From 4431566e48faec501dae430ac0b6121e1259bdfd Mon Sep 17 00:00:00 2001 From: cbizon Date: Tue, 13 Feb 2024 16:53:30 -0500 Subject: [PATCH 1/2] handled contributes_to --- src/rules/Notes | 2 + .../rules_with_types_cleaned_finalized.json | 531 +----------------- 2 files changed, 8 insertions(+), 525 deletions(-) diff --git a/src/rules/Notes b/src/rules/Notes index 4a799c7..e80f519 100644 --- a/src/rules/Notes +++ b/src/rules/Notes @@ -29,5 +29,7 @@ x ?b activity_or_abundance_biolink:affects ?a ?a increased_activity_or_abund x ?b biolink:affects_response_to ?a ?a increased_activity_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b "?b biolink:increases_response_to ?a ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b +Subsequently removed several rules or modified the node types where "contributes_to" was involved in chemical-gene rules. + This process is obviously roundabout and we are going to clarify it in the next round of rule minings. diff --git a/src/rules/kara_typed_rules/rules_with_types_cleaned_finalized.json b/src/rules/kara_typed_rules/rules_with_types_cleaned_finalized.json index ec4f30d..568842f 100644 --- a/src/rules/kara_typed_rules/rules_with_types_cleaned_finalized.json +++ b/src/rules/kara_typed_rules/rules_with_types_cleaned_finalized.json @@ -4065,7 +4065,7 @@ }, "f": { "categories": [ - "biolink:BiologicalEntity" + "biolink:DiseaseOrPhenotypicFeature" ] } }, @@ -4662,7 +4662,7 @@ }, "f": { "categories": [ - "biolink:NamedThing" + "biolink:DiseaseOrPhenotypicFeature" ] } }, @@ -5116,59 +5116,6 @@ } } }, - { - "Rule": "?f biolink:affects_response_to ?a ?b biolink:contributes_to ?f => ?a increased_activity_biolink:affects ?b", - "Head Coverage": "0.000219675", - "Std Confidence": "0.072847682", - "PCA Confidence": "0.089430894", - "Positive Examples": "11", - "Body size": "151", - "PCA Body size": "123", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - }, - "f": { - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "f", - "object": "$source", - "predicates": [ - "biolink:affects_response_to" - ] - }, - "edge_1": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:contributes_to" - ] - } - } - } - } - }, { "Rule": "?b biolink:biomarker_for ?f ?a biolink:interacts_with ?f => ?a increased_activity_biolink:affects ?b", "Head Coverage": "0.000718936", @@ -5462,73 +5409,6 @@ } } }, - { - "Rule": "?f biolink:contributes_to ?b ?a increased_activity_or_abundance_biolink:affects ?f => ?a increased_activity_biolink:affects ?b", - "Head Coverage": "0.030754483", - "Std Confidence": "0.048176187", - "PCA Confidence": "0.060255106", - "Positive Examples": "1540", - "Body size": "31966", - "PCA Body size": "25558", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - }, - "f": { - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "f", - "object": "$target", - "predicates": [ - "biolink:contributes_to" - ] - }, - "edge_1": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?b biolink:affects_response_to ?a => ?a increased_activity_biolink:affects ?b", "Head Coverage": "0.00497264", @@ -6157,7 +6037,7 @@ }, "f": { "categories": [ - "biolink:BiologicalEntity" + "biolink:DiseaseOrPhenotypicFeature" ] } }, @@ -6906,59 +6786,6 @@ } } }, - { - "Rule": "?a biolink:binds ?f ?b biolink:contributes_to ?f => ?a decreased_activity_biolink:affects ?b", - "Head Coverage": "0.000072254", - "Std Confidence": "0.302325581", - "PCA Confidence": "0.65", - "Positive Examples": "26", - "Body size": "86", - "PCA Body size": "40", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - }, - "f": { - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:binds" - ] - }, - "edge_1": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:contributes_to" - ] - } - } - } - } - }, { "Rule": "?a biolink:binds ?b => ?a decreased_activity_biolink:affects ?b", "Head Coverage": "0.010549016", @@ -7295,59 +7122,6 @@ } } }, - { - "Rule": "?f biolink:affects_response_to ?a ?b biolink:contributes_to ?f => ?a decreased_activity_biolink:affects ?b", - "Head Coverage": "0.000047243", - "Std Confidence": "0.112582781", - "PCA Confidence": "0.129770992", - "Positive Examples": "17", - "Body size": "151", - "PCA Body size": "131", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - }, - "f": { - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "f", - "object": "$source", - "predicates": [ - "biolink:affects_response_to" - ] - }, - "edge_1": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:contributes_to" - ] - } - } - } - } - }, { "Rule": "?e decreased_activity_or_abundance_biolink:affects ?b ?e biolink:similar_to ?a => ?a decreased_activity_biolink:affects ?b", "Head