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update examples to conform to TRAPI 2.0 #555

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Merged
edeutsch merged 11 commits into from
Mar 19, 2026
Merged

update examples to conform to TRAPI 2.0 #555

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a973517
update examples to conform to TRAPI 2.0
vdancik Mar 12, 2026
cfd99ee
update pathfinder specification
uhbrar Mar 12, 2026
537d28c
remove empty analyses
vdancik Mar 12, 2026
86b0f08
Merge branch '2.0-examples-update' of https://github.com/NCATSTransla…
vdancik Mar 12, 2026
7c9157f
add set interpretation
vdancik Mar 12, 2026
812e1ba
remove empty constrains and cleanup attributes
vdancik Mar 12, 2026
a3aa7f2
update node bindings
vdancik Mar 12, 2026
81ec297
pathfinder spec: make complete messages valid json
colleenXu Mar 13, 2026
e55b4d2
pathfinder spec: add resource_id to complete examples
colleenXu Mar 13, 2026
e3f7bd5
pathfinder spec: make example scores valid floats from json POV
colleenXu Mar 13, 2026
ee37bdc
pathfinder spec: fix some json syntax, add resource_id across doc
colleenXu Mar 13, 2026
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74 changes: 39 additions & 35 deletions ImplementationGuidance/DataExamples/causes_predicate_vs_qualifier.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,24 +22,15 @@
"predicates": [
"biolink:affects"
],
"qualifier_constraints": [
{
"qualifier_set": [
{
"qualifier_type_id": "biolink:object_aspect_qualifier",
"qualifier_value": "activity"
},
{
"qualifier_type_id": "biolink:object_modifier_qualifier",
"qualifier_value": "increased"
},
{
"qualifier_type_id": "biolink:qualified_predicate",
"qualifier_value": "biolink:causes"
}
]
}
]
"constraints": {
"qualifiers": [
{
"biolink:object_aspect_qualifier": "activity",
"biolink:object_modifier_qualifier": "increased",
"biolink:qualified_predicate": "biolink:causes"
}
]
}
}
}
},
Expand Down Expand Up @@ -80,30 +71,43 @@
"qualifier_type_id": "biolink:causal_mechanism_qualifier",
"qualifier_value": "binding"
}
]
],
"sources": [
{
"resource_id": "infores:chembl",
"resource_role": "primary_knowledge_source"
}
],
"knowledge_level": "knowledge_assertion",
"agent_type": "manual_agent"
}
},
"results": [
{
"node_bindings": {
"n0": [
{
"id": "PUBCHEM.COMPOUND:6623"
}
],
"n1": [
{
"id": "HGNC:3467"
}
]
"n0": {
"ids": [
"PUBCHEM.COMPOUND:6623"
]
},
"n1": {
"ids": [
"HGNC:3467"
]
}
},
"edge_bindings": {
"e01": [
{
"id": "x17770"
"analyses": [
{
"resource_id": "infores:arax",
"edge_bindings": {
"e01": {
"ids": [
"x17770"
]
}
}
]
}
}
]
}
]
}
Expand Down
89 changes: 42 additions & 47 deletions ImplementationGuidance/DataExamples/complex_gocam_qualifiers.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,36 +25,18 @@
"predicates": [
"biolink:regulates"
],
"qualifier_constraints": [
{
"qualifier_set": [
{
"qualifier_type_id": "biolink:subject_aspect_qualifier",
"qualifier_value": "GO:0043539"
},
{
"qualifier_type_id": "biolink:subject_context_qualifier",
"qualifier_value": "GO:0005886"
},
{
"qualifier_type_id": "biolink:object_aspect_qualifier",
"qualifier_value": "GO:0004708"
},
{
"qualifier_type_id": "biolink:object_context_qualifier",
