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Trapi 1.4 #115

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merged 2 commits into from
May 1, 2023
Merged

Trapi 1.4 #115

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f625975
Updating to TRAPI 1.4 provenance
edgargaticaCU Apr 28, 2023
e4675fa
Removing the last vestiges of CHEBI
edgargaticaCU May 1, 2023
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70 changes: 36 additions & 34 deletions text_mining/smartapi.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -414,7 +414,7 @@ components:
If "fields=all", all available fields will be returned.


Note that it supports dot notation as well, e.g., you can pass "chebi.name".
Note that it supports dot notation as well, e.g., you can pass "mondo.name".
Default: "fields=all".
The parameter "filter" is an alias for this parameter.
in: query
Expand Down Expand Up @@ -604,12 +604,12 @@ components:
## - for reverse operations, some edge attributes may seem odd (reversed subj/obj)
## - don't use subject.type/object.type in q, that came from SRI ID resolver and differs a lot between IDs of same namespace
## - use heuristics to specify input / output type. BTE will handle any discrepancies w/ SRI ID resolver...
## - CHEBI, DRUGBANK :SmallMolecule
## - DRUGBANK :SmallMolecule
## - MONDO: Disease
## - HP: PhenotypicFeaure
## - UniProtKB: Gene
## - currently we can't express _exists_ with this kind of query: useful for setting the output
## - currently, BTE handles prefix (CHEBI / MONDO / HP keep their prefixes, DRUGBANK / UniProtKB does not).
## - currently, BTE handles prefix (MONDO / HP keep their prefixes, DRUGBANK / UniProtKB does not).
## in the future, could edit parser + queries to handle prefixes
## - joinSafe is only needed if the delimiter isn't a comma
drugbank-treats-mondo:
Expand All @@ -628,7 +628,7 @@ components:
"scopes": ["subject.DRUGBANK", "association.edge_label"]
}
parameters:
fields: object.MONDO,association.edge_attributes
fields: object.MONDO,association.edge_attributes,association.sources
size: 1000
outputs:
- id: MONDO
Expand All @@ -655,7 +655,7 @@ components:
"scopes": ["object.MONDO", "association.edge_label"]
}
parameters:
fields: subject.DRUGBANK,association.edge_attributes
fields: subject.DRUGBANK,association.edge_attributes,association.sources
size: 1000
outputs:
- id: DRUGBANK
Expand All @@ -682,7 +682,7 @@ components:
"scopes": ["subject.DRUGBANK", "association.edge_label"]
}
parameters:
fields: object.HP,association.edge_attributes
fields: object.HP,association.edge_attributes,association.sources
size: 1000
outputs:
- id: HP
Expand All @@ -709,7 +709,7 @@ components:
"scopes": ["object.HP", "association.edge_label"]
}
parameters:
fields: subject.DRUGBANK,association.edge_attributes
fields: subject.DRUGBANK,association.edge_attributes,association.sources
size: 1000
outputs:
- id: DRUGBANK
Expand All @@ -735,7 +735,7 @@ components:
"scopes": ["subject.DRUGBANK", "association.edge_label"]
}
parameters:
fields: object.UniProtKB,association.edge_attributes
fields: object.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand Down Expand Up @@ -767,7 +767,7 @@ components:
"scopes": ["object.UniProtKB", "association.edge_label"]
}
parameters:
fields: subject.DRUGBANK,association.edge_attributes
fields: subject.DRUGBANK,association.edge_attributes,association.sources
size: 1000
outputs:
- id: DRUGBANK
Expand Down Expand Up @@ -798,7 +798,7 @@ components:
"scopes": ["subject.DRUGBANK", "association.edge_label"]
}
parameters:
fields: object.UniProtKB,association.edge_attributes
fields: object.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand Down Expand Up @@ -830,7 +830,7 @@ components:
"scopes": ["object.UniProtKB", "association.edge_label"]
}
parameters:
fields: subject.DRUGBANK,association.edge_attributes
fields: subject.DRUGBANK,association.edge_attributes,association.sources
size: 1000
outputs:
- id: DRUGBANK
Expand Down Expand Up @@ -861,7 +861,7 @@ components:
"scopes": ["subject.UniProtKB", "association.edge_label"]
}
parameters:
fields: object.UniProtKB,association.edge_attributes
fields: object.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand Down Expand Up @@ -891,7 +891,7 @@ components:
"scopes": ["object.UniProtKB", "association.edge_label"]
}
parameters:
fields: subject.UniProtKB,association.edge_attributes
fields: subject.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand Down Expand Up @@ -921,7 +921,7 @@ components:
"scopes": ["subject.UniProtKB", "association.edge_label"]
}
parameters:
fields: object.UniProtKB,association.edge_attributes
fields: object.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand Down Expand Up @@ -951,7 +951,7 @@ components:
"scopes": ["object.UniProtKB", "association.edge_label"]
}
parameters:
fields: subject.UniProtKB,association.edge_attributes
