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openapi.yml
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openapi: 3.0.3
info:
contact:
email: [email protected]
name: BioThings Team
x-id: https://github.com/biothings
x-role: responsible organization
description: >-
Documentation of the BioThings API for [DGIdb](https://dgidb.org/)
drug-gene interaction data.
termsOfService: https://biothings.io/about
title: BioThings DGIdb API
version: '4.2.0'
x-translator:
infores: "infores:biothings-dgidb"
component: KP
team:
- Service Provider
biolink-version: "4.2.2"
servers:
- description: Encrypted Production server
url: https://biothings.ncats.io/dgidb
x-maturity: production
- url: https://biothings.test.transltr.io/dgidb
description: ITRB Test server
x-maturity: testing
- url: https://biothings.ci.transltr.io/dgidb
description: ITRB CI server
x-maturity: staging
tags:
- name: gene
- name: chemical
- name: association
- name: annotation
- name: query
- name: translator
- name: biothings
- name: biothings_graph
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: "1fb7c7f0ef333cd2"
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"
# - "$ref": "#/components/parameters/format"
requestBody:
content:
application/json:
example:
ids:
- "1fb7c7f0ef333cd2"
- "f91c68378f89f4c8"
schema:
type: object
properties:
ids:
description: >-
Accepts multiple association ids. Note that currently we only take the input ids
up to 1000 maximum, the rest will be omitted.
type: array
items:
type: string
responses:
'200':
description: A 200 status code indicates a successful query, and is accompanied by the query response payload.
tags:
- association
"/metadata":
get:
description: Get metadata about the data available from the API
## these are noted in the https://mychem.info/v1/spec endpoint; commenting out for now
# parameters:
# - "$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"
# - "$ref": "#/components/parameters/prefix"
responses:
'200':
description: A 200 status code indicates a successful query, and is accompanied by the query response payload.
tags:
- metadata
"/query":
get:
description: >-
Query service. In the output, "total" in the output gives the total number
of matching hits, while the actual hits are returned under "hits" field.
parameters:
- name: q
description: >-
Required, passing user query. The detailed query syntax for parameter is explained
[here for a core BioThings
API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).
in: query
required: true
example: "subject.CHEMBL_COMPOUND:CHEMBL1017"
schema:
type: string
- "$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"
# - "$ref": "#/components/parameters/format"
requestBody:
content:
application/json:
example:
q:
- "CHEMBL266510"
- "CHEMBL1200833"
scopes:
- "subject.CHEMBL_COMPOUND"
schema:
type: object
properties:
q:
description: >-
Accepts multiple values separated by commas. Note that currently we only take the input values
up to 1000 maximum, the rest will be omitted.
type: array
items:
type: string
scopes:
description: >-
Specify one or more fields (separated by commas) to search. Default: _id
type: array
items:
type: string
responses:
'200':
description: A 200 status code indicates a successful query, and is accompanied by the query response payload.
## commenting out schemas and other status codes for now
# content:
# application/json:
# schema:
# "$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
## 12 sets (24 operations)
x-bte-kgs-operations:
- $ref: '#/components/x-bte-kgs-operations/activator'
- $ref: '#/components/x-bte-kgs-operations/activator-rev'
- $ref: '#/components/x-bte-kgs-operations/agonist'
- $ref: '#/components/x-bte-kgs-operations/agonist-rev'
- $ref: '#/components/x-bte-kgs-operations/allosteric_modulator'
- $ref: '#/components/x-bte-kgs-operations/allosteric_modulator-rev'
- $ref: '#/components/x-bte-kgs-operations/antagonist'
- $ref: '#/components/x-bte-kgs-operations/antagonist-rev'
- $ref: '#/components/x-bte-kgs-operations/antibody'
- $ref: '#/components/x-bte-kgs-operations/antibody-rev'
## commenting out because there's only 4 records for this set of operations
# - $ref: '#/components/x-bte-kgs-operations/antisense_oligonucleotide'
# - $ref: '#/components/x-bte-kgs-operations/antisense_oligonucleotide-rev'
- $ref: '#/components/x-bte-kgs-operations/blocker'
- $ref: '#/components/x-bte-kgs-operations/blocker-rev'
## commenting out because there's only 1 record for this set of operations
# - $ref: '#/components/x-bte-kgs-operations/inducer'
# - $ref: '#/components/x-bte-kgs-operations/inducer-rev'
- $ref: '#/components/x-bte-kgs-operations/inhibitor'