"qualifier_value": "GO:0005737"
},
{
"qualifier_type_id": "biolink:object_direction_qualifier",
"qualifier_value": "increased"
},
{
"qualifier_type_id": "biolink:pathway_context_qualifier",
"qualifier_value": "GO:0038134"
}
]
}
]
"constraints": {
"qualifiers": [
{
"biolink:subject_aspect_qualifier": "GO:0043539",
"biolink:subject_context_qualifier": "GO:0005886",
"biolink:object_aspect_qualifier": "GO:0004708",
"biolink:object_context_qualifier": "GO:0005737",
"biolink:object_direction_qualifier": "increased",
"biolink:pathway_context_qualifier": "GO:0038134"
}
]
}
}
}
},
Expand Down Expand Up @@ -103,31 +85,44 @@
"qualifier_type_id": "biolink:pathway_context_qualifier",
"qualifier_value": "GO:0038134"
}
]
],
"sources": [
{
"resource_id": "infores:chembl",
"resource_role": "primary_knowledge_source"
}
],
"knowledge_level": "knowledge_assertion",
"agent_type": "manual_agent"
}
}
},
"results": [
{
"node_bindings": {
"n0": [
{
"id": "FB:FBgn0003205"
}
],
"n1": [
{
"id": "FB:FBgn0003079"
}
]
"n0": {
"ids": [
"FB:FBgn0003205"
]
},
"n1": {
"ids": [
"FB:FBgn0003079"
]
}
},
"edge_bindings": {
"e01": [
{
"id": "x17770"
"analyses": [
{
"resource_id": "infores:arax",
"edge_bindings": {
"e01": {
"ids": [
"x17770"
]
}
}
]
}
}
]
}
]
}
96 changes: 53 additions & 43 deletions ImplementationGuidance/DataExamples/localization_or_transport.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,8 @@
"n0": {
"categories": [
"biolink:ChemicalEntity"
]
],
"set_interpretation": "COLLATE"
},
"n1": {
"categories": [
Expand All @@ -22,24 +23,16 @@
"predicates": [
"biolink:affects"
],
"qualifier_constraints": [
{
"qualifier_set": [
{
"qualifier_type_id": "biolink:object_aspect_qualifier",
"qualifier_value": "localization"
}
]
},
{
"qualifier_set": [
{
"qualifier_type_id": "biolink:object_aspect_qualifier",
"qualifier_value": "transport"
}
]
}
]
"constraints": {
"qualifiers": [
{
"biolink:object_aspect_qualifier": "localization"
},
{
"biolink:object_aspect_qualifier": "transport"
}
]
}
}
}
},
Expand Down Expand Up @@ -74,7 +67,15 @@
"qualifier_type_id": "biolink:object_aspect_qualifier",
"qualifier_value": "localization"
}
]
],
"sources": [
{
"resource_id": "infores:chembl",
"resource_role": "primary_knowledge_source"
}
],
"knowledge_level": "knowledge_assertion",
"agent_type": "manual_agent"
},
"x17771": {
"predicate": "biolink:affects",
Expand All @@ -85,37 +86,46 @@
"qualifier_type_id": "biolink:object_aspect_qualifier",
"qualifier_value": "transport"
}
]
],
"sources": [
{
"resource_id": "infores:chembl",
"resource_role": "primary_knowledge_source"
}
],
"knowledge_level": "knowledge_assertion",
"agent_type": "manual_agent"
}
}
},
"results": [
{
"node_bindings": {
"n0": [
{
"id": "PUBCHEM.COMPOUND:6623"
},
{
"id": "PUBCHEM.COMPOUND:6625"
}
],
"n1": [
{
"id": "HGNC:3467"
}
]
"n0": {
"ids": [
"PUBCHEM.COMPOUND:6623",
"PUBCHEM.COMPOUND:6625"
]
},
"n1": {
"ids": [
"HGNC:3467"
]
}
},
"edge_bindings": {
"e01": [
{
"id": "x17770"
},
{
"id": "x17771"
"analyses": [
{
"resource_id": "infores:arax",
"edge_bindings": {
"e01": {
"ids": [
"x17770",
"x17771"
]
}
}
]
}
}
]
}
]
}
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