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fix: remove covid_phenotype-based operations from mydisease x-bte ann…
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colleenXu committed Aug 23, 2021
1 parent bede883 commit f77f111
Showing 1 changed file with 0 additions and 52 deletions.
52 changes: 0 additions & 52 deletions mydisease.info/smartapi.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -226,7 +226,6 @@ paths:
- "$ref": "#/components/x-bte-kgs-operations/disease-variant"
- "$ref": "#/components/x-bte-kgs-operations/disease-phenotype"
- "$ref": "#/components/x-bte-kgs-operations/disease-phenotype2"
- "$ref": "#/components/x-bte-kgs-operations/disease-phenotype3" ## for covid_phenotypes
- "$ref": "#/components/x-bte-kgs-operations/disease-chemical"
- "$ref": "#/components/x-bte-kgs-operations/disease-chemical2"
# - "$ref": "#/components/x-bte-kgs-operations/disease-pathway"
Expand All @@ -235,7 +234,6 @@ paths:
- "$ref": "#/components/x-bte-kgs-operations/variant-disease"
- "$ref": "#/components/x-bte-kgs-operations/phenotype-disease"
- "$ref": "#/components/x-bte-kgs-operations/phenotype-disease2"
- "$ref": "#/components/x-bte-kgs-operations/phenotype-disease3" ## for covid_phenotypes
- "$ref": "#/components/x-bte-kgs-operations/chemical-disease"
- "$ref": "#/components/x-bte-kgs-operations/chemical-disease2"
# - "$ref": "#/components/x-bte-kgs-operations/pathway-disease"
Expand Down Expand Up @@ -445,8 +443,6 @@ components:
modifier: hpo.phenotype_related_to_disease.modifier
sex: hpo.phenotype_related_to_disease.sex
biocuration: hpo.phenotype_related_to_disease.biocuration
disease-phenotype2:
HP: covid_phenotypes.hp ## HAS PREFIX (HP)
disease-chemical:
MESH: ctd.chemical_related_to_disease.mesh_chemical_id ## no prefix
## direct_evidence has two values, 'marker/mechanism' or 'therapeutic'
Expand Down Expand Up @@ -586,29 +582,6 @@ components:
source: "infores:hpo-annotations"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/disease-phenotype"
disease-phenotype3: ## covid only
## could be updated based on Automat's current tool?
- supportBatch: true
inputSeparator: ","
parameters:
fields: covid_phenotypes.hp
requestBody:
body:
q: "{inputs[0]}" ## HAS PREFIX (MONDO)
## example: put MONDO:0100096 here (only possible input)
## should get HP:0011899 (Hyperfibrinogenemia) in response
scopes: mondo.mondo
header: application/x-www-form-urlencoded
inputs:
- id: MONDO
semantic: Disease
outputs:
- id: HP
semantic: PhenotypicFeature
predicate: has_phenotype
source: "infores:automat-covid-phenotypes" ## but an older downloaded version...
response_mapping:
"$ref": "#/components/x-bte-response-mapping/disease-phenotype2"
## for ctd-based operations:
## - when the mydisease parser maps the resources' IDs to MONDO, are there situations where a MESH and a OMIM ID map to the same MONDO?
## If so, 1) Is only one of them kept?,
Expand Down Expand Up @@ -851,31 +824,6 @@ components:
source: "infores:hpo-annotations"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/orphanet"
phenotype-disease3: ## covid only
- path: "/query"
method: post
supportBatch: true
inputSeparator: ","
parameters:
fields: mondo.mondo
requestBody:
body:
q: "{inputs[0]}" ## HAS PREFIX (HP)
## example: put HP:0011899 here (Hyperfibrinogenemia)
## should get MONDO:0100096 in response (COVID-19)
## somewhat restricted set of possible inputs (~20)
scopes: covid_phenotypes.hp
header: application/x-www-form-urlencoded
inputs:
- id: HP
semantic: PhenotypicFeature
outputs:
- id: MONDO
semantic: Disease
predicate: phenotype_of
source: "infores:automat-covid-phenotypes"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/mondo"
chemical-disease:
- path: "/query"
method: post
Expand Down

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