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Merged
edeutsch merged 3 commits into from
Feb 12, 2026
Merged

Combine classes #544

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fc41591
consolodate classes
uhbrar Feb 12, 2026
848550a
make analyses not required
uhbrar Feb 12, 2026
f595a95
changes from trapi meeting
uhbrar Feb 12, 2026
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211 changes: 211 additions & 0 deletions ImplementationGuidance/DataExamples/single_node_example.json
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Original file line number Diff line number Diff line change
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{
"message": {
"query_graph": {
"nodes": {
"n0": {
"categories": [
"biolink:Disease"
],
"constraints": [],
"ids": [
"MONDO:0004979"
]
}
}
},
"knowledge_graph": {
"nodes": {
"MONDO:0004979": {
"categories": [
"biolink:BiologicalEntity",
"biolink:Disease",
"biolink:ThingWithTaxon",
"biolink:NamedThing",
"biolink:DiseaseOrPhenotypicFeature"
],
"name": "asthma",
"attributes": [
{
"attribute_type_id": "biolink:log_odds_ratio_95_ci",
"value": 100.0,
"value_type_id": "EDAM:data_0006",
"original_attribute_name": "information_content"
},
{
"attribute_type_id": "biolink:Attribute",
"value": 77.1,
"original_attribute_name": "information_content"
},
{
"attribute_type_id": "biolink:description",
"value": "Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing. [HPO:probinson]; UMLS Semantic Type: STY:T047; Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing.; Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing.; ; Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing.",
"value_type_id": "metatype:String",
"attribute_source": "infores:rtx-kg2"
},
{
"attribute_type_id": "biolink:Attribute",
"value": true,
"original_attribute_name": "MONDO_SUPERCLASS_disease"
},
{
"attribute_type_id": "dct:description",
"value": "A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety.",
"value_type_id": "EDAM:data_0006",
"original_attribute_name": "description"
},
{
"attribute_type_id": "biolink:Attribute",
"value": 77.4,
"original_attribute_name": "information_content"
},
{
"attribute_type_id": "biolink:Attribute",
"value": true,
"original_attribute_name": "MONDO_SUPERCLASS_lower_respiratory_tract_disorder"
},
{
"attribute_type_id": "biolink:Attribute",
"value": [
"MEDDRA:10003553",
"MEDDRA:10037993",
"MONDO:0004979",
"MEDDRA:10003560",
"ICD10:J45",
"UMLS:C3714497",
"KEGG.DISEASE:05310",
"UMLS:C0004096",
"MEDDRA:10003565",
"MEDDRA:10066863",
"MESH:D001249",
"MEDDRA:10066091",
"MEDDRA:10003555",
"ICD9:493",
"NCIT:C28397",
"MESH:D016535",
"SNOMEDCT:195967001",
"MEDDRA:10003561",
"UMLS:C0085129",
"MEDDRA:10056285",
"HP:0002099",
"MEDDRA:10006450",
"MEDDRA:10082852",
"UMLS:C0340062",
"DOID:2841",
"SNOMEDCT:991000119106",
"icd11.foundation:1656445230",
"medgen:2109"
],
"original_attribute_name": "equivalent_identifiers"
},
{
"attribute_type_id": "biolink:description",
"value": "A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety.",
"value_type_id": "dct:description",
"original_attribute_name": "description"
},
{
"attribute_type_id": "biolink:Attribute",
"value": [
"MONDO:0004979",
"DOID:2841",
"UMLS:C0004096",
"UMLS:C0085129",
"UMLS:C0340062",
"UMLS:C3714497",
"MESH:D001249",
"MESH:D016535",
"MEDDRA:10003553",
"MEDDRA:10003555",
"MEDDRA:10003560",
"MEDDRA:10003561",
"MEDDRA:10003565",
"MEDDRA:10006450",
"MEDDRA:10037993",
"MEDDRA:10056285",
"MEDDRA:10066091",
"MEDDRA:10066863",
"MEDDRA:10082852",
"NCIT:C28397",
"SNOMEDCT:195967001",
"SNOMEDCT:991000119106",
"ICD10:J45",
"ICD9:493",
"KEGG.DISEASE:05310",
"HP:0002099"
],
"original_attribute_name": "equivalent_identifiers"
},
{
"attribute_type_id": "biolink:Attribute",
"value": true,
"original_attribute_name": "MONDO_SUPERCLASS_human_disease"
},
{
"attribute_type_id": "biolink:synonym",
"value": [
"Asthma",
"Reactive airway disease",
"bronchial hyperreactivity",
"asthma",
"Bronchial Hyperreactivity"
],
"value_type_id": "metatype:String",
"attribute_source": "infores:rtx-kg2",
"description": "Names of all nodes in this synonym set in RTX-KG2."
},
{
"attribute_type_id": "biolink:IriType",
"value": "http://purl.obolibrary.org/obo/MONDO_0004979",
"value_type_id": "metatype:Uri",
"attribute_source": "infores:rtx-kg2"
},
{
"attribute_type_id": "biolink:log_odds_ratio_95_ci",
"value": [
"MONDO:0004979",
"DOID:2841",
"UMLS:C0004099",
"MESH:D001249",
"MESH:D001250",
"MEDDRA:10003557",
"MEDDRA:10015649",
"MEDDRA:10079895",
"NCIT:C28397",
"SNOMEDCT:31387002",
"medgen:2109",
"ICD10:J45",
"ICD9:493",
"KEGG.DISEASE:05310",
"HP:0012652"
],
"value_type_id": "EDAM:data_0006",
"original_attribute_name": "equivalent_identifiers"
},
{
"attribute_type_id": "biolink:Attribute",
"value": true,
"original_attribute_name": "MONDO_SUPERCLASS_respiratory_system_disorder"
},
{
"attribute_type_id": "biolink:Attribute",
"value": 78.2,
"original_attribute_name": "information_content"
}
]
}
}
},
"results": [
{
"node_bindings": {
"n0": [
{
"id": "MONDO:0004979",
"attributes": []
}
]
}
}
]
}
}
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