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2.0 migration guide #556

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7279a91
migration guide: filled out section 1
colleenXu Mar 12, 2026
8ccc0dd
migration guide: filled out section 2
colleenXu Mar 12, 2026
bcd4614
migration guide: filled out section 3
colleenXu Mar 12, 2026
b56285c
migration guide: filled out section 4
colleenXu Mar 12, 2026
a68fbcc
migration guide: filled out section 5
colleenXu Mar 12, 2026
a9a605c
migration guide: filled out other changes section
colleenXu Mar 12, 2026
10debc8
Merge branch '2.0' into 2.0-migration-guide-plus
colleenXu Mar 13, 2026
f5d20fe
migration guide: incorporate yaml change from today
colleenXu Mar 13, 2026
3145c92
migration guide: put section 1 examples into folded sections
colleenXu Mar 13, 2026
c6423de
migration guide: add examples to section 2
colleenXu Mar 13, 2026
8b2206d
migration guide: adjust KL in examples
colleenXu Mar 13, 2026
615fbab
migration guide: add full 1.6.0-beta example
colleenXu Mar 13, 2026
99a62ce
migration guide: add full 2.0 corresponding example
colleenXu Mar 13, 2026
33b1744
Update docs/reference.md [no ci]
colleenXu Mar 13, 2026
8fc0355
binding spec: starting point
colleenXu Mar 13, 2026
38ff291
migration guide: adjust ARA infores in examples
colleenXu Mar 13, 2026
3ff26dd
migration guide: fix typos, format in binding section
colleenXu Mar 16, 2026
7cb3c1b
binding spec: draft written
colleenXu Mar 16, 2026
9eabba5
qedge constraints spec: draft written
colleenXu Mar 16, 2026
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357 changes: 357 additions & 0 deletions ImplementationGuidance/DataExamples/1-6_example_response.json
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Original file line number Diff line number Diff line change
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{
"message": {
"query_graph": {
"nodes": {
"nA": {
"ids": null,
"categories": [
"biolink:Drug"
],
"set_interpretation": "BATCH",
"constraints": [],
"member_ids": []
},
"nI": {
"ids": null,
"categories": [
"biolink:Gene"
],
"set_interpretation": "BATCH",
"constraints": [],
"member_ids": []
},
"nB": {
"ids": [
"MONDO:111"
],
"categories": [
"biolink:Disease"
],
"set_interpretation": "BATCH",
"constraints": [],
"member_ids": []
}
},
"edges": {
"e1": {
"subject": "nA",
"object": "nI",
"knowledge_type": null,
"predicates": null,
"attribute_constraints": [
{
"id": "biolink:knowledge_source",
"name": "special key to query on sources info",
"not": true,
"operator": "==",
"value": "infores:semmeddb"
}
],
"qualifier_constraints": [
{
"qualifier_set": [
{
"qualifier_type_id": "biolink:object_direction_qualifier",
"qualifier_value": "increased"
},
{
"qualifier_type_id": "biolink:object_aspect_qualifier",
"qualifier_value": "activity_or_abundance"
}
]
}
]
},
"e2": {
"subject": "nI",
"object": "nB",
"knowledge_type": null,
"predicates": null,
"attribute_constraints": [
{
"id": "biolink:knowledge_level",
"name": "knowledge level",
"operator": "==",
"value": [
"knowledge_assertion",
"text_co_occurrence"
]
},
{
"id": "biolink:agent_type",
"name": "agent type",
"operator": "==",
"value": "automated_agent"
},
{
"id": "biolink:z_score",
"name": "z-score",
"operator": ">",
"value": 5
}
],
"qualifier_constraints": []
}
}
},
"knowledge_graph": {
"nodes": {
"MONDO:111": {
"categories": [
"biolink:Disease"
],
"attributes": [],
"name": "type 1 diabetes mellitus"
},
"CHEBI:1234": {
"categories": [
"biolink:Drug"
],
"attributes": [],
"name": "Metformin"
},
"NCBIGene:7777": {
"categories": [
"biolink:Gene"
