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agr.yaml
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openapi: 3.0.3
info:
contact:
email: help@biothings.io
name: BioThings Team
x-id: https://github.com/biothings
x-role: responsible developers
description: >-
Documentation of the BioThings API for
[AGR](https://www.alliancegenome.org/downloads) disease associations data.
termsOfService: https://biothings.io/about
title: BioThings AGR API
version: '2021-08-19' ## data / parser may be this old...
x-translator:
infores: "infores:biothings-agr"
component: KP
team:
- Service Provider
biolink-version: "3.5.3"
servers:
- description: Encrypted Production server
url: https://biothings.ncats.io/agr
x-maturity: production
- description: Production server
url: http://biothings.ncats.io/agr
x-maturity: production
tags:
- name: association
- name: gene
- name: disease
- name: metadata
- name: query
- name: translator
- name: biothings
paths:
"/association/{id}":
get:
description: >-
By default, this will return the complete association in JSON format. If the input is not valid,
404 (NOT FOUND) will be returned.
Optionally, you can pass a "fields" parameter to return only the annotation you want
(by filtering returned object fields). "fields" accepts any attributes (a.k.a fields) available
from the association. Multiple attributes should be separated by commas. If an attribute is not
available for a specific association, it will be ignored. Note that the attribute names are
case-sensitive.
Just like the query service, you can also pass a "callback" parameter to make a JSONP call.
parameters:
- name: id
in: path
required: true
example: "MGI:2386296"
schema:
type: string
- "$ref": "#/components/parameters/fields"
- "$ref": "#/components/parameters/callback"
- "$ref": "#/components/parameters/email"
## this is useful even when it's not noted in the docs
- "$ref": "#/components/parameters/size"
## these are noted in the /spec endpoint; commenting out for now
# - "$ref": "#/components/parameters/raw"
# - "$ref": "#/components/parameters/rawquery"
# - "$ref": "#/components/parameters/dotfield"
# - "$ref": "#/components/parameters/_sorted"
# - "$ref": "#/components/parameters/always_list"
# - "$ref": "#/components/parameters/allow_null"
# - "$ref": "#/components/parameters/format"
responses:
'200':
description: A 200 status code indicates a successful query, and is accompanied by the query response payload.
## commenting out schemas and other status codes for now
# content:
# application/json:
# schema:
# $ref: '#/components/schemas/Association'
# '404':
# description: A response indicating an unknown association ID
tags:
- association
"/association":
post:
description: >-
Although making simple GET requests above to our service is sufficient in most use cases,
there are some times you might find it easier to batch query (e.g., retrieving multiple associations).
Fortunately, you can also make batch queries via POST requests when you need to.
parameters:
- name: ids
description: >-
Accepts multiple association ids separated by commas. Note that currently we only take ids up to
1000 maximum, the rest will be omitted.
The request body can also be used to provide these ids.
in: query
## setting to false since putting this info in the request body seems to work as well
required: false
schema:
type: string
- "$ref": "#/components/parameters/fields"
- "$ref": "#/components/parameters/email"
## this is useful even when it's not noted in the docs
- "$ref": "#/components/parameters/size"
## these are noted in the /spec endpoint; commenting out for now
# - "$ref": "#/components/parameters/raw"
# - "$ref": "#/components/parameters/rawquery"
# - "$ref": "#/components/parameters/dotfield"
# - "$ref": "#/components/parameters/_sorted"
# - "$ref": "#/components/parameters/always_list"
# - "$ref": "#/components/parameters/allow_null"
# - "$ref": "#/components/parameters/format"
requestBody:
content:
application/json:
example:
ids:
- "MGI:2384568"
- "RGD:2320289"
schema:
type: object
properties:
ids:
description: >-
Accepts multiple association ids. Note that currently we only take the input ids
up to 1000 maximum, the rest will be omitted.
type: array
items:
type: string
responses:
'200':
description: A 200 status code indicates a successful query, and is accompanied by the query response payload.
