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dgidb: fix comments, update directly_interacts_with predicate for qua…
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…lifier refactor
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colleenXu committed Oct 27, 2022
1 parent f951fcd commit 923f5f8
Showing 1 changed file with 44 additions and 34 deletions.
78 changes: 44 additions & 34 deletions dgidb/openapi.yml
Original file line number Diff line number Diff line change
Expand Up @@ -577,7 +577,7 @@ components:
outputs:
- id: NCBIGene
semantic: Gene
## for biolink 2.2.8, DGIdb:agonist maps to increases_activity_of
## for biolink 2.4.8, DGIdb:agonist maps to increases_activity_of
predicate: affects
## nesting allows this main key to stay the same even with future changes
qualifiers:
Expand Down Expand Up @@ -616,7 +616,7 @@ components:
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.2.8, DGIdb:agonist maps to the inverse of increases_activity_of
## for biolink 2.4.8, DGIdb:agonist maps to the inverse of increases_activity_of
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
Expand Down Expand Up @@ -652,7 +652,7 @@ components:
outputs:
- id: NCBIGene
semantic: Gene
## for biolink 2.2.8, DGIdb:allosteric_modulator maps to affects_activity_of
## for biolink 2.4.8, DGIdb:allosteric_modulator maps to affects_activity_of
predicate: affects
qualifiers:
object_aspect_qualifier: activity
Expand Down Expand Up @@ -684,7 +684,7 @@ components:
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.2.8, DGIdb:allosteric_modulator maps to the inverse of affects_activity_of
## for biolink 2.4.8, DGIdb:allosteric_modulator maps to the inverse of affects_activity_of
predicate: affected_by
qualifiers:
subject_aspect_qualifier: activity
Expand Down Expand Up @@ -718,7 +718,7 @@ components:
outputs:
- id: NCBIGene
semantic: Gene
## for biolink 2.2.8, DGIdb:antagonist maps to decreases_activity_of
## for biolink 2.4.8, DGIdb:antagonist maps to decreases_activity_of
predicate: affects
qualifiers:
qualified_predicate: causes
Expand Down Expand Up @@ -761,7 +761,7 @@ components:
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.2.8, DGIdb:antagonist maps to the inverse of decreases_activity_of
## for biolink 2.4.8, DGIdb:antagonist maps to the inverse of decreases_activity_of
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
Expand Down Expand Up @@ -797,8 +797,13 @@ components:
outputs:
- id: NCBIGene
semantic: Gene
## biolink 2.2.8: using the mapping for GAMMA:antibody, rather than mapping for the relation (molecularly_interacts_with)
predicate: directly_interacts_with
## for biolink 2.4.8, was using directly_interacts_with (mapping for GAMMA:antibody)
predicate: affects
qualifiers:
qualified_predicate: causes
object_aspect_qualifier: activity
object_direction_qualifier: decreased
causal_mechanism_qualifier: "antibody inhibition" ## extra since DGIdb labels these as "antibody"
source: "infores:dgidb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/forward"
Expand Down Expand Up @@ -826,8 +831,13 @@ components:
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## biolink 2.2.8: using the mapping for GAMMA:antibody, rather than mapping for the relation (molecularly_interacts_with)
predicate: directly_interacts_with
## for biolink 2.4.8, was using directly_interacts_with (mapping for GAMMA:antibody)
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
subject_aspect_qualifier: activity
subject_direction_qualifier: decreased
causal_mechanism_qualifier: "antibody inhibition" ## extra since DGIdb labels these as "antibody"
source: "infores:dgidb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/reverse"
Expand Down Expand Up @@ -858,7 +868,7 @@ components:
# outputs:
# - id: NCBIGene
# semantic: Gene
# ## for biolink 2.2.8, DGIdb:antisense_oligonucleotide maps to decreases_expression_of
# ## for biolink 2.4.8, DGIdb:antisense_oligonucleotide maps to decreases_expression_of
# ## but dgidb definition is: translation from mRNA to protein is inhibited..
# predicate: affects
# qualifiers:
Expand Down Expand Up @@ -892,7 +902,7 @@ components:
# outputs:
# - id: "CHEMBL.COMPOUND"
# semantic: SmallMolecule
# ## for biolink 2.2.8, DGIdb:antisense_oligonucleotide maps to the inverse of decreases_expression_of
# ## for biolink 2.4.8, DGIdb:antisense_oligonucleotide maps to the inverse of decreases_expression_of
# ## but dgidb definition is: translation from mRNA to protein is inhibited..
# predicate: affected_by
# qualifiers:
Expand Down Expand Up @@ -930,7 +940,7 @@ components:
semantic: Gene
## CX: has the same issue as "antagonist"
## - def https://dgidb.org/interaction_types and https://en.wikipedia.org/wiki/Receptor_antagonist
## for biolink 2.2.8, DGIdb:blocker maps to decreases_activity_of
## for biolink 2.4.8, DGIdb:blocker maps to decreases_activity_of
predicate: affects
qualifiers:
qualified_predicate: causes
Expand Down Expand Up @@ -967,7 +977,7 @@ components:
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.2.8, DGIdb:blocker maps to the inverse of decreases_activity_of
## for biolink 2.4.8, DGIdb:blocker maps to the inverse of decreases_activity_of
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
Expand Down Expand Up @@ -1004,7 +1014,7 @@ components:
# outputs:
# - id: NCBIGene
# semantic: Gene
# ## for biolink 2.2.8, DGIdb:inducer maps to increases_activity_of
# ## for biolink 2.4.8, DGIdb:inducer maps to increases_activity_of
# predicate: affects
# qualifiers:
# qualified_predicate: causes
Expand Down Expand Up @@ -1038,7 +1048,7 @@ components:
# outputs:
# - id: "CHEMBL.COMPOUND"
# semantic: SmallMolecule
# ## for biolink 2.2.8, DGIdb:inducer maps to the inverse of increases_activity_of
# ## for biolink 2.4.8, DGIdb:inducer maps to the inverse of increases_activity_of
# predicate: affected_by
# qualifiers:
# qualified_predicate: caused_by
Expand Down Expand Up @@ -1074,7 +1084,7 @@ components:
outputs:
- id: NCBIGene
semantic: Gene
## for biolink 2.2.8, DGIdb:inhibitor maps to decreases_activity_of
## for biolink 2.4.8, DGIdb:inhibitor maps to decreases_activity_of
predicate: affects
qualifiers:
qualified_predicate: causes
Expand Down Expand Up @@ -1108,7 +1118,7 @@ components:
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.2.8, DGIdb:inhibitor maps to the inverse of decreases_activity_of
## for biolink 2.4.8, DGIdb:inhibitor maps to the inverse of decreases_activity_of
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
Expand Down Expand Up @@ -1145,7 +1155,7 @@ components:
# outputs:
# - id: NCBIGene
# semantic: Gene
# ## for biolink 2.2.8, DGIdb:inhibitory_allosteric_modulator maps to decreases_activity_of
# ## for biolink 2.4.8, DGIdb:inhibitory_allosteric_modulator maps to decreases_activity_of
# predicate: affects
# qualifiers:
# qualified_predicate: causes
Expand Down Expand Up @@ -1179,7 +1189,7 @@ components:
# outputs:
# - id: "CHEMBL.COMPOUND"
# semantic: SmallMolecule
# ## for biolink 2.2.8, DGIdb:inhibitory_allosteric_modulator maps to the inverse of decreases_activity_of
# ## for biolink 2.4.8, DGIdb:inhibitory_allosteric_modulator maps to the inverse of decreases_activity_of
# predicate: affected_by
# qualifiers:
# qualified_predicate: caused_by
Expand Down Expand Up @@ -1215,7 +1225,7 @@ components:
outputs:
- id: NCBIGene
semantic: Gene
## for biolink 2.2.8, DGIdb:inverse_agonist maps to decreases_activity_of
## for biolink 2.4.8, DGIdb:inverse_agonist maps to decreases_activity_of
predicate: affects
qualifiers:
qualified_predicate: causes
Expand Down Expand Up @@ -1249,7 +1259,7 @@ components:
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.2.8, DGIdb:inverse_agonist maps to the inverse of decreases_activity_of
## for biolink 2.4.8, DGIdb:inverse_agonist maps to the inverse of decreases_activity_of
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
Expand Down Expand Up @@ -1286,7 +1296,7 @@ components:
- id: NCBIGene
semantic: Gene
## could also use "entity regulates entity"? see def: https://dgidb.org/interaction_types
## for biolink 2.2.8, DGIdb:modulator maps to affects_activity_of
## for biolink 2.4.8, DGIdb:modulator maps to affects_activity_of
predicate: affects
qualifiers:
object_aspect_qualifier: activity
Expand Down Expand Up @@ -1318,7 +1328,7 @@ components:
