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smartapi.yaml
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openapi: 3.0.3
info:
contact:
email: help@biothings.io
name: BioThings Team
x-role: responsible developers
description: >-
Documentation of the BioThings API for [Therapeutic Target Database](https://db.idrblab.net/ttd/).
This KP contains drug-disease, target-disease, drug-protein target, and biomarker-disease associations.
termsOfService: https://biothings.io/about
title: Biothings Therapeutic Target Database API
version: '1.0' ## API version, KP version is 8.1.01
x-translator:
infores: "infores:biothings-ttd"
component: KP
team:
- Service Provider
biolink-version: "3.5.0"
servers:
- description: Encrypted Production server
url: https://biothings.ncats.io/ttd
x-maturity: production
- description: Production server
url: http://biothings.ncats.io/ttd
x-maturity: production
tags:
- name: gene
- name: disease
- name: chemical
- name: association
- name: annotation
- name: query
- name: translator
- name: biothings
- name: metadata
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.
parameters:
- name: id
in: path
required: true
example: "101481444_interacts_with_O60885"
schema:
type: string
## fields is the most useful parameter
- "$ref": "#/components/parameters/fields"
# - "$ref": "#/components/parameters/raw"
# - "$ref": "#/components/parameters/rawquery"
- "$ref": "#/components/parameters/dotfield"
- "$ref": "#/components/parameters/always_list"
- "$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:
# $ref: '#/components/schemas/Association'
'404':
description: A response indicating an unknown association ID
summary: >-
Retrieve association based on ID
tags:
- association
"/association":
post:
description: >-
Although making simple GET requests above to our service is sufficient in most use cases,
there are some times you might find it easier to batch query (e.g., retrieving multiple associations).
Fortunately, you can also make batch queries via POST requests when you need to.
parameters:
- name: ids
description: >-
Accepts multiple association ids separated by commas. Note that currently we only take ids up to
1000 maximum, the rest will be omitted.
The request body can also be used to provide these ids.
in: query
## setting to false since putting this info in the request body seems to work as well
required: false
schema:
type: string
- "$ref": "#/components/parameters/fields"
# - "$ref": "#/components/parameters/raw"
# - "$ref": "#/components/parameters/rawquery"
- "$ref": "#/components/parameters/dotfield"
- "$ref": "#/components/parameters/always_list"
- "$ref": "#/components/parameters/allow_null"
- "$ref": "#/components/parameters/format"
requestBody:
content:
application/json:
example:
ids:
- "136183441_interacts_with_Q16548"
- "P17301_target_for_0005301"
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.
## No '404' is included in the post due to batch query
tags:
- association
"/metadata":
get:
description: Get metadata about the data available from the API
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
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: "object.mondo:0005083"
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"
- "$ref": "#/components/parameters/dotfield"
- "$ref": "#/components/parameters/aggs"
## these are noted in the /spec endpoint; commenting out for now
# - "$ref": "#/components/parameters/userquery"
# - "$ref": "#/components/parameters/explain"
# - "$ref": "#/components/parameters/raw"
# - "$ref": "#/components/parameters/rawquery"
- "$ref": "#/components/parameters/always_list"