fields: subject.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand Down Expand Up @@ -981,7 +981,7 @@ components:
"scopes": ["subject.UniProtKB", "association.edge_label"]
}
parameters:
fields: object.MONDO,association.edge_attributes
fields: object.MONDO,association.edge_attributes,association.sources
size: 1000
outputs:
- id: MONDO
Expand All @@ -1008,7 +1008,7 @@ components:
"scopes": ["object.MONDO", "association.edge_label"]
}
parameters:
fields: subject.UniProtKB,association.edge_attributes
fields: subject.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand All @@ -1034,7 +1034,7 @@ components:
"scopes": ["subject.UniProtKB", "association.edge_label"]
}
parameters:
fields: object.HP,association.edge_attributes
fields: object.HP,association.edge_attributes,association.sources
size: 1000
outputs:
- id: HP
Expand All @@ -1061,7 +1061,7 @@ components:
"scopes": ["object.HP", "association.edge_label"]
}
parameters:
fields: subject.UniProtKB,association.edge_attributes
fields: subject.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand All @@ -1087,7 +1087,7 @@ components:
"scopes": ["subject.DRUGBANK", "association.edge_label"]
}
parameters:
fields: object.HP,association.edge_attributes
fields: object.HP,association.edge_attributes,association.sources
size: 1000
outputs:
- id: HP
Expand All @@ -1110,7 +1110,7 @@ components:
"scopes": ["object.HP", "association.edge_label"]
}
parameters:
fields: subject.DRUGBANK,association.edge_attributes
fields: subject.DRUGBANK,association.edge_attributes,association.sources
size: 1000
outputs:
- id: DRUGBANK
Expand All @@ -1133,7 +1133,7 @@ components:
"scopes": ["subject.DRUGBANK", "association.edge_label"]
}
parameters:
fields: object.MONDO,association.edge_attributes
fields: object.MONDO,association.edge_attributes,association.sources
size: 1000
outputs:
- id: MONDO
Expand All @@ -1156,7 +1156,7 @@ components:
"scopes": ["object.MONDO", "association.edge_label"]
}
parameters:
fields: subject.DRUGBANK,association.edge_attributes
fields: subject.DRUGBANK,association.edge_attributes,association.sources
size: 1000
outputs:
- id: DRUGBANK
Expand All @@ -1179,7 +1179,7 @@ components:
"scopes": ["subject.UniProtKB", "association.edge_label"]
}
parameters:
fields: object.HP,association.edge_attributes
fields: object.HP,association.edge_attributes,association.sources
size: 1000
outputs:
- id: HP
Expand Down Expand Up @@ -1208,7 +1208,7 @@ components:
"scopes": ["object.HP", "association.edge_label"]
}
parameters:
fields: subject.UniProtKB,association.edge_attributes
fields: subject.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand Down Expand Up @@ -1237,7 +1237,7 @@ components:
"scopes": ["subject.UniProtKB", "association.edge_label"]
}
parameters:
fields: object.MONDO,association.edge_attributes
fields: object.MONDO,association.edge_attributes,association.sources
size: 1000
outputs:
- id: MONDO
Expand Down Expand Up @@ -1266,7 +1266,7 @@ components:
"scopes": ["object.MONDO", "association.edge_label"]
}
parameters:
fields: subject.UniProtKB,association.edge_attributes
fields: subject.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand Down Expand Up @@ -1295,7 +1295,7 @@ components:
"scopes": ["subject.UniProtKB", "association.edge_label"]
}
parameters:
fields: object.HP,association.edge_attributes
fields: object.HP,association.edge_attributes,association.sources
size: 1000
outputs:
- id: HP
Expand Down Expand Up @@ -1324,7 +1324,7 @@ components:
"scopes": ["object.HP", "association.edge_label"]
}
parameters:
fields: subject.UniProtKB,association.edge_attributes
fields: subject.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand Down Expand Up @@ -1353,7 +1353,7 @@ components:
"scopes": ["subject.UniProtKB", "association.edge_label"]
}
parameters:
fields: object.MONDO,association.edge_attributes
fields: object.MONDO,association.edge_attributes,association.sources
size: 1000
outputs:
- id: MONDO
Expand Down Expand Up @@ -1382,7 +1382,7 @@ components:
"scopes": ["object.MONDO", "association.edge_label"]
}
parameters:
fields: subject.UniProtKB,association.edge_attributes
fields: subject.UniProtKB,association.edge_attributes,association.sources
size: 1000
outputs:
- id: UniProtKB
Expand All @@ -1400,18 +1400,20 @@ components:
mondo-object:
MONDO: object.MONDO
edge-attributes: association.edge_attributes
chebi-subject:
CHEBI: subject.CHEBI
edge-attributes: association.edge_attributes
trapi_sources: association.sources
hp-object:
HP: object.HP
edge-attributes: association.edge_attributes
trapi_sources: association.sources
drugbank-subject:
DRUGBANK: subject.DRUGBANK
edge-attributes: association.edge_attributes
trapi_sources: association.sources
uniprotkb-object:
UniProtKB: object.UniProtKB
edge-attributes: association.edge_attributes
trapi_sources: association.sources
uniprotkb-subject:
UniProtKB: subject.UniProtKB
edge-attributes: association.edge_attributes
trapi_sources: association.sources