- $ref: '#/components/x-bte-kgs-operations/inhibitor-rev'
## commenting out because there's only 1 record for this set of operations
# - $ref: '#/components/x-bte-kgs-operations/inhibitory_allosteric_modulator'
# - $ref: '#/components/x-bte-kgs-operations/inhibitory_allosteric_modulator-rev'
- $ref: '#/components/x-bte-kgs-operations/inverse_agonist'
- $ref: '#/components/x-bte-kgs-operations/inverse_agonist-rev'
- $ref: '#/components/x-bte-kgs-operations/modulator'
- $ref: '#/components/x-bte-kgs-operations/modulator-rev'
## commenting out because there's only 5 records for this set of operations
# - $ref: '#/components/x-bte-kgs-operations/negative_modulator'
# - $ref: '#/components/x-bte-kgs-operations/negative_modulator-rev'
- $ref: '#/components/x-bte-kgs-operations/no_dgidb_relationship'
- $ref: '#/components/x-bte-kgs-operations/no_dgidb_relationship-rev'
- $ref: '#/components/x-bte-kgs-operations/partial_agonist'
- $ref: '#/components/x-bte-kgs-operations/partial_agonist-rev'
- $ref: '#/components/x-bte-kgs-operations/positive_modulator'
- $ref: '#/components/x-bte-kgs-operations/positive_modulator-rev'
## commenting out because there's only 1 record for this set of operations
# - $ref: '#/components/x-bte-kgs-operations/suppressor'
# - $ref: '#/components/x-bte-kgs-operations/suppressor-rev'
## commenting out because there's only 8 records for this set of operations
# - $ref: '#/components/x-bte-kgs-operations/vaccine'
# - $ref: '#/components/x-bte-kgs-operations/vaccine-rev'
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:
## - future: we could ingest subject.drug_name and object.SYMBOL fields
## - we will only use records with subject.CHEMBL_COMPOUND
## - only 154 records don't have this field: https://biothings.ncats.io/dgidb/query?q=NOT%20_exists_:subject.CHEMBL_COMPOUND
## those drugs may have had a name or wikidata ID that couldn't be mapped to chembl in MyChem.
## - all records have object.NCBIGene
## - for interaction_claim_source info, see https://www.dgidb.org/browse/sources
## - for interaction_types info, see https://www.dgidb.org/about#interaction-types
## Most records did not have a value for that column. We put the value to "not_applicable" in those cases...
## - for interaction_group_score info, see https://www.dgidb.org/about#interaction-scores
## - only some records have PMIDs. all records have interaction_group_score, interaction_claim_source
## - in the future, could edit parser + queries to handle prefixes
## - joinSafe is only needed if the delimiter isn't a comma
activator:
## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:activator
## 195 records
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
requestBody:
body:
q: "{{ queryInputs }}"
scopes: subject.CHEMBL_COMPOUND
parameters:
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# object.NCBIGene,association.interaction_group_score,
# association.interaction_claim_source,association.pmids,association.interaction_types
fields: >-
object.NCBIGene,association.pmids
size: 1000
filter: association.interaction_types:activator
outputs:
- id: NCBIGene
semantic: Gene
predicate: affects
## nesting allows this main key to stay the same even with future changes
qualifiers:
## key is the "qualifier_type_id", value is the "qualifier_value" in the TRAPI Edge.qualifiers spec
qualified_predicate: causes
object_aspect_qualifier: activity
object_direction_qualifier: increased
causal_mechanism_qualifier: activation ## extra since DGIdb labels these as "activator"
source: "infores:dgidb"
knowledge_level: knowledge_assertion
agent_type: automated_agent
response_mapping:
"$ref": "#/components/x-bte-response-mapping/forward"
testExamples:
- qInput: "CHEMBL.COMPOUND:CHEMBL266510" ## FLINDOKALNER
oneOutput: "NCBIGene:9132" ## KCNQ4
activator-rev:
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}"
scopes: object.NCBIGene
parameters:
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# subject.CHEMBL_COMPOUND,association.interaction_group_score,
# association.interaction_claim_source,association.pmids,association.interaction_types
fields: >-
subject.CHEMBL_COMPOUND,association.pmids
size: 1000
filter: association.interaction_types:activator
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## biolink 2.4.8: used entity_positively_regulated_by_entity
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
subject_aspect_qualifier: activity
subject_direction_qualifier: increased
causal_mechanism_qualifier: activation ## extra since DGIdb labels these as "activator"