tags:
- association
"/metadata":
get:
description: Get metadata about the data available from the API
## these are noted in the https://mychem.info/v1/spec endpoint; commenting out for now
# parameters:
# - "$ref": "#/components/parameters/format"
# - "$ref": "#/components/parameters/raw"
responses:
'200':
description: A 200 status code indicates a successful query, and is accompanied by the query response payload.
tags:
- metadata
"/metadata/fields":
get:
description: Get metadata about the data fields available from the API
## these are noted in the https://mychem.info/v1/spec endpoint; commenting out for now
# parameters:
# - "$ref": "#/components/parameters/format"
# - "$ref": "#/components/parameters/raw"
# - "$ref": "#/components/parameters/search"
# - "$ref": "#/components/parameters/prefix"
responses:
'200':
description: A 200 status code indicates a successful query, and is accompanied by the query response payload.
tags:
- metadata
"/query":
get:
description: >-
Query service. In the output, "total" in the output gives the total number
of matching hits, while the actual hits are returned under "hits" field.
parameters:
- name: q
description: >-
Required, passing user query. The detailed query syntax for parameter is explained
[here for a core BioThings
API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).
in: query
required: true
example: "agr.symbol:Kank2"
schema:
type: string
- "$ref": "#/components/parameters/fields"
- "$ref": "#/components/parameters/size"
- "$ref": "#/components/parameters/from"
- "$ref": "#/components/parameters/fetch_all"
- "$ref": "#/components/parameters/scroll_id"
- "$ref": "#/components/parameters/sort"
- "$ref": "#/components/parameters/facets"
- "$ref": "#/components/parameters/facet_size"
- "$ref": "#/components/parameters/callback"
- "$ref": "#/components/parameters/dotfield"
- "$ref": "#/components/parameters/email"
## these are noted in the /spec endpoint; commenting out for now
# - "$ref": "#/components/parameters/aggs"
# - "$ref": "#/components/parameters/userquery"
# - "$ref": "#/components/parameters/explain"
# - "$ref": "#/components/parameters/raw"
# - "$ref": "#/components/parameters/rawquery"
# - "$ref": "#/components/parameters/_sorted"
# - "$ref": "#/components/parameters/always_list"
# - "$ref": "#/components/parameters/allow_null"
# - "$ref": "#/components/parameters/format"
responses:
'200':
description: A 200 status code indicates a successful query, and is accompanied by the query response payload.
## commenting out schemas and other status codes for now
# content:
# application/json:
# schema:
# "$ref": "#/components/schemas/QueryResult"
# '400':
# content:
# application/json:
# schema:
# "$ref": "#/components/schemas/ErrorResult"
# description: A response indicating an improperly formatted query
# summary: Make queries and return matching gene hits. Supports JSONP and CORS
# as well.
tags:
- query
post:
description: >-
Although making simple GET requests above to our query service is sufficient for most use cases,
there are times you might find it more efficient to make batch queries (e.g., retrieving data
for multiple inputs). Fortunately, you can also make batch queries via POST requests when you need to.
The "query” field in the returned object indicates the matching query term. If a query term has no match,
it will return with a “notfound” field with the value “true”.
parameters:
- name: q
description: >-
Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000
maximum, the rest will be omitted.
The request body can also be used to provide these ids.
in: query
## setting to false since putting this info in the request body seems to work as well
required: false
schema:
type: array
items:
type: string
- name: scopes
description: >-
Optional, specify one or more fields (separated by commas) to search. Default: _id
The request body can also be used to provide this information.
in: query
## setting to false since putting this info in the request body seems to work as well
required: false
schema:
type: string
- "$ref": "#/components/parameters/fields"
- "$ref": "#/components/parameters/email"
## this is useful even when it's not noted in the docs
- "$ref": "#/components/parameters/size"
- "$ref": "#/components/parameters/from"
- "$ref": "#/components/parameters/fetch_all"
- "$ref": "#/components/parameters/scroll_id"
## these are noted in the https://mychem.info/v1/spec endpoint; commenting out for now
# - "$ref": "#/components/parameters/sort"
# - "$ref": "#/components/parameters/raw"
# - "$ref": "#/components/parameters/rawquery"
# - "$ref": "#/components/parameters/dotfield"
# - "$ref": "#/components/parameters/_sorted"
# - "$ref": "#/components/parameters/always_list"
# - "$ref": "#/components/parameters/allow_null"
# - "$ref": "#/components/parameters/format"
requestBody:
content:
application/json:
example:
q:
- "Acot2"
- "Kank2"
scopes:
- "agr.symbol"
schema:
type: object
properties:
q:
description: >-
Accepts multiple values separated by commas. Note that currently we only take the input values
up to 1000 maximum, the rest will be omitted.
