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openapi_full.yml
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openapi: 3.0.3
info:
contact:
email: help@mygene.info
name: Chunlei Wu
x-id: https://github.com/newgene
x-role: responsible developer
description: Documentation of the MyGene.info Gene Query web services. Learn more about [MyGene.info](https://docs.mygene.info/en/latest/index.html)
termsOfService: "http://mygene.info/terms/"
title: MyGene.info API
version: "3.0"
x-translator:
infores: "infores:mygene-info"
component: KP
team:
- "Service Provider"
biolink-version: "4.2.2"
servers:
- description: Encrypted Production server
url: https://mygene.info/v3
x-maturity: production
tags:
- name: gene
- name: annotation
- name: query
- name: translator
- name: biothings
paths:
"/gene/{id}":
get:
description: >-
By default, this will return the complete gene annotation object in JSON format.
See [here](https://docs.mygene.info/en/latest/doc/annotation_service.html#returned-object)
for an example and [here](https://docs.mygene.info/en/latest/doc/data.html#gene-object)
for more details. If the input gene ID 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 gene object. Multiple attributes should be separated by commas. If an attribute is not
available for a specific gene object, it will be ignored. Note that the attribute names are
case-sensitive.
Just like the gene query service, you can also pass a "callback" parameter to make a JSONP call.
parameters:
## these are provided in the docs https://docs.mygene.info/en/latest/doc/annotation_service.html
- name: id
description: >-
Entrez ("1017") or Ensembl gene id ("ENSG00000123374"). A retired Entrez Gene id works too if it is
replaced by a new one, e.g., 245794. But a "discontinued" gene id will not return any hit, e.g., 138.
in: path
required: true
example: "1017"
schema:
type: string
## species, species_facet_filter are special parameters for MyGene
- "$ref": "#/components/parameters/species"
- "$ref": "#/components/parameters/fields"
- "$ref": "#/components/parameters/callback"
- "$ref": "#/components/parameters