source: "infores:dgidb"
knowledge_level: knowledge_assertion
agent_type: automated_agent
response_mapping:
"$ref": "#/components/x-bte-response-mapping/reverse"
testExamples:
- qInput: "NCBIGene:2983" ## GUCY1B1
oneOutput: "CHEMBL.COMPOUND:CHEMBL730" ## NITROGLYCERIN
agonist:
## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:agonist
## 2234 records
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
requestBody:
body:
q: "{{ queryInputs }}"
scopes: subject.CHEMBL_COMPOUND
parameters:
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# object.NCBIGene,association.interaction_group_score,
# association.interaction_claim_source,association.pmids,association.interaction_types
fields: >-
object.NCBIGene,association.pmids
size: 1000
filter: association.interaction_types:agonist
outputs:
- id: NCBIGene
semantic: Gene
## for biolink 2.4.8, DGIdb:agonist maps to increases_activity_of
predicate: affects
qualifiers:
qualified_predicate: causes
object_aspect_qualifier: activity
object_direction_qualifier: increased
causal_mechanism_qualifier: agonism ## extra since DGIdb labels these as "agonist"
source: "infores:dgidb"
knowledge_level: knowledge_assertion
agent_type: automated_agent
response_mapping:
"$ref": "#/components/x-bte-response-mapping/forward"
testExamples:
- qInput: "CHEMBL.COMPOUND:CHEMBL1200833" ## DIPIVEFRIN HYDROCHLORIDE
oneOutput: "NCBIGene:155" ## ADRB3
## some records have multiple interaction_types
## 1 record, agonist + allosteric_modulator: https://biothings.ncats.io/dgidb/query?q=association.interaction_types:agonist%20AND%20association.interaction_types:allosteric_modulator
## 17 records, agonist + antagonist: https://biothings.ncats.io/dgidb/query?q=association.interaction_types:agonist%20AND%20association.interaction_types:antagonist
agonist-rev:
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}"
scopes: object.NCBIGene
parameters:
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# subject.CHEMBL_COMPOUND,association.interaction_group_score,
# association.interaction_claim_source,association.pmids,association.interaction_types
fields: >-
subject.CHEMBL_COMPOUND,association.pmids
size: 1000
filter: association.interaction_types:agonist
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.4.8, DGIdb:agonist maps to the inverse of increases_activity_of
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
subject_aspect_qualifier: activity
subject_direction_qualifier: increased
causal_mechanism_qualifier: agonism ## extra since DGIdb labels these as "agonist"
source: "infores:dgidb"
knowledge_level: knowledge_assertion
agent_type: automated_agent
response_mapping:
"$ref": "#/components/x-bte-response-mapping/reverse"
testExamples:
- qInput: "NCBIGene:1814" ## DRD3
oneOutput: "CHEMBL.COMPOUND:CHEMBL2146110" ## SARIZOTAN HYDROCHLORIDE
allosteric_modulator:
## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:allosteric_modulator
## 170 records
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
requestBody:
body:
q: "{{ queryInputs }}"
scopes: subject.CHEMBL_COMPOUND
parameters:
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# object.NCBIGene,association.interaction_group_score,
# association.interaction_claim_source,association.pmids,association.interaction_types
fields: >-
object.NCBIGene,association.pmids
size: 1000
filter: association.interaction_types:allosteric_modulator
outputs:
- id: NCBIGene
semantic: Gene
## for biolink 2.4.8, DGIdb:allosteric_modulator maps to affects_activity_of
predicate: affects
qualifiers:
object_aspect_qualifier: activity
## no causal_mechanism_qualifier for "allosteric modulator" (not negative or positive)
source: "infores:dgidb"
knowledge_level: knowledge_assertion
agent_type: automated_agent
response_mapping:
"$ref": "#/components/x-bte-response-mapping/forward"
testExamples:
- qInput: "CHEMBL.COMPOUND:CHEMBL3305985" ## ALCURONIUM
oneOutput: "NCBIGene:1132" ## CHRM4
allosteric_modulator-rev:
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}"
scopes: object.NCBIGene
parameters:
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# subject.CHEMBL_COMPOUND,association.interaction_group_score,
# association.interaction_claim_source,association.pmids,association.interaction_types
fields: >-
subject.CHEMBL_COMPOUND,association.pmids
size: 1000
filter: association.interaction_types:allosteric_modulator
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.4.8, DGIdb:allosteric_modulator maps to the inverse of affects_activity_of
predicate: affected_by
qualifiers:
subject_aspect_qualifier: activity