type: array
items:
type: string
scopes:
description: >-
Specify one or more fields (separated by commas) to search. Default: _id
type: array
items:
type: string
responses:
'200':
description: A 200 status code indicates a successful query, and is accompanied by the query response payload.
## commenting out schemas and other status codes for now
# content:
# application/json:
# schema:
# "$ref": "#/components/schemas/QueryPOSTResult"
# '400':
# content:
# application/json:
# schema:
# "$ref": "#/components/schemas/ErrorResult"
# description: A response indicating an improperly formatted query
# summary: Make batch gene queries and return matching gene hits
tags:
- query
## 37 operations (9 sets of 3 and 5 sets of 2)
x-bte-kgs-operations:
- $ref: '#/components/x-bte-kgs-operations/hgnc-to-doid-isMarkerFor'
- $ref: '#/components/x-bte-kgs-operations/doid-to-hgnc-bothBiomarker'
- $ref: '#/components/x-bte-kgs-operations/rgd-to-doid-isMarkerFor'
- $ref: '#/components/x-bte-kgs-operations/doid-to-rgd-bothBiomarker'
- $ref: '#/components/x-bte-kgs-operations/hgnc-to-doid-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/mgi-to-doid-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/doid-to-mgi-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/rgd-to-doid-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/zfin-to-doid-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/doid-to-zfin-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/fb-to-doid-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/doid-to-fb-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/wb-to-doid-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/doid-to-wb-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/sgd-to-doid-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/doid-to-sgd-biomarkerViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/hgnc-to-doid-isImplicatedIn'
- $ref: '#/components/x-bte-kgs-operations/doid-to-hgnc-bothImplicated'
- $ref: '#/components/x-bte-kgs-operations/mgi-to-doid-isImplicatedIn'
- $ref: '#/components/x-bte-kgs-operations/doid-to-mgi-bothImplicated'
- $ref: '#/components/x-bte-kgs-operations/rgd-to-doid-isImplicatedIn'
- $ref: '#/components/x-bte-kgs-operations/doid-to-rgd-bothImplicated'
- $ref: '#/components/x-bte-kgs-operations/zfin-to-doid-isImplicatedIn'
- $ref: '#/components/x-bte-kgs-operations/doid-to-zfin-bothImplicated'
- $ref: '#/components/x-bte-kgs-operations/fb-to-doid-isImplicatedIn'
- $ref: '#/components/x-bte-kgs-operations/doid-to-fb-bothImplicated'
- $ref: '#/components/x-bte-kgs-operations/wb-to-doid-isImplicatedIn'
- $ref: '#/components/x-bte-kgs-operations/doid-to-wb-bothImplicated'
- $ref: '#/components/x-bte-kgs-operations/sgd-to-doid-isImplicatedIn'
- $ref: '#/components/x-bte-kgs-operations/doid-to-sgd-bothImplicated'
- $ref: '#/components/x-bte-kgs-operations/hgnc-to-doid-implicatedViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/mgi-to-doid-implicatedViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/rgd-to-doid-implicatedViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/zfin-to-doid-implicatedViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/fb-to-doid-implicatedViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/wb-to-doid-implicatedViaOrthology'
- $ref: '#/components/x-bte-kgs-operations/sgd-to-doid-implicatedViaOrthology'
components:
parameters:
callback:
name: callback
description: >-
Optional, you can pass a "callback" parameter to make a JSONP call.
in: query
required: false
schema:
type: string
dotfield:
name: dotfield
description: >-
Optional, can be used to control the format of the returned object.