Coverage": "0.000052801", @@ -7514,7 +7288,7 @@ }, "f": { "categories": [ - "biolink:NamedThing" + "biolink:DiseaseOrPhenotypicFeature" ] } }, @@ -7648,7 +7422,7 @@ }, "f": { "categories": [ - "biolink:BiologicalEntity" + "biolink:DiseaseOrPhenotypicFeature" ] } }, @@ -8620,126 +8394,6 @@ } } }, - { - "Rule": "?f biolink:affects_response_to ?a ?b biolink:contributes_to ?f => ?a increased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.000284129", - "Std Confidence": "0.112582781", - "PCA Confidence": "0.137096774", - "Positive Examples": "17", - "Body size": "151", - "PCA Body size": "124", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - }, - "f": { - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "f", - "object": "$source", - "predicates": [ - "biolink:affects_response_to" - ] - }, - "edge_1": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:contributes_to" - ] - } - } - } - } - }, - { - "Rule": "?e biolink:contributes_to ?a ?e increased_synthesis_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.000350983", - "Std Confidence": "0.109947644", - "PCA Confidence": "1", - "Positive Examples": "21", - "Body size": "191", - "PCA Body size": "21", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "e", - "object": "$source", - "predicates": [ - "biolink:contributes_to" - ] - }, - "edge_1": { - "subject": "e", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "synthesis" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?b decreased_metabolic_processing_biolink:affects ?a => ?a increased_activity_or_abundance_biolink:affects ?b", "Head Coverage": "0.000233989", @@ -9205,73 +8859,6 @@ } } }, - { - "Rule": "?f biolink:contributes_to ?b ?a increased_activity_or_abundance_biolink:affects ?f => ?a increased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.02971654", - "Std Confidence": "0.055621598", - "PCA Confidence": "0.055621598", - "Positive Examples": "1778", - "Body size": "31966", - "PCA Body size": "31966", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - }, - "f": { - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "f", - "object": "$target", - "predicates": [ - "biolink:contributes_to" - ] - }, - "edge_1": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?a biolink:similar_to ?f ?f decreased_molecular_interaction_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b", "Head Coverage": "0.001370504", @@ -9560,7 +9147,7 @@ }, "f": { "categories": [ - "biolink:BiologicalEntity" + "biolink:DiseaseOrPhenotypicFeature" ] } }, @@ -10364,59 +9951,6 @@ } } }, - { - "Rule": "?a biolink:binds ?f ?b biolink:contributes_to ?f => ?a decreased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.000071122", - "Std Confidence": "0.302325581", - "PCA Confidence": "0.65", - "Positive Examples": "26", - "Body size": "86", - "PCA Body size": "40", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - }, - "f": { - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:binds" - ] - }, - "edge_1": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:contributes_to" - ] - } - } - } - } - }, { "Rule": "?b biolink:affects_response_to ?a ?a biolink:interacts_with ?b => ?a decreased_activity_or_abundance_biolink:affects ?b", "Head Coverage": "0.000054709", @@ -10863,59 +10397,6 @@ } } }, - { - "Rule": "?f biolink:affects_response_to ?a ?b biolink:contributes_to ?f => ?a decreased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.000054709", - "Std Confidence": "0.132450331", - "PCA Confidence": "0.151515152", - "Positive Examples": "20", - "Body size": "151", - "PCA Body size": "132", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - }, - "f": { - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "f", - "object": "$source", - "predicates": [ - "biolink:affects_response_to" - ] - }, - "edge_1": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:contributes_to" - ] - } - } - } - } - }, { "Rule": "?e decreased_activity_or_abundance_biolink:affects ?b ?e biolink:similar_to ?a => ?a decreased_activity_or_abundance_biolink:affects ?b", "Head Coverage": "0.000051974", From 6a20cf027132bc09dc8e5425381728d35849a807 Mon Sep 17 00:00:00 2001 From: cbizon Date: Fri, 16 Feb 2024 15:03:19 -0500 Subject: [PATCH 2/2] Update openapi-config.yaml --- openapi-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openapi-config.yaml b/openapi-config.yaml index d77ffa1..af28af0 100644 --- a/openapi-config.yaml +++ b/openapi-config.yaml @@ -11,7 +11,7 @@ servers: # url: http://127.0.0.1:5000 termsOfService: http://robokop.renci.org:7055/tos?service_long=ARAGORN&provider_long=RENCI title: ARAGORN -version: 2.6.1 +version: 2.6.2 tags: - name: translator - name: ARA