- "$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"
## 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:
- "6323491"
- "136183441"
scopes:
- "subject.pubchem_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
x-bte-kgs-operations:
# - $ref: '#/components/x-bte-kgs-operations/chebi_treats_mondo'
# - $ref: '#/components/x-bte-kgs-operations/chebi_treats_mondo-rev'
# - $ref: '#/components/x-bte-kgs-operations/chebi_treats_icd11'
# - $ref: '#/components/x-bte-kgs-operations/chebi_treats_icd11-rev'
- $ref: '#/components/x-bte-kgs-operations/pubchem_treats_mondo'
- $ref: '#/components/x-bte-kgs-operations/pubchem_treats_mondo-rev'
- $ref: '#/components/x-bte-kgs-operations/pubchem_treats_icd11'
- $ref: '#/components/x-bte-kgs-operations/pubchem_treats_icd11-rev'
- $ref: '#/components/x-bte-kgs-operations/ttd_drug_id_treats_mondo'
- $ref: '#/components/x-bte-kgs-operations/ttd_drug_id_treats_mondo-rev'
- $ref: '#/components/x-bte-kgs-operations/ttd_drug_id_treats_icd11'
- $ref: '#/components/x-bte-kgs-operations/ttd_drug_id_treats_icd11-rev'
- $ref: '#/components/x-bte-kgs-operations/uniprotkb_target_for_mondo'
- $ref: '#/components/x-bte-kgs-operations/uniprotkb_target_for_mondo-rev'
- $ref: '#/components/x-bte-kgs-operations/uniprotkb_target_for_icd11'
- $ref: '#/components/x-bte-kgs-operations/uniprotkb_target_for_icd11-rev'
- $ref: '#/components/x-bte-kgs-operations/ttd_target_id_target_for_mondo'
- $ref: '#/components/x-bte-kgs-operations/ttd_target_id_target_for_mondo-rev'
- $ref: '#/components/x-bte-kgs-operations/ttd_target_id_target_for_icd11'
- $ref: '#/components/x-bte-kgs-operations/ttd_target_id_target_for_icd11-rev'
# - $ref: '#/components/x-bte-kgs-operations/chebi_interacts_with_uniprotkb'
# - $ref: '#/components/x-bte-kgs-operations/chebi_interacts_with_uniprotkb-rev'
# - $ref: '#/components/x-bte-kgs-operations/chebi_interacts_with_ttd_target_id'
# - $ref: '#/components/x-bte-kgs-operations/chebi_interacts_with_ttd_target_id-rev'
- $ref: '#/components/x-bte-kgs-operations/pubchem_interacts_with_uniprotkb'
- $ref: '#/components/x-bte-kgs-operations/pubchem_interacts_with_uniprotkb-rev'
- $ref: '#/components/x-bte-kgs-operations/pubchem_interacts_with_ttd_target_id'
- $ref: '#/components/x-bte-kgs-operations/pubchem_interacts_with_ttd_target_id-rev'
- $ref: '#/components/x-bte-kgs-operations/ttd_drug_id_interacts_with_uniprotkb'
- $ref: '#/components/x-bte-kgs-operations/ttd_drug_id_interacts_with_uniprotkb-rev'
- $ref: '#/components/x-bte-kgs-operations/ttd_drug_id_interacts_with_ttd_target_id'
- $ref: '#/components/x-bte-kgs-operations/ttd_drug_id_interacts_with_ttd_target_id-rev'
# TODO: Not doing operation right now. But can potentially map some of the biomarkers to gene/protein
# - $ref: '#/components/x-bte-kgs-operations/biomarker_id_biomarker_for_mondo'
# - $ref: '#/components/x-bte-kgs-operations/biomarker_id_biomarker_for_mondo-rev'
# - $ref: '#/components/x-bte-kgs-operations/biomarker_id_biomarker_for_icd11'
# - $ref: '#/components/x-bte-kgs-operations/biomarker_id_biomarker_for_icd11-rev'
# - $ref: '#/components/x-bte-kgs-operations/biomarker_id_biomarker_for_icd10'
# - $ref: '#/components/x-bte-kgs-operations/biomarker_id_biomarker_for_icd10-rev'
# - $ref: '#/components/x-bte-kgs-operations/biomarker_id_biomarker_for_icd9'
# - $ref: '#/components/x-bte-kgs-operations/biomarker_id_biomarker_for_icd9-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
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:
## in the API's records:
## - subjects and objects can be Gene/Protein (UniprotKB), SmallMolecule (PUBCHEM.COMPOUND, CHEBI),
## Disease (MONDO, ICD11, ICD10, ICD9)
## - predicates can be treats, target_for, interacts_with
## SmallMolecule_treats_Disease, Gene_target_for_Disease, SmallMolecule_interacts_with_Gene
## - BTE automatically puts prefix on MONDO IDs, but prefix has to be added to other ID inputs
## - currently, BTE will also accept response with Translator-prefix (api-response-transform module).
## - joinSafe is only needed if the delimiter isn't a comma
## - fields not included due to data-processing / biolink-modeling issues:
## - association.clinical_trial.status:has lots of possible values
## 'investigative', 'patented', 'phase 2', 'approved', 'phase 1', 'terminated', 'phase 3',
## 'discontinued in phase 2', 'phase 1/2', 'discontinued in phase 1', 'preclinical', 'discontinued in phase 3',
## 'phase 2/3', 'clinical trial', 'withdrawn from market', 'phase 4', 'phase 3 trial', 'discontinued in phase1/2',
## 'phase 2 trial', 'discontinued in preregistration', 'phase 2/3 trial', 'preregistration', 'phase 2a',
## 'phase 1 trial', 'phase 0', 'registered', 'approved (orphan drug)', 'phase 1b', 'phase 2b',
## 'discontinued in phase2/3', 'NDA filed', 'phase 1/2 trial', 'phase 1/2a', 'discontinued in phase 1 trial',
## 'discontinued in phase 4', 'phase 1b/2a', 'application submitted', 'approval submitted', 'BLA submitted',
## 'discontinued in phase 2a', 'discontinued in phase 2b'
## - subject.bioclass. TODO: list the values (if too many, make a notes, need to make keys that are certain vocabularies)
## - subject.target_type. TODO: list the values (if too many, makes notes)
# chebi_treats_mondo:
# ## https://biothings.transltr.io/ttd/query?q=_exists_:subject.chebi%20AND%20association.predicate:%22biolink:treats%22%20AND%20_exists_:object.mondo
# ## 543 records
# - supportBatch: true
# useTemplating: true ## flag to say templating is being used below
# inputs:
# - id: CHEBI
# semantic: SmallMolecule
# requestBodyType: object
# requestBody:
# body: >-
# {
# "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:treats"]') }} ],
# "scopes": ["subject.chebi", "association.predicate"]
# }
# outputs:
# - id: MONDO
# semantic: Disease
# parameters:
# ## not including these fields due to data-processing / biolink-modeling issues
# ## - association.clinical_trial.status
# fields: >-
# object.mondo,
# object.name,
# subject.name
# size: 1000
# predicate: treats
# source: "infores:ttd"
# response_mapping:
# "$ref": "#/components/x-bte-response-mapping/mondo-object"
# # testExamples:
# # - qInput: "CHEBI:6960" ## Moexipril
# # oneOutput: "MONDO:0001134" ## Hypertension
# chebi_treats_mondo-rev:
# - supportBatch: true
# useTemplating: true
# inputs:
# - id: MONDO
# semantic: Disease
# requestBodyType: object
# requestBody:
# body: >- ## take out mondo prefix
# {
# "q": [ {{ queryInputs | rmPrefix() | wrap( '["' , '","biolink:treats"]') }} ],
# "scopes": ["object.mondo", "association.predicate"]
# }
# outputs:
# - id: CHEBI
# semantic: SmallMolecule
# parameters:
# fields: >-
# subject.chebi,
# subject.name,
# object.name
# size: 1000
# predicate: treated_by
# source: "infores:ttd"
# response_mapping:
# "$ref": "#/components/x-bte-response-mapping/chebi-subject"
# # testExamples:
# # - qInput: "MONDO:0005180" ## Parkinson disease
# # oneOutput: "CHEBI:134699" ## Opicapone
# chebi_treats_icd11:
# ## url: https://biothings.transltr.io/ttd/query?q=\_exists_:subject.chebi%20AND%20association.predicate:%22biolink:treats%22%20AND%20_exists_:object.icd11
# ## 3806 records
# - supportBatch: true
# useTemplating: true ## flag to say templating is being used below
# inputs:
# - id: CHEBI
# semantic: SmallMolecule
# requestBodyType: object
# requestBody: ## no prefix
# body: >-
# {"q": {{ queryInputs | replPrefix('association.predicate:"biolink:treats"
# AND (NOT _exists_:subject.pubchem_compound) AND (NOT _exists:object.mondo) AND subject.chebi')| dump}},
# "scopes": []
# }
# outputs:
# - id: ICD11
# semantic: Disease
# parameters:
# ## not including these fields due to data-processing / biolink-modeling issues
# ## - association.clinical_trial.status
# ## - object.mondo Not all object node has mondo
# fields: >-
# object.icd11,
# object.name,
# subject.name
# size: 1000
# predicate: treats
# source: "infores:ttd"
# response_mapping:
# "$ref": "#/components/x-bte-response-mapping/icd11-object"
# # testExamples:
# # - qInput: "CHEBI:107601" ## Savirin
# # oneOutput: "ICD11:1B5Y" ## Staphylococcus