],
"attributes": [],
"name": "EIF2_AK3"
},
"NCBIGene:5555": {
"categories": [
"biolink:Gene"
],
"attributes": [],
"name": "HMOX1"
}
},
"edges": {
"e2_B": {
"predicate": "biolink:affects",
"subject": "NCBIGene:7777",
"object": "MONDO:111",
"sources": [
{
"resource_id": "infores:ctd",
"resource_role": "primary_knowledge_source"
}
],
"attributes": [
{
"attribute_type_id": "biolink:knowledge_level",
"value": "knowledge_assertion"
},
{
"attribute_type_id": "biolink:agent_type",
"value": "automated_agent"
},
{
"attribute_type_id": "biolink:z_score",
"value": 7.963
}
],
"qualifiers": []
},
"e1_B": {
"predicate": "biolink:affects",
"subject": "CHEBI:1234",
"object": "NCBIGene:7777",
"sources": [
{
"resource_id": "infores:text-mining-provider-targeted",
"resource_role": "primary_knowledge_source"
}
],
"attributes": [
{
"attribute_type_id": "biolink:knowledge_level",
"value": "not_provided"
},
{
"attribute_type_id": "biolink:agent_type",
"value": "text_mining_agent"
}
],
"qualifiers": [
{
"qualifier_type_id": "biolink:qualified_predicate",
"qualifier_value": "biolink:causes"
},
{
"qualifier_type_id": "biolink:object_direction_qualifier",
"qualifier_value": "increased"
},
{
"qualifier_type_id": "biolink:object_aspect_qualifier",
"qualifier_value": "activity_or_abundance"
}
]
},
"e2_A": {
"predicate": "biolink:occurs_together_in_literature_with",
"subject": "NCBIGene:5555",
"object": "MONDO:111",
"sources": [
{
"resource_id": "infores:diseases",
"resource_role": "primary_knowledge_source"
}
],
"attributes": [
{
"attribute_type_id": "biolink:knowledge_level",
"value": "text_co_occurrence"
},
{
"attribute_type_id": "biolink:agent_type",
"value": "data_analysis_pipeline"
},
{
"attribute_type_id": "biolink:z_score",
"value": 6.435
}
],
"qualifiers": []
},
"e1_A": {
"predicate": "biolink:affects",
"subject": "CHEBI:1234",
"object": "NCBIGene:5555",
"sources": [
{
"resource_id": "infores:chembl",
"resource_role": "primary_knowledge_source"
}
],
"attributes": [
{
"attribute_type_id": "biolink:knowledge_level",
"value": "knowledge_assertion"
},
{
"attribute_type_id": "biolink:agent_type",
"value": "manual_agent"
}
],
"qualifiers": [
{
"qualifier_type_id": "biolink:qualified_predicate",
"qualifier_value": "biolink:causes"
},
{
"qualifier_type_id": "biolink:object_direction_qualifier",
"qualifier_value": "increased"
},
{
"qualifier_type_id": "biolink:object_aspect_qualifier",
"qualifier_value": "activity_or_abundance"
}
]
}
}
},
"results": [
{
"node_bindings": {
"nA": [
{
"id": "CHEBI:1234",
"attributes": []
}
],
"nI": [
{
"id": "NCBIGene:5555",
"attributes": []
}
],
"nB": [
{
"id": "MONDO:111",
"attributes": []
}
]
},
"analyses": [
{
"resource_id": "infores:retriever",
"edge_bindings": {
"e1": [
{
"id": "e1_A",
"attributes": []
}
],
"e2": [
{
"id": "e2_A",
"attributes": []
}
]
}
}
]
},
{
"node_bindings": {
"nA": [
{
"id": "CHEBI:1234",
"attributes": []
}
],
"nI": [
{
"id": "NCBIGene:7777",
"attributes": []
}
],
"nB": [
{
"id": "MONDO:111",
"attributes": []
}
]
},
"analyses": [
{
"resource_id": "infores:retriever",
"edge_bindings": {
"e1": [
{
"id": "e1_B",
"attributes": []
}
]
},
"e2": [
{
"id": "e2_B",
"attributes": []
}
]
}
]
}
],
"auxiliary_graphs": {}
},
"log_level": "DEBUG",
"bypass_cache": true,
"biolink_version": "4.3.2",
"schema_version": "1.6.0",
"workflow": null,
"status": "Complete",
"logs": [
{
"level": "INFO",
"message": "Begin processing...",
"timestamp": "1"
},
{
"level": "DEBUG",
"message": "Found 2 starting branches...",
"timestamp": "2"
}
]
}
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