diff --git a/src/rules/parse_to_trapi.py b/src/rules/parse_to_trapi.py index 4f09c9f..d822852 100644 --- a/src/rules/parse_to_trapi.py +++ b/src/rules/parse_to_trapi.py @@ -83,8 +83,9 @@ def parse_line(line, header, source, rule_conf, qmap): if float(rule["Std Confidence"]) <= minconf: return {} # Is the rule going to bring back too many results? - maxbody = source.get("max_body_size", 99999999999) - if int(rule["Body size"]) >= maxbody: + maxnegs = source.get("max_negative_examples", 99999999999) + negatives = int(rule["Body size"]) - int(rule["Positive Examples"]) + if int(negatives) >= maxnegs: return {} template = rule_to_trapi(rule['Rule'],rule_conf,qmap) if template is not None: diff --git a/src/rules/rule_config.json b/src/rules/rule_config.json index aca709c..eb43df4 100644 --- a/src/rules/rule_config.json +++ b/src/rules/rule_config.json @@ -5,9 +5,9 @@ "AMIE_inputs": [ { "input_file": "robokop_biolink3_fixed_treats_len3_correct_rules.txt", - "min_positive_example": 2000, - "min_std_confidence": 0.001, - "max_body_size": 100000 + "min_positive_example": 1000, + "min_std_confidence": 0.01, + "max_negative_examples": 10000 } ], "source": "biolink:ChemicalEntity", diff --git a/src/rules/rules.json b/src/rules/rules.json index 7615b88..1a39383 100644 --- a/src/rules/rules.json +++ b/src/rules/rules.json @@ -66,13 +66,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?a biolink:similar_to ?h ?h biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.0705439", - "Std Confidence": "0.990714949", - "PCA Confidence": "0.991021672", - "Positive Examples": "3201", - "Body size": "3231", - "PCA Body size": "3230", + "Rule": "?a biolink:ameliorates ?b ?b biolink:associated_with ?f ?a biolink:treats ?f => ?a biolink:treats ?b", + "Head Coverage": "0.022721262", + "Std Confidence": "0.995173745", + "PCA Confidence": "0.995173745", + "Positive Examples": "1031", + "Body size": "1036", + "PCA Body size": "1036", "Functional variable": "?a", "template": { "query_graph": { @@ -93,7 +93,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "h": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -108,15 +108,15 @@ ] }, "edge_1": { - "subject": "$source", - "object": "h", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:similar_to" + "biolink:associated_with" ] }, "edge_2": { - "subject": "h", - "object": "$target", + "subject": "$source", + "object": "f", "predicates": [ "biolink:treats" ] @@ -126,13 +126,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?h biolink:has_phenotype ?b ?a biolink:treats ?h => ?a biolink:treats ?b", - "Head Coverage": "0.084339739", - "Std Confidence": "0.989144482", - "PCA Confidence": "0.989144482", - "Positive Examples": "3827", - "Body size": "3869", - "PCA Body size": "3869", + "Rule": "?a biolink:ameliorates ?b ?b biolink:correlated_with ?f ?a biolink:treats ?f => ?a biolink:treats ?b", + "Head Coverage": "0.022434767", + "Std Confidence": "0.995112414", + "PCA Confidence": "0.995112414", + "Positive Examples": "1018", + "Body size": "1023", + "PCA Body size": "1023", "Functional variable": "?a", "template": { "query_graph": { @@ -153,7 +153,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "h": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -168,15 +168,15 @@ ] }, "edge_1": { - "subject": "h", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:has_phenotype" + "biolink:correlated_with" ] }, "edge_2": { "subject": "$source", - "object": "h", + "object": "f", "predicates": [ "biolink:treats" ] @@ -186,13 +186,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?g biolink:similar_to ?a ?g biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.071249118", - "Std Confidence": "0.987175573", - "PCA Confidence": "0.987477092", - "Positive Examples": "3233", - "Body size": "3275", - "PCA Body size": "3274", + "Rule": "?a biolink:ameliorates ?b ?a biolink:similar_to ?h ?h biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.0705439", + "Std Confidence": "0.990714949", + "PCA Confidence": "0.991021672", + "Positive Examples": "3201", + "Body size": "3231", + "PCA Body size": "3230", "Functional variable": "?a", "template": { "query_graph": { @@ -213,7 +213,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "g": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -228,14 +228,14 @@ ] }, "edge_1": { - "subject": "g", - "object": "$source", + "subject": "$source", + "object": "h", "predicates": [ "biolink:similar_to" ] }, "edge_2": { - "subject": "g", + "subject": "h", "object": "$target", "predicates": [ "biolink:treats" @@ -246,13 +246,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?g biolink:genetic_association ?b ?g biolink:increases_response_to ?a => ?a biolink:treats ?b", - "Head Coverage": "0.048219323", - "Std Confidence": "0.983370787", - "PCA Confidence": "0.984255511", - "Positive Examples": "2188", - "Body size": "2225", - "PCA Body size": "2223", + "Rule": "?a biolink:ameliorates ?b ?h biolink:has_phenotype ?b ?a biolink:treats ?h => ?a biolink:treats ?b", + "Head Coverage": "0.084339739", + "Std Confidence": "0.989144482", + "PCA Confidence": "0.989144482", + "Positive Examples": "3827", + "Body size": "3869", + "PCA Body size": "3869", "Functional variable": "?a", "template": { "query_graph": { @@ -273,7 +273,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "g": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -288,17 +288,17 @@ ] }, "edge_1": { - "subject": "g", + "subject": "h", "object": "$target", "predicates": [ - "biolink:genetic_association" + "biolink:has_phenotype" ] }, "edge_2": { - "subject": "g", - "object": "$source", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:increases_response_to" + "biolink:treats" ] } } @@ -306,13 +306,13 @@ } }, { - "Rule": "?g biolink:affects_response_to ?a ?a biolink:ameliorates ?b ?g biolink:genetic_association ?b => ?a biolink:treats ?b", - "Head Coverage": "0.056505642", - "Std Confidence": "0.981623277", - "PCA Confidence": "0.981999234", - "Positive Examples": "2564", - "Body size": "2612", - "PCA Body size": "2611", + "Rule": "?a biolink:ameliorates ?b ?g biolink:similar_to ?a ?g biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.071249118", + "Std Confidence": "0.987175573", + "PCA Confidence": "0.987477092", + "Positive Examples": "3233", + "Body size": "3275", + "PCA Body size": "3274", "Functional variable": "?a", "template": { "query_graph": { @@ -341,24 +341,24 @@ }, "edges": { "edge_0": { - "subject": "g", - "object": "$source", + "subject": "$source", + "object": "$target", "predicates": [ - "biolink:affects_response_to" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "$source", - "object": "$target", + "subject": "g", + "object": "$source", "predicates": [ - "biolink:ameliorates" + "biolink:similar_to" ] }, "edge_2": { "subject": "g", "object": "$target", "predicates": [ - "biolink:genetic_association" + "biolink:treats" ] } } @@ -366,13 +366,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?h biolink:has_adverse_event ?b ?a biolink:similar_to ?h => ?a biolink:treats ?b", - "Head Coverage": "0.047359838", - "Std Confidence": "0.977707006", - "PCA Confidence": "0.977707006", - "Positive Examples": "2149", - "Body size": "2198", - "PCA Body size": "2198", + "Rule": "?a biolink:ameliorates ?b ?g biolink:decreases_response_to ?a ?g biolink:genetic_association ?b => ?a biolink:treats ?b", + "Head Coverage": "0.041409556", + "Std Confidence": "0.986869748", + "PCA Confidence": "0.986869748", + "Positive Examples": "1879", + "Body size": "1904", + "PCA Body size": "1904", "Functional variable": "?a", "template": { "query_graph": { @@ -393,7 +393,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "h": { + "g": { "categories": [ "biolink:NamedThing" ] @@ -408,17 +408,17 @@ ] }, "edge_1": { - "subject": "h", - "object": "$target", + "subject": "g", + "object": "$source", "predicates": [ - "biolink:has_adverse_event" + "biolink:decreases_response_to" ] }, "edge_2": { - "subject": "$source", - "object": "h", + "subject": "g", + "object": "$target", "predicates": [ - "biolink:similar_to" + "biolink:genetic_association" ] } } @@ -426,13 +426,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?h biolink:genetic_association ?b ?a increased_expression_biolink:affects ?h => ?a biolink:treats ?b", - "Head Coverage": "0.045751058", - "Std Confidence": "0.976941176", - "PCA Confidence": "0.978322337", - "Positive Examples": "2076", - "Body size": "2125", - "PCA Body size": "2122", + "Rule": "?a biolink:ameliorates ?b ?a biolink:related_to ?h ?h biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.036803597", + "Std Confidence": "0.985250737", + "PCA Confidence": "0.986414649", + "Positive Examples": "1670", + "Body size": "1695", + "PCA Body size": "1693", "Functional variable": "?a", "template": { "query_graph": { @@ -468,31 +468,17 @@ ] }, "edge_1": { - "subject": "h", - "object": "$target", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:genetic_association" + "biolink:related_to" ] }, "edge_2": { - "subject": "$source", - "object": "h", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "expression" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } + "biolink:treats" ] } } @@ -500,13 +486,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?g biolink:has_adverse_event ?b ?g biolink:similar_to ?a => ?a biolink:treats ?b", - "Head Coverage": "0.047095381", - "Std Confidence": "0.975799087", - "PCA Confidence": "0.975799087", - "Positive Examples": "2137", - "Body size": "2190", - "PCA Body size": "2190", + "Rule": "?a biolink:ameliorates ?b ?g biolink:genetic_association ?b ?g biolink:increases_response_to ?a => ?a biolink:treats ?b", + "Head Coverage": "0.048219323", + "Std Confidence": "0.983370787", + "PCA Confidence": "0.984255511", + "Positive Examples": "2188", + "Body size": "2225", + "PCA Body size": "2223", "Functional variable": "?a", "template": { "query_graph": { @@ -545,14 +531,14 @@ "subject": "g", "object": "$target", "predicates": [ - "biolink:has_adverse_event" + "biolink:genetic_association" ] }, "edge_2": { "subject": "g", "object": "$source", "predicates": [ - "biolink:similar_to" + "biolink:increases_response_to" ] } } @@ -560,13 +546,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?h biolink:ameliorates ?b ?a biolink:similar_to ?h => ?a biolink:treats ?b", - "Head Coverage": "0.060296192", - "Std Confidence": "0.975053457", - "PCA Confidence": "0.97574893", - "Positive Examples": "2736", - "Body size": "2806", - "PCA Body size": "2804", + "Rule": "?a biolink:ameliorates ?b ?g biolink:causes ?b ?g biolink:similar_to ?a => ?a biolink:treats ?b", + "Head Coverage": "0.034709979", + "Std Confidence": "0.982532751", + "PCA Confidence": "0.982532751", + "Positive Examples": "1575", + "Body size": "1603", + "PCA Body size": "1603", "Functional variable": "?a", "template": { "query_graph": { @@ -587,7 +573,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "h": { + "g": { "categories": [ "biolink:NamedThing" ] @@ -602,15 +588,15 @@ ] }, "edge_1": { - "subject": "h", + "subject": "g", "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:causes" ] }, "edge_2": { - "subject": "$source", - "object": "h", + "subject": "g", + "object": "$source", "predicates": [ "biolink:similar_to" ] @@ -620,13 +606,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?g biolink:ameliorates ?b ?g biolink:similar_to ?a => ?a biolink:treats ?b", - "Head Coverage": "0.060141925", - "Std Confidence": "0.974991068", - "PCA Confidence": "0.975688237", - "Positive Examples": "2729", - "Body size": "2799", - "PCA Body size": "2797", + "Rule": "?g biolink:affects_response_to ?a ?a biolink:ameliorates ?b ?g biolink:genetic_association ?b => ?a biolink:treats ?b", + "Head Coverage": "0.056505642", + "Std Confidence": "0.981623277", + "PCA Confidence": "0.981999234", + "Positive Examples": "2564", + "Body size": "2612", + "PCA Body size": "2611", "Functional variable": "?a", "template": { "query_graph": { @@ -655,14 +641,14 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "$target", + "subject": "g", + "object": "$source", "predicates": [ - "biolink:ameliorates" + "biolink:affects_response_to" ] }, "edge_1": { - "subject": "g", + "subject": "$source", "object": "$target", "predicates": [ "biolink:ameliorates" @@ -670,9 +656,9 @@ }, "edge_2": { "subject": "g", - "object": "$source", + "object": "$target", "predicates": [ - "biolink:similar_to" + "biolink:genetic_association" ] } } @@ -680,13 +666,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?a biolink:ameliorates ?h ?h biolink:has_phenotype ?b => ?a biolink:treats ?b", - "Head Coverage": "0.082047779", - "Std Confidence": "0.973333333", - "PCA Confidence": "0.977165354", - "Positive Examples": "3723", - "Body size": "3825", - "PCA Body size": "3810", + "Rule": "?a biolink:ameliorates ?b ?h biolink:ameliorates ?b ?a biolink:related_to ?h => ?a biolink:treats ?b", + "Head Coverage": "0.033057123", + "Std Confidence": "0.980392157", + "PCA Confidence": "0.981675393", + "Positive Examples": "1500", + "Body size": "1530", + "PCA Body size": "1528", "Functional variable": "?a", "template": { "query_graph": { @@ -722,17 +708,17 @@ ] }, "edge_1": { - "subject": "$source", - "object": "h", + "subject": "h", + "object": "$target", "predicates": [ "biolink:ameliorates" ] }, "edge_2": { - "subject": "h", - "object": "$target", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:has_phenotype" + "biolink:related_to" ] } } @@ -740,13 +726,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b ?a biolink:has_adverse_event ?b => ?a biolink:treats ?b", - "Head Coverage": "0.05917225", - "Std Confidence": "0.968964273", - "PCA Confidence": "0.968964273", - "Positive Examples": "2685", - "Body size": "2771", - "PCA Body size": "2771", + "Rule": "?a biolink:ameliorates ?b ?h biolink:causes ?b ?a biolink:similar_to ?h => ?a biolink:treats ?b", + "Head Coverage": "0.038169958", + "Std Confidence": "0.980192417", + "PCA Confidence": "0.980192417", + "Positive Examples": "1732", + "Body size": "1767", + "PCA Body size": "1767", "Functional variable": "?a", "template": { "query_graph": { @@ -766,6 +752,11 @@ "categories": [ "biolink:DiseaseOrPhenotypicFeature" ] + }, + "h": { + "categories": [ + "biolink:NamedThing" + ] } }, "edges": { @@ -777,10 +768,17 @@ ] }, "edge_1": { - "subject": "$source", + "subject": "h", "object": "$target", "predicates": [ - "biolink:has_adverse_event" + "biolink:causes" + ] + }, + "edge_2": { + "subject": "$source", + "object": "h", + "predicates": [ + "biolink:similar_to" ] } } @@ -788,13 +786,13 @@ } }, { - "Rule": "?e biolink:ameliorates ?b ?i biolink:has_input ?a ?i biolink:has_input ?e => ?a biolink:treats ?b", - "Head Coverage": "0.082907264", - "Std Confidence": "0.963133641", - "PCA Confidence": "0.966349859", - "Positive Examples": "3762", - "Body size": "3906", - "PCA Body size": "3893", + "Rule": "?a biolink:ameliorates ?b ?h biolink:genetic_association ?b ?a decreased_expression_biolink:affects ?h => ?a biolink:treats ?b", + "Head Coverage": "0.04215885", + "Std Confidence": "0.9790174", + "PCA Confidence": "0.979518689", + "Positive Examples": "1913", + "Body size": "1954", + "PCA Body size": "1953", "Functional variable": "?a", "template": { "query_graph": { @@ -815,12 +813,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -828,24 +821,38 @@ }, "edges": { "edge_0": { - "subject": "e", + "subject": "$source", "object": "$target", "predicates": [ "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "$source", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:has_input" + "biolink:genetic_association" ] }, "edge_2": { - "subject": "i", - "object": "e", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:has_input" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "expression" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] } } @@ -853,13 +860,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b => ?a biolink:treats ?b", - "Head Coverage": "0.707444464", - "Std Confidence": "0.958582179", - "PCA Confidence": "0.968239127", - "Positive Examples": "32101", - "Body size": "33488", - "PCA Body size": "33154", + "Rule": "?a biolink:ameliorates ?b ?a biolink:causes ?b => ?a biolink:treats ?b", + "Head Coverage": "0.029288611", + "Std Confidence": "0.977924945", + "PCA Confidence": "0.977924945", + "Positive Examples": "1329", + "Body size": "1359", + "PCA Body size": "1359", "Functional variable": "?a", "template": { "query_graph": { @@ -888,19 +895,26 @@ "predicates": [ "biolink:ameliorates" ] + }, + "edge_1": { + "subject": "$source", + "object": "$target", + "predicates": [ + "biolink:causes" + ] } } } } }, { - "Rule": "?i biolink:has_output ?a ?i biolink:has_output ?e ?e biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.048285437", - "Std Confidence": "0.888123227", - "PCA Confidence": "0.947254648", - "Positive Examples": "2191", - "Body size": "2467", - "PCA Body size": "2313", + "Rule": "?a biolink:ameliorates ?b ?h biolink:has_adverse_event ?b ?a biolink:similar_to ?h => ?a biolink:treats ?b", + "Head Coverage": "0.047359838", + "Std Confidence": "0.977707006", + "PCA Confidence": "0.977707006", + "Positive Examples": "2149", + "Body size": "2198", + "PCA Body size": "2198", "Functional variable": "?a", "template": { "query_graph": { @@ -921,12 +935,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "e": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -934,24 +943,24 @@ }, "edges": { "edge_0": { - "subject": "i", - "object": "$source", + "subject": "$source", + "object": "$target", "predicates": [ - "biolink:has_output" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "e", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:has_output" + "biolink:has_adverse_event" ] }, "edge_2": { - "subject": "e", - "object": "$target", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:treats" + "biolink:similar_to" ] } } @@ -959,13 +968,13 @@ } }, { - "Rule": "?a biolink:has_part ?f ?i biolink:has_part ?f ?i biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.04894658", - "Std Confidence": "0.692763568", - "PCA Confidence": "0.915876289", - "Positive Examples": "2221", - "Body size": "3206", - "PCA Body size": "2425", + "Rule": "?a biolink:ameliorates ?b ?h biolink:genetic_association ?b ?a increased_expression_biolink:affects ?h => ?a biolink:treats ?b", + "Head Coverage": "0.045751058", + "Std Confidence": "0.976941176", + "PCA Confidence": "0.978322337", + "Positive Examples": "2076", + "Body size": "2125", + "PCA Body size": "2122", "Functional variable": "?a", "template": { "query_graph": { @@ -986,12 +995,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -1000,23 +1004,37 @@ "edges": { "edge_0": { "subject": "$source", - "object": "f", + "object": "$target", "predicates": [ - "biolink:has_part" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "f", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:has_part" + "biolink:genetic_association" ] }, "edge_2": { - "subject": "i", - "object": "$target", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:treats" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "expression" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "increased" + } + ] + } ] } } @@ -1024,13 +1042,13 @@ } }, { - "Rule": "?i biolink:has_part ?a ?i biolink:has_part ?e ?e biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.143181417", - "Std Confidence": "0.676700344", - "PCA Confidence": "0.779110205", - "Positive Examples": "6497", - "Body size": "9601", - "PCA Body size": "8339", + "Rule": "?a biolink:ameliorates ?b ?g biolink:has_adverse_event ?b ?g biolink:similar_to ?a => ?a biolink:treats ?b", + "Head Coverage": "0.047095381", + "Std Confidence": "0.975799087", + "PCA Confidence": "0.975799087", + "Positive Examples": "2137", + "Body size": "2190", + "PCA Body size": "2190", "Functional variable": "?a", "template": { "query_graph": { @@ -1051,12 +1069,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "e": { + "g": { "categories": [ "biolink:NamedThing" ] @@ -1064,24 +1077,24 @@ }, "edges": { "edge_0": { - "subject": "i", - "object": "$source", + "subject": "$source", + "object": "$target", "predicates": [ - "biolink:has_part" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "e", + "subject": "g", + "object": "$target", "predicates": [ - "biolink:has_part" + "biolink:has_adverse_event" ] }, "edge_2": { - "subject": "e", - "object": "$target", + "subject": "g", + "object": "$source", "predicates": [ - "biolink:treats" + "biolink:similar_to" ] } } @@ -1089,13 +1102,13 @@ } }, { - "Rule": "?e biolink:ameliorates ?b ?i biolink:has_part ?a ?i biolink:has_part ?e => ?a biolink:treats ?b", - "Head Coverage": "0.090400212", - "Std Confidence": "0.623688612", - "PCA Confidence": "0.72345679", - "Positive Examples": "4102", - "Body size": "6577", - "PCA Body size": "5670", + "Rule": "?a biolink:ameliorates ?b ?a biolink:has_adverse_event ?h ?h biolink:has_phenotype ?b => ?a biolink:treats ?b", + "Head Coverage": "0.033938646", + "Std Confidence": "0.975300823", + "PCA Confidence": "0.975300823", + "Positive Examples": "1540", + "Body size": "1579", + "PCA Body size": "1579", "Functional variable": "?a", "template": { "query_graph": { @@ -1116,12 +1129,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -1129,24 +1137,24 @@ }, "edges": { "edge_0": { - "subject": "e", + "subject": "$source", "object": "$target", "predicates": [ "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "$source", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:has_part" + "biolink:has_adverse_event" ] }, "edge_2": { - "subject": "i", - "object": "e", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:has_part" + "biolink:has_phenotype" ] } } @@ -1154,13 +1162,13 @@ } }, { - "Rule": "?f biolink:has_phenotype ?b ?b biolink:has_phenotype ?f ?a biolink:treats ?f => ?a biolink:treats ?b", - "Head Coverage": "0.055800423", - "Std Confidence": "0.617259873", - "PCA Confidence": "0.617259873", - "Positive Examples": "2532", - "Body size": "4102", - "PCA Body size": "4102", + "Rule": "?a biolink:ameliorates ?b ?h biolink:ameliorates ?b ?a biolink:similar_to ?h => ?a biolink:treats ?b", + "Head Coverage": "0.060296192", + "Std Confidence": "0.975053457", + "PCA Confidence": "0.97574893", + "Positive Examples": "2736", + "Body size": "2806", + "PCA Body size": "2804", "Functional variable": "?a", "template": { "query_graph": { @@ -1181,7 +1189,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -1189,24 +1197,24 @@ }, "edges": { "edge_0": { - "subject": "f", + "subject": "$source", "object": "$target", "predicates": [ - "biolink:has_phenotype" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "$target", - "object": "f", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:has_phenotype" + "biolink:ameliorates" ] }, "edge_2": { "subject": "$source", - "object": "f", + "object": "h", "predicates": [ - "biolink:treats" + "biolink:similar_to" ] } } @@ -1214,13 +1222,13 @@ } }, { - "Rule": "?e biolink:treats ?b ?i decreased_metabolic_processing_biolink:affects ?a ?i decreased_metabolic_processing_biolink:affects ?e => ?a biolink:treats ?b", - "Head Coverage": "0.049321227", - "Std Confidence": "0.27571763", - "PCA Confidence": "0.292931937", - "Positive Examples": "2238", - "Body size": "8117", - "PCA Body size": "7640", + "Rule": "?a biolink:ameliorates ?b ?g biolink:ameliorates ?b ?g biolink:similar_to ?a => ?a biolink:treats ?b", + "Head Coverage": "0.060141925", + "Std Confidence": "0.974991068", + "PCA Confidence": "0.975688237", + "Positive Examples": "2729", + "Body size": "2799", + "PCA Body size": "2797", "Functional variable": "?a", "template": { "query_graph": { @@ -1241,12 +1249,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "g": { "categories": [ "biolink:NamedThing" ] @@ -1254,52 +1257,24 @@ }, "edges": { "edge_0": { - "subject": "e", + "subject": "$source", "object": "$target", "predicates": [ - "biolink:treats" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "$source", + "subject": "g", + "object": "$target", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "metabolic_processing" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:ameliorates" ] }, "edge_2": { - "subject": "i", - "object": "e", + "subject": "g", + "object": "$source", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "metabolic_processing" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:similar_to" ] } } @@ -1307,13 +1282,13 @@ } }, { - "Rule": "?i biolink:associated_with ?b ?i biolink:correlated_with ?f ?a biolink:treats ?f => ?a biolink:treats ?b", - "Head Coverage": "0.211323166", - "Std Confidence": "0.274953405", - "PCA Confidence": "0.274953405", - "Positive Examples": "9589", - "Body size": "34875", - "PCA Body size": "34875", + "Rule": "?a biolink:ameliorates ?b ?h biolink:genetic_association ?b ?a biolink:interacts_with ?h => ?a biolink:treats ?b", + "Head Coverage": "0.026071051", + "Std Confidence": "0.97446458", + "PCA Confidence": "0.976072607", + "Positive Examples": "1183", + "Body size": "1214", + "PCA Body size": "1212", "Functional variable": "?a", "template": { "query_graph": { @@ -1334,12 +1309,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "f": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -1347,24 +1317,24 @@ }, "edges": { "edge_0": { - "subject": "i", + "subject": "$source", "object": "$target", "predicates": [ - "biolink:associated_with" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "f", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:correlated_with" + "biolink:genetic_association" ] }, "edge_2": { "subject": "$source", - "object": "f", + "object": "h", "predicates": [ - "biolink:treats" + "biolink:interacts_with" ] } } @@ -1372,13 +1342,13 @@ } }, { - "Rule": "?i biolink:associated_with ?f ?i biolink:correlated_with ?b ?a biolink:treats ?f => ?a biolink:treats ?b", - "Head Coverage": "0.210992595", - "Std Confidence": "0.273652318", - "PCA Confidence": "0.273652318", - "Positive Examples": "9574", - "Body size": "34986", - "PCA Body size": "34986", + "Rule": "?a biolink:ameliorates ?b ?h biolink:genetic_association ?b ?a increased_secretion_biolink:affects ?h => ?a biolink:treats ?b", + "Head Coverage": "0.029553068", + "Std Confidence": "0.973856209", + "PCA Confidence": "0.973856209", + "Positive Examples": "1341", + "Body size": "1377", + "PCA Body size": "1377", "Functional variable": "?a", "template": { "query_graph": { @@ -1399,12 +1369,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "f": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -1412,24 +1377,38 @@ }, "edges": { "edge_0": { - "subject": "i", - "object": "f", + "subject": "$source", + "object": "$target", "predicates": [ - "biolink:associated_with" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", + "subject": "h", "object": "$target", "predicates": [ - "biolink:correlated_with" + "biolink:genetic_association" ] }, "edge_2": { "subject": "$source", - "object": "f", + "object": "h", "predicates": [ - "biolink:treats" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "secretion" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "increased" + } + ] + } ] } } @@ -1437,13 +1416,13 @@ } }, { - "Rule": "?i biolink:associated_with ?b ?i biolink:associated_with ?f ?a biolink:treats ?f => ?a biolink:treats ?b", - "Head Coverage": "0.214276269", - "Std Confidence": "0.271047056", - "PCA Confidence": "0.271047056", - "Positive Examples": "9723", - "Body size": "35872", - "PCA Body size": "35872", + "Rule": "?a biolink:ameliorates ?b ?a biolink:ameliorates ?h ?h biolink:has_phenotype ?b => ?a biolink:treats ?b", + "Head Coverage": "0.082047779", + "Std Confidence": "0.973333333", + "PCA Confidence": "0.977165354", + "Positive Examples": "3723", + "Body size": "3825", + "PCA Body size": "3810", "Functional variable": "?a", "template": { "query_graph": { @@ -1464,12 +1443,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "f": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -1477,24 +1451,24 @@ }, "edges": { "edge_0": { - "subject": "i", + "subject": "$source", "object": "$target", "predicates": [ - "biolink:associated_with" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "f", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:associated_with" + "biolink:ameliorates" ] }, "edge_2": { - "subject": "$source", - "object": "f", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:treats" + "biolink:has_phenotype" ] } } @@ -1502,13 +1476,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?f ?i biolink:associated_with ?b ?i biolink:correlated_with ?f => ?a biolink:treats ?b", - "Head Coverage": "0.162508815", - "Std Confidence": "0.264519138", - "PCA Confidence": "0.267280438", - "Positive Examples": "7374", - "Body size": "27877", - "PCA Body size": "27589", + "Rule": "?g abundance_biolink:affects ?a ?a biolink:ameliorates ?b ?g biolink:genetic_association ?b => ?a biolink:treats ?b", + "Head Coverage": "0.03113981", + "Std Confidence": "0.973140496", + "PCA Confidence": "0.973811165", + "Positive Examples": "1413", + "Body size": "1452", + "PCA Body size": "1451", "Functional variable": "?a", "template": { "query_graph": { @@ -1529,12 +1503,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "g": { "categories": [ "biolink:NamedThing" ] @@ -1542,24 +1511,34 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "f", + "subject": "g", + "object": "$source", "predicates": [ - "biolink:ameliorates" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "abundance" + } + ] + } ] }, "edge_1": { - "subject": "i", + "subject": "$source", "object": "$target", "predicates": [ - "biolink:associated_with" + "biolink:ameliorates" ] }, "edge_2": { - "subject": "i", - "object": "f", + "subject": "g", + "object": "$target", "predicates": [ - "biolink:correlated_with" + "biolink:genetic_association" ] } } @@ -1567,13 +1546,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?f ?i biolink:associated_with ?f ?i biolink:correlated_with ?b => ?a biolink:treats ?b", - "Head Coverage": "0.162486777", - "Std Confidence": "0.26295517", - "PCA Confidence": "0.265731997", - "Positive Examples": "7373", - "Body size": "28039", - "PCA Body size": "27746", + "Rule": "?a biolink:ameliorates ?b ?h biolink:genetic_association ?b ?a decreased_secretion_biolink:affects ?h => ?a biolink:treats ?b", + "Head Coverage": "0.037971615", + "Std Confidence": "0.969066367", + "PCA Confidence": "0.969066367", + "Positive Examples": "1723", + "Body size": "1778", + "PCA Body size": "1778", "Functional variable": "?a", "template": { "query_graph": { @@ -1594,12 +1573,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -1608,23 +1582,37 @@ "edges": { "edge_0": { "subject": "$source", - "object": "f", + "object": "$target", "predicates": [ "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "f", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:associated_with" + "biolink:genetic_association" ] }, "edge_2": { - "subject": "i", - "object": "$target", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:correlated_with" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "secretion" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] } } @@ -1632,13 +1620,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?f ?i biolink:associated_with ?b ?i biolink:associated_with ?f => ?a biolink:treats ?b", - "Head Coverage": "0.165395804", - "Std Confidence": "0.260174721", - "PCA Confidence": "0.263028774", - "Positive Examples": "7505", - "Body size": "28846", - "PCA Body size": "28533", + "Rule": "?a biolink:ameliorates ?b ?a biolink:has_adverse_event ?b => ?a biolink:treats ?b", + "Head Coverage": "0.05917225", + "Std Confidence": "0.968964273", + "PCA Confidence": "0.968964273", + "Positive Examples": "2685", + "Body size": "2771", + "PCA Body size": "2771", "Functional variable": "?a", "template": { "query_graph": { @@ -1658,38 +1646,21 @@ "categories": [ "biolink:DiseaseOrPhenotypicFeature" ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { - "categories": [ - "biolink:NamedThing" - ] } }, "edges": { "edge_0": { "subject": "$source", - "object": "f", + "object": "$target", "predicates": [ "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", + "subject": "$source", "object": "$target", "predicates": [ - "biolink:associated_with" - ] - }, - "edge_2": { - "subject": "i", - "object": "f", - "predicates": [ - "biolink:associated_with" + "biolink:has_adverse_event" ] } } @@ -1697,13 +1668,13 @@ } }, { - "Rule": "?i biolink:has_part ?e ?i biolink:related_to ?a ?e biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.146332863", - "Std Confidence": "0.226923208", - "PCA Confidence": "0.390864139", - "Positive Examples": "6640", - "Body size": "29261", - "PCA Body size": "16988", + "Rule": "?a biolink:ameliorates ?b ?h biolink:genetic_association ?b ?a decreased_molecular_interaction_biolink:affects ?h => ?a biolink:treats ?b", + "Head Coverage": "0.025982898", + "Std Confidence": "0.968775678", + "PCA Confidence": "0.971169687", + "Positive Examples": "1179", + "Body size": "1217", + "PCA Body size": "1214", "Functional variable": "?a", "template": { "query_graph": { @@ -1724,12 +1695,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "e": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -1737,24 +1703,38 @@ }, "edges": { "edge_0": { - "subject": "i", - "object": "e", + "subject": "$source", + "object": "$target", "predicates": [ - "biolink:has_part" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "$source", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:genetic_association" ] }, "edge_2": { - "subject": "e", - "object": "$target", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:treats" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "molecular_interaction" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] } } @@ -1762,13 +1742,13 @@ } }, { - "Rule": "?j biolink:ameliorates ?b ?e biolink:has_part ?j ?e biolink:related_to ?a => ?a biolink:treats ?b", - "Head Coverage": "0.093529619", - "Std Confidence": "0.208182086", - "PCA Confidence": "0.357088767", - "Positive Examples": "4244", - "Body size": "20386", - "PCA Body size": "11885", + "Rule": "?e biolink:ameliorates ?b ?i biolink:has_input ?a ?i biolink:has_input ?e => ?a biolink:treats ?b", + "Head Coverage": "0.082907264", + "Std Confidence": "0.963133641", + "PCA Confidence": "0.966349859", + "Positive Examples": "3762", + "Body size": "3906", + "PCA Body size": "3893", "Functional variable": "?a", "template": { "query_graph": { @@ -1789,12 +1769,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "j": { + "e": { "categories": [ "biolink:NamedThing" ] }, - "e": { + "i": { "categories": [ "biolink:NamedThing" ] @@ -1802,24 +1782,65 @@ }, "edges": { "edge_0": { - "subject": "j", + "subject": "e", "object": "$target", "predicates": [ "biolink:ameliorates" ] }, "edge_1": { - "subject": "e", - "object": "j", + "subject": "i", + "object": "$source", "predicates": [ - "biolink:has_part" + "biolink:has_input" ] }, "edge_2": { - "subject": "e", - "object": "$source", + "subject": "i", + "object": "e", "predicates": [ - "biolink:related_to" + "biolink:has_input" + ] + } + } + } + } + }, + { + "Rule": "?a biolink:ameliorates ?b => ?a biolink:treats ?b", + "Head Coverage": "0.707444464", + "Std Confidence": "0.958582179", + "PCA Confidence": "0.968239127", + "Positive Examples": "32101", + "Body size": "33488", + "PCA Body size": "33154", + "Functional variable": "?a", + "template": { + "query_graph": { + "nodes": { + "$source": { + "ids": [ + "$source_id" + ], + "categories": [ + "biolink:ChemicalEntity" + ] + }, + "$target": { + "ids": [ + "$target_id" + ], + "categories": [ + "biolink:DiseaseOrPhenotypicFeature" + ] + } + }, + "edges": { + "edge_0": { + "subject": "$source", + "object": "$target", + "predicates": [ + "biolink:ameliorates" ] } } @@ -1827,13 +1848,13 @@ } }, { - "Rule": "?i biolink:treats ?b ?a decreased_localization_biolink:affects ?f ?i decreased_localization_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.071778032", - "Std Confidence": "0.205930703", - "PCA Confidence": "0.240938009", - "Positive Examples": "3257", - "Body size": "15816", - "PCA Body size": "13518", + "Rule": "?i biolink:has_output ?a ?i biolink:has_output ?e ?e biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.048285437", + "Std Confidence": "0.888123227", + "PCA Confidence": "0.947254648", + "Positive Examples": "2191", + "Body size": "2467", + "PCA Body size": "2313", "Functional variable": "?a", "template": { "query_graph": { @@ -1859,7 +1880,7 @@ "biolink:NamedThing" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -1868,51 +1889,23 @@ "edges": { "edge_0": { "subject": "i", - "object": "$target", + "object": "$source", "predicates": [ - "biolink:treats" + "biolink:has_output" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "i", + "object": "e", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "localization" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:has_output" ] }, "edge_2": { - "subject": "i", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "localization" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:treats" ] } } @@ -1920,13 +1913,13 @@ } }, { - "Rule": "?i biolink:negatively_correlated_with ?b ?i biolink:negatively_correlated_with ?f ?a biolink:treats ?f => ?a biolink:treats ?b", - "Head Coverage": "0.104306241", - "Std Confidence": "0.202715436", - "PCA Confidence": "0.202715436", - "Positive Examples": "4733", - "Body size": "23348", - "PCA Body size": "23348", + "Rule": "?e biolink:ameliorates ?b ?i biolink:has_output ?a ?i biolink:has_output ?e => ?a biolink:treats ?b", + "Head Coverage": "0.036495063", + "Std Confidence": "0.857586743", + "PCA Confidence": "0.917960089", + "Positive Examples": "1656", + "Body size": "1931", + "PCA Body size": "1804", "Functional variable": "?a", "template": { "query_graph": { @@ -1947,12 +1940,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { + "e": { "categories": [ "biolink:NamedThing" ] }, - "f": { + "i": { "categories": [ "biolink:NamedThing" ] @@ -1960,24 +1953,24 @@ }, "edges": { "edge_0": { - "subject": "i", + "subject": "e", "object": "$target", "predicates": [ - "biolink:negatively_correlated_with" + "biolink:ameliorates" ] }, "edge_1": { "subject": "i", - "object": "f", + "object": "$source", "predicates": [ - "biolink:negatively_correlated_with" + "biolink:has_output" ] }, "edge_2": { - "subject": "$source", - "object": "f", + "subject": "i", + "object": "e", "predicates": [ - "biolink:treats" + "biolink:has_output" ] } } @@ -1985,13 +1978,13 @@ } }, { - "Rule": "?i biolink:related_to ?b ?i biolink:related_to ?f ?a biolink:treats ?f => ?a biolink:treats ?b", - "Head Coverage": "0.161252645", - "Std Confidence": "0.202227627", - "PCA Confidence": "0.202227627", - "Positive Examples": "7317", - "Body size": "36182", - "PCA Body size": "36182", + "Rule": "?i biolink:has_part ?b ?i biolink:related_to ?f ?a biolink:treats ?f => ?a biolink:treats ?b", + "Head Coverage": "0.025321756", + "Std Confidence": "0.839298758", + "PCA Confidence": "0.839298758", + "Positive Examples": "1149", + "Body size": "1369", + "PCA Body size": "1369", "Functional variable": "?a", "template": { "query_graph": { @@ -2028,7 +2021,7 @@ "subject": "i", "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:has_part" ] }, "edge_1": { @@ -2050,13 +2043,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?f ?i biolink:negatively_correlated_with ?b ?i biolink:negatively_correlated_with ?f => ?a biolink:treats ?b", - "Head Coverage": "0.087843794", - "Std Confidence": "0.199270109", - "PCA Confidence": "0.201181043", - "Positive Examples": "3986", - "Body size": "20003", - "PCA Body size": "19813", + "Rule": "?i biolink:has_part ?b ?i biolink:has_part ?f ?a biolink:treats ?f => ?a biolink:treats ?b", + "Head Coverage": "0.025343794", + "Std Confidence": "0.823192555", + "PCA Confidence": "0.823192555", + "Positive Examples": "1150", + "Body size": "1397", + "PCA Body size": "1397", "Functional variable": "?a", "template": { "query_graph": { @@ -2077,12 +2070,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "i": { "categories": [ "biolink:NamedThing" ] }, - "i": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -2090,24 +2083,24 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "f", + "subject": "i", + "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:has_part" ] }, "edge_1": { "subject": "i", - "object": "$target", + "object": "f", "predicates": [ - "biolink:negatively_correlated_with" + "biolink:has_part" ] }, "edge_2": { - "subject": "i", + "subject": "$source", "object": "f", "predicates": [ - "biolink:negatively_correlated_with" + "biolink:treats" ] } } @@ -2115,13 +2108,13 @@ } }, { - "Rule": "?i biolink:ameliorates ?b ?a decreased_localization_biolink:affects ?f ?i decreased_localization_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.058092384", - "Std Confidence": "0.19736448", - "PCA Confidence": "0.229317094", - "Positive Examples": "2636", - "Body size": "13356", - "PCA Body size": "11495", + "Rule": "?i biolink:ameliorates ?b ?a biolink:has_part ?f ?i biolink:has_part ?f => ?a biolink:treats ?b", + "Head Coverage": "0.036715444", + "Std Confidence": "0.726559093", + "PCA Confidence": "0.919426049", + "Positive Examples": "1666", + "Body size": "2293", + "PCA Body size": "1812", "Functional variable": "?a", "template": { "query_graph": { @@ -2165,42 +2158,14 @@ "subject": "$source", "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "localization" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:has_part" ] }, "edge_2": { "subject": "i", "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "localization" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:has_part" ] } } @@ -2208,13 +2173,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?f ?i biolink:related_to ?b ?i biolink:related_to ?f => ?a biolink:treats ?b", - "Head Coverage": "0.127953103", - "Std Confidence": "0.192200742", - "PCA Confidence": "0.193927653", - "Positive Examples": "5806", - "Body size": "30208", - "PCA Body size": "29939", + "Rule": "?a biolink:has_part ?f ?i biolink:has_part ?f ?i biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.04894658", + "Std Confidence": "0.692763568", + "PCA Confidence": "0.915876289", + "Positive Examples": "2221", + "Body size": "3206", + "PCA Body size": "2425", "Functional variable": "?a", "template": { "query_graph": { @@ -2251,21 +2216,21 @@ "subject": "$source", "object": "f", "predicates": [ - "biolink:ameliorates" + "biolink:has_part" ] }, "edge_1": { "subject": "i", - "object": "$target", + "object": "f", "predicates": [ - "biolink:related_to" + "biolink:has_part" ] }, "edge_2": { "subject": "i", - "object": "f", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:treats" ] } } @@ -2273,13 +2238,13 @@ } }, { - "Rule": "?e biolink:treats ?b ?i increased_secretion_biolink:affects ?a ?i increased_secretion_biolink:affects ?e => ?a biolink:treats ?b", - "Head Coverage": "0.05055536", - "Std Confidence": "0.174302865", - "PCA Confidence": "0.229606646", - "Positive Examples": "2294", - "Body size": "13161", - "PCA Body size": "9991", + "Rule": "?i biolink:has_part ?f ?i biolink:related_to ?b ?a biolink:treats ?f => ?a biolink:treats ?b", + "Head Coverage": "0.025321756", + "Std Confidence": "0.692585895", + "PCA Confidence": "0.692585895", + "Positive Examples": "1149", + "Body size": "1659", + "PCA Body size": "1659", "Functional variable": "?a", "template": { "query_graph": { @@ -2300,12 +2265,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "i": { "categories": [ "biolink:NamedThing" ] }, - "i": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -2313,52 +2278,24 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$target", + "subject": "i", + "object": "f", "predicates": [ - "biolink:treats" + "biolink:has_part" ] }, "edge_1": { "subject": "i", - "object": "$source", + "object": "$target", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "secretion" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } + "biolink:related_to" ] }, "edge_2": { - "subject": "i", - "object": "e", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "secretion" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } + "biolink:treats" ] } } @@ -2366,13 +2303,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?j ?b biolink:associated_with ?f ?j biolink:associated_with ?f => ?a biolink:treats ?b", - "Head Coverage": "0.063050952", - "Std Confidence": "0.165022784", - "PCA Confidence": "0.166968194", - "Positive Examples": "2861", - "Body size": "17337", - "PCA Body size": "17135", + "Rule": "?i biolink:has_part ?a ?i biolink:has_part ?e ?e biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.143181417", + "Std Confidence": "0.676700344", + "PCA Confidence": "0.779110205", + "Positive Examples": "6497", + "Body size": "9601", + "PCA Body size": "8339", "Functional variable": "?a", "template": { "query_graph": { @@ -2393,12 +2330,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "j": { + "i": { "categories": [ "biolink:NamedThing" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -2406,24 +2343,24 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "j", + "subject": "i", + "object": "$source", "predicates": [ - "biolink:ameliorates" + "biolink:has_part" ] }, "edge_1": { - "subject": "$target", - "object": "f", + "subject": "i", + "object": "e", "predicates": [ - "biolink:associated_with" + "biolink:has_part" ] }, "edge_2": { - "subject": "j", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:associated_with" + "biolink:treats" ] } } @@ -2431,13 +2368,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?j ?b biolink:associated_with ?f ?j biolink:correlated_with ?f => ?a biolink:treats ?b", - "Head Coverage": "0.061574401", - "Std Confidence": "0.163717333", - "PCA Confidence": "0.165766835", - "Positive Examples": "2794", - "Body size": "17066", - "PCA Body size": "16855", + "Rule": "?e biolink:ameliorates ?b ?i biolink:has_part ?a ?i biolink:has_part ?e => ?a biolink:treats ?b", + "Head Coverage": "0.090400212", + "Std Confidence": "0.623688612", + "PCA Confidence": "0.72345679", + "Positive Examples": "4102", + "Body size": "6577", + "PCA Body size": "5670", "Functional variable": "?a", "template": { "query_graph": { @@ -2458,12 +2395,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "j": { + "e": { "categories": [ "biolink:NamedThing" ] }, - "f": { + "i": { "categories": [ "biolink:NamedThing" ] @@ -2471,24 +2408,24 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "j", + "subject": "e", + "object": "$target", "predicates": [ "biolink:ameliorates" ] }, "edge_1": { - "subject": "$target", - "object": "f", + "subject": "i", + "object": "$source", "predicates": [ - "biolink:associated_with" + "biolink:has_part" ] }, "edge_2": { - "subject": "j", - "object": "f", + "subject": "i", + "object": "e", "predicates": [ - "biolink:correlated_with" + "biolink:has_part" ] } } @@ -2496,13 +2433,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?j ?b biolink:correlated_with ?f ?j biolink:correlated_with ?f => ?a biolink:treats ?b", - "Head Coverage": "0.06238981", - "Std Confidence": "0.162244255", - "PCA Confidence": "0.164220662", - "Positive Examples": "2831", - "Body size": "17449", - "PCA Body size": "17239", + "Rule": "?f biolink:has_phenotype ?b ?b biolink:has_phenotype ?f ?a biolink:treats ?f => ?a biolink:treats ?b", + "Head Coverage": "0.055800423", + "Std Confidence": "0.617259873", + "PCA Confidence": "0.617259873", + "Positive Examples": "2532", + "Body size": "4102", + "PCA Body size": "4102", "Functional variable": "?a", "template": { "query_graph": { @@ -2523,11 +2460,6 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "j": { - "categories": [ - "biolink:NamedThing" - ] - }, "f": { "categories": [ "biolink:NamedThing" @@ -2536,24 +2468,24 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "j", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:has_phenotype" ] }, "edge_1": { "subject": "$target", "object": "f", "predicates": [ - "biolink:correlated_with" + "biolink:has_phenotype" ] }, "edge_2": { - "subject": "j", + "subject": "$source", "object": "f", "predicates": [ - "biolink:correlated_with" + "biolink:treats" ] } } @@ -2561,13 +2493,13 @@ } }, { - "Rule": "?i biolink:has_part ?f ?a biolink:related_to ?f ?i biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.048924542", - "Std Confidence": "0.161854768", - "PCA Confidence": "0.783621603", - "Positive Examples": "2220", - "Body size": "13716", - "PCA Body size": "2833", + "Rule": "?a biolink:ameliorates ?f ?f biolink:has_phenotype ?b ?b biolink:has_phenotype ?f => ?a biolink:treats ?b", + "Head Coverage": "0.041233251", + "Std Confidence": "0.588735053", + "PCA Confidence": "0.591527031", + "Positive Examples": "1871", + "Body size": "3178", + "PCA Body size": "3163", "Functional variable": "?a", "template": { "query_graph": { @@ -2588,11 +2520,6 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, "f": { "categories": [ "biolink:NamedThing" @@ -2601,24 +2528,24 @@ }, "edges": { "edge_0": { - "subject": "i", + "subject": "$source", "object": "f", "predicates": [ - "biolink:has_part" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:has_phenotype" ] }, "edge_2": { - "subject": "i", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:treats" + "biolink:has_phenotype" ] } } @@ -2626,13 +2553,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?j ?j biolink:associated_with ?f ?b biolink:correlated_with ?f => ?a biolink:treats ?b", - "Head Coverage": "0.061442172", - "Std Confidence": "0.159624413", - "PCA Confidence": "0.161454714", - "Positive Examples": "2788", - "Body size": "17466", - "PCA Body size": "17268", + "Rule": "?j biolink:associated_with ?b ?f biolink:associated_with ?j ?a biolink:treats ?f => ?a biolink:treats ?b", + "Head Coverage": "0.022104196", + "Std Confidence": "0.5747851", + "PCA Confidence": "0.5747851", + "Positive Examples": "1003", + "Body size": "1745", + "PCA Body size": "1745", "Functional variable": "?a", "template": { "query_graph": { @@ -2666,24 +2593,24 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "j", + "subject": "j", + "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:associated_with" ] }, "edge_1": { - "subject": "j", - "object": "f", + "subject": "f", + "object": "j", "predicates": [ "biolink:associated_with" ] }, "edge_2": { - "subject": "$target", + "subject": "$source", "object": "f", "predicates": [ - "biolink:correlated_with" + "biolink:treats" ] } } @@ -2691,13 +2618,13 @@ } }, { - "Rule": "?b biolink:correlated_with ?f ?j biolink:correlated_with ?f ?a biolink:treats ?j => ?a biolink:treats ?b", - "Head Coverage": "0.086521509", - "Std Confidence": "0.159224561", - "PCA Confidence": "0.159224561", - "Positive Examples": "3926", - "Body size": "24657", - "PCA Body size": "24657", + "Rule": "?e biolink:treats ?b ?i decreased_uptake_biolink:affects ?a ?i decreased_uptake_biolink:affects ?e => ?a biolink:treats ?b", + "Head Coverage": "0.031889104", + "Std Confidence": "0.489512855", + "PCA Confidence": "0.498965517", + "Positive Examples": "1447", + "Body size": "2956", + "PCA Body size": "2900", "Functional variable": "?a", "template": { "query_graph": { @@ -2718,12 +2645,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] }, - "j": { + "i": { "categories": [ "biolink:NamedThing" ] @@ -2731,24 +2658,52 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:correlated_with" + "biolink:treats" ] }, "edge_1": { - "subject": "j", - "object": "f", + "subject": "i", + "object": "$source", "predicates": [ - "biolink:correlated_with" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "uptake" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] }, "edge_2": { - "subject": "$source", - "object": "j", + "subject": "i", + "object": "e", "predicates": [ - "biolink:treats" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "uptake" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] } } @@ -2756,13 +2711,13 @@ } }, { - "Rule": "?j biolink:associated_with ?f ?b biolink:correlated_with ?f ?a biolink:treats ?j => ?a biolink:treats ?b", - "Head Coverage": "0.085662024", - "Std Confidence": "0.156305292", - "PCA Confidence": "0.156305292", - "Positive Examples": "3887", - "Body size": "24868", - "PCA Body size": "24868", + "Rule": "?b biolink:disrupts ?f ?j biolink:disrupts ?f ?a biolink:treats ?j => ?a biolink:treats ?b", + "Head Coverage": "0.025343794", + "Std Confidence": "0.487494701", + "PCA Confidence": "0.487494701", + "Positive Examples": "1150", + "Body size": "2359", + "PCA Body size": "2359", "Functional variable": "?a", "template": { "query_graph": { @@ -2783,12 +2738,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "j": { + "f": { "categories": [ "biolink:NamedThing" ] }, - "f": { + "j": { "categories": [ "biolink:NamedThing" ] @@ -2796,17 +2751,17 @@ }, "edges": { "edge_0": { - "subject": "j", + "subject": "$target", "object": "f", "predicates": [ - "biolink:associated_with" + "biolink:disrupts" ] }, "edge_1": { - "subject": "$target", + "subject": "j", "object": "f", "predicates": [ - "biolink:correlated_with" + "biolink:disrupts" ] }, "edge_2": { @@ -2821,13 +2776,13 @@ } }, { - "Rule": "?b biolink:associated_with ?f ?j biolink:correlated_with ?f ?a biolink:treats ?j => ?a biolink:treats ?b", - "Head Coverage": "0.086036671", - "Std Confidence": "0.155954141", - "PCA Confidence": "0.155954141", - "Positive Examples": "3904", - "Body size": "25033", - "PCA Body size": "25033", + "Rule": "?e biolink:ameliorates ?b ?i decreased_uptake_biolink:affects ?a ?i decreased_uptake_biolink:affects ?e => ?a biolink:treats ?b", + "Head Coverage": "0.024682652", + "Std Confidence": "0.484638685", + "PCA Confidence": "0.49382716", + "Positive Examples": "1120", + "Body size": "2311", + "PCA Body size": "2268", "Functional variable": "?a", "template": { "query_graph": { @@ -2848,12 +2803,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] }, - "j": { + "i": { "categories": [ "biolink:NamedThing" ] @@ -2861,24 +2816,52 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:associated_with" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "j", - "object": "f", + "subject": "i", + "object": "$source", "predicates": [ - "biolink:correlated_with" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "uptake" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] }, "edge_2": { - "subject": "$source", - "object": "j", + "subject": "i", + "object": "e", "predicates": [ - "biolink:treats" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "uptake" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] } } @@ -2886,13 +2869,13 @@ } }, { - "Rule": "?b biolink:associated_with ?f ?j biolink:associated_with ?f ?a biolink:treats ?j => ?a biolink:treats ?b", - "Head Coverage": "0.088130289", - "Std Confidence": "0.155675802", - "PCA Confidence": "0.155675802", - "Positive Examples": "3999", - "Body size": "25688", - "PCA Body size": "25688", + "Rule": "?a biolink:has_adverse_event ?b ?a biolink:similar_to ?h ?h biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.029486953", + "Std Confidence": "0.326979472", + "PCA Confidence": "0.328182487", + "Positive Examples": "1338", + "Body size": "4092", + "PCA Body size": "4077", "Functional variable": "?a", "template": { "query_graph": { @@ -2913,12 +2896,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - }, - "j": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -2926,22 +2904,22 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "$source", + "object": "$target", "predicates": [ - "biolink:associated_with" + "biolink:has_adverse_event" ] }, "edge_1": { - "subject": "j", - "object": "f", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:associated_with" + "biolink:similar_to" ] }, "edge_2": { - "subject": "$source", - "object": "j", + "subject": "h", + "object": "$target", "predicates": [ "biolink:treats" ] @@ -2951,13 +2929,13 @@ } }, { - "Rule": "?a biolink:decreases_response_to ?f ?i biolink:decreases_response_to ?f ?i biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.095887694", - "Std Confidence": "0.137637606", - "PCA Confidence": "0.16366372", - "Positive Examples": "4351", - "Body size": "31612", - "PCA Body size": "26585", + "Rule": "?a biolink:has_adverse_event ?b ?g biolink:similar_to ?a ?g biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.028385049", + "Std Confidence": "0.303773585", + "PCA Confidence": "0.304275927", + "Positive Examples": "1288", + "Body size": "4240", + "PCA Body size": "4233", "Functional variable": "?a", "template": { "query_graph": { @@ -2978,12 +2956,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "g": { "categories": [ "biolink:NamedThing" ] @@ -2992,20 +2965,20 @@ "edges": { "edge_0": { "subject": "$source", - "object": "f", + "object": "$target", "predicates": [ - "biolink:decreases_response_to" + "biolink:has_adverse_event" ] }, "edge_1": { - "subject": "i", - "object": "f", + "subject": "g", + "object": "$source", "predicates": [ - "biolink:decreases_response_to" + "biolink:similar_to" ] }, "edge_2": { - "subject": "i", + "subject": "g", "object": "$target", "predicates": [ "biolink:treats" @@ -3016,13 +2989,13 @@ } }, { - "Rule": "?i biolink:ameliorates ?b ?a biolink:decreases_response_to ?f ?i biolink:decreases_response_to ?f => ?a biolink:treats ?b", - "Head Coverage": "0.079447285", - "Std Confidence": "0.128428928", - "PCA Confidence": "0.15331944", - "Positive Examples": "3605", - "Body size": "28070", - "PCA Body size": "23513", + "Rule": "?e biolink:ameliorates ?b ?i decreased_metabolic_processing_biolink:affects ?a ?i decreased_metabolic_processing_biolink:affects ?e => ?a biolink:treats ?b", + "Head Coverage": "0.035525388", + "Std Confidence": "0.286221591", + "PCA Confidence": "0.302552553", + "Positive Examples": "1612", + "Body size": "5632", + "PCA Body size": "5328", "Functional variable": "?a", "template": { "query_graph": { @@ -3043,12 +3016,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { + "e": { "categories": [ "biolink:NamedThing" ] }, - "f": { + "i": { "categories": [ "biolink:NamedThing" ] @@ -3056,24 +3029,52 @@ }, "edges": { "edge_0": { - "subject": "i", + "subject": "e", "object": "$target", "predicates": [ "biolink:ameliorates" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "i", + "object": "$source", "predicates": [ - "biolink:decreases_response_to" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "metabolic_processing" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] }, "edge_2": { "subject": "i", - "object": "f", + "object": "e", "predicates": [ - "biolink:decreases_response_to" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "metabolic_processing" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] } } @@ -3081,13 +3082,13 @@ } }, { - "Rule": "?i biolink:treats ?b ?a increased_localization_biolink:affects ?f ?i increased_localization_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.102168547", - "Std Confidence": "0.127104239", - "PCA Confidence": "0.192269409", - "Positive Examples": "4636", - "Body size": "36474", - "PCA Body size": "24112", + "Rule": "?e biolink:treats ?b ?i decreased_metabolic_processing_biolink:affects ?a ?i decreased_metabolic_processing_biolink:affects ?e => ?a biolink:treats ?b", + "Head Coverage": "0.049321227", + "Std Confidence": "0.27571763", + "PCA Confidence": "0.292931937", + "Positive Examples": "2238", + "Body size": "8117", + "PCA Body size": "7640", "Functional variable": "?a", "template": { "query_graph": { @@ -3108,12 +3109,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { + "e": { "categories": [ "biolink:NamedThing" ] }, - "f": { + "i": { "categories": [ "biolink:NamedThing" ] @@ -3121,15 +3122,15 @@ }, "edges": { "edge_0": { - "subject": "i", + "subject": "e", "object": "$target", "predicates": [ "biolink:treats" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "i", + "object": "$source", "predicates": [ "biolink:affects" ], @@ -3138,11 +3139,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "localization" + "qualifier_value": "metabolic_processing" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" + "qualifier_value": "decreased" } ] } @@ -3150,7 +3151,7 @@ }, "edge_2": { "subject": "i", - "object": "f", + "object": "e", "predicates": [ "biolink:affects" ], @@ -3159,11 +3160,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "localization" + "qualifier_value": "metabolic_processing" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" + "qualifier_value": "decreased" } ] } @@ -3174,13 +3175,13 @@ } }, { - "Rule": "?i biolink:ameliorates ?b ?a increased_localization_biolink:affects ?f ?i increased_localization_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.080416961", - "Std Confidence": "0.124764933", - "PCA Confidence": "0.189312581", - "Positive Examples": "3649", - "Body size": "29247", - "PCA Body size": "19275", + "Rule": "?e biolink:treats ?b ?i increased_synthesis_biolink:affects ?a ?i increased_synthesis_biolink:affects ?e => ?a biolink:treats ?b", + "Head Coverage": "0.039580395", + "Std Confidence": "0.268259895", + "PCA Confidence": "0.434235977", + "Positive Examples": "1796", + "Body size": "6695", + "PCA Body size": "4136", "Functional variable": "?a", "template": { "query_graph": { @@ -3201,12 +3202,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { + "e": { "categories": [ "biolink:NamedThing" ] }, - "f": { + "i": { "categories": [ "biolink:NamedThing" ] @@ -3214,15 +3215,15 @@ }, "edges": { "edge_0": { - "subject": "i", + "subject": "e", "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:treats" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "i", + "object": "$source", "predicates": [ "biolink:affects" ], @@ -3231,7 +3232,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "localization" + "qualifier_value": "synthesis" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -3243,7 +3244,7 @@ }, "edge_2": { "subject": "i", - "object": "f", + "object": "e", "predicates": [ "biolink:affects" ], @@ -3252,7 +3253,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "localization" + "qualifier_value": "synthesis" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -3267,13 +3268,13 @@ } }, { - "Rule": "?i biolink:ameliorates ?b ?a decreased_molecular_modification_biolink:affects ?f ?i decreased_molecular_modification_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.046059591", - "Std Confidence": "0.122072309", - "PCA Confidence": "0.129741138", - "Positive Examples": "2090", - "Body size": "17121", - "PCA Body size": "16109", + "Rule": "?f biolink:associated_with ?b ?a biolink:treats ?f => ?a biolink:treats ?b", + "Head Coverage": "0.029663258", + "Std Confidence": "0.260953858", + "PCA Confidence": "0.260953858", + "Positive Examples": "1346", + "Body size": "5158", + "PCA Body size": "5158", "Functional variable": "?a", "template": { "query_graph": { @@ -3294,11 +3295,6 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, "f": { "categories": [ "biolink:NamedThing" @@ -3307,52 +3303,17 @@ }, "edges": { "edge_0": { - "subject": "i", + "subject": "f", "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:associated_with" ] }, "edge_1": { "subject": "$source", "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_modification" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - }, - "edge_2": { - "subject": "i", - "object": "f", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_modification" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:treats" ] } } @@ -3360,13 +3321,13 @@ } }, { - "Rule": "?i biolink:treats ?b ?a decreased_molecular_modification_biolink:affects ?f ?i decreased_molecular_modification_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.053861072", - "Std Confidence": "0.118784933", - "PCA Confidence": "0.126220111", - "Positive Examples": "2444", - "Body size": "20575", - "PCA Body size": "19363", + "Rule": "?f biolink:correlated_with ?b ?a biolink:treats ?f => ?a biolink:treats ?b", + "Head Coverage": "0.028869887", + "Std Confidence": "0.259046866", + "PCA Confidence": "0.259046866", + "Positive Examples": "1310", + "Body size": "5057", + "PCA Body size": "5057", "Functional variable": "?a", "template": { "query_graph": { @@ -3387,11 +3348,6 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, "f": { "categories": [ "biolink:NamedThing" @@ -3400,52 +3356,17 @@ }, "edges": { "edge_0": { - "subject": "i", + "subject": "f", "object": "$target", "predicates": [ - "biolink:treats" + "biolink:correlated_with" ] }, "edge_1": { "subject": "$source", "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_modification" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - }, - "edge_2": { - "subject": "i", - "object": "f", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_modification" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:treats" ] } } @@ -3453,13 +3374,13 @@ } }, { - "Rule": "?e biolink:ameliorates ?b ?i increased_uptake_biolink:affects ?a ?i increased_uptake_biolink:affects ?e => ?a biolink:treats ?b", - "Head Coverage": "0.059568935", - "Std Confidence": "0.106702984", - "PCA Confidence": "0.138388286", - "Positive Examples": "2703", - "Body size": "25332", - "PCA Body size": "19532", + "Rule": "?e biolink:ameliorates ?b ?i increased_synthesis_biolink:affects ?a ?i increased_synthesis_biolink:affects ?e => ?a biolink:treats ?b", + "Head Coverage": "0.027944288", + "Std Confidence": "0.252791069", + "PCA Confidence": "0.410754778", + "Positive Examples": "1268", + "Body size": "5016", + "PCA Body size": "3087", "Functional variable": "?a", "template": { "query_graph": { @@ -3510,7 +3431,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "uptake" + "qualifier_value": "synthesis" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -3531,7 +3452,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "uptake" + "qualifier_value": "synthesis" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -3546,13 +3467,13 @@ } }, { - "Rule": "?e biolink:treats ?b ?i increased_uptake_biolink:affects ?a ?i increased_uptake_biolink:affects ?e => ?a biolink:treats ?b", - "Head Coverage": "0.081078103", - "Std Confidence": "0.105051255", - "PCA Confidence": "0.135257353", - "Positive Examples": "3679", - "Body size": "35021", - "PCA Body size": "27200", + "Rule": "?e biolink:treats ?b ?i increased_activity_biolink:affects ?a ?i increased_activity_biolink:affects ?e => ?a biolink:treats ?b", + "Head Coverage": "0.022148272", + "Std Confidence": "0.21446863", + "PCA Confidence": "0.509893455", + "Positive Examples": "1005", + "Body size": "4686", + "PCA Body size": "1971", "Functional variable": "?a", "template": { "query_graph": { @@ -3603,7 +3524,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "uptake" + "qualifier_value": "activity" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -3624,7 +3545,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "uptake" + "qualifier_value": "activity" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -3639,13 +3560,13 @@ } }, { - "Rule": "?a biolink:increases_response_to ?f ?i biolink:increases_response_to ?f ?i biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.045420487", - "Std Confidence": "0.104175091", - "PCA Confidence": "0.108132214", - "Positive Examples": "2061", - "Body size": "19784", - "PCA Body size": "19060", + "Rule": "?h biolink:genetic_association ?b ?a biolink:has_adverse_event ?b ?a increased_activity_biolink:affects ?h => ?a biolink:treats ?b", + "Head Coverage": "0.023492595", + "Std Confidence": "0.204842429", + "PCA Confidence": "0.205276334", + "Positive Examples": "1066", + "Body size": "5204", + "PCA Body size": "5193", "Functional variable": "?a", "template": { "query_graph": { @@ -3666,12 +3587,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -3679,24 +3595,38 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "f", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:increases_response_to" + "biolink:genetic_association" ] }, "edge_1": { - "subject": "i", - "object": "f", + "subject": "$source", + "object": "$target", "predicates": [ - "biolink:increases_response_to" + "biolink:has_adverse_event" ] }, "edge_2": { - "subject": "i", - "object": "$target", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:treats" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "increased" + } + ] + } ] } } @@ -3704,13 +3634,13 @@ } }, { - "Rule": "?b biolink:similar_to ?f ?j biolink:similar_to ?f ?a biolink:treats ?j => ?a biolink:treats ?b", - "Head Coverage": "0.081254408", - "Std Confidence": "0.099043679", - "PCA Confidence": "0.099043679", - "Positive Examples": "3687", - "Body size": "37226", - "PCA Body size": "37226", + "Rule": "?b biolink:associated_with ?f ?f biolink:correlated_with ?j ?a biolink:treats ?j => ?a biolink:treats ?b", + "Head Coverage": "0.023228138", + "Std Confidence": "0.185302391", + "PCA Confidence": "0.185302391", + "Positive Examples": "1054", + "Body size": "5688", + "PCA Body size": "5688", "Functional variable": "?a", "template": { "query_graph": { @@ -3747,14 +3677,14 @@ "subject": "$target", "object": "f", "predicates": [ - "biolink:similar_to" + "biolink:associated_with" ] }, "edge_1": { - "subject": "j", - "object": "f", + "subject": "f", + "object": "j", "predicates": [ - "biolink:similar_to" + "biolink:correlated_with" ] }, "edge_2": { @@ -3769,13 +3699,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?j ?b biolink:similar_to ?f ?j biolink:similar_to ?f => ?a biolink:treats ?b", - "Head Coverage": "0.064373237", - "Std Confidence": "0.093980245", - "PCA Confidence": "0.094573593", - "Positive Examples": "2921", - "Body size": "31081", - "PCA Body size": "30886", + "Rule": "?e biolink:ameliorates ?b ?i increased_secretion_biolink:affects ?a ?i increased_secretion_biolink:affects ?e => ?a biolink:treats ?b", + "Head Coverage": "0.036296721", + "Std Confidence": "0.182351639", + "PCA Confidence": "0.24234844", + "Positive Examples": "1647", + "Body size": "9032", + "PCA Body size": "6796", "Functional variable": "?a", "template": { "query_graph": { @@ -3796,12 +3726,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "j": { + "e": { "categories": [ "biolink:NamedThing" ] }, - "f": { + "i": { "categories": [ "biolink:NamedThing" ] @@ -3809,24 +3739,52 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "j", + "subject": "e", + "object": "$target", "predicates": [ "biolink:ameliorates" ] }, "edge_1": { - "subject": "$target", - "object": "f", + "subject": "i", + "object": "$source", "predicates": [ - "biolink:similar_to" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "secretion" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "increased" + } + ] + } ] }, "edge_2": { - "subject": "j", - "object": "f", + "subject": "i", + "object": "e", "predicates": [ - "biolink:similar_to" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "secretion" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "increased" + } + ] + } ] } } @@ -3834,13 +3792,13 @@ } }, { - "Rule": "?e biolink:affects_response_to ?a ?i biolink:ameliorates ?b ?i biolink:binds ?e => ?a biolink:treats ?b", - "Head Coverage": "0.070103138", - "Std Confidence": "0.093531314", - "PCA Confidence": "0.113603086", - "Positive Examples": "3181", - "Body size": "34010", - "PCA Body size": "28001", + "Rule": "?h biolink:genetic_association ?b ?a biolink:has_adverse_event ?b ?a decreased_activity_biolink:affects ?h => ?a biolink:treats ?b", + "Head Coverage": "0.037288434", + "Std Confidence": "0.173183214", + "PCA Confidence": "0.173770155", + "Positive Examples": "1692", + "Body size": "9770", + "PCA Body size": "9737", "Functional variable": "?a", "template": { "query_graph": { @@ -3861,12 +3819,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -3874,24 +3827,38 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$source", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:affects_response_to" + "biolink:genetic_association" ] }, "edge_1": { - "subject": "i", + "subject": "$source", "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:has_adverse_event" ] }, "edge_2": { - "subject": "i", - "object": "e", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:binds" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] } } @@ -3899,13 +3866,13 @@ } }, { - "Rule": "?i biolink:similar_to ?b ?i biolink:similar_to ?f ?a biolink:treats ?f => ?a biolink:treats ?b", - "Head Coverage": "0.083370063", - "Std Confidence": "0.092180609", - "PCA Confidence": "0.092180609", - "Positive Examples": "3783", - "Body size": "41039", - "PCA Body size": "41039", + "Rule": "?a biolink:ameliorates ?h ?a biolink:has_adverse_event ?b ?h biolink:has_phenotype ?b => ?a biolink:treats ?b", + "Head Coverage": "0.022500882", + "Std Confidence": "0.164916815", + "PCA Confidence": "0.165130196", + "Positive Examples": "1021", + "Body size": "6191", + "PCA Body size": "6183", "Functional variable": "?a", "template": { "query_graph": { @@ -3926,12 +3893,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "f": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -3939,24 +3901,24 @@ }, "edges": { "edge_0": { - "subject": "i", - "object": "$target", + "subject": "$source", + "object": "h", "predicates": [ - "biolink:similar_to" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", - "object": "f", + "subject": "$source", + "object": "$target", "predicates": [ - "biolink:similar_to" + "biolink:has_adverse_event" ] }, "edge_2": { - "subject": "$source", - "object": "f", + "subject": "h", + "object": "$target", "predicates": [ - "biolink:treats" + "biolink:has_phenotype" ] } } @@ -3964,13 +3926,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?f ?i biolink:similar_to ?b ?i biolink:similar_to ?f => ?a biolink:treats ?b", - "Head Coverage": "0.067656911", - "Std Confidence": "0.089734596", - "PCA Confidence": "0.090315368", - "Positive Examples": "3070", - "Body size": "34212", - "PCA Body size": "33992", + "Rule": "?a biolink:directly_physically_interacts_with ?h ?h biolink:genetic_association ?b ?a biolink:has_adverse_event ?b => ?a biolink:treats ?b", + "Head Coverage": "0.039051481", + "Std Confidence": "0.159323863", + "PCA Confidence": "0.15949595", + "Positive Examples": "1772", + "Body size": "11122", + "PCA Body size": "11110", "Functional variable": "?a", "template": { "query_graph": { @@ -3991,12 +3953,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -4005,23 +3962,23 @@ "edges": { "edge_0": { "subject": "$source", - "object": "f", + "object": "h", "predicates": [ - "biolink:ameliorates" + "biolink:directly_physically_interacts_with" ] }, "edge_1": { - "subject": "i", + "subject": "h", "object": "$target", "predicates": [ - "biolink:similar_to" + "biolink:genetic_association" ] }, "edge_2": { - "subject": "i", - "object": "f", + "subject": "$source", + "object": "$target", "predicates": [ - "biolink:similar_to" + "biolink:has_adverse_event" ] } } @@ -4029,13 +3986,13 @@ } }, { - "Rule": "?j biolink:affects_response_to ?a ?e biolink:binds ?j ?e biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.083678597", - "Std Confidence": "0.088417474", - "PCA Confidence": "0.106480832", - "Positive Examples": "3797", - "Body size": "42944", - "PCA Body size": "35659", + "Rule": "?b biolink:associated_with ?f ?f biolink:associated_with ?j ?a biolink:treats ?j => ?a biolink:treats ?b", + "Head Coverage": "0.023404443", + "Std Confidence": "0.158271237", + "PCA Confidence": "0.158271237", + "Positive Examples": "1062", + "Body size": "6710", + "PCA Body size": "6710", "Functional variable": "?a", "template": { "query_graph": { @@ -4056,12 +4013,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "j": { + "f": { "categories": [ "biolink:NamedThing" ] }, - "e": { + "j": { "categories": [ "biolink:NamedThing" ] @@ -4069,22 +4026,22 @@ }, "edges": { "edge_0": { - "subject": "j", - "object": "$source", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:affects_response_to" + "biolink:associated_with" ] }, "edge_1": { - "subject": "e", + "subject": "f", "object": "j", "predicates": [ - "biolink:binds" + "biolink:associated_with" ] }, "edge_2": { - "subject": "e", - "object": "$target", + "subject": "$source", + "object": "j", "predicates": [ "biolink:treats" ] @@ -4094,13 +4051,13 @@ } }, { - "Rule": "?a biolink:similar_to ?f ?f biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.147655148", - "Std Confidence": "0.087572541", - "PCA Confidence": "0.099711284", - "Positive Examples": "6700", - "Body size": "76508", - "PCA Body size": "67194", + "Rule": "?a biolink:has_adverse_event ?b ?h biolink:has_phenotype ?b ?a biolink:treats ?h => ?a biolink:treats ?b", + "Head Coverage": "0.026688117", + "Std Confidence": "0.154208583", + "PCA Confidence": "0.154208583", + "Positive Examples": "1211", + "Body size": "7853", + "PCA Body size": "7853", "Functional variable": "?a", "template": { "query_graph": { @@ -4121,7 +4078,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "h": { "categories": [ "biolink:NamedThing" ] @@ -4130,14 +4087,21 @@ "edges": { "edge_0": { "subject": "$source", - "object": "f", + "object": "$target", "predicates": [ - "biolink:similar_to" + "biolink:has_adverse_event" ] }, "edge_1": { - "subject": "f", + "subject": "h", "object": "$target", + "predicates": [ + "biolink:has_phenotype" + ] + }, + "edge_2": { + "subject": "$source", + "object": "h", "predicates": [ "biolink:treats" ] @@ -4147,13 +4111,13 @@ } }, { - "Rule": "?i biolink:treats ?b ?a decreased_degradation_biolink:affects ?f ?i decreased_degradation_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.076009344", - "Std Confidence": "0.086951041", - "PCA Confidence": "0.110283302", - "Positive Examples": "3449", - "Body size": "39666", - "PCA Body size": "31274", + "Rule": "?i biolink:ameliorates ?b ?i biolink:has_part ?f ?a biolink:related_to ?f => ?a biolink:treats ?b", + "Head Coverage": "0.036737482", + "Std Confidence": "0.147235471", + "PCA Confidence": "0.768911439", + "Positive Examples": "1667", + "Body size": "11322", + "PCA Body size": "2168", "Functional variable": "?a", "template": { "query_graph": { @@ -4190,49 +4154,21 @@ "subject": "i", "object": "$target", "predicates": [ - "biolink:treats" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "$source", + "subject": "i", "object": "f", "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" - } - ] - } + "biolink:has_part" ] }, "edge_2": { - "subject": "i", + "subject": "$source", "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "degradation" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:related_to" ] } } @@ -4240,13 +4176,13 @@ } }, { - "Rule": "?i biolink:decreases_response_to ?f ?i biolink:treats ?b ?a decreased_expression_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.046147743", - "Std Confidence": "0.086859134", - "PCA Confidence": "0.098643301", - "Positive Examples": "2094", - "Body size": "24108", - "PCA Body size": "21228", + "Rule": "?i biolink:affects_response_to ?a ?e biolink:treats ?b ?i decreased_uptake_biolink:affects ?e => ?a biolink:treats ?b", + "Head Coverage": "0.022412729", + "Std Confidence": "0.14113239", + "PCA Confidence": "0.166095051", + "Positive Examples": "1017", + "Body size": "7206", + "PCA Body size": "6123", "Functional variable": "?a", "template": { "query_graph": { @@ -4272,7 +4208,7 @@ "biolink:NamedThing" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -4281,21 +4217,21 @@ "edges": { "edge_0": { "subject": "i", - "object": "f", + "object": "$source", "predicates": [ - "biolink:decreases_response_to" + "biolink:affects_response_to" ] }, "edge_1": { - "subject": "i", + "subject": "e", "object": "$target", "predicates": [ "biolink:treats" ] }, "edge_2": { - "subject": "$source", - "object": "f", + "subject": "i", + "object": "e", "predicates": [ "biolink:affects" ], @@ -4304,7 +4240,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "expression" + "qualifier_value": "uptake" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -4319,13 +4255,13 @@ } }, { - "Rule": "?i biolink:ameliorates ?b ?a decreased_degradation_biolink:affects ?f ?i decreased_degradation_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.067017807", - "Std Confidence": "0.084469876", - "PCA Confidence": "0.107198252", - "Positive Examples": "3041", - "Body size": "36001", - "PCA Body size": "28368", + "Rule": "?i biolink:ameliorates ?b ?a biolink:negatively_correlated_with ?f ?i biolink:negatively_correlated_with ?f => ?a biolink:treats ?b", + "Head Coverage": "0.026137165", + "Std Confidence": "0.134117381", + "PCA Confidence": "0.2259478", + "Positive Examples": "1186", + "Body size": "8843", + "PCA Body size": "5249", "Functional variable": "?a", "template": { "query_graph": { @@ -4369,42 +4305,14 @@ "subject": "$source", "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "degradation" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:negatively_correlated_with" ] }, "edge_2": { "subject": "i", "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "degradation" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:negatively_correlated_with" ] } } @@ -4412,13 +4320,13 @@ } }, { - "Rule": "?e biolink:similar_to ?a ?e biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.147478843", - "Std Confidence": "0.082030915", - "PCA Confidence": "0.092685697", - "Positive Examples": "6692", - "Body size": "81579", - "PCA Body size": "72201", + "Rule": "?a biolink:negatively_correlated_with ?f ?i biolink:negatively_correlated_with ?f ?i biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.032351904", + "Std Confidence": "0.133600291", + "PCA Confidence": "0.229590241", + "Positive Examples": "1468", + "Body size": "10988", + "PCA Body size": "6394", "Functional variable": "?a", "template": { "query_graph": { @@ -4439,7 +4347,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { + "categories": [ + "biolink:NamedThing" + ] + }, + "i": { "categories": [ "biolink:NamedThing" ] @@ -4447,14 +4360,21 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:similar_to" + "biolink:negatively_correlated_with" ] }, "edge_1": { - "subject": "e", + "subject": "i", + "object": "f", + "predicates": [ + "biolink:negatively_correlated_with" + ] + }, + "edge_2": { + "subject": "i", "object": "$target", "predicates": [ "biolink:treats" @@ -4465,13 +4385,13 @@ } }, { - "Rule": "?i biolink:related_to ?f ?i biolink:treats ?b ?a decreased_expression_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.046169781", - "Std Confidence": "0.079101378", - "PCA Confidence": "0.092474068", - "Positive Examples": "2095", - "Body size": "26485", - "PCA Body size": "22655", + "Rule": "?f biolink:causes ?b ?a biolink:similar_to ?f ?f biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.026181241", + "Std Confidence": "0.11998788", + "PCA Confidence": "0.135973446", + "Positive Examples": "1188", + "Body size": "9901", + "PCA Body size": "8737", "Functional variable": "?a", "template": { "query_graph": { @@ -4492,11 +4412,6 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, "f": { "categories": [ "biolink:NamedThing" @@ -4505,38 +4420,24 @@ }, "edges": { "edge_0": { - "subject": "i", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:causes" ] }, "edge_1": { - "subject": "i", - "object": "$target", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:treats" + "biolink:similar_to" ] }, "edge_2": { - "subject": "$source", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "expression" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:treats" ] } } @@ -4544,13 +4445,13 @@ } }, { - "Rule": "?e biolink:binds ?j ?j biolink:increases_response_to ?a ?e biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.046103667", - "Std Confidence": "0.077498703", - "PCA Confidence": "0.100761006", - "Positive Examples": "2092", - "Body size": "26994", - "PCA Body size": "20762", + "Rule": "?e biolink:causes ?b ?e biolink:similar_to ?a ?e biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.026666079", + "Std Confidence": "0.118325836", + "PCA Confidence": "0.131952017", + "Positive Examples": "1210", + "Body size": "10226", + "PCA Body size": "9170", "Functional variable": "?a", "template": { "query_graph": { @@ -4575,26 +4476,21 @@ "categories": [ "biolink:NamedThing" ] - }, - "j": { - "categories": [ - "biolink:NamedThing" - ] } }, "edges": { "edge_0": { "subject": "e", - "object": "j", + "object": "$target", "predicates": [ - "biolink:binds" + "biolink:causes" ] }, "edge_1": { - "subject": "j", + "subject": "e", "object": "$source", "predicates": [ - "biolink:increases_response_to" + "biolink:similar_to" ] }, "edge_2": { @@ -4609,13 +4505,13 @@ } }, { - "Rule": "?f biolink:ameliorates ?b ?a biolink:similar_to ?f => ?a biolink:treats ?b", - "Head Coverage": "0.085111072", - "Std Confidence": "0.077079674", - "PCA Confidence": "0.087170459", - "Positive Examples": "3862", - "Body size": "50104", - "PCA Body size": "44304", + "Rule": "?e biolink:ameliorates ?b ?i transport_biolink:affects ?a ?i transport_biolink:affects ?e => ?a biolink:treats ?b", + "Head Coverage": "0.025938822", + "Std Confidence": "0.113151317", + "PCA Confidence": "0.150742828", + "Positive Examples": "1177", + "Body size": "10402", + "PCA Body size": "7808", "Functional variable": "?a", "template": { "query_graph": { @@ -4636,7 +4532,12 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { + "categories": [ + "biolink:NamedThing" + ] + }, + "i": { "categories": [ "biolink:NamedThing" ] @@ -4644,17 +4545,44 @@ }, "edges": { "edge_0": { - "subject": "f", + "subject": "e", "object": "$target", "predicates": [ "biolink:ameliorates" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "i", + "object": "$source", "predicates": [ - "biolink:similar_to" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "transport" + } + ] + } + ] + }, + "edge_2": { + "subject": "i", + "object": "e", + "predicates": [ + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "transport" + } + ] + } ] } } @@ -4662,13 +4590,13 @@ } }, { - "Rule": "?e biolink:affects_response_to ?a ?i biolink:ameliorates ?b ?i biolink:interacts_with ?e => ?a biolink:treats ?b", - "Head Coverage": "0.090818935", - "Std Confidence": "0.075306544", - "PCA Confidence": "0.089303515", - "Positive Examples": "4121", - "Body size": "54723", - "PCA Body size": "46146", + "Rule": "?f biolink:ameliorates ?b ?f biolink:has_adverse_event ?b ?a biolink:similar_to ?f => ?a biolink:treats ?b", + "Head Coverage": "0.027591678", + "Std Confidence": "0.112813119", + "PCA Confidence": "0.128094946", + "Positive Examples": "1252", + "Body size": "11098", + "PCA Body size": "9774", "Functional variable": "?a", "template": { "query_graph": { @@ -4689,12 +4617,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -4702,24 +4625,24 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$source", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:affects_response_to" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "i", + "subject": "f", "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:has_adverse_event" ] }, "edge_2": { - "subject": "i", - "object": "e", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:interacts_with" + "biolink:similar_to" ] } } @@ -4727,13 +4650,13 @@ } }, { - "Rule": "?f abundance_biolink:affects ?j ?j biolink:ameliorates ?b ?a decreased_expression_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.049717913", - "Std Confidence": "0.070647919", - "PCA Confidence": "0.087040395", - "Positive Examples": "2256", - "Body size": "31933", - "PCA Body size": "25919", + "Rule": "?a activity_biolink:affects ?f ?i activity_biolink:affects ?f ?i biolink:treats ?b => ?a biolink:treats ?b", + "Head Coverage": "0.026269394", + "Std Confidence": "0.111977454", + "PCA Confidence": "0.310093652", + "Positive Examples": "1192", + "Body size": "10645", + "PCA Body size": "3844", "Functional variable": "?a", "template": { "query_graph": { @@ -4759,7 +4682,7 @@ "biolink:NamedThing" ] }, - "j": { + "i": { "categories": [ "biolink:NamedThing" ] @@ -4767,8 +4690,8 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "j", + "subject": "$source", + "object": "f", "predicates": [ "biolink:affects" ], @@ -4777,21 +4700,14 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "abundance" + "qualifier_value": "activity" } ] } ] }, "edge_1": { - "subject": "j", - "object": "$target", - "predicates": [ - "biolink:ameliorates" - ] - }, - "edge_2": { - "subject": "$source", + "subject": "i", "object": "f", "predicates": [ "biolink:affects" @@ -4801,28 +4717,33 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "expression" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" + "qualifier_value": "activity" } ] } ] + }, + "edge_2": { + "subject": "i", + "object": "$target", + "predicates": [ + "biolink:treats" + ] } } } } - }, + } + ], + "{\"predicate\": \"biolink:contraindicated_for\"}": [ { - "Rule": "?j biolink:affects_response_to ?a ?e biolink:interacts_with ?j ?e biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.110432828", - "Std Confidence": "0.070242084", - "PCA Confidence": "0.083312551", - "Positive Examples": "5011", - "Body size": "71339", - "PCA Body size": "60147", + "Rule": "?a biolink:contraindicated_for ?f ?f biolink:correlated_with ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.040336578", + "Std Confidence": "0.381377096", + "PCA Confidence": "0.381377096", + "Positive Examples": "1069", + "Body size": "2803", + "PCA Body size": "2803", "Functional variable": "?a", "template": { "query_graph": { @@ -4843,12 +4764,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "j": { - "categories": [ - "biolink:NamedThing" - ] - }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -4856,24 +4772,17 @@ }, "edges": { "edge_0": { - "subject": "j", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:affects_response_to" + "biolink:contraindicated_for" ] }, "edge_1": { - "subject": "e", - "object": "j", - "predicates": [ - "biolink:interacts_with" - ] - }, - "edge_2": { - "subject": "e", + "subject": "f", "object": "$target", "predicates": [ - "biolink:treats" + "biolink:correlated_with" ] } } @@ -4881,13 +4790,13 @@ } }, { - "Rule": "?e biolink:treats ?b ?i increased_transport_biolink:affects ?a ?i increased_transport_biolink:affects ?e => ?a biolink:treats ?b", - "Head Coverage": "0.098973025", - "Std Confidence": "0.069631146", - "PCA Confidence": "0.09923546", - "Positive Examples": "4491", - "Body size": "64497", - "PCA Body size": "45256", + "Rule": "?f biolink:associated_with ?b ?a biolink:contraindicated_for ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.041128971", + "Std Confidence": "0.381252186", + "PCA Confidence": "0.381252186", + "Positive Examples": "1090", + "Body size": "2859", + "PCA Body size": "2859", "Functional variable": "?a", "template": { "query_graph": { @@ -4908,12 +4817,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -4921,2268 +4825,15 @@ }, "edges": { "edge_0": { - "subject": "e", + "subject": "f", "object": "$target", "predicates": [ - "biolink:treats" + "biolink:associated_with" ] }, "edge_1": { - "subject": "i", - "object": "$source", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "transport" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - }, - "edge_2": { - "subject": "i", - "object": "e", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "transport" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?e biolink:ameliorates ?b ?e biolink:similar_to ?a => ?a biolink:treats ?b", - "Head Coverage": "0.084648272", - "Std Confidence": "0.069517846", - "PCA Confidence": "0.078483858", - "Positive Examples": "3841", - "Body size": "55252", - "PCA Body size": "48940", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "e", - "object": "$target", - "predicates": [ - "biolink:ameliorates" - ] - }, - "edge_1": { - "subject": "e", - "object": "$source", - "predicates": [ - "biolink:similar_to" - ] - } - } - } - } - }, - { - "Rule": "?e biolink:treats ?b ?i metabolic_processing_biolink:affects ?a ?i metabolic_processing_biolink:affects ?e => ?a biolink:treats ?b", - "Head Coverage": "0.105275917", - "Std Confidence": "0.06933941", - "PCA Confidence": "0.096273605", - "Positive Examples": "4777", - "Body size": "68893", - "PCA Body size": "49619", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "e", - "object": "$target", - "predicates": [ - "biolink:treats" - ] - }, - "edge_1": { - "subject": "i", - "object": "$source", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "metabolic_processing" - } - ] - } - ] - }, - "edge_2": { - "subject": "i", - "object": "e", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "metabolic_processing" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?e biolink:ameliorates ?b ?i increased_transport_biolink:affects ?a ?i increased_transport_biolink:affects ?e => ?a biolink:treats ?b", - "Head Coverage": "0.079293018", - "Std Confidence": "0.069204285", - "PCA Confidence": "0.100100156", - "Positive Examples": "3598", - "Body size": "51991", - "PCA Body size": "35944", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "e", - "object": "$target", - "predicates": [ - "biolink:ameliorates" - ] - }, - "edge_1": { - "subject": "i", - "object": "$source", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "transport" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - }, - "edge_2": { - "subject": "i", - "object": "e", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "transport" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?j biolink:ameliorates ?b ?e metabolic_processing_biolink:affects ?a ?e metabolic_processing_biolink:affects ?j => ?a biolink:treats ?b", - "Head Coverage": "0.081562941", - "Std Confidence": "0.069058815", - 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"PCA Body size": "99020", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:ameliorates" - ] - }, - "edge_1": { - "subject": "i", - "object": "f", - "predicates": [ - "biolink:negatively_correlated_with" - ] - }, - "edge_2": { - "subject": "i", - "object": "$target", - "predicates": [ - "biolink:treats" - ] - } - } - } - } - }, - { - "Rule": "?i abundance_biolink:affects ?e ?i biolink:decreases_response_to ?a ?e biolink:treats ?b => ?a biolink:treats ?b", - "Head Coverage": "0.052318406", - "Std Confidence": "0.053785853", - "PCA Confidence": "0.072801987", - "Positive Examples": "2374", - "Body size": "44138", - "PCA Body size": "32609", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "i", - "object": "e", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "abundance" - } - ] - } - ] - }, - "edge_1": { - "subject": "i", - "object": "$source", - "predicates": [ - "biolink:decreases_response_to" - ] - }, - "edge_2": { - "subject": "e", - "object": "$target", - "predicates": [ - "biolink:treats" - ] - } - } - } - } - }, - { - "Rule": "?i biolink:treats ?b ?a decreased_expression_biolink:affects ?f ?i increased_secretion_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.048968618", - "Std Confidence": "0.053713015", - "PCA Confidence": "0.062067039", - "Positive Examples": "2222", - "Body size": "41368", - "PCA Body size": "35800", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "i", - "object": "$target", - "predicates": [ - "biolink:treats" - ] - }, - "edge_1": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "expression" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - }, - "edge_2": { - "subject": "i", - "object": "f", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "secretion" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?i biolink:ameliorates ?b ?i biolink:negatively_correlated_with ?f ?a biolink:treats ?f => ?a biolink:treats ?b", - "Head Coverage": "0.107744182", - "Std Confidence": "0.053132064", - "PCA Confidence": "0.053132064", - "Positive Examples": "4889", - "Body size": "92016", - "PCA Body size": "92016", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "i", - "object": "$target", - "predicates": [ - "biolink:ameliorates" - ] - }, - "edge_1": { - "subject": "i", - "object": "f", - "predicates": [ - "biolink:negatively_correlated_with" - ] - }, - "edge_2": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:treats" - ] - } - } - } - } - }, - { - "Rule": "?i biolink:ameliorates ?b ?e biolink:increases_response_to ?a ?i increased_molecular_interaction_biolink:affects ?e => ?a biolink:treats ?b", - "Head Coverage": "0.053839034", - "Std Confidence": "0.052873066", - "PCA Confidence": "0.074766641", - "Positive Examples": "2443", - "Body size": "46205", - "PCA Body size": "32675", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "i", - "object": "$target", - "predicates": [ - "biolink:ameliorates" - ] - }, - "edge_1": { - "subject": "e", - "object": "$source", - "predicates": [ - "biolink:increases_response_to" - ] - }, - "edge_2": { - "subject": "i", - "object": "e", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_interaction" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?i biolink:treats ?b ?a decreased_expression_biolink:affects ?f ?i increased_degradation_biolink:affects ?f => ?a biolink:treats ?b", - "Head Coverage": "0.046191819", - "Std Confidence": "0.052254992", - "PCA Confidence": "0.059849804", - "Positive Examples": "2096", - "Body size": "40111", - "PCA Body size": "35021", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "i", - "object": "$target", - "predicates": [ - "biolink:treats" - ] - }, - "edge_1": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "expression" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - }, - "edge_2": { - "subject": "i", - "object": "f", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "degradation" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?i biolink:ameliorates ?b ?a biolink:ameliorates ?f ?i biolink:negatively_correlated_with ?f => ?a biolink:treats ?b", - "Head Coverage": "0.09271421", - "Std Confidence": "0.052220002", - "PCA Confidence": "0.052677711", - "Positive Examples": "4207", - "Body size": "80563", - "PCA Body size": "79863", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "i": { - "categories": [ - "biolink:NamedThing" - ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "i", - "object": "$target", - "predicates": [ - "biolink:ameliorates" - ] - }, - "edge_1": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:ameliorates" - ] - }, - "edge_2": { - "subject": "i", - "object": "f", - "predicates": [ - "biolink:negatively_correlated_with" - ] - } - } - } - } - }, - { - "Rule": "?e biolink:affects_response_to ?a ?j biolink:ameliorates ?b ?e metabolic_processing_biolink:affects ?j => ?a biolink:treats ?b", - "Head Coverage": "0.046830924", - "Std Confidence": "0.052139562", - "PCA Confidence": "0.071628409", - "Positive Examples": "2125", - "Body size": "40756", - "PCA Body size": "29667", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "e": { - "categories": [ - "biolink:NamedThing" - ] - }, - "j": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "e", - "object": "$source", - "predicates": [ - "biolink:affects_response_to" - ] - }, - "edge_1": { - "subject": "j", - "object": "$target", - "predicates": [ - "biolink:ameliorates" - ] - }, - "edge_2": { - "subject": "e", - "object": "j", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "metabolic_processing" - } - ] - } - ] - } - } - } - } - } - ], - "{\"predicate\": \"biolink:contraindicated_for\"}": [ - { - "Rule": "?a biolink:contraindicated_for ?f ?f biolink:correlated_with ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.040336578", - "Std Confidence": "0.381377096", - "PCA Confidence": "0.381377096", - "Positive Examples": "1069", - "Body size": "2803", - "PCA Body size": "2803", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:contraindicated_for" - ] - }, - "edge_1": { - "subject": "f", - "object": "$target", - "predicates": [ - "biolink:correlated_with" - ] - } - } - } - } - }, - { - "Rule": "?f biolink:associated_with ?b ?a biolink:contraindicated_for ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.041128971", - "Std Confidence": "0.381252186", - "PCA Confidence": "0.381252186", - "Positive Examples": "1090", - "Body size": "2859", - "PCA Body size": "2859", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "f", - "object": "$target", - "predicates": [ - "biolink:associated_with" - ] - }, - "edge_1": { - "subject": "$source", - "object": "f", + "subject": "$source", + "object": "f", "predicates": [ "biolink:contraindicated_for" ] @@ -8284,13 +5935,13 @@ } }, { - "Rule": "?a biolink:contributes_to ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.064221568", - "Std Confidence": "0.026687155", - "PCA Confidence": "0.06218033", - "Positive Examples": "1702", - "Body size": "63776", - "PCA Body size": "27372", + "Rule": "?a biolink:causes ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.159120066", + "Std Confidence": "0.030438643", + "PCA Confidence": "0.037518461", + "Positive Examples": "4217", + "Body size": "138541", + "PCA Body size": "112398", "Functional variable": "?a", "template": { "query_graph": { @@ -8317,7 +5968,7 @@ "subject": "$source", "object": "$target", "predicates": [ - "biolink:contributes_to" + "biolink:causes" ] } } @@ -8325,13 +5976,13 @@ } }, { - "Rule": "?f biolink:contraindicated_for ?b ?a biolink:has_part ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.006942872", - "Std Confidence": "0.025977693", - "PCA Confidence": "1", - "Positive Examples": "184", - "Body size": "7083", - "PCA Body size": "184", + "Rule": "?a biolink:contributes_to ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.064221568", + "Std Confidence": "0.026687155", + "PCA Confidence": "0.06218033", + "Positive Examples": "1702", + "Body size": "63776", + "PCA Body size": "27372", "Functional variable": "?a", "template": { "query_graph": { @@ -8351,26 +6002,14 @@ "categories": [ "biolink:DiseaseOrPhenotypicFeature" ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] } }, "edges": { "edge_0": { - "subject": "f", - "object": "$target", - "predicates": [ - "biolink:contraindicated_for" - ] - }, - "edge_1": { "subject": "$source", - "object": "f", + "object": "$target", "predicates": [ - "biolink:has_part" + "biolink:contributes_to" ] } } @@ -8378,13 +6017,13 @@ } }, { - "Rule": "?a biolink:has_adverse_event ?f ?b biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.011659497", - "Std Confidence": "0.0240336", - "PCA Confidence": "0.030663888", - "Positive Examples": "309", - "Body size": "12857", - "PCA Body size": "10077", + "Rule": "?f biolink:contraindicated_for ?b ?a biolink:has_part ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.006942872", + "Std Confidence": "0.025977693", + "PCA Confidence": "1", + "Positive Examples": "184", + "Body size": "7083", + "PCA Body size": "184", "Functional variable": "?a", "template": { "query_graph": { @@ -8413,17 +6052,17 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:has_adverse_event" + "biolink:contraindicated_for" ] }, "edge_1": { - "subject": "$target", + "subject": "$source", "object": "f", "predicates": [ - "biolink:similar_to" + "biolink:has_part" ] } } @@ -8431,13 +6070,13 @@ } }, { - "Rule": "?f biolink:contributes_to ?b ?a biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.083012603", - "Std Confidence": "0.022729151", - "PCA Confidence": "0.034155657", - "Positive Examples": "2200", - "Body size": "96792", - "PCA Body size": "64411", + "Rule": "?a biolink:has_adverse_event ?f ?b biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.011659497", + "Std Confidence": "0.0240336", + "PCA Confidence": "0.030663888", + "Positive Examples": "309", + "Body size": "12857", + "PCA Body size": "10077", "Functional variable": "?a", "template": { "query_graph": { @@ -8466,14 +6105,14 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "$target", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:contributes_to" + "biolink:has_adverse_event" ] }, "edge_1": { - "subject": "$source", + "subject": "$target", "object": "f", "predicates": [ "biolink:similar_to" @@ -8484,13 +6123,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e secretion_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000415063", - "Std Confidence": "0.022494888", - "PCA Confidence": "0.046218487", - "Positive Examples": "11", - "Body size": "489", - "PCA Body size": "238", + "Rule": "?e biolink:contributes_to ?b ?e biolink:similar_to ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.089427213", + "Std Confidence": "0.023198677", + "PCA Confidence": "0.034028256", + "Positive Examples": "2370", + "Body size": "102161", + "PCA Body size": "69648", "Functional variable": "?a", "template": { "query_graph": { @@ -8522,75 +6161,12 @@ "subject": "e", "object": "$target", "predicates": [ - "biolink:genetic_association" + "biolink:contributes_to" ] }, "edge_1": { "subject": "e", "object": "$source", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "secretion" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?a biolink:causes ?f ?b biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.006339144", - "Std Confidence": "0.022325581", - "PCA Confidence": "0.02607481", - "Positive Examples": "168", - "Body size": "7525", - "PCA Body size": "6443", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" - ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:causes" - ] - }, - "edge_1": { - "subject": "$target", - "object": "f", "predicates": [ "biolink:similar_to" ] @@ -8600,13 +6176,13 @@ } }, { - "Rule": "?f biolink:correlated_with ?b ?a biolink:treats ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.00415063", - "Std Confidence": "0.021752027", - "PCA Confidence": "0.0413845", - "Positive Examples": "110", - "Body size": "5057", - "PCA Body size": "2658", + "Rule": "?f biolink:contributes_to ?b ?a biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.083012603", + "Std Confidence": "0.022729151", + "PCA Confidence": "0.034155657", + "Positive Examples": "2200", + "Body size": "96792", + "PCA Body size": "64411", "Functional variable": "?a", "template": { "query_graph": { @@ -8638,28 +6214,28 @@ "subject": "f", "object": "$target", "predicates": [ - "biolink:correlated_with" + "biolink:contributes_to" ] }, "edge_1": { "subject": "$source", "object": "f", "predicates": [ - "biolink:treats" + "biolink:similar_to" ] } } } } }, - { - "Rule": "?f biolink:associated_with ?b ?a biolink:treats ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.004226096", - "Std Confidence": "0.021713843", - "PCA Confidence": "0.040742088", - "Positive Examples": "112", - "Body size": "5158", - "PCA Body size": "2749", + { + "Rule": "?e biolink:genetic_association ?b ?e secretion_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000415063", + "Std Confidence": "0.022494888", + "PCA Confidence": "0.046218487", + "Positive Examples": "11", + "Body size": "489", + "PCA Body size": "238", "Functional variable": "?a", "template": { "query_graph": { @@ -8680,7 +6256,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -8688,17 +6264,27 @@ }, "edges": { "edge_0": { - "subject": "f", + "subject": "e", "object": "$target", "predicates": [ - "biolink:associated_with" + "biolink:genetic_association" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "e", + "object": "$source", "predicates": [ - "biolink:treats" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "secretion" + } + ] + } ] } } @@ -8706,13 +6292,13 @@ } }, { - "Rule": "?a biolink:causes ?f ?f biolink:correlated_with ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.01433854", - "Std Confidence": "0.017534955", - "PCA Confidence": "0.054723502", - "Positive Examples": "380", - "Body size": "21671", - "PCA Body size": "6944", + "Rule": "?a biolink:causes ?f ?b biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.006339144", + "Std Confidence": "0.022325581", + "PCA Confidence": "0.02607481", + "Positive Examples": "168", + "Body size": "7525", + "PCA Body size": "6443", "Functional variable": "?a", "template": { "query_graph": { @@ -8748,10 +6334,10 @@ ] }, "edge_1": { - "subject": "f", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:correlated_with" + "biolink:similar_to" ] } } @@ -8759,13 +6345,13 @@ } }, { - "Rule": "?a biolink:causes ?f ?f biolink:similar_to ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.00528262", - "Std Confidence": "0.016839067", - "PCA Confidence": "0.019734987", - "Positive Examples": "140", - "Body size": "8314", - "PCA Body size": "7094", + "Rule": "?f biolink:correlated_with ?b ?a biolink:treats ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.00415063", + "Std Confidence": "0.021752027", + "PCA Confidence": "0.0413845", + "Positive Examples": "110", + "Body size": "5057", + "PCA Body size": "2658", "Functional variable": "?a", "template": { "query_graph": { @@ -8794,17 +6380,17 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:causes" + "biolink:correlated_with" ] }, "edge_1": { - "subject": "f", - "object": "$target", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:similar_to" + "biolink:treats" ] } } @@ -8812,13 +6398,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?f ?f biolink:correlated_with ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.002188514", - "Std Confidence": "0.015675676", - "PCA Confidence": "0.035409035", - "Positive Examples": "58", - "Body size": "3700", - "PCA Body size": "1638", + "Rule": "?f biolink:associated_with ?b ?a biolink:treats ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.004226096", + "Std Confidence": "0.021713843", + "PCA Confidence": "0.040742088", + "Positive Examples": "112", + "Body size": "5158", + "PCA Body size": "2749", "Functional variable": "?a", "template": { "query_graph": { @@ -8847,17 +6433,17 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:associated_with" ] }, "edge_1": { - "subject": "f", - "object": "$target", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:correlated_with" + "biolink:treats" ] } } @@ -8865,13 +6451,13 @@ } }, { - "Rule": "?a biolink:has_adverse_event ?f ?f biolink:similar_to ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.007131537", - "Std Confidence": "0.015316045", - "PCA Confidence": "0.020016946", - "Positive Examples": "189", - "Body size": "12340", - "PCA Body size": "9442", + "Rule": "?a biolink:has_adverse_event ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.134216286", + "Std Confidence": "0.020644225", + "PCA Confidence": "0.026577105", + "Positive Examples": "3557", + "Body size": "172300", + "PCA Body size": "133837", "Functional variable": "?a", "template": { "query_graph": { @@ -8891,26 +6477,14 @@ "categories": [ "biolink:DiseaseOrPhenotypicFeature" ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] } }, "edges": { "edge_0": { "subject": "$source", - "object": "f", - "predicates": [ - "biolink:has_adverse_event" - ] - }, - "edge_1": { - "subject": "f", "object": "$target", "predicates": [ - "biolink:similar_to" + "biolink:has_adverse_event" ] } } @@ -8918,13 +6492,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?f ?f biolink:associated_with ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.002113048", - "Std Confidence": "0.015106555", - "PCA Confidence": "0.033836858", - "Positive Examples": "56", - "Body size": "3707", - "PCA Body size": "1655", + "Rule": "?a biolink:causes ?f ?f biolink:correlated_with ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.01433854", + "Std Confidence": "0.017534955", + "PCA Confidence": "0.054723502", + "Positive Examples": "380", + "Body size": "21671", + "PCA Body size": "6944", "Functional variable": "?a", "template": { "query_graph": { @@ -8956,14 +6530,14 @@ "subject": "$source", "object": "f", "predicates": [ - "biolink:ameliorates" + "biolink:causes" ] }, "edge_1": { "subject": "f", "object": "$target", "predicates": [ - "biolink:associated_with" + "biolink:correlated_with" ] } } @@ -8971,13 +6545,13 @@ } }, { - "Rule": "?a biolink:contributes_to ?f ?b biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.004226096", - "Std Confidence": "0.014386641", - "PCA Confidence": "0.04770017", - "Positive Examples": "112", - "Body size": "7785", - "PCA Body size": "2348", + "Rule": "?e biolink:causes ?b ?e biolink:similar_to ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.175307524", + "Std Confidence": "0.016919217", + "PCA Confidence": "0.024800491", + "Positive Examples": "4646", + "Body size": "274599", + "PCA Body size": "187335", "Functional variable": "?a", "template": { "query_graph": { @@ -8998,7 +6572,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -9006,15 +6580,15 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:contributes_to" + "biolink:causes" ] }, "edge_1": { - "subject": "$target", - "object": "f", + "subject": "e", + "object": "$source", "predicates": [ "biolink:similar_to" ] @@ -9024,13 +6598,13 @@ } }, { - "Rule": "?a biolink:similar_to ?f ?f biolink:treats ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.040789374", - "Std Confidence": "0.014129241", - "PCA Confidence": "0.021156255", - "Positive Examples": "1081", - "Body size": "76508", - "PCA Body size": "51096", + "Rule": "?a biolink:causes ?f ?f biolink:similar_to ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.00528262", + "Std Confidence": "0.016839067", + "PCA Confidence": "0.019734987", + "Positive Examples": "140", + "Body size": "8314", + "PCA Body size": "7094", "Functional variable": "?a", "template": { "query_graph": { @@ -9062,14 +6636,14 @@ "subject": "$source", "object": "f", "predicates": [ - "biolink:similar_to" + "biolink:causes" ] }, "edge_1": { "subject": "f", "object": "$target", "predicates": [ - "biolink:treats" + "biolink:similar_to" ] } } @@ -9077,13 +6651,13 @@ } }, { - "Rule": "?e biolink:similar_to ?a ?e biolink:treats ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.042789223", - "Std Confidence": "0.013900636", - "PCA Confidence": "0.020446432", - "Positive Examples": "1134", - "Body size": "81579", - "PCA Body size": "55462", + "Rule": "?f biolink:causes ?b ?a biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.175835786", + "Std Confidence": "0.016502644", + "PCA Confidence": "0.024176143", + "Positive Examples": "4660", + "Body size": "282379", + "PCA Body size": "192752", "Functional variable": "?a", "template": { "query_graph": { @@ -9104,7 +6678,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -9112,17 +6686,17 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$source", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:similar_to" + "biolink:causes" ] }, "edge_1": { - "subject": "e", - "object": "$target", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:treats" + "biolink:similar_to" ] } } @@ -9130,13 +6704,13 @@ } }, { - "Rule": "?b biolink:similar_to ?f ?a biolink:treats ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.006339144", - "Std Confidence": "0.013814653", - "PCA Confidence": "0.031360836", - "Positive Examples": "168", - "Body size": "12161", - "PCA Body size": "5357", + "Rule": "?a biolink:ameliorates ?f ?f biolink:correlated_with ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.002188514", + "Std Confidence": "0.015675676", + "PCA Confidence": "0.035409035", + "Positive Examples": "58", + "Body size": "3700", + "PCA Body size": "1638", "Functional variable": "?a", "template": { "query_graph": { @@ -9165,17 +6739,17 @@ }, "edges": { "edge_0": { - "subject": "$target", + "subject": "$source", "object": "f", "predicates": [ - "biolink:similar_to" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:treats" + "biolink:correlated_with" ] } } @@ -9183,13 +6757,13 @@ } }, { - "Rule": "?f biolink:ameliorates ?b ?a biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.025658441", - "Std Confidence": "0.013571771", - "PCA Confidence": "0.020349533", - "Positive Examples": "680", - "Body size": "50104", - "PCA Body size": "33416", + "Rule": "?a biolink:has_adverse_event ?f ?f biolink:similar_to ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.007131537", + "Std Confidence": "0.015316045", + "PCA Confidence": "0.020016946", + "Positive Examples": "189", + "Body size": "12340", + "PCA Body size": "9442", "Functional variable": "?a", "template": { "query_graph": { @@ -9218,15 +6792,15 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "$target", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:ameliorates" + "biolink:has_adverse_event" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ "biolink:similar_to" ] @@ -9236,13 +6810,13 @@ } }, { - "Rule": "?f biolink:contraindicated_for ?b ?a biolink:related_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.007244736", - "Std Confidence": "0.013200413", - "PCA Confidence": "0.583586626", - "Positive Examples": "192", - "Body size": "14545", - "PCA Body size": "329", + "Rule": "?a biolink:ameliorates ?f ?f biolink:associated_with ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.002113048", + "Std Confidence": "0.015106555", + "PCA Confidence": "0.033836858", + "Positive Examples": "56", + "Body size": "3707", + "PCA Body size": "1655", "Functional variable": "?a", "template": { "query_graph": { @@ -9271,17 +6845,17 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "$target", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:contraindicated_for" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:associated_with" ] } } @@ -9289,13 +6863,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?f ?b biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.004603426", - "Std Confidence": "0.012914153", - "PCA Confidence": "0.031754295", - "Positive Examples": "122", - "Body size": "9447", - "PCA Body size": "3842", + "Rule": "?a biolink:contributes_to ?f ?b biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.004226096", + "Std Confidence": "0.014386641", + "PCA Confidence": "0.04770017", + "Positive Examples": "112", + "Body size": "7785", + "PCA Body size": "2348", "Functional variable": "?a", "template": { "query_graph": { @@ -9327,7 +6901,7 @@ "subject": "$source", "object": "f", "predicates": [ - "biolink:ameliorates" + "biolink:contributes_to" ] }, "edge_1": { @@ -9342,13 +6916,13 @@ } }, { - "Rule": "?e biolink:ameliorates ?b ?e biolink:similar_to ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.026865897", - "Std Confidence": "0.012886411", - "PCA Confidence": "0.019022683", - "Positive Examples": "712", - "Body size": "55252", - "PCA Body size": "37429", + "Rule": "?a biolink:similar_to ?f ?f biolink:treats ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.040789374", + "Std Confidence": "0.014129241", + "PCA Confidence": "0.021156255", + "Positive Examples": "1081", + "Body size": "76508", + "PCA Body size": "51096", "Functional variable": "?a", "template": { "query_graph": { @@ -9369,7 +6943,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -9377,17 +6951,17 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$target", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:ameliorates" + "biolink:similar_to" ] }, "edge_1": { - "subject": "e", - "object": "$source", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:similar_to" + "biolink:treats" ] } } @@ -9395,13 +6969,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e decreased_metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.002452645", - "Std Confidence": "0.012712693", - "PCA Confidence": "0.029385172", - "Positive Examples": "65", - "Body size": "5113", - "PCA Body size": "2212", + "Rule": "?e biolink:similar_to ?a ?e biolink:treats ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.042789223", + "Std Confidence": "0.013900636", + "PCA Confidence": "0.020446432", + "Positive Examples": "1134", + "Body size": "81579", + "PCA Body size": "55462", "Functional variable": "?a", "template": { "query_graph": { @@ -9431,30 +7005,16 @@ "edges": { "edge_0": { "subject": "e", - "object": "$target", + "object": "$source", "predicates": [ - "biolink:genetic_association" + "biolink:similar_to" ] }, "edge_1": { "subject": "e", - "object": "$source", + "object": "$target", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "metabolic_processing" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:treats" ] } } @@ -9462,13 +7022,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a decreased_molecular_interaction_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.004792091", - "Std Confidence": "0.012147298", - "PCA Confidence": "0.057727273", - "Positive Examples": "127", - "Body size": "10455", - "PCA Body size": "2200", + "Rule": "?b biolink:similar_to ?f ?a biolink:treats ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.006339144", + "Std Confidence": "0.013814653", + "PCA Confidence": "0.031360836", + "Positive Examples": "168", + "Body size": "12161", + "PCA Body size": "5357", "Functional variable": "?a", "template": { "query_graph": { @@ -9500,28 +7060,14 @@ "subject": "$target", "object": "f", "predicates": [ - "biolink:related_to" + "biolink:similar_to" ] }, "edge_1": { "subject": "$source", "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_interaction" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:treats" ] } } @@ -9529,13 +7075,13 @@ } }, { - "Rule": "?e biolink:contributes_to ?b ?e biolink:has_part ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.002943174", - "Std Confidence": "0.012085528", - "PCA Confidence": "0.057906459", - "Positive Examples": "78", - "Body size": "6454", - "PCA Body size": "1347", + "Rule": "?f biolink:ameliorates ?b ?a biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.025658441", + "Std Confidence": "0.013571771", + "PCA Confidence": "0.020349533", + "Positive Examples": "680", + "Body size": "50104", + "PCA Body size": "33416", "Functional variable": "?a", "template": { "query_graph": { @@ -9556,7 +7102,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -9564,17 +7110,17 @@ }, "edges": { "edge_0": { - "subject": "e", + "subject": "f", "object": "$target", "predicates": [ - "biolink:contributes_to" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "e", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:has_part" + "biolink:similar_to" ] } } @@ -9582,13 +7128,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a decreased_secretion_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.005622217", - "Std Confidence": "0.01189146", - "PCA Confidence": "0.041596873", - "Positive Examples": "149", - "Body size": "12530", - "PCA Body size": "3582", + "Rule": "?f biolink:contraindicated_for ?b ?a biolink:related_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.007244736", + "Std Confidence": "0.013200413", + "PCA Confidence": "0.583586626", + "Positive Examples": "192", + "Body size": "14545", + "PCA Body size": "329", "Functional variable": "?a", "template": { "query_graph": { @@ -9617,31 +7163,17 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:contraindicated_for" ] }, "edge_1": { "subject": "$source", "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "secretion" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:related_to" ] } } @@ -9649,13 +7181,13 @@ } }, { - "Rule": "?f biolink:affects_response_to ?a ?b biolink:related_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.008640857", - "Std Confidence": "0.011550489", - "PCA Confidence": "0.03469697", - "Positive Examples": "229", - "Body size": "19826", - "PCA Body size": "6600", + "Rule": "?a biolink:ameliorates ?f ?b biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.004603426", + "Std Confidence": "0.012914153", + "PCA Confidence": "0.031754295", + "Positive Examples": "122", + "Body size": "9447", + "PCA Body size": "3842", "Functional variable": "?a", "template": { "query_graph": { @@ -9684,17 +7216,17 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:affects_response_to" + "biolink:ameliorates" ] }, "edge_1": { "subject": "$target", "object": "f", "predicates": [ - "biolink:related_to" + "biolink:similar_to" ] } } @@ -9702,13 +7234,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a increased_molecular_modification_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000641461", - "Std Confidence": "0.011541073", - "PCA Confidence": "0.049132948", - "Positive Examples": "17", - "Body size": "1473", - "PCA Body size": "346", + "Rule": "?e biolink:ameliorates ?b ?e biolink:similar_to ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.026865897", + "Std Confidence": "0.012886411", + "PCA Confidence": "0.019022683", + "Positive Examples": "712", + "Body size": "55252", + "PCA Body size": "37429", "Functional variable": "?a", "template": { "query_graph": { @@ -9729,7 +7261,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -9737,31 +7269,17 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:related_to" - ] - }, - "edge_1": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_modification" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } + "subject": "e", + "object": "$target", + "predicates": [ + "biolink:ameliorates" + ] + }, + "edge_1": { + "subject": "e", + "object": "$source", + "predicates": [ + "biolink:similar_to" ] } } @@ -9769,13 +7287,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a decreased_expression_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.004943023", - "Std Confidence": "0.01146207", - "PCA Confidence": "0.035026738", - "Positive Examples": "131", - "Body size": "11429", - "PCA Body size": "3740", + "Rule": "?e biolink:genetic_association ?b ?e decreased_metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.002452645", + "Std Confidence": "0.012712693", + "PCA Confidence": "0.029385172", + "Positive Examples": "65", + "Body size": "5113", + "PCA Body size": "2212", "Functional variable": "?a", "template": { "query_graph": { @@ -9796,7 +7314,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -9804,15 +7322,15 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:genetic_association" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "e", + "object": "$source", "predicates": [ "biolink:affects" ], @@ -9821,7 +7339,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "expression" + "qualifier_value": "metabolic_processing" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -9836,13 +7354,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a decreased_molecular_modification_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000452796", - "Std Confidence": "0.010507881", - "PCA Confidence": "0.04137931", - "Positive Examples": "12", - "Body size": "1142", - "PCA Body size": "290", + "Rule": "?b biolink:related_to ?f ?a decreased_molecular_interaction_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.004792091", + "Std Confidence": "0.012147298", + "PCA Confidence": "0.057727273", + "Positive Examples": "127", + "Body size": "10455", + "PCA Body size": "2200", "Functional variable": "?a", "template": { "query_graph": { @@ -9888,7 +7406,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_modification" + "qualifier_value": "molecular_interaction" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -9903,13 +7421,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?f ?f biolink:similar_to ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.003584635", - "Std Confidence": "0.01038819", - "PCA Confidence": "0.024154589", - "Positive Examples": "95", - "Body size": "9145", - "PCA Body size": "3933", + "Rule": "?e biolink:contributes_to ?b ?e biolink:has_part ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.002943174", + "Std Confidence": "0.012085528", + "PCA Confidence": "0.057906459", + "Positive Examples": "78", + "Body size": "6454", + "PCA Body size": "1347", "Functional variable": "?a", "template": { "query_graph": { @@ -9930,7 +7448,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -9938,17 +7456,17 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:contributes_to" ] }, "edge_1": { - "subject": "f", - "object": "$target", + "subject": "e", + "object": "$source", "predicates": [ - "biolink:similar_to" + "biolink:has_part" ] } } @@ -9956,13 +7474,13 @@ } }, { - "Rule": "?f biolink:similar_to ?b ?a biolink:treats ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.004339295", - "Std Confidence": "0.010057723", - "PCA Confidence": "0.021515435", - "Positive Examples": "115", - "Body size": "11434", - "PCA Body size": "5345", + "Rule": "?b biolink:related_to ?f ?a decreased_secretion_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.005622217", + "Std Confidence": "0.01189146", + "PCA Confidence": "0.041596873", + "Positive Examples": "149", + "Body size": "12530", + "PCA Body size": "3582", "Functional variable": "?a", "template": { "query_graph": { @@ -9991,17 +7509,31 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:similar_to" + "biolink:related_to" ] }, "edge_1": { "subject": "$source", "object": "f", "predicates": [ - "biolink:treats" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "secretion" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] } } @@ -10009,13 +7541,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?f metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.001169723", - "Std Confidence": "0.009983897", - "PCA Confidence": "0.040951123", - "Positive Examples": "31", - "Body size": "3105", - "PCA Body size": "757", + "Rule": "?f biolink:affects_response_to ?a ?b biolink:related_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.008640857", + "Std Confidence": "0.011550489", + "PCA Confidence": "0.03469697", + "Positive Examples": "229", + "Body size": "19826", + "PCA Body size": "6600", "Functional variable": "?a", "template": { "query_graph": { @@ -10044,27 +7576,17 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "f", + "object": "$source", "predicates": [ - "biolink:related_to" + "biolink:affects_response_to" ] }, "edge_1": { - "subject": "f", - "object": "$source", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "metabolic_processing" - } - ] - } + "biolink:related_to" ] } } @@ -10072,13 +7594,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e decreased_secretion_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.001396121", - "Std Confidence": "0.009759958", - "PCA Confidence": "0.022519781", - "Positive Examples": "37", - "Body size": "3791", - "PCA Body size": "1643", + "Rule": "?b biolink:related_to ?f ?a increased_molecular_modification_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000641461", + "Std Confidence": "0.011541073", + "PCA Confidence": "0.049132948", + "Positive Examples": "17", + "Body size": "1473", + "PCA Body size": "346", "Functional variable": "?a", "template": { "query_graph": { @@ -10099,7 +7621,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -10107,15 +7629,15 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:genetic_association" + "biolink:related_to" ] }, "edge_1": { - "subject": "e", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ "biolink:affects" ], @@ -10124,11 +7646,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "secretion" + "qualifier_value": "molecular_modification" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" + "qualifier_value": "increased" } ] } @@ -10139,13 +7661,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?f decreased_metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000716927", - "Std Confidence": "0.009758603", - "PCA Confidence": "0.072796935", - "Positive Examples": "19", - "Body size": "1947", - "PCA Body size": "261", + "Rule": "?b biolink:related_to ?f ?a decreased_expression_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.004943023", + "Std Confidence": "0.01146207", + "PCA Confidence": "0.035026738", + "Positive Examples": "131", + "Body size": "11429", + "PCA Body size": "3740", "Functional variable": "?a", "template": { "query_graph": { @@ -10181,8 +7703,8 @@ ] }, "edge_1": { - "subject": "f", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ "biolink:affects" ], @@ -10191,7 +7713,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "metabolic_processing" + "qualifier_value": "expression" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -10206,13 +7728,13 @@ } }, { - "Rule": "?f biolink:increases_response_to ?a ?b biolink:related_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.006980605", - "Std Confidence": "0.009711286", - "PCA Confidence": "0.038042361", - "Positive Examples": "185", - "Body size": "19050", - "PCA Body size": "4863", + "Rule": "?f biolink:has_adverse_event ?b ?a biolink:similar_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.152214927", + "Std Confidence": "0.011332479", + "PCA Confidence": "0.016701652", + "Positive Examples": "4034", + "Body size": "355968", + "PCA Body size": "241533", "Functional variable": "?a", "template": { "query_graph": { @@ -10242,16 +7764,16 @@ "edges": { "edge_0": { "subject": "f", - "object": "$source", + "object": "$target", "predicates": [ - "biolink:increases_response_to" + "biolink:has_adverse_event" ] }, "edge_1": { - "subject": "$target", + "subject": "$source", "object": "f", "predicates": [ - "biolink:related_to" + "biolink:similar_to" ] } } @@ -10259,13 +7781,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e decreased_activity_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000905592", - "Std Confidence": "0.009584665", - "PCA Confidence": "0.041450777", - "Positive Examples": "24", - "Body size": "2504", - "PCA Body size": "579", + "Rule": "?e biolink:has_adverse_event ?b ?e biolink:similar_to ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.157082484", + "Std Confidence": "0.011080915", + "PCA Confidence": "0.016153378", + "Positive Examples": "4163", + "Body size": "375691", + "PCA Body size": "257717", "Functional variable": "?a", "template": { "query_graph": { @@ -10297,28 +7819,14 @@ "subject": "e", "object": "$target", "predicates": [ - "biolink:genetic_association" + "biolink:has_adverse_event" ] }, "edge_1": { "subject": "e", "object": "$source", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } + "biolink:similar_to" ] } } @@ -10326,13 +7834,13 @@ } }, { - "Rule": "?f biolink:decreases_response_to ?a ?b biolink:related_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.005093955", - "Std Confidence": "0.009322561", - "PCA Confidence": "0.033632287", - "Positive Examples": "135", - "Body size": "14481", - "PCA Body size": "4014", + "Rule": "?b biolink:related_to ?f ?a decreased_molecular_modification_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000452796", + "Std Confidence": "0.010507881", + "PCA Confidence": "0.04137931", + "Positive Examples": "12", + "Body size": "1142", + "PCA Body size": "290", "Functional variable": "?a", "template": { "query_graph": { @@ -10361,17 +7869,31 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "$source", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:decreases_response_to" + "biolink:related_to" ] }, "edge_1": { - "subject": "$target", + "subject": "$source", "object": "f", "predicates": [ - "biolink:related_to" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "molecular_modification" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] } } @@ -10379,13 +7901,13 @@ } }, { - "Rule": "?a biolink:contributes_to ?f ?f biolink:similar_to ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.002905441", - "Std Confidence": "0.009228188", - "PCA Confidence": "0.030362776", - "Positive Examples": "77", - "Body size": "8344", - "PCA Body size": "2536", + "Rule": "?a biolink:ameliorates ?f ?f biolink:similar_to ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.003584635", + "Std Confidence": "0.01038819", + "PCA Confidence": "0.024154589", + "Positive Examples": "95", + "Body size": "9145", + "PCA Body size": "3933", "Functional variable": "?a", "template": { "query_graph": { @@ -10417,7 +7939,7 @@ "subject": "$source", "object": "f", "predicates": [ - "biolink:contributes_to" + "biolink:ameliorates" ] }, "edge_1": { @@ -10432,13 +7954,13 @@ } }, { - "Rule": "?a biolink:treats ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.015696929", - "Std Confidence": "0.009167842", - "PCA Confidence": "0.018075954", - "Positive Examples": "416", - "Body size": "45376", - "PCA Body size": "23014", + "Rule": "?f biolink:similar_to ?b ?a biolink:treats ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.004339295", + "Std Confidence": "0.010057723", + "PCA