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Treats refactor tmkp #143

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merged 6 commits into from
Mar 7, 2024
Merged

Treats refactor tmkp #143

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76dd93e
Merge pull request #4 from NCATS-Tangerine/master
edgargaticaCU Mar 7, 2024
709a7ed
Revert "treats refactor"
edgargaticaCU Mar 7, 2024
215183a
Revert "Merge branch 'master' into master"
colleenXu Mar 7, 2024
51a4eb3
Merge branch 'master' into master
edgargaticaCU Mar 7, 2024
7ae9108
Merge pull request #5 from NCATS-Tangerine/master
edgargaticaCU Mar 7, 2024
baf4b13
treats refactor
edgargaticaCU Mar 7, 2024
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50 changes: 23 additions & 27 deletions text_mining/smartapi.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,12 @@ info:
- Service Provider
biolink-version: "4.1.6"
servers:
- description: Encrypted Production server
url: https://biothings.ncats.io/text_mining_targeted_association
x-maturity: production
- url: https://biothings.test.transltr.io/text_mining_targeted_association
description: ITRB Test server
x-maturity: testing
- url: https://biothings.ci.transltr.io/text_mining_targeted_association
description: ITRB CI server
x-maturity: staging
tags:
- name: gene
- name: chemical
Expand Down Expand Up @@ -605,6 +608,7 @@ 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...
## - DRUGBANK :SmallMolecule
## - MONDO: Disease
## - HP: PhenotypicFeaure
## - UniProtKB: Gene
Expand All @@ -620,15 +624,13 @@ components:
- id: DRUGBANK
semantic: SmallMolecule
requestBody:
body: >-
{
"q": [ {{ queryInputs | wrap( '["' , '","treats_or_applied_or_studied_to_treat"]') }} ],
"scopes": ["subject.DRUGBANK", "association.edge_label"]
}
body:
q: "{{ queryInputs }}"
scopes: subject.DRUGBANK
parameters:
fields: object.MONDO,association.edge_attributes,association.sources
size: 1000
filter: _exists_:subject.DRUGBANK AND association.edge_label:treats AND _exists_:object.MONDO
filter: _exists_:subject.DRUGBANK AND association.edge_label:treats_or_applied_or_studied_to_treat AND _exists_:object.MONDO
outputs:
- id: MONDO
semantic: Disease
Expand All @@ -647,15 +649,13 @@ components:
- id: MONDO
semantic: Disease
requestBody:
body: >-
{
"q": [ {{ queryInputs | wrap( '["' , '","treats_or_applied_or_studied_to_treat"]') }} ],
"scopes": ["object.MONDO", "association.edge_label"]
}
body:
q: "{{ queryInputs }}"
scopes: object.MONDO
parameters:
fields: subject.DRUGBANK,association.edge_attributes,association.sources
size: 1000
filter: _exists_:subject.DRUGBANK AND association.edge_label:treats AND _exists_:object.MONDO
filter: _exists_:subject.DRUGBANK AND association.edge_label:treats_or_applied_or_studied_to_treat AND _exists_:object.MONDO
outputs:
- id: DRUGBANK
semantic: SmallMolecule
Expand All @@ -674,15 +674,13 @@ components:
- id: DRUGBANK
semantic: SmallMolecule
requestBody:
body: >-
{
"q": [ {{ queryInputs | wrap( '["' , '","treats_or_applied_or_studied_to_treat"]') }} ],
"scopes": ["subject.DRUGBANK", "association.edge_label"]
}
body:
q: "{{ queryInputs }}"
scopes: subject.DRUGBANK
parameters:
fields: object.HP,association.edge_attributes,association.sources
size: 1000
filter: _exists_:subject.DRUGBANK AND association.edge_label:treats AND _exists_:object.HP
filter: _exists_:subject.DRUGBANK AND association.edge_label:treats_or_applied_or_studied_to_treat AND _exists_:object.HP
outputs:
- id: HP
semantic: PhenotypicFeature
Expand All @@ -701,15 +699,13 @@ components:
- id: HP
semantic: PhenotypicFeature
requestBody:
body: >-
{
"q": [ {{ queryInputs | wrap( '["' , '","treats_or_applied_or_studied_to_treat"]') }} ],
"scopes": ["object.HP", "association.edge_label"]
}
body:
q: "{{ queryInputs }}"
scopes: object.HP
parameters:
fields: subject.DRUGBANK,association.edge_attributes,association.sources
size: 1000
filter: _exists_:subject.DRUGBANK AND association.edge_label:treats AND _exists_:object.HP
filter: _exists_:subject.DRUGBANK AND association.edge_label:treats_or_applied_or_studied_to_treat AND _exists_:object.HP
outputs:
- id: DRUGBANK
semantic: SmallMolecule
Expand Down