knowledge_level": "knowledge_assertion", + "agent_type": "manual_agent" } } }, "results": [ { "node_bindings": { - "n0": [ - { - "id": "PUBCHEM.COMPOUND:6137" - } - ], - "n1": [ - { - "id": "HGNC:286" - } - ] + "n0": { + "ids": [ + "PUBCHEM.COMPOUND:6137" + ] + }, + "n1": { + "ids": [ + "HGNC:286" + ] + } }, - "edge_bindings": { - "e01": [ - { - "id": "x17770" + "analyses": [ + { + "resource_id": "infores:arax", + "edge_bindings": { + "e01": { + "ids": [ + "x17770" + ] + } } - ] - } + } + ] } ] } diff --git a/ImplementationGuidance/Specifications/pathfinder_query_specification.md b/ImplementationGuidance/Specifications/pathfinder_query_specification.md index db951d59..9b00bcf9 100644 --- a/ImplementationGuidance/Specifications/pathfinder_query_specification.md +++ b/ImplementationGuidance/Specifications/pathfinder_query_specification.md @@ -26,7 +26,7 @@ The QueryGraph still has a field for Nodes, as a traditional QueryGraph would, b has a field for Paths. This example shows a query that requests Paths connecting Crohn's Disease with Parkinson's. All paths returned must connect these two nodes. -``` +```json "query_graph": { "nodes": { "n0": { @@ -55,7 +55,7 @@ which requires that all returned paths contain at least one node matching the sp In the example below, the intermediate category constraint listed requires that paths have at least one `Gene` node between them. -``` +```json "query_graph": { "nodes": { "n0": { @@ -93,7 +93,7 @@ and Edges both follow the same rules as all other queries, although for the sake contain all the required information typically found in a valid knowledge graph node and edge, such as knowledge level or source. -``` +```json "knowledge_graph": { "nodes": { "MONDO:0005011": { @@ -109,12 +109,12 @@ level or source. "categories": ["biolink:Cell"] } }, - "edges" { + "edges": { "e0": { "subject": "MONDO:0005011", "object": "NCBIGene:120892", "predicate": "biolink:condition_associated_with_gene" - } + }, "e1": { "subject": "NCBIGene:120892", "object": "MONDO:0005180", @@ -153,7 +153,7 @@ between two nodes are allowed. Using the Knowledge Graph above, we can construct the AuxiliaryGraphs shown in the example below: -``` +```json "auxiliary_graphs": { "a0": { "edges": [ @@ -173,7 +173,7 @@ Using the Knowledge Graph above, we can construct the AuxiliaryGraphs shown in t "edges": [ "e5" ] - }, + } } ``` @@ -189,7 +189,7 @@ constraints would yield a slightly different set of paths. As show below in the AuxiliaryGraphs, `a2` is removed because it does not contain any `Gene` nodes. Therefore, it is not a valid Path for the constrained version of the query. -``` +```json "auxiliary_graphs": { "a0": { "edges": [ @@ -221,53 +221,54 @@ Each analysis no longer contains EdgeBindings, with no QueryGraph edges to bind PathBindings to bind to QPath. Each Path Binding binds an Auxiliary Graph by `id` to a QPath. This is similar to how EdgeBindings bind a KnowledgeGraph Edge, by id, to a QueryGraph Edge. -``` +```json "results": [ { "node_bindings": { - "n0": [ - { - "id": "MONDO:0005011", - "attributes": [] - } - ], - "n1": [ - { - "id": "MONDO:0005180", - "attributes": [] - } - ] + "n0": { + "ids": [ + "MONDO:0005011" + ] + }, + "n1": { + "ids": [ + "MONDO:0005180" + ] + } }, "analyses": [ { + "resource_id": "infores:shepherd-aragorn", "path_bindings": { - "p0": [ - { - "id": "a0" - } - ], + "p0": { + "ids": [ + "a0" + ] + } }, - "score": .85 + "score": 0.85 }, { + "resource_id": "infores:shepherd-aragorn", "path_bindings": { - "p0": [ - { - "id": "a1" - } - ], + "p0": { + "ids": [ + "a1" + ] + } }, - "score": .7 + "score": 0.7 }, { + "resource_id": "infores:shepherd-aragorn", "path_bindings": { - "p0": [ - { - "id": "a2" - } - ], + "p0": { + "ids": [ + "a2" + ] + } }, - "score": .9 + "score": 0.9 } ] } @@ -277,43 +278,43 @@ This is similar to how EdgeBindings bind a KnowledgeGraph Edge, by id, to a Quer This is only valid for the unconstrained version of the query. The `intermediate_categories` constraint version would look like this. -``` +```json "results": [ { "node_bindings": { - "n0": [ - { - "id": "MONDO:0005011", - "attributes": [] - } - ], - "n1": [ - { - "id": "MONDO:0005180", - "attributes": [] - } - ] + "n0": { + "ids": [ + "MONDO:0005011" + ] + }, + "n1": { + "ids": [ + "MONDO:0005180" + ] + } }, "analyses": [ { + "resource_id": "infores:shepherd-aragorn", "path_bindings": { - "p0": [ - { - "id": "a0" - } - ], + "p0": { + "ids": [ + "a0" + ] + } }, - "score": .85 + "score": 0.85 }, { + "resource_id": "infores:shepherd-aragorn", "path_bindings": { - "p0": [ - { - "id": "a1" - } - ], + "p0": { + "ids": [ + "a1" + ] + } }, - "score": .7 + "score": 0.7 } ] } @@ -329,9 +330,9 @@ and Results all included. The constrained version is shown after that. ### Unconstrained -``` +```json { - "message" { + "message": { "query_graph": { "nodes": { "n0": { @@ -368,12 +369,12 @@ and Results all included. The constrained version is shown after that. "categories": ["biolink:Cell"] } }, - "edges" { + "edges": { "e0": { "subject": "MONDO:0005011", "object": "NCBIGene:120892", "predicate": "biolink:condition_associated_with_gene" - } + }, "e1": { "subject": "NCBIGene:120892", "object": "MONDO:0005180", @@ -420,54 +421,55 @@ and Results all included. The constrained version is shown after that. "edges": [ "e5" ] - }, + } }, "results": [ { "node_bindings": { - "n0": [ - { - "id": "MONDO:0005011", - "attributes": [] - } - ], - "n1": [ - { - "id": "MONDO:0005180", - "attributes": [] - } - ] + "n0": { + "ids": [ + "MONDO:0005011" + ] + }, + "n1": { + "ids": [ + "MONDO:0005180" + ] + } }, "analyses": [ { + "resource_id": "infores:shepherd-aragorn", "path_bindings": { - "p0": [ - { - "id": "a0" - } - ], + "p0": { + "ids": [ + "a0" + ] + } }, - "score": .85 + "score": 0.85 }, { + "resource_id": "infores:shepherd-aragorn", "path_bindings": { - "p0": [ - { - "id": "a1" - } - ], + "p0": { + "ids": [ + "a1" + ] + } }, - "score": .7 + "score": 0.7 }, { + "resource_id": "infores:shepherd-aragorn", "path_bindings": { - "p0": [ - { - "id": "a2" - } - ], + "p0": { + "ids": [ + "a2" + ] + } }, - "score": .9 + "score": 0.9 } ] } @@ -478,9 +480,9 @@ and Results all included. The constrained version is shown after that. ### Constrained -``` +```json { - "message" { + "message": { "query_graph": { "nodes": { "n0": { @@ -521,12 +523,12 @@ and Results all included. The constrained version is shown after that. "categories": ["biolink:Cell"] } }, - "edges" { + "edges": { "e0": { "subject": "MONDO:0005011", "object": "NCBIGene:120892", "predicate": "biolink:condition_associated_with_gene" - } + }, "e1": { "subject": "NCBIGene:120892", "object": "MONDO:0005180", @@ -568,43 +570,43 @@ and Results all included. The constrained version is shown after that. "results": [ { "node_bindings": { - "n0": [ - { - "id": "MONDO:0005011", - "attributes": [] - } - ], - "n1": [ - { - "id": "MONDO:0005180", - "attributes": [] - } - ] + "n0": { + "ids": [ + "MONDO:0005011" + ] + }, + "n1": { + "ids": [ + "MONDO:0005180" + ] + } }, "analyses": [ { + "resource_id": "infores:shepherd-aragorn", "path_bindings": { - "p0": [ - { - "id": "a0" - } - ], + "p0": { + "ids": [ + "a0" + ] + } }, - "score": .85 + "score": 0.85 }, { + "resource_id": "infores:shepherd-aragorn", "path_bindings": { - "p0": [ - { - "id": "a1" - } - ], + "p0": { + "ids": [ + "a1" + ] + } }, - "score": .7 + "score": 0.7 } ] } ] } } -``` \ No newline at end of file +```