infection
# chebi_treats_icd11-rev:
# - supportBatch: true
# useTemplating: true
# inputs:
# - id: ICD11
# semantic: Disease
# requestBodyType: object
# requestBody: ## no prefix
# body: >-
# {"q": {{ queryInputs | replPrefix('association.predicate:"biolink:treats"
# AND (NOT _exists_:subject.pubchem_compound) AND (NOT _exists:object.mondo) AND object.icd11')| dump}},
# "scopes": []
# }
# outputs:
# - id: CHEBI
# semantic: SmallMolecule
# parameters:
# ## not including these fields due to data-processing / biolink-modeling issues
# ## - association.clinical_trial.status
# fields: >-
# subject.chebi,
# subject.name,
# object.name
# size: 1000
# predicate: treated_by
# source: "infores:ttd"
# response_mapping:
# "$ref": "#/components/x-bte-response-mapping/chebi-subject"
# # testExamples:
# # - qInput: "ICD11:CB03.4" ## Pulmonary fibrosis
# # oneOutput: "CHEBI:144367" ## 3PO
pubchem_treats_mondo:
## https://biothings.transltr.io/ttd/query?q=_exists_:subject.pubchem_compound%20AND%20_exists_:object.mondo%20AND%20association.predicate:%22biolink:treats%22
## 1604 records
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: "PUBCHEM.COMPOUND"
semantic: SmallMolecule
requestBody: ## no prefix
body:
q: "{{ queryInputs | rmPrefix() }}"
scopes: subject.pubchem_compound
outputs:
- id: MONDO
semantic: Disease
parameters:
## not including these fields due to data-processing / biolink-modeling issues
## - association.clinical_trial.status
fields: >-
object.mondo,
object.name,
subject.name
size: 1000
filter: _exists_:subject.pubchem_compound AND _exists_:object.mondo AND association.predicate:"biolink:treats"
predicate: treats
source: "infores:ttd"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/mondo-object"
# testExamples:
# - qInput: "PUBCHEM.COMPOUND:118063735" ## LMB763 (Nidufexor)
# oneOutput: "MONDO:0004790" ## fatty liver disease
pubchem_treats_mondo-rev:
- supportBatch: true
useTemplating: true
inputs:
- id: MONDO
semantic: Disease
requestBody: ## no prefix
body:
q: "{{ queryInputs | rmPrefix() }}"
scopes: object.mondo
outputs:
- id: "PUBCHEM.COMPOUND"
semantic: SmallMolecule
parameters:
fields: >-
subject.pubchem_compound,
subject.name,
object.name
size: 1000
filter: _exists_:subject.pubchem_compound AND _exists_:object.mondo AND association.predicate:"biolink:treats"
predicate: treated_by
source: "infores:ttd"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/pubchem-subject"
# testExamples:
# - qInput: "MONDO:0021094" ## Human immunodeficiency virus infection
# oneOutput: "PUBCHEM.COMPOUND:103596027" ## GS-1156 (8-(3-Chloro-5-(trifluoromethyl)pyridin-2-yl)-8-azabicyclo[3.2.1]octan-3-one)
pubchem_treats_icd11:
## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.pubchem_compound%20AND%20_exists_:object.icd11%20AND%20(NOT%20_exists_:object.mondo)%20AND%20association.predicate:%22biolink:treats%22
## 9985 records
## exists: subject.pubchem_compound, association.predicate.biolink:treats, object.icd11
## not exists: object.mondo
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: "PUBCHEM.COMPOUND"
semantic: SmallMolecule
requestBody: ## no prefix
body:
q: "{{ queryInputs | rmPrefix() }}"
scopes: subject.pubchem_compound
outputs:
- id: ICD11
semantic: Disease
parameters:
## not including these fields due to data-processing / biolink-modeling issues
## - association.clinical_trial.status
fields: >-
object.icd11,
object.name,
subject.name
size: 1000
filter: _exists_:subject.pubchem_compound AND _exists_:object.icd11 AND (NOT _exists_:object.mondo) AND association.predicate:"biolink:treats"
predicate: treats
source: "infores:ttd"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/icd11-object"
# testExamples:
# - qInput: "PUBCHEM.COMPOUND:126843189" ## AVN-101 (AVN-101 HCl)
# oneOutput: "ICD11:6D71" ## Cognitive impairment
pubchem_treats_icd11-rev:
- supportBatch: true
useTemplating: true
inputs:
- id: ICD11
semantic: Disease
requestBody: ## no prefix
body:
q: "{{ queryInputs | rmPrefix() }}"
scopes: object.icd11
outputs:
- id: "PUBCHEM.COMPOUND"
semantic: SmallMolecule
parameters:
fields: >-
subject.pubchem_compound,
subject.name,
object.name
size: 1000
filter: _exists_:subject.pubchem_compound AND _exists_:object.icd11 AND (NOT _exists_:object.mondo) AND association.predicate:"biolink:treats"
predicate: treated_by
source: "infores:ttd"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/pubchem-subject"
# testExamples:
# - qInput: "ICD11:MG51" ## Multidrug resistant infection
# oneOutput: "PUBCHEM.COMPOUND:139600308" ## SPR206
ttd_drug_id_treats_mondo:
## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.ttd_drug_id%20AND%20(NOT%20_exists_:subject.pubchem_compound)%20AND%20_exists_:object.mondo%20AND%20association.predicate:%22biolink:treats%22
## 2240 records
## exists: subject.ttd_drug_id, association.predicate.biolink:treats, object.mondo
## not exists: subject.pubchem_compound
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: "TTD.DRUG"
semantic: SmallMolecule
requestBody: ## no prefix
body:
q: "{{ queryInputs | rmPrefix() }}"
scopes: subject.ttd_drug_id
outputs:
- id: MONDO
semantic: Disease
parameters:
## not including these fields due to data-processing / biolink-modeling issues
## - association.clinical_trial.status
fields: >-
object.mondo,
object.name,
subject.name
size: 1000
filter: _exists_:subject.ttd_drug_id AND (NOT _exists_:subject.pubchem_compound) AND _exists_:object.mondo AND association.predicate:"biolink:treats"
predicate: treats
source: "infores:ttd"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/mondo-object"
# testExamples:
# - qInput: "TTD.DRUG:DZJ3D5" ## PF-07220060
# oneOutput: "MONDO:0008315" ## Prostate cancer
ttd_drug_id_treats_mondo-rev:
- supportBatch: true
useTemplating: true
inputs:
- id: MONDO
semantic: Disease
requestBody: ## no prefix
body:
q: "{{ queryInputs | rmPrefix() }}"
scopes: object.mondo
outputs:
- id: "TTD.DRUG"
semantic: SmallMolecule
parameters:
fields: >-
subject.ttd_drug_id,
subject.name,
object.name
size: 1000
filter: _exists_:subject.ttd_drug_id AND (NOT _exists_:subject.pubchem_compound) AND _exists_:object.mondo AND association.predicate:"biolink:treats"
predicate: treated_by
source: "infores:ttd"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/ttd_drug_id-subject"
# testExamples:
# - qInput: "MONDO:0019056" ## Myasthenia gravis
# oneOutput: "TTD.DRUG:DZA98D" ## ARGX-113
ttd_drug_id_treats_icd11:
## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.ttd_drug_id%20AND%20association.predicate:%22biolink:treats%22%20AND%20_exists_:object.icd11%20AND%20NOT%20_exists_:object.mondoAND%20NOT%20_exists_:subject.pubchem_compound
## 16,956 records
## exists: subject.ttd_drug_id, association.predicate.biolink:treats, object.icd11
## not exists: subject.pubchem_compound, object.mondo
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: "TTD.DRUG"
semantic: SmallMolecule
requestBody: ## no prefix
body:
q: "{{ queryInputs | rmPrefix() }}"
scopes: subject.ttd_drug_id
outputs:
- id: ICD11
semantic: Disease
parameters:
## not including these fields due to data-processing / biolink-modeling issues
## - association.clinical_trial.status
## - object.mondo Not all object node has mondo
fields: >-
object.icd11,
object.name,
subject.name
size: 1000
filter: >-
_exists_:subject.ttd_drug_id AND (NOT _exists_:subject.pubchem_compound) AND
_exists_:object.icd11 AND (NOT _exists_:object.mondo) AND
association.predicate:"biolink:treats"
predicate: treats
source: "infores:ttd"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/icd11-object"
# testExamples:
# - qInput: "TTD.DRUG:DZW53X" ## GSK4069889
# oneOutput: "ICD11:2C25" ## Non-small cell lung cancer
ttd_drug_id_treats_icd11-rev:
- supportBatch: true
useTemplating: true
inputs:
- id: ICD11
semantic: Disease
requestBody: ## no prefix
body:
q: "{{ queryInputs | rmPrefix() }}"
scopes: object.icd11
outputs:
- id: "TTD.DRUG"
semantic: SmallMolecule
parameters:
## not including these fields due to data-processing / biolink-modeling issues
## - association.clinical_trial.status
fields: >-
subject.ttd_drug_id,
subject.name,
object.name
size: 1000
filter: >-
_exists_:subject.ttd_drug_id AND (NOT _exists_:subject.pubchem_compound) AND
_exists_:object.icd11 AND (NOT _exists_:object.mondo) AND
association.predicate:"biolink:treats"
predicate: treated_by
source: "infores:ttd"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/ttd_drug_id-subject"
# testExamples:
# - qInput: "ICD11:1D48" ## Zika virus infection
# oneOutput: "TTD.DRUG:DZTL59" ## INO-A002
uniprotkb_target_for_mondo:
## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.uniprotkb%20AND%20association.predicate:%22biolink:target_for%22%20AND%20_exists_:object.mondo
## 601 records
- supportBatch: true
useTemplating: true ## flag to say templating is being used below
inputs:
- id: UniProtKB
semantic: Gene
requestBody: ## no prefix
body:
q: "{{ queryInputs | rmPrefix() }}"
scopes: subject.uniprotkb
outputs:
- id: MONDO
semantic: Disease
parameters:
## not including these fields due to data-processing / biolink-modeling issues
## - association.clinical_trial.status
## - subject.bioclass