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retrieval_provenance_refactor_20220505.js
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retrieval_provenance_refactor_20220505.js
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## See Goodle Doc here for background, a description of modeled retrieval scenarios, and rationale behind each modeling proposal: https://docs.google.com/document/d/11RKh4d4XPGV0a6V--xvpjBFO7RnnT2BZkNzGbakt0a0/edit#
## ----------
## SCENARIO 1 EXAMPLES
## Abrar Original Proposal
{
"edges": {
"id": "e719492"
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"provenance": [
{
"id": "p0"
"original_knowledge_source": "infores:KS"
},
{
"id": "p1"
"aggregator_knowledge_source": "infores:KP_1",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
},
{
"id": "p2"
"aggregator_knowledge_source": "infores:KP_2",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
},
{
"id": "p3"
"aggregator_knowledge_source": "infores:KP_3",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
},
{
"id": "p4"
"aggregator_knowledge_source": "infores:ARA_1",
"adjacency_list": [
{
"parent": "p1",
"method": "query"
},
{
"parent": "p2",
"method": "contains"
}
]
},
{
"id":"p5"
"aggregator_knowledge_source": "infores:ARA_2",
"adjacency_list": [
{
"parent": "p1",
"method": "query"
},
{
"parent": "p3",
"method": "query"
}
]
},
{
"id": "p6":
"aggregator_knowledge_source": "infores:WR",
"adjacency_list": [
{
"parent": "p4",
"method": "query"
},
{
"parent": "p5",
"method": "query"
}
]
}
}
#----------------------------------------------------#
## Proposal 2: Biolink-Based Renaming/Reframing of Abrar's Original Proposal (same structure as Abrar's, more Biolink-based semantics)
## Ilustrates Proposal 2 in the Gdoc here: https://docs.google.com/document/d/11RKh4d4XPGV0a6V--xvpjBFO7RnnT2BZkNzGbakt0a0/edit#
{
"edges": {
"id": "e719492"
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"sources": [
{
"id": "s24b72cca732kb", # A SourceMetadata object
"resource": "infores:KS1",
"resource_type": "original"
},
{
"id": "s8bc318ab77kp1", # A SourceMetadata object
"resource": "infores:KP_1",
"resource_role": "aggregator",
"retrievals": [
{
"retreived_from": "infores:KS1", # A RetrievalMetadata object
"method": "consumed"
}
]
},
{
"id": "s3b57ca75b3kp2", # A SourceMetadata object
"resource": "infores:KP_2",
"resource_role": "aggregator",
"retrievals": [
{
"retrieved_from": "infores:KS1", # A RetrievalMetadata object
"method": "consumed"
}
]
},
{
"id": "s93bb579a87kp3", # A SourceMetadata object
"resource": "infores:KP_3",
"resource_role": "aggregator",
"retrievals": [
{
"retrieved_from": "infores:KS1", # A RetrievalMetadata object
"method": "consumed"
}
]
},
{
"id": "s7cc840a95bara1", # A SourceMetadata object
"resource": "infores:ARA_1",
"resource_role": "aggregator",
"retrievals": [
{
"retrieved_from": "infores:KP_1", # A RetrievalMetadata object
"method": "query"
},
{
"retrieved_from": "infores:KP_2", # A RetrievalMetadata object
"method": "contains"
}
]
},
{
"id": "s32b64cc8a6ara2", # A SourceMetadata object
"reource": "infores:ARA_2",
"resource_role": "aggregator",
"retrievals": [
{
"retrieved_from": "infores:KP_1", # A RetrievalMetadata object
"method": "query"
},
{
"retrieved_from": "infores:KP_3", # A RetrievalMetadata object
"method": "query"
}
]
},
{
"id": "s84a76abb2wr4", # A SourceMetadata object
"resource": "infores:WR",
"resource_role": "aggregator",
"retrievals": [
{
"retrieved_from": "infores:ARA_1", # A RetrievalMetadata object
"method": "query"
},
{
"retrieved_from": "infores:ARA_2", # A RetrievalMetadata object
"method": "query"
}
]
}
}
#----------------------------------------------------#
## Proposal 3: Biolink-Based Restructuring of Abrar's Original Proposal (moves from a 2-level to a 1-level representation, using more Biolink-based semantics)
## Ilustrates Proposal 3 in the Gdoc here: https://docs.google.com/document/d/11RKh4d4XPGV0a6V--xvpjBFO7RnnT2BZkNzGbakt0a0/edit#
## Note that I think we decided the 'preceded_by' fields are not needed (which perhaps means that the hash IDs for SourceMetadata and RetrievalMetadata are also not needed)
{
"edges": {
"id": "e719491"
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"retrievals": [
{
"id": "re25ac984b7kbkp1",
"source": "infores:KS",
"source_role": "original",
"target": "infores:KP_1",
"target_role": "aggregator",
"method": "consumed"
},
{
"id": "re83bb198c8kbkp2",
"source": "infores:KS",
"source_role": "original",
"target": "infores:KP_2",
"target_role": "aggregator",
"method": "consumed"
},
{
"id": "re75bb123a8kbkp3",
"source": "infores:KS",
"source_role": "original",
"target": "infores:KP_3",
"target_role": "aggregator",
"method": "consumed"
},
{
"id": "re41ac943b2kp1ara1",
"source": "infores:KP1",
"source_role": "aggregator",
"target": "infores:ARA_1",