## no causal_mechanism_qualifier for "allosteric modulator" (not negative or positive)
source: "infores:dgidb"
knowledge_level: knowledge_assertion
agent_type: automated_agent
response_mapping:
"$ref": "#/components/x-bte-response-mapping/reverse"
testExamples:
- qInput: "NCBIGene:207" ## AKT1
oneOutput: "CHEMBL.COMPOUND:CHEMBL1079175" ## MK-2206
antagonist:
## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:antagonist
## 2330 records
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
requestBody:
body:
q: "{{ queryInputs }}"
scopes: subject.CHEMBL_COMPOUND
parameters:
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# object.NCBIGene,association.interaction_group_score,
# association.interaction_claim_source,association.pmids,association.interaction_types
fields: >-
object.NCBIGene,association.pmids
size: 1000
filter: association.interaction_types:antagonist
outputs:
- id: NCBIGene
semantic: Gene
## for biolink 2.4.8, DGIdb:antagonist maps to decreases_activity_of
predicate: affects
qualifiers:
qualified_predicate: causes
object_aspect_qualifier: activity
object_direction_qualifier: decreased
causal_mechanism_qualifier: antagonism ## extra since DGIdb labels these as "antagonist"
source: "infores:dgidb"
knowledge_level: knowledge_assertion
agent_type: automated_agent
response_mapping:
"$ref": "#/components/x-bte-response-mapping/forward"
testExamples:
- qInput: "CHEMBL.COMPOUND:CHEMBL3545038" ## S-237648
oneOutput: "NCBIGene:4889" ## NPY5R
## some records have multiple interaction_types
## 1 record, antagonist + allosteric_modulator: https://biothings.ncats.io/dgidb/query?q=association.interaction_types:allosteric_modulator%20AND%20association.interaction_types:antagonist
antagonist-rev:
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}"
scopes: object.NCBIGene
parameters:
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# subject.CHEMBL_COMPOUND,association.interaction_group_score,
# association.interaction_claim_source,association.pmids,association.interaction_types
fields: >-
subject.CHEMBL_COMPOUND,association.pmids
size: 1000
filter: association.interaction_types:antagonist
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.4.8, DGIdb:antagonist maps to the inverse of decreases_activity_of
predicate: affected_by
qualifiers:
qualified_predicate: caused_by
subject_aspect_qualifier: activity
subject_direction_qualifier: decreased
causal_mechanism_qualifier: antagonism ## extra since DGIdb labels these as "antagonist"
source: "infores:dgidb"
knowledge_level: knowledge_assertion
agent_type: automated_agent
response_mapping:
"$ref": "#/components/x-bte-response-mapping/reverse"
testExamples:
- qInput: "NCBIGene:185" ## AGTR1
oneOutput: "CHEMBL.COMPOUND:CHEMBL1017" ## TELMISARTAN
antibody:
## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:antibody
## 222 records
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
requestBody:
body:
q: "{{ queryInputs }}"
scopes: subject.CHEMBL_COMPOUND
parameters:
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# object.NCBIGene,association.interaction_group_score,
# association.interaction_claim_source,association.pmids,association.interaction_types
fields: >-
object.NCBIGene,association.pmids
size: 1000
filter: association.interaction_types:antibody
outputs:
- id: NCBIGene
semantic: Gene
## for biolink 2.4.8, was using directly_interacts_with (mapping for GAMMA:antibody)
predicate: physically_interacts_with
qualifiers:
causal_mechanism_qualifier: antibody_inhibition ## extra since DGIdb labels these as "antibody"
source: "infores:dgidb"
knowledge_level: knowledge_assertion
agent_type: automated_agent
response_mapping:
"$ref": "#/components/x-bte-response-mapping/forward"
testExamples:
- qInput: "CHEMBL.COMPOUND:CHEMBL4297570" ## AMP-224
oneOutput: "NCBIGene:80380" ## PDCD1LG2
antibody-rev:
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}"
scopes: object.NCBIGene
parameters:
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# subject.CHEMBL_COMPOUND,association.interaction_group_score,
# association.interaction_claim_source,association.pmids,association.interaction_types
fields: >-
subject.CHEMBL_COMPOUND,association.pmids
size: 1000
filter: association.interaction_types:antibody
outputs:
- id: "CHEMBL.COMPOUND"
semantic: SmallMolecule
## for biolink 2.4.8, was using directly_interacts_with (mapping for GAMMA:antibody)
predicate: physically_interacts_with
qualifiers:
causal_mechanism_qualifier: antibody_inhibition ## extra since DGIdb labels these as "antibody"
source: "infores:dgidb"
knowledge_level: knowledge_assertion
agent_type: automated_agent