If "dotfield" is true, the returned data object is returned flattened (no nested objects)
using dotfield notation for key names. Default: false.
in: query
required: false
schema:
type: boolean
default: false
email:
name: email
description: >-
Optional, if you are regular users of our services, we encourage you to provide us an email,
so that we can better track the usage or follow up with you.
in: query
required: false
schema:
type: string
facet_size:
name: facet_size
description: >-
Optional, an integer (1 <= facet_size <= 1000) that specifies how many buckets to return in a
[faceted query](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries).
in: query
required: false
schema:
type: integer
default: 10
facets:
name: facets
description: >-
Optional, a single field or comma-separated fields to return facets, can only be used on non-free text fields.
E.g. “facets=chembl.molecule_properties.full_mwt”. See [examples of faceted queries for a core BioThings
API](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries).
in: query
required: false
schema:
type: array
items:
type: string
fetch_all:
name: fetch_all
description: >-
Optional, a boolean, which when TRUE, allows fast retrieval of all unsorted query hits.
The return object contains a _scroll_id field, which when passed as a parameter to the query endpoint
(see the scroll_id parameter), returns the next 1000 query results. Setting fetch_all = TRUE causes
the results to be inherently unsorted, therefore the sort parameter is ignored. For more information,
see [examples using fetch_all for a core BioThings
API](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries).
Default: FALSE.
in: query
required: false
schema:
type: boolean
default: false
fields:
name: fields
description: >-
Optional, can be a comma-separated list to limit the fields returned from the object.
If "fields=all", all available fields will be returned.
Note that it supports dot notation as well, e.g., you can pass "chebi.name".
Default: "fields=all".
The parameter "filter" is an alias for this parameter.
in: query
required: false
schema:
type: string
default: all
from:
name: from
description: >-
Optional, the number of matching hits to skip, starting from 0. Default: 0.
in: query
required: false
schema:
type: integer
default: 0
scroll_id:
name: scroll_id
description: >-
Optional, a string containing the _scroll_id returned from a query request with fetch_all = TRUE.
Supplying a valid scroll_id will return the next 1000 unordered results. If the next results are
not obtained within 1 minute of the previous set of results, the scroll_id becomes stale, and a
new one must be obtained with another query request with fetch_all = TRUE. All other parameters are
ignored when the scroll_id parameter is supplied. For more information see [examples using scroll_id
for a core BioThings
API](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries).
in: query
required: false
schema:
type: string
size:
name: size
description: >-
Optional, the maximum number of matching hits to return (with a cap of 1000 at the moment). Default: 10.
The combination of "size" and "from" parameters can be used to get paging for a large query.
in: query
required: false
schema:
type: integer
default: 10
sort:
name: sort
description: >-
Optional, the comma-separated fields to sort on. Prefix with "-" for descending order, otherwise in ascending order.
Default: sort by matching scores in descending order.
in: query
required: false
schema:
type: array
items:
type: string
## these are noted in the https://mychem.info/v1/spec endpoint; commenting out for now
# _sorted:
# name: _sorted
# in: query
# required: false
# schema:
# type: boolean
# default: true
# aggs:
# name: aggs
# in: query
# required: false
# schema:
# type: array
# items:
# type: string
# allow_null:
# name: allow_null
# in: query
# required: false
# schema:
# type: array
# items:
# type: string
# always_list:
# name: always_list
# in: query
# required: false
# schema:
# type: array
# items:
# type: string
# explain:
# name: explain
# in: query
# required: false
# schema:
# type: boolean
# format:
# name: format
# description: 'controls output format of server response, currently supports:
# "json", "jsonld", "html". Type: string. Default: json.'
# in: query
# required: false
# schema:
# type: string
# default: json
# prefix:
# name: prefix
# in: query
# required: false
# schema:
# type: string
# raw:
# name: raw
# in: query
# required: false
# schema:
# type: boolean
# rawquery:
# name: rawquery
# in: query
# required: false
# schema:
# type: boolean
# search:
# name: search
# in: query
# required: false
# schema:
# type: string
# userquery:
# name: userquery
# in: query
# required: false
# schema:
# type: string
## commenting out schemas and other status codes for now
# schemas:
# Association:
# properties:
# _id:
# type: string
# required:
# - _id
# type: object
# ErrorResult:
# properties:
# message:
# type: string
# success:
# type: boolean
# type: object
# QueryPOSTResult:
# items:
# allOf:
# - $ref: '#/components/schemas/Association'
# - properties:
# _score:
# format: float
# type: number
# query:
# type: string
# type: object
# type: array
# QueryResult:
# properties:
# hits:
# items:
# $ref: '#/components/schemas/Association'
# type: array
# max_score:
# format: float
# type: number
# took:
# type: integer
# total:
# type: integer
# type: object
# int64_or_array:
# oneOf:
# - items:
# format: int64
# type: integer
# type: array
# - format: int64
# type: integer
# string_or_array:
# oneOf:
# - items:
# type: string
# type: array
# - type: string
x-bte-kgs-operations:
## API includes gene-disease data. ref? https://www.alliancegenome.org/help#disease
## - relationship meanings: https://www.alliancegenome.org/glossary
## is_marker_for only had 2 Gene ID namespaces (HGNC, RGD)
## - Gene: Multiple ID types possible, IDs include prefix (field: _id)
## - HGNC Gene ID
## - Mouse Genome Database (MGI)
## - Rat Genome Database (RGD)
## - Saccharomyces Genome Database (SGD)
## - Zebrafish Information Network (ZFIN)
## - FlyBase (FB)
## - WormBase (WB)
## - Xenbase (Xenbase) - couldn't find later
## - GO Consortium (GO) - couldn't find later
## - Disease: DOID ID with prefixes (field: "doid")
## Other fields: I don't have the full list of terms/namespaces. Would need to analyze original data to get this
## - date: could be usable w/ JQ processing?
## not clear what kind of date this is
## biolink-model has date-related terms that can be edge-attribute ids
## - evidence_code: can use with "biolink:has_evidence"?
## not using because BTE seems to merge values for diff diseases (in same hit)
## ref? https://www.alliancegenome.org/help#docodes and https://www.alliancegenome.org/help#gocodes
## - ECO:0000033 / author statement supported by traceable reference
## - ECO:0000250 / sequence similarity evidence used in manual assertion
## - ECO:0000270 / expression pattern evidence used in manual assertion
## - ECO:0000304 / author statement supported by traceable reference used in manual assertion
## - ECO:0000314 / direct assay evidence used in manual assertion
## - ECO:0000315 / mutant phenotype evidence used in manual assertion
## - ECO:0000501 / evidence used in automatic assertion
## - ECO:0007013 / combinatorial experimental and author inference evidence used in manual assertion
## - ECO:0007191 / inference by association of genotype from phenotype used in manual assertion
## - reference: could be usable w/ JQ processing?
## - PMID rarely?
## - MGI
## - source: string term for deeper provenance
## - Alliance
## - FB
## - WB
## - SGD
## - with_orthologs: not sure if the evidence is from this gene
## - RGD
## - HGNC
## - ZFIN
## - MGI
hgnc-to-doid-isMarkerFor:
## 1769 records
- supportBatch: true
useTemplating: true
inputs:
- id: HGNC
semantic: Gene
requestBody:
body:
## API data has prefix
## joinSafe is only needed if the delimiter isn't a comma
q: "{{ queryInputs | replPrefix('HGNC') }}"
scopes: _id
outputs:
- id: DOID
semantic: Disease
parameters:
## ID field has prefix (DOID)
fields: >-
agr.is_marker_for.doid,
agr.is_marker_for.term_name,
agr.symbol
filter: agr.taxon:"NCBITaxon:9606"
size: 1000
predicate: biomarker_for
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/isMarkerFor-doid"
# testExamples:
# - qInput: "HGNC:10615" ## CCL17
# oneOutput: "DOID:3082" ## interstitial lung disease
doid-to-hgnc-bothBiomarker:
- supportBatch: true
useTemplating: true
inputs:
- id: DOID
semantic: Disease
requestBody:
body:
q: "{{ queryInputs | replPrefix('DOID') }}"
scopes: agr.biomarker_via_orthology.doid,agr.is_marker_for.doid
outputs:
- id: HGNC
semantic: Gene
parameters:
fields: >-
_id,
agr.symbol
filter: agr.taxon:"NCBITaxon:9606"
size: 1000
predicate: has_biomarker
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/hgnc"
# testExamples:
## for biomarker_via_orthology
# - qInput: "DOID:0080322" ## polycystic kidney disease
# oneOutput: "HGNC:1043" ## BGLAP
## for is_marker_for
# - qInput: "DOID:0080600" ## COVID-19
# oneOutput: "HGNC:10626" ## CCL27
rgd-to-doid-isMarkerFor:
## 1534 records
- supportBatch: true
useTemplating: true
inputs:
- id: RGD
semantic: Gene
requestBody:
body:
q: "{{ queryInputs | replPrefix('RGD') }}"
scopes: _id
outputs:
- id: DOID
semantic: Disease
parameters:
fields: >-
agr.is_marker_for.doid,
agr.is_marker_for.term_name,
agr.symbol
filter: agr.taxon:"NCBITaxon:10116"
size: 1000
predicate: biomarker_for
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/isMarkerFor-doid"
# testExamples:
# - qInput: "RGD:1303018" ## Mcm7
# oneOutput: "DOID:684" ## hepatocellular carcinoma
doid-to-rgd-bothBiomarker:
- supportBatch: true
useTemplating: true
inputs:
- id: DOID
semantic: Disease
requestBody:
body:
q: "{{ queryInputs | replPrefix('DOID') }}"
scopes: agr.biomarker_via_orthology.doid,agr.is_marker_for.doid
outputs:
- id: RGD
semantic: Gene
parameters:
fields: >-
_id,
agr.symbol
filter: agr.taxon:"NCBITaxon:10116"
size: 1000
predicate: has_biomarker
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/rgd"
# testExamples:
## for biomarker_via_orthology
# - qInput: "DOID:3587" ## pancreatic ductal carcinoma
# oneOutput: "RGD:1303018" ## Mcm7
## for is_marker_for
# - qInput: "DOID:10325" ## silicosis
# oneOutput: "RGD:1303058" ## Chia
hgnc-to-doid-biomarkerViaOrthology:
## 1581 records
- supportBatch: true
useTemplating: true
inputs:
- id: HGNC
semantic: Gene
requestBody:
body:
## API data has prefix
## joinSafe is only needed if the delimiter isn't a comma
q: "{{ queryInputs | replPrefix('HGNC') }}"
scopes: _id
outputs:
- id: DOID
semantic: Disease
parameters:
## ID field has prefix (DOID)
fields: >-
agr.biomarker_via_orthology.doid,
agr.biomarker_via_orthology.term_name,
agr.symbol
filter: agr.taxon:"NCBITaxon:9606"
size: 1000
## not sure if this predicate is okay for "via orthology"
predicate: biomarker_for
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid"
# testExamples:
# - qInput: "HGNC:1037" ## CFB
# oneOutput: "DOID:0080322" ## polycystic kidney disease
mgi-to-doid-biomarkerViaOrthology:
## 2590 records
- supportBatch: true
useTemplating: true
inputs:
- id: MGI
semantic: Gene
requestBody:
body:
q: "{{ queryInputs | replPrefix('MGI') }}"