Confidence": "0.021515435", + "Positive Examples": "115", + "Body size": "11434", + "PCA Body size": "5345", "Functional variable": "?a", "template": { "query_graph": { @@ -10458,12 +7980,24 @@ "categories": [ "biolink:DiseaseOrPhenotypicFeature" ] + }, + "f": { + "categories": [ + "biolink:NamedThing" + ] } }, "edges": { "edge_0": { - "subject": "$source", + "subject": "f", "object": "$target", + "predicates": [ + "biolink:similar_to" + ] + }, + "edge_1": { + "subject": "$source", + "object": "f", "predicates": [ "biolink:treats" ] @@ -10473,13 +8007,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e decreased_synthesis_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.001547053", - "Std Confidence": "0.009141583", - "PCA Confidence": "0.039767216", - "Positive Examples": "41", - "Body size": "4485", - "PCA Body size": "1031", + "Rule": "?b biolink:related_to ?f ?f metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.001169723", + "Std Confidence": "0.009983897", + "PCA Confidence": "0.040951123", + "Positive Examples": "31", + "Body size": "3105", + "PCA Body size": "757", "Functional variable": "?a", "template": { "query_graph": { @@ -10500,7 +8034,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -10508,14 +8042,14 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:genetic_association" + "biolink:related_to" ] }, "edge_1": { - "subject": "e", + "subject": "f", "object": "$source", "predicates": [ "biolink:affects" @@ -10525,11 +8059,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "synthesis" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" + "qualifier_value": "metabolic_processing" } ] } @@ -10540,13 +8070,13 @@ } }, { - "Rule": "?e biolink:contraindicated_for ?b ?e biolink:related_to ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.007207003", - "Std Confidence": "0.009118251", - "PCA Confidence": "0.312091503", - "Positive Examples": "191", - "Body size": "20947", - "PCA Body size": "612", + "Rule": "?e biolink:genetic_association ?b ?e decreased_secretion_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.001396121", + "Std Confidence": "0.009759958", + "PCA Confidence": "0.022519781", + "Positive Examples": "37", + "Body size": "3791", + "PCA Body size": "1643", "Functional variable": "?a", "template": { "query_graph": { @@ -10578,14 +8108,28 @@ "subject": "e", "object": "$target", "predicates": [ - "biolink:contraindicated_for" + "biolink:genetic_association" ] }, "edge_1": { "subject": "e", "object": "$source", "predicates": [ - "biolink:related_to" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "secretion" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } ] } } @@ -10593,13 +8137,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?f increased_synthesis_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000943325", - "Std Confidence": "0.009094216", - "PCA Confidence": "0.069060773", - "Positive Examples": "25", - "Body size": "2749", - "PCA Body size": "362", + "Rule": "?b biolink:related_to ?f ?f decreased_metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000716927", + "Std Confidence": "0.009758603", + "PCA Confidence": "0.072796935", + "Positive Examples": "19", + "Body size": "1947", + "PCA Body size": "261", "Functional variable": "?a", "template": { "query_graph": { @@ -10645,11 +8189,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "synthesis" + "qualifier_value": "metabolic_processing" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" + "qualifier_value": "decreased" } ] } @@ -10660,13 +8204,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e increased_secretion_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.004829824", - "Std Confidence": "0.008564737", - "PCA Confidence": "0.021761306", - "Positive Examples": "128", - "Body size": "14945", - "PCA Body size": "5882", + "Rule": "?f biolink:increases_response_to ?a ?b biolink:related_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.006980605", + "Std Confidence": "0.009711286", + "PCA Confidence": "0.038042361", + "Positive Examples": "185", + "Body size": "19050", + "PCA Body size": "4863", "Functional variable": "?a", "template": { "query_graph": { @@ -10687,7 +8231,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -10695,31 +8239,17 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$target", + "subject": "f", + "object": "$source", "predicates": [ - "biolink:genetic_association" + "biolink:increases_response_to" ] }, "edge_1": { - "subject": "e", - "object": "$source", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "secretion" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } + "biolink:related_to" ] } } @@ -10727,13 +8257,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?f increased_uptake_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000415063", - "Std Confidence": "0.008390542", - "PCA Confidence": "0.041509434", - "Positive Examples": "11", - "Body size": "1311", - "PCA Body size": "265", + "Rule": "?e biolink:genetic_association ?b ?e decreased_activity_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000905592", + "Std Confidence": "0.009584665", + "PCA Confidence": "0.041450777", + "Positive Examples": "24", + "Body size": "2504", + "PCA Body size": "579", "Functional variable": "?a", "template": { "query_graph": { @@ -10754,7 +8284,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -10762,14 +8292,14 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:genetic_association" ] }, "edge_1": { - "subject": "f", + "subject": "e", "object": "$source", "predicates": [ "biolink:affects" @@ -10779,11 +8309,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "uptake" + "qualifier_value": "activity" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" + "qualifier_value": "decreased" } ] } @@ -10794,13 +8324,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?f increased_metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.001811184", - "Std Confidence": "0.007735697", - "PCA Confidence": "0.037825059", - "Positive Examples": "48", - "Body size": "6205", - "PCA Body size": "1269", + "Rule": "?f biolink:decreases_response_to ?a ?b biolink:related_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.005093955", + "Std Confidence": "0.009322561", + "PCA Confidence": "0.033632287", + "Positive Examples": "135", + "Body size": "14481", + "PCA Body size": "4014", "Functional variable": "?a", "template": { "query_graph": { @@ -10829,31 +8359,17 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:related_to" - ] - }, - "edge_1": { "subject": "f", "object": "$source", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "metabolic_processing" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } + "biolink:decreases_response_to" + ] + }, + "edge_1": { + "subject": "$target", + "object": "f", + "predicates": [ + "biolink:related_to" ] } } @@ -10861,13 +8377,13 @@ } }, { - "Rule": "?e biolink:has_part ?a ?e biolink:treats ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000981058", - "Std Confidence": "0.007454128", - "PCA Confidence": "0.03190184", - "Positive Examples": "26", - "Body size": "3488", - "PCA Body size": "815", + "Rule": "?a biolink:contributes_to ?f ?f biolink:similar_to ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.002905441", + "Std Confidence": "0.009228188", + "PCA Confidence": "0.030362776", + "Positive Examples": "77", + "Body size": "8344", + "PCA Body size": "2536", "Functional variable": "?a", "template": { "query_graph": { @@ -10888,7 +8404,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -10896,17 +8412,17 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:has_part" + "biolink:contributes_to" ] }, "edge_1": { - "subject": "e", + "subject": "f", "object": "$target", "predicates": [ - "biolink:treats" + "biolink:similar_to" ] } } @@ -10914,13 +8430,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a increased_secretion_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.007320202", - "Std Confidence": "0.007258306", - "PCA Confidence": "0.042330351", - "Positive Examples": "194", - "Body size": "26728", - "PCA Body size": "4583", + "Rule": "?a biolink:treats ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.015696929", + "Std Confidence": "0.009167842", + "PCA Confidence": "0.018075954", + "Positive Examples": "416", + "Body size": "45376", + "PCA Body size": "23014", "Functional variable": "?a", "template": { "query_graph": { @@ -10940,40 +8456,14 @@ "categories": [ "biolink:DiseaseOrPhenotypicFeature" ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] } }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:related_to" - ] - }, - "edge_1": { "subject": "$source", - "object": "f", + "object": "$target", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "secretion" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } + "biolink:treats" ] } } @@ -10981,13 +8471,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a increased_expression_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.007056071", - "Std Confidence": "0.00721228", - "PCA Confidence": "0.029191383", - "Positive Examples": "187", - "Body size": "25928", - "PCA Body size": "6406", + "Rule": "?e biolink:genetic_association ?b ?e decreased_synthesis_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.001547053", + "Std Confidence": "0.009141583", + "PCA Confidence": "0.039767216", + "Positive Examples": "41", + "Body size": "4485", + "PCA Body size": "1031", "Functional variable": "?a", "template": { "query_graph": { @@ -11008,7 +8498,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -11016,15 +8506,15 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:genetic_association" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "e", + "object": "$source", "predicates": [ "biolink:affects" ], @@ -11033,11 +8523,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "expression" + "qualifier_value": "synthesis" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" + "qualifier_value": "decreased" } ] } @@ -11048,13 +8538,13 @@ } }, { - "Rule": "?a biolink:ameliorates ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.00905592", - "Std Confidence": "0.007166746", - "PCA Confidence": "0.017867778", - "Positive Examples": "240", - "Body size": "33488", - "PCA Body size": "13432", + "Rule": "?e biolink:contraindicated_for ?b ?e biolink:related_to ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.007207003", + "Std Confidence": "0.009118251", + "PCA Confidence": "0.312091503", + "Positive Examples": "191", + "Body size": "20947", + "PCA Body size": "612", "Functional variable": "?a", "template": { "query_graph": { @@ -11074,14 +8564,26 @@ "categories": [ "biolink:DiseaseOrPhenotypicFeature" ] + }, + "e": { + "categories": [ + "biolink:NamedThing" + ] } }, "edges": { "edge_0": { - "subject": "$source", + "subject": "e", "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:contraindicated_for" + ] + }, + "edge_1": { + "subject": "e", + "object": "$source", + "predicates": [ + "biolink:related_to" ] } } @@ -11089,13 +8591,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a increased_molecular_interaction_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.002603577", - "Std Confidence": "0.007113402", - "PCA Confidence": "0.0283135", - "Positive Examples": "69", - "Body size": "9700", - "PCA Body size": "2437", + "Rule": "?b biolink:related_to ?f ?f increased_synthesis_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000943325", + "Std Confidence": "0.009094216", + "PCA Confidence": "0.069060773", + "Positive Examples": "25", + "Body size": "2749", + "PCA Body size": "362", "Functional variable": "?a", "template": { "query_graph": { @@ -11131,8 +8633,8 @@ ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "f", + "object": "$source", "predicates": [ "biolink:affects" ], @@ -11141,7 +8643,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_interaction" + "qualifier_value": "synthesis" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -11156,13 +8658,13 @@ } }, { - "Rule": "?e biolink:ameliorates ?b ?e biolink:has_part ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000679194", - "Std Confidence": "0.006744099", - "PCA Confidence": "0.028391167", - "Positive Examples": "18", - "Body size": "2669", - "PCA Body size": "634", + "Rule": "?e biolink:genetic_association ?b ?e increased_secretion_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.004829824", + "Std Confidence": "0.008564737", + "PCA Confidence": "0.021761306", + "Positive Examples": "128", + "Body size": "14945", + "PCA Body size": "5882", "Functional variable": "?a", "template": { "query_graph": { @@ -11194,14 +8696,28 @@ "subject": "e", "object": "$target", "predicates": [ - "biolink:ameliorates" + "biolink:genetic_association" ] }, "edge_1": { "subject": "e", "object": "$source", "predicates": [ - "biolink:has_part" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "secretion" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "increased" + } + ] + } ] } } @@ -11209,13 +8725,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e synthesis_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000792393", - "Std Confidence": "0.006469501", - "PCA Confidence": "0.031065089", - "Positive Examples": "21", - "Body size": "3246", - "PCA Body size": "676", + "Rule": "?b biolink:related_to ?f ?f increased_uptake_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000415063", + "Std Confidence": "0.008390542", + "PCA Confidence": "0.041509434", + "Positive Examples": "11", + "Body size": "1311", + "PCA Body size": "265", "Functional variable": "?a", "template": { "query_graph": { @@ -11236,7 +8752,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -11244,14 +8760,14 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:genetic_association" + "biolink:related_to" ] }, "edge_1": { - "subject": "e", + "subject": "f", "object": "$source", "predicates": [ "biolink:affects" @@ -11261,7 +8777,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "synthesis" + "qualifier_value": "uptake" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "increased" } ] } @@ -11272,13 +8792,66 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.003660101", - "Std Confidence": "0.005898449", - "PCA Confidence": "0.019897436", - "Positive Examples": "97", - "Body size": "16445", - "PCA Body size": "4875", + "Rule": "?a biolink:causes ?f ?f biolink:has_phenotype ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.034337031", + "Std Confidence": "0.008046617", + "PCA Confidence": "0.009682293", + "Positive Examples": "910", + "Body size": "113091", + "PCA Body size": "93986", + "Functional variable": "?a", + "template": { + "query_graph": { + "nodes": { + "$source": { + "ids": [ + "$source_id" + ], + "categories": [ + "biolink:ChemicalEntity" + ] + }, + "$target": { + "ids": [ + "$target_id" + ], + "categories": [ + "biolink:DiseaseOrPhenotypicFeature" + ] + }, + "f": { + "categories": [ + "biolink:NamedThing" + ] + } + }, + "edges": { + "edge_0": { + "subject": "$source", + "object": "f", + "predicates": [ + "biolink:causes" + ] + }, + "edge_1": { + "subject": "f", + "object": "$target", + "predicates": [ + "biolink:has_phenotype" + ] + } + } + } + } + }, + { + "Rule": "?b biolink:related_to ?f ?f increased_metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.001811184", + "Std Confidence": "0.007735697", + "PCA Confidence": "0.037825059", + "Positive Examples": "48", + "Body size": "6205", + "PCA Body size": "1269", "Functional variable": "?a", "template": { "query_graph": { @@ -11299,7 +8872,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -11307,14 +8880,14 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:genetic_association" + "biolink:related_to" ] }, "edge_1": { - "subject": "e", + "subject": "f", "object": "$source", "predicates": [ "biolink:affects" @@ -11325,6 +8898,10 @@ { "qualifier_type_id": "biolink:object_aspect_qualifier", "qualifier_value": "metabolic_processing" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "increased" } ] } @@ -11335,13 +8912,13 @@ } }, { - "Rule": "?f biolink:genetic_association ?b ?a increased_molecular_modification_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.001924383", - "Std Confidence": "0.005836576", - "PCA Confidence": "0.023932426", - "Positive Examples": "51", - "Body size": "8738", - "PCA Body size": "2131", + "Rule": "?a biolink:has_adverse_event ?f ?f biolink:has_phenotype ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.040827107", + "Std Confidence": "0.007507216", + "PCA Confidence": "0.009790792", + "Positive Examples": "1082", + "Body size": "144128", + "PCA Body size": "110512", "Functional variable": "?a", "template": { "query_graph": { @@ -11370,31 +8947,17 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "$target", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:genetic_association" + "biolink:has_adverse_event" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_modification" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } + "biolink:has_phenotype" ] } } @@ -11402,13 +8965,13 @@ } }, { - "Rule": "?a activity_biolink:affects ?f ?b biolink:related_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000415063", - "Std Confidence": "0.005801688", - "PCA Confidence": "0.056994819", - "Positive Examples": "11", - "Body size": "1896", - "PCA Body size": "193", + "Rule": "?e biolink:has_part ?a ?e biolink:treats ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000981058", + "Std Confidence": "0.007454128", + "PCA Confidence": "0.03190184", + "Positive Examples": "26", + "Body size": "3488", + "PCA Body size": "815", "Functional variable": "?a", "template": { "query_graph": { @@ -11429,7 +8992,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -11437,27 +9000,17 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "f", + "subject": "e", + "object": "$source", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - } - ] - } + "biolink:has_part" ] }, "edge_1": { - "subject": "$target", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:treats" ] } } @@ -11465,13 +9018,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a decreased_degradation_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000603728", - "Std Confidence": "0.005774089", - "PCA Confidence": "0.034707158", - "Positive Examples": "16", - "Body size": "2771", - "PCA Body size": "461", + "Rule": "?b biolink:related_to ?f ?a increased_secretion_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.007320202", + "Std Confidence": "0.007258306", + "PCA Confidence": "0.042330351", + "Positive Examples": "194", + "Body size": "26728", + "PCA Body size": "4583", "Functional variable": "?a", "template": { "query_graph": { @@ -11517,11 +9070,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "degradation" + "qualifier_value": "secretion" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" + "qualifier_value": "increased" } ] } @@ -11532,13 +9085,13 @@ } }, { - "Rule": "?f biolink:genetic_association ?b ?a decreased_secretion_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.019130632", - "Std Confidence": "0.005390291", - "PCA Confidence": "0.017667352", - "Positive Examples": "507", - "Body size": "94058", - "PCA Body size": "28697", + "Rule": "?b biolink:related_to ?f ?a increased_expression_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.007056071", + "Std Confidence": "0.00721228", + "PCA Confidence": "0.029191383", + "Positive Examples": "187", + "Body size": "25928", + "PCA Body size": "6406", "Functional variable": "?a", "template": { "query_graph": { @@ -11567,10 +9120,10 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:genetic_association" + "biolink:related_to" ] }, "edge_1": { @@ -11584,11 +9137,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "secretion" + "qualifier_value": "expression" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" + "qualifier_value": "increased" } ] } @@ -11599,13 +9152,13 @@ } }, { - "Rule": "?b biolink:associated_with ?f ?a biolink:has_adverse_event ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.019319297", - "Std Confidence": "0.0053345", - "PCA Confidence": "0.00714495", - "Positive Examples": "512", - "Body size": "95979", - "PCA Body size": "71659", + "Rule": "?a biolink:ameliorates ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.00905592", + "Std Confidence": "0.007166746", + "PCA Confidence": "0.017867778", + "Positive Examples": "240", + "Body size": "33488", + "PCA Body size": "13432", "Functional variable": "?a", "template": { "query_graph": { @@ -11625,26 +9178,14 @@ "categories": [ "biolink:DiseaseOrPhenotypicFeature" ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] } }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:associated_with" - ] - }, - "edge_1": { "subject": "$source", - "object": "f", + "object": "$target", "predicates": [ - "biolink:has_adverse_event" + "biolink:ameliorates" ] } } @@ -11652,13 +9193,13 @@ } }, { - "Rule": "?f biolink:genetic_association ?b ?a decreased_expression_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.015810128", - "Std Confidence": "0.005297092", - "PCA Confidence": "0.016211406", - "Positive Examples": "419", - "Body size": "79100", - "PCA Body size": "25846", + "Rule": "?b biolink:related_to ?f ?a increased_molecular_interaction_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.002603577", + "Std Confidence": "0.007113402", + "PCA Confidence": "0.0283135", + "Positive Examples": "69", + "Body size": "9700", + "PCA Body size": "2437", "Functional variable": "?a", "template": { "query_graph": { @@ -11687,10 +9228,10 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:genetic_association" + "biolink:related_to" ] }, "edge_1": { @@ -11704,11 +9245,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "expression" + "qualifier_value": "molecular_interaction" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" + "qualifier_value": "increased" } ] } @@ -11719,13 +9260,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a increased_localization_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000716927", - "Std Confidence": "0.005277778", - "PCA Confidence": "0.026425591", - "Positive Examples": "19", - "Body size": "3600", - "PCA Body size": "719", + "Rule": "?e biolink:ameliorates ?b ?e biolink:has_part ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000679194", + "Std Confidence": "0.006744099", + "PCA Confidence": "0.028391167", + "Positive Examples": "18", + "Body size": "2669", + "PCA Body size": "634", "Functional variable": "?a", "template": { "query_graph": { @@ -11746,7 +9287,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -11754,45 +9295,31 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:ameliorates" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "e", + "object": "$source", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "localization" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } + "biolink:has_part" ] } } } - } - }, - { - "Rule": "?f biolink:genetic_association ?b ?a decreased_molecular_interaction_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.013998943", - "Std Confidence": "0.005273107", - "PCA Confidence": "0.023684883", - "Positive Examples": "371", - "Body size": "70357", - "PCA Body size": "15664", + } + }, + { + "Rule": "?e biolink:genetic_association ?b ?e synthesis_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000792393", + "Std Confidence": "0.006469501", + "PCA Confidence": "0.031065089", + "Positive Examples": "21", + "Body size": "3246", + "PCA Body size": "676", "Functional variable": "?a", "template": { "query_graph": { @@ -11813,7 +9340,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -11821,15 +9348,15 @@ }, "edges": { "edge_0": { - "subject": "f", + "subject": "e", "object": "$target", "predicates": [ "biolink:genetic_association" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "e", + "object": "$source", "predicates": [ "biolink:affects" ], @@ -11838,11 +9365,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_interaction" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" + "qualifier_value": "synthesis" } ] } @@ -11853,13 +9376,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e increased_metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.006452343", - "Std Confidence": "0.004955085", - "PCA Confidence": "0.022688072", - "Positive Examples": "171", - "Body size": "34510", - "PCA Body size": "7537", + "Rule": "?e biolink:genetic_association ?b ?e metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.003660101", + "Std Confidence": "0.005898449", + "PCA Confidence": "0.019897436", + "Positive Examples": "97", + "Body size": "16445", + "PCA Body size": "4875", "Functional variable": "?a", "template": { "query_graph": { @@ -11906,10 +9429,6 @@ { "qualifier_type_id": "biolink:object_aspect_qualifier", "qualifier_value": "metabolic_processing" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" } ] } @@ -11920,13 +9439,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e transport_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.001056524", - "Std Confidence": "0.004691689", - "PCA Confidence": "0.016184971", - "Positive Examples": "28", - "Body size": "5968", - "PCA Body size": "1730", + "Rule": "?f biolink:genetic_association ?b ?a increased_molecular_modification_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.001924383", + "Std Confidence": "0.005836576", + "PCA Confidence": "0.023932426", + "Positive Examples": "51", + "Body size": "8738", + "PCA Body size": "2131", "Functional variable": "?a", "template": { "query_graph": { @@ -11947,7 +9466,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -11955,15 +9474,15 @@ }, "edges": { "edge_0": { - "subject": "e", + "subject": "f", "object": "$target", "predicates": [ "biolink:genetic_association" ] }, "edge_1": { - "subject": "e", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ "biolink:affects" ], @@ -11972,7 +9491,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "transport" + "qualifier_value": "molecular_modification" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "increased" } ] } @@ -11983,13 +9506,13 @@ } }, { - "Rule": "?a biolink:decreases_response_to ?f ?f biolink:genetic_association ?b => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.003999698", - "Std Confidence": "0.004650143", - "PCA Confidence": "0.018841095", - "Positive Examples": "106", - "Body size": "22795", - "PCA Body size": "5626", + "Rule": "?a activity_biolink:affects ?f ?b biolink:related_to ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000415063", + "Std Confidence": "0.005801688", + "PCA Confidence": "0.056994819", + "Positive Examples": "11", + "Body size": "1896", + "PCA Body size": "193", "Functional variable": "?a", "template": { "query_graph": { @@ -12021,14 +9544,24 @@ "subject": "$source", "object": "f", "predicates": [ - "biolink:decreases_response_to" + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity" + } + ] + } ] }, "edge_1": { - "subject": "f", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:genetic_association" + "biolink:related_to" ] } } @@ -12036,13 +9569,13 @@ } }, { - "Rule": "?f biolink:genetic_association ?b ?a decreased_molecular_modification_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.001056524", - "Std Confidence": "0.004450095", - "PCA Confidence": "0.01771031", - "Positive Examples": "28", - "Body size": "6292", - "PCA Body size": "1581", + "Rule": "?b biolink:related_to ?f ?a decreased_degradation_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000603728", + "Std Confidence": "0.005774089", + "PCA Confidence": "0.034707158", + "Positive Examples": "16", + "Body size": "2771", + "PCA Body size": "461", "Functional variable": "?a", "template": { "query_graph": { @@ -12071,10 +9604,10 @@ }, "edges": { "edge_0": { - "subject": "f", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:genetic_association" + "biolink:related_to" ] }, "edge_1": { @@ -12088,7 +9621,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_modification" + "qualifier_value": "degradation" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -12103,13 +9636,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a increased_degradation_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.002226247", - "Std Confidence": "0.004410226", - "PCA Confidence": "0.029222387", - "Positive Examples": "59", - "Body size": "13378", - "PCA Body size": "2019", + "Rule": "?f biolink:genetic_association ?b ?a decreased_secretion_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.019130632", + "Std Confidence": "0.005390291", + "PCA Confidence": "0.017667352", + "Positive Examples": "507", + "Body size": "94058", + "PCA Body size": "28697", "Functional variable": "?a", "template": { "query_graph": { @@ -12138,10 +9671,10 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "f", + "object": "$target", "predicates": [ - "biolink:related_to" + "biolink:genetic_association" ] }, "edge_1": { @@ -12155,11 +9688,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "degradation" + "qualifier_value": "secretion" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" + "qualifier_value": "decreased" } ] } @@ -12170,13 +9703,13 @@ } }, { - "Rule": "?e biolink:causes ?b ?e biolink:has_part ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.002867708", - "Std Confidence": "0.004065911", - "PCA Confidence": "0.036138849", - "Positive Examples": "76", - "Body size": "18692", - "PCA Body size": "2103", + "Rule": "?b biolink:associated_with ?f ?a biolink:has_adverse_event ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.019319297", + "Std Confidence": "0.0053345", + "PCA Confidence": "0.00714495", + "Positive Examples": "512", + "Body size": "95979", + "PCA Body size": "71659", "Functional variable": "?a", "template": { "query_graph": { @@ -12197,7 +9730,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -12205,17 +9738,17 @@ }, "edges": { "edge_0": { - "subject": "e", - "object": "$target", + "subject": "$target", + "object": "f", "predicates": [ - "biolink:causes" + "biolink:associated_with" ] }, "edge_1": { - "subject": "e", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:has_part" + "biolink:has_adverse_event" ] } } @@ -12223,13 +9756,13 @@ } }, { - "Rule": "?f biolink:genetic_association ?b ?a increased_molecular_interaction_biolink:affects ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.007999396", - "Std Confidence": "0.003779303", - "PCA Confidence": "0.016115545", - "Positive Examples": "212", - "Body size": "56095", - "PCA Body size": "13155", + "Rule": "?f biolink:genetic_association ?b ?a decreased_expression_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.015810128", + "Std Confidence": "0.005297092", + "PCA Confidence": "0.016211406", + "Positive Examples": "419", + "Body size": "79100", + "PCA Body size": "25846", "Functional variable": "?a", "template": { "query_graph": { @@ -12275,11 +9808,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_interaction" + "qualifier_value": "expression" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" + "qualifier_value": "decreased" } ] } @@ -12290,13 +9823,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a upregulated_biolink:regulates ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.011093502", - "Std Confidence": "0.003753064", - "PCA Confidence": "0.014846235", - "Positive Examples": "294", - "Body size": "78336", - "PCA Body size": "19803", + "Rule": "?e biolink:affects_response_to ?a ?e biolink:genetic_association ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.028111086", + "Std Confidence": "0.005292321", + "PCA Confidence": "0.015218057", + "Positive Examples": "745", + "Body size": "140770", + "PCA Body size": "48955", "Functional variable": "?a", "template": { "query_graph": { @@ -12317,7 +9850,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -12325,27 +9858,17 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", + "subject": "e", + "object": "$source", "predicates": [ - "biolink:related_to" + "biolink:affects_response_to" ] }, "edge_1": { - "subject": "$source", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:regulates" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "upregulated" - } - ] - } + "biolink:genetic_association" ] } } @@ -12353,13 +9876,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?a downregulated_biolink:regulates ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.010263376", - "Std Confidence": "0.003685537", - "PCA Confidence": "0.011567085", - "Positive Examples": "272", - "Body size": "73802", - "PCA Body size": "23515", + "Rule": "?a biolink:contributes_to ?f ?f biolink:has_phenotype ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.020451287", + "Std Confidence": "0.005286", + "PCA Confidence": "0.016417775", + "Positive Examples": "542", + "Body size": "102535", + "PCA Body size": "33013", "Functional variable": "?a", "template": { "query_graph": { @@ -12388,80 +9911,17 @@ }, "edges": { "edge_0": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:related_to" - ] - }, - "edge_1": { "subject": "$source", "object": "f", "predicates": [ - "biolink:regulates" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "downregulated" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?f biolink:genetic_association ?b ?a biolink:increases_response_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.001282922", - "Std Confidence": "0.00355537", - "PCA Confidence": "0.010391198", - "Positive Examples": "34", - "Body size": "9563", - "PCA Body size": "3272", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:DiseaseOrPhenotypicFeature" + "biolink:contributes_to" ] }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { + "edge_1": { "subject": "f", "object": "$target", "predicates": [ - "biolink:genetic_association" - ] - }, - "edge_1": { - "subject": "$source", - "object": "f", - "predicates": [ - "biolink:increases_response_to" + "biolink:has_phenotype" ] } } @@ -12469,13 +9929,13 @@ } }, { - "Rule": "?b biolink:related_to ?f ?f decreased_secretion_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000603728", - "Std Confidence": "0.003542958", - "PCA Confidence": "0.07960199", - "Positive Examples": "16", - "Body size": "4516", - "PCA Body size": "201", + "Rule": "?b biolink:related_to ?f ?a increased_localization_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.000716927", + "Std Confidence": "0.005277778", + "PCA Confidence": "0.026425591", + "Positive Examples": "19", + "Body size": "3600", + "PCA Body size": "719", "Functional variable": "?a", "template": { "query_graph": { @@ -12511,8 +9971,8 @@ ] }, "edge_1": { - "subject": "f", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ "biolink:affects" ], @@ -12521,11 +9981,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "secretion" + "qualifier_value": "localization" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" + "qualifier_value": "increased" } ] } @@ -12536,13 +9996,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e increased_synthesis_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.002188514", - "Std Confidence": "0.003378969", - "PCA Confidence": "0.023135221", - "Positive Examples": "58", - "Body size": "17165", - "PCA Body size": "2507", + "Rule": "?f biolink:genetic_association ?b ?a decreased_molecular_interaction_biolink:affects ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.013998943", + "Std Confidence": "0.005273107", + "PCA Confidence": "0.023684883", + "Positive Examples": "371", + "Body size": "70357", + "PCA Body size": "15664", "Functional variable": "?a", "template": { "query_graph": { @@ -12563,7 +10023,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -12571,15 +10031,15 @@ }, "edges": { "edge_0": { - "subject": "e", + "subject": "f", "object": "$target", "predicates": [ "biolink:genetic_association" ] }, "edge_1": { - "subject": "e", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ "biolink:affects" ], @@ -12588,11 +10048,11 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "synthesis" + "qualifier_value": "molecular_interaction" }, { "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" + "qualifier_value": "decreased" } ] } @@ -12603,13 +10063,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e increased_molecular_interaction_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000452796", - "Std Confidence": "0.003305785", - "PCA Confidence": "0.023255814", - "Positive Examples": "12", - "Body size": "3630", - "PCA Body size": "516", + "Rule": "?f biolink:has_phenotype ?b ?a biolink:treats ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.025318844", + "Std Confidence": "0.005229155", + "PCA Confidence": "0.011333694", + "Positive Examples": "671", + "Body size": "128319", + "PCA Body size": "59204", "Functional variable": "?a", "template": { "query_graph": { @@ -12630,7 +10090,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "e": { + "f": { "categories": [ "biolink:NamedThing" ] @@ -12638,31 +10098,17 @@ }, "edges": { "edge_0": { - "subject": "e", + "subject": "f", "object": "$target", "predicates": [ - "biolink:genetic_association" + "biolink:has_phenotype" ] }, "edge_1": { - "subject": "e", - "object": "$source", + "subject": "$source", + "object": "f", "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_interaction" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } + "biolink:treats" ] } } @@ -12670,13 +10116,13 @@ } }, { - "Rule": "?a biolink:has_adverse_event ?f ?b biolink:has_part ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000792393", - "Std Confidence": "0.003161222", - "PCA Confidence": "0.004021448", - "Positive Examples": "21", - "Body size": "6643", - "PCA Body size": "5222", + "Rule": "?e biolink:genetic_association ?b ?e biolink:increases_response_to ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.022337937", + "Std Confidence": "0.005053696", + "PCA Confidence": "0.015498194", + "Positive Examples": "592", + "Body size": "117142", + "PCA Body size": "38198", "Functional variable": "?a", "template": { "query_graph": { @@ -12697,7 +10143,7 @@ "biolink:DiseaseOrPhenotypicFeature" ] }, - "f": { + "e": { "categories": [ "biolink:NamedThing" ] @@ -12705,17 +10151,17 @@ }, "edges": { "edge_0": { - "subject": "$source", - "object": "f", + "subject": "e", + "object": "$target", "predicates": [ - "biolink:has_adverse_event" + "biolink:genetic_association" ] }, "edge_1": { - "subject": "$target", - "object": "f", + "subject": "e", + "object": "$source", "predicates": [ - "biolink:has_part" + "biolink:increases_response_to" ] } } @@ -12723,13 +10169,13 @@ } }, { - "Rule": "?e biolink:genetic_association ?b ?e increased_activity_biolink:affects ?a => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.000641461", - "Std Confidence": "0.00314291", - "PCA Confidence": "0.024495677", - "Positive Examples": "17", - "Body size": "5409", - "PCA Body size": "694", + "Rule": "?e biolink:genetic_association ?b ?e increased_metabolic_processing_biolink:affects ?a => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.006452343", + "Std Confidence": "0.004955085", + "PCA Confidence": "0.022688072", + "Positive Examples": "171", + "Body size": "34510", + "PCA Body size": "7537", "Functional variable": "?a", "template": { "query_graph": { @@ -12775,7 +10221,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" + "qualifier_value": "metabolic_processing" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -12790,13 +10236,13 @@ } }, { - "Rule": "?a biolink:binds ?f ?b biolink:related_to ?f => ?a biolink:contraindicated_for ?b", - "Head Coverage": "0.005886348", - "Std Confidence": "0.003100159", - "PCA Confidence": "0.05163853", - "Positive Examples": "156", - "Body size": "50320", - "PCA Body size": "3021", + "Rule": "?a biolink:ameliorates ?f ?f biolink:has_phenotype ?b => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.019017433", + "Std Confidence": "0.00486618", + "PCA Confidence": "0.011054086", + "Positive Examples": "504", + "Body size": "103572", + "PCA Body size": "45594", "Functional variable": "?a", "template": { "query_graph": { @@ -12828,14 +10274,67 @@ "subject": "$source", "object": "f", "predicates": [ - "biolink:binds" + "biolink:ameliorates" ] }, "edge_1": { + "subject": "f", + "object": "$target", + "predicates": [ + "biolink:has_phenotype" + ] + } + } + } + } + }, + { + "Rule": "?b biolink:associated_with ?f ?a biolink:causes ?f => ?a biolink:contraindicated_for ?b", + "Head Coverage": "0.022677534", + "Std Confidence": "0.004845172", + "PCA Confidence": "0.005899734", + "Positive Examples": "601", + "Body size": "124041", + "PCA Body size": "101869", + "Functional variable": "?a", + "template": { + "query_graph": { + "nodes": { + "$source": { + "ids": [ + "$source_id" + ], + "categories": [ + "biolink:ChemicalEntity" + ] + }, + "$target": { + "ids": [ + "$target_id" + ], + "categories": [ + "biolink:DiseaseOrPhenotypicFeature" + ] + }, + "f": { + "categories": [ + "biolink:NamedThing" + ] + } + }, + "edges": { + "edge_0": { "subject": "$target", "object": "f", "predicates": [ - "biolink:related_to" + "biolink:associated_with" + ] + }, + "edge_1": { + "subject": "$source", + "object": "f", + "predicates": [ + "biolink:causes" ] } } @@ -23297,6 +20796,73 @@ } } }, + { + "Rule": "?f biolink:contributes_to ?b ?a decreased_activity_biolink:affects ?f => ?a decreased_activity_biolink:affects ?b", + "Head Coverage": "0.020258779", + "Std Confidence": "0.053836497", + "PCA Confidence": "0.053836497", + "Positive Examples": "7290", + "Body size": "135410", + "PCA Body size": "135410", + "Functional variable": "?a", + "template": { + "query_graph": { + "nodes": { + "$source": { + "ids": [ + "$source_id" + ], + "categories": [ + "biolink:ChemicalEntity" + ] + }, + "$target": { + "ids": [ + "$target_id" + ], + "categories": [ + "biolink:Gene" + ] + }, + "f": { + "categories": [ + "biolink:NamedThing" + ] + } + }, + "edges": { + "edge_0": { + "subject": "f", + "object": "$target", + "predicates": [ + "biolink:contributes_to" + ] + }, + "edge_1": { + "subject": "$source", + "object": "f", + "predicates": [ + "biolink:affects" + ], + "qualifier_constraints": [ + { + "qualifier_set": [ + { + "qualifier_type_id": "biolink:object_aspect_qualifier", + "qualifier_value": "activity" + }, + { + "qualifier_type_id": "biolink:object_direction_qualifier", + "qualifier_value": "decreased" + } + ] + } + ] + } + } + } + } + }, { "Rule": "?b increased_uptake_biolink:affects ?a => ?a decreased_activity_biolink:affects ?b", "Head Coverage": "0.000066696", @@ -24305,73 +21871,6 @@ } } } - }, - { - "Rule": "?f biolink:similar_to ?a ?b increased_uptake_biolink:affects ?f => ?a decreased_activity_biolink:affects ?b", - "Head Coverage": "0.000033348", - "Std Confidence": "0.02970297", - "PCA Confidence": "0.036809816", - "Positive Examples": "12", - "Body size": "404", - "PCA Body size": "326", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - }, - "f": { - "categories": [ - "biolink:NamedThing" - ] - } - }, - "edges": { - "edge_0": { - "subject": "f", - "object": "$source", - "predicates": [ - "biolink:similar_to" - ] - }, - "edge_1": { - "subject": "$target", - "object": "f", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "uptake" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } } ] } \ No newline at end of file diff --git a/src/service_aggregator.py b/src/service_aggregator.py index cf1cf4a..6f49b54 100644 --- a/src/service_aggregator.py +++ b/src/service_aggregator.py @@ -498,8 +498,8 @@ async def aragorn_lookup(input_message, params, guid, infer, answer_qnode): # Now it's an infer query. messages = expand_query(input_message, params, guid) print(len(messages)) - #nrules_per_batch = int(os.environ.get("MULTISTRIDER_BATCH_SIZE", 101)) - nrules_per_batch = int(os.environ.get("MULTISTRIDER_BATCH_SIZE", 1)) + nrules_per_batch = int(os.environ.get("MULTISTRIDER_BATCH_SIZE", 101)) + #nrules_per_batch = int(os.environ.get("MULTISTRIDER_BATCH_SIZE", 1)) # nrules = int(os.environ.get("MAXIMUM_MULTISTRIDER_RULES",len(messages))) nrules = int(os.environ.get("MAXIMUM_MULTISTRIDER_RULES", 101)) result_messages = [] @@ -528,6 +528,8 @@ async def aragorn_lookup(input_message, params, guid, infer, answer_qnode): result["message"]["results"].extend(rm["message"]["results"]) mergedresults = merge_results_by_node(result, answer_qnode) logger.info(f"{guid}: results merged") + with open('junk.json','w') as outf: + json.dump(mergedresults,outf) return mergedresults, sc @@ -698,7 +700,7 @@ async def make_one_request(client, automat_url, message, sem): async def robokop_infer(input_message, guid, question_qnode, answer_qnode): automat_url = os.environ.get("ROBOKOPKG_URL", "https://automat.transltr.io/robokopkg/1.3/") - max_conns = os.environ.get("MAX_CONNECTIONS", 21) + max_conns = os.environ.get("MAX_CONNECTIONS", 5) nrules = int(os.environ.get("MAXIMUM_ROBOKOPKG_RULES", 101)) messages = expand_query(input_message, {}, guid) logger.info(f"{guid}: {len(messages)} to send to {automat_url}") @@ -737,6 +739,7 @@ async def robokop_infer(input_message, guid, question_qnode, answer_qnode): mergedresults = {"message": {"knowledge_graph": {"nodes": {}, "edges": {}}, "results": []}} # The merged results will have some expanded query, we want the original query. mergedresults["message"]["query_graph"] = input_message["message"]["query_graph"] + return mergedresults, 200