"target_role": "aggregator",
"method": "query",
"preceded_by": ["re25ac984b7kbkp1"]
},
{
"id": "re82ab873a9kp2ara1",
"source": "infores:KP2",
"source_role": "aggregator",
"target": "infores:ARA_1",
"target_role": "aggregator",
"method": "contained",
"preceded_by": ["re83bb198c8kbkp2"]
},
{
"id": "re47aa825c7kp1ara2",
"source": "infores:KP1",
"source_role": "aggregator",
"target": "infores:ARA_2",
"target_role": "aggregator",
"method": "query",
"preceded_by": ["re25ac984b7kbkp1"]
},
{
"id": "re34bb814c6kp3ara21",
"source": "infores:KP3",
"source_role": "aggregator",
"target": "infores:ARA_2",
"target_role": "aggregator",
"method": "query",
"preceded_by": ["re75bb123a8kbkp3"]
},
{
"id": "re61bb249a4ara1wr",
"source": "infores:ARA1",
"source_role": "aggregator",
"target": "infores:WR",
"target_role": "aggregator",
"method": "query",
"preceded_by": ["re41ac943b2kp1ara1", "re82ab873a9kp2ara1"]
},
{
"id": "re32bb725c9ara2wr",
"source": "infores:ARA2",
"source_role": "aggregator",
"target": "infores:WR",
"target_role": "aggregator",
"method": "query",
"preceded_by": ["re47aa825c7kp1ara2", "re34bb814c6kp3ara2"]
}
]
}
# -------------------------------------------------------------
## Proposal 4: Bare Bones Model proposed on 5-10-22 Call . . . and even simpler one level representation
## Ilustrates Proposal 4 in the Gdoc here: https://docs.google.com/document/d/11RKh4d4XPGV0a6V--xvpjBFO7RnnT2BZkNzGbakt0a0/edit#
{
"edges": {
"id": "e719491",
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"sources": [
{
"id": "re25ac984b7kb1",
"resource": "infores:KS_1",
"resource_role": "primary"
},
{
"id": "re25ac984b7kp1ks1",
"resource": "infores:KP_1",
"resource_role": "primary",
"upstream_resource": ["infores:KS_1"]
},
{
"id": "re25ac984b7kp2ks1",
"resource": "infores:KP_2",
"resource_role": "primary",
"upstream_resource": ["infores:KS_1"]
},
{
"id": "re25ac984b7kp3ks1",
"resource": "infores:KP_3",
"resource_role": "primary",
"upstream_resource": ["infores:KS_1"]
},
{
"id": "re25ac984b7ara1kp1kp2",
"resource": "infores:ARA_1",
"resource_role": "primary",
"upstream_resource": ["infores:KP_1", "infores:KP_2"]
},
{
"id": "re25ac984b7ara2kp1kp3",
"resource": "infores:ARA_2",
"resource_role": "primary",
"upstream_resource": ["infores:KP_1", "infores:KP_3"]
},
{
"id": "re25ac984b7wrara1ara2",
"resource": "infores:WR",
"resource_role": "primary",
"upstream_resource": ["infores:ARA_1", "infores:ARA_2"]
}
]
}
}
# -------------------------------------------------------------
## SCENARIO 2 EXAMPLES (Scenario 2 overview in Gdoc here: https://docs.google.com/document/d/11RKh4d4XPGV0a6V--xvpjBFO7RnnT2BZkNzGbakt0a0/edit#)
## One-level representation of an expanded scenario that include a second external source / original source that KP1 pulls from.
## e.g. MolePro pulls the edge/association ChemX-binds-GeneY from ChemBL and StringDB. Same SPOQ semantics, but different original/primary source.
## Because our merge criteria include identity of the primary/original source, these two Edges never get merged into a single Association/Edge object (although the UI might ultimately display them as one).
## Only the second Edge is shown below, which would complement the Edge already shown above.
## This second edge is retrieved from KS2 by KP1, then goes through ARA1 and ARA2, on its way to the WR.
{
"edges": {
"id": "e21aa4542" # A different Edge gets created for the assertion originating in KS2, even though it states the same knowledge as the assertion originating in KS1 and represented in the edge above
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"retrievals": [
{
"id": "re52ba891b4kb2kp1",
"source": "infores:KS2",
"source_role": "original",
"target": "infores:KP_1",
"target_role": "aggregator",
"method": "consumed"
},
{
"id": "re43ab256b7kp1ara1", # note that the content of this object is identical to that of one in the other edge - which would give the same hashed id, unless we include the edge id in computing the hash (which I think we should for this reason . . . we want these hash ids to be different)
"source": "infores:KP1",
"source_role": "aggregator",
"target": "infores:ARA_1",
"target_role": "aggregator",
"method": "query",
"preceded_by": ["re52ba891b4kb2kp1"]
},
{
"id": "re68aa815c7kp1ara2",
"source": "infores:KP1",
"source_role": "aggregator",
"target": "infores:ARA_2",
"target_role": "aggregator",
"method": "query",
"preceded_by": ["re52ba891b4kb2kp1"]
},
{
"id": "re72ba249b3ara1wr",
"source": "infores:ARA1",
"source_role": "aggregator",
"target": "infores:WR",
"target_role": "aggregator",
"method": "query",
"preceded_by": ["re43ab256b7kp1ara1"]
},
{
"id": "re72bc725c7ara2wr",
"source": "infores:ARA2",
"source_role": "aggregator",
"target": "infores:WR",
"target_role": "aggregator",
"method": "query",
"preceded_by": ["re68aa815c7kp1ara2"]
}
]
}