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.2.8, DGIdb:modulator maps to the inverse of affects_activity_of
## for biolink 2.4.8, DGIdb:modulator maps to the inverse of affects_activity_of
predicate: affected_by
qualifiers:
subject_aspect_qualifier: activity
Expand Down Expand Up @@ -1353,7 +1363,7 @@ components:
# outputs:
# - id: NCBIGene
# semantic: Gene
# ## for biolink 2.2.8, DGIdb:negative_modulator maps to decreases_activity_of
# ## for biolink 2.4.8, DGIdb:negative_modulator maps to decreases_activity_of
# predicate: affects
# qualifiers:
# qualified_predicate: causes
Expand Down Expand Up @@ -1387,7 +1397,7 @@ components:
# outputs:
# - id: "CHEMBL.COMPOUND"
# semantic: SmallMolecule
# ## for biolink 2.2.8, DGIdb:negative_modulator maps to the inverse of decreases_activity_of
# ## for biolink 2.4.8, DGIdb:negative_modulator maps to the inverse of decreases_activity_of
# predicate: affected_by
# qualifiers:
# qualified_predicate: caused_by
Expand Down Expand Up @@ -1484,7 +1494,7 @@ components:
outputs:
- id: NCBIGene
semantic: Gene
## for biolink 2.2.8, DGIdb:partial_agonist maps to increases_activity_of
## for biolink 2.4.8, DGIdb:partial_agonist maps to increases_activity_of
predicate: affects
qualifiers:
qualified_predicate: causes
Expand Down Expand Up @@ -1518,7 +1528,7 @@ components:
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.2.8, DGIdb:partial_agonist maps to the inverse of increases_activity_of
## for biolink 2.4.8, DGIdb:partial_agonist maps to the inverse of increases_activity_of
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
Expand Down Expand Up @@ -1554,7 +1564,7 @@ components:
outputs:
- id: NCBIGene
semantic: Gene
## biolink 2.2.8: using mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term. using increases_activity_of
## biolink 2.4.8: using mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term. using increases_activity_of
predicate: affects
qualifiers:
qualified_predicate: causes
Expand Down Expand Up @@ -1588,7 +1598,7 @@ components:
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## biolink 2.2.8: using inverse of mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term (activity_increased_by)
## biolink 2.4.8: using inverse of mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term (activity_increased_by)
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
Expand Down Expand Up @@ -1625,7 +1635,7 @@ components:
# outputs:
# - id: NCBIGene
# semantic: Gene
# ## biolink 2.2.8: using mapping for GAMMA:suppressor, so using decreases_activity_of
# ## biolink 2.4.8: using mapping for GAMMA:suppressor, so using decreases_activity_of
# predicate: affects
# qualifiers:
# qualified_predicate: causes
Expand Down Expand Up @@ -1659,7 +1669,7 @@ components:
# outputs:
# - id: "CHEMBL.COMPOUND"
# semantic: SmallMolecule
# ## biolink 2.2.8: using inverse of mapping for GAMMA:suppressor (so using activity_decreased_by)
# ## biolink 2.4.8: using inverse of mapping for GAMMA:suppressor (so using activity_decreased_by)
# predicate: affected_by
# qualifiers:
# qualified_predicate: caused_by
Expand Down Expand Up @@ -1696,7 +1706,7 @@ components:
# outputs:
# - id: NCBIGene
# semantic: Gene
# ## using a different predicate than the biolink 2.2.8 mapping (decreases_activity_of)
# ## using a different predicate than the biolink 2.4.8 mapping (decreases_activity_of)
# ## reasoning: thought its def https://dgidb.org/interaction_types was similar to https://github.com/biolink/biolink-model/blob/c73899cd33753c5d2ff937213b6c5911c579b001/biolink-model.yaml#L2918
# predicate: affects_response_to
# source: "infores:dgidb"
Expand Down Expand Up @@ -1726,7 +1736,7 @@ components:
# outputs:
# - id: "CHEMBL.COMPOUND"
# semantic: SmallMolecule
# ## using a different predicate than the biolink 2.2.8 mapping (decreases_activity_of)
# ## using a different predicate than the biolink 2.4.8 mapping (decreases_activity_of)
# ## reasoning: thought its def https://dgidb.org/interaction_types was similar to https://github.com/biolink/biolink-model/blob/c73899cd33753c5d2ff937213b6c5911c579b001/biolink-model.yaml#L2918
# predicate: response_affected_by
# source: "infores:dgidb"
Expand Down

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