scopes: _id
outputs:
- id: DOID
semantic: Disease
parameters:
fields: >-
agr.biomarker_via_orthology.doid,
agr.biomarker_via_orthology.term_name,
agr.symbol
filter: agr.taxon:"NCBITaxon:10090"
size: 1000
predicate: biomarker_for
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid"
# testExamples:
# - qInput: "MGI:109384" ## Atf3
# oneOutput: "DOID:10283" ## prostate cancer
doid-to-mgi-biomarkerViaOrthology:
- supportBatch: true
useTemplating: true
inputs:
- id: DOID
semantic: Disease
requestBody:
body:
q: "{{ queryInputs | replPrefix('DOID') }}"
scopes: agr.biomarker_via_orthology.doid
outputs:
- id: MGI
semantic: Gene
parameters:
fields: >-
_id,
agr.symbol
filter: agr.taxon:"NCBITaxon:10090"
size: 1000
predicate: has_biomarker
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/mgi"
# testExamples:
# - qInput: "DOID:0050758" ## metabolic acidosis
# oneOutput: "MGI:109393" ## Slc4a1
rgd-to-doid-biomarkerViaOrthology:
## 1879 records
- supportBatch: true
useTemplating: true
inputs:
- id: RGD
semantic: Gene
requestBody:
body:
q: "{{ queryInputs | replPrefix('RGD') }}"
scopes: _id
outputs:
- id: DOID
semantic: Disease
parameters:
fields: >-
agr.biomarker_via_orthology.doid,
agr.biomarker_via_orthology.term_name,
agr.symbol
filter: agr.taxon:"NCBITaxon:10116"
size: 1000
predicate: biomarker_for
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid"
# testExamples:
# - qInput: "RGD:1302977" ## Slpil3
# oneOutput: "DOID:2945" ## severe acute respiratory syndrome
zfin-to-doid-biomarkerViaOrthology:
## 2800 records
- supportBatch: true
useTemplating: true
inputs:
- id: ZFIN
semantic: Gene
requestBody:
body:
q: "{{ queryInputs | replPrefix('ZFIN') }}"
scopes: _id
outputs:
- id: DOID
semantic: Disease
parameters:
fields: >-
agr.biomarker_via_orthology.doid,
agr.biomarker_via_orthology.term_name,
agr.symbol
filter: agr.taxon:"NCBITaxon:7955"
size: 1000
predicate: biomarker_for
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid"
# testExamples:
# - qInput: "ZFIN:ZDB-GENE-011205-17" ## mt-cyb
# oneOutput: "DOID:9352" ## type 2 diabetes mellitus
doid-to-zfin-biomarkerViaOrthology:
- supportBatch: true
useTemplating: true
inputs:
- id: DOID
semantic: Disease
requestBody:
body:
q: "{{ queryInputs | replPrefix('DOID') }}"
scopes: agr.biomarker_via_orthology.doid
outputs:
- id: ZFIN
semantic: Gene
parameters:
fields: >-
_id,
agr.symbol
filter: agr.taxon:"NCBITaxon:7955"
size: 1000
predicate: has_biomarker
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/zfin"
# testExamples:
# - qInput: "DOID:7997" ## thyrotoxicosis
# oneOutput: "ZFIN:ZDB-GENE-011205-17" ## mt-cyb
fb-to-doid-biomarkerViaOrthology:
## 1630 records
- supportBatch: true
useTemplating: true
inputs:
- id: FB
semantic: Gene
requestBody:
body:
q: "{{ queryInputs | replPrefix('FB') }}"
scopes: _id
outputs:
- id: DOID
semantic: Disease
parameters:
fields: >-
agr.biomarker_via_orthology.doid,
agr.biomarker_via_orthology.term_name,
agr.symbol
filter: agr.taxon:"NCBITaxon:7227"
size: 1000
predicate: biomarker_for
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid"
# testExamples:
# - qInput: "FB:FBgn0023518" ## trr
# oneOutput: "DOID:5517" ## stomach carcinoma
doid-to-fb-biomarkerViaOrthology:
- supportBatch: true
useTemplating: true
inputs:
- id: DOID
semantic: Disease
requestBody:
body:
q: "{{ queryInputs | replPrefix('DOID') }}"
scopes: agr.biomarker_via_orthology.doid
outputs:
- id: FB
semantic: Gene
parameters:
fields: >-
_id,
agr.symbol
filter: agr.taxon:"NCBITaxon:7227"
size: 1000
predicate: has_biomarker
source: "infores:agrkb"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/fb"
# testExamples:
# - qInput: "DOID:8634" ## prostate carcinoma in situ
# oneOutput: "FB:FBgn0024227" ## aurB
wb-to-doid-biomarkerViaOrthology:
## 1670 records
- supportBatch: true
useTemplating: true
inputs:
- id: WB
semantic: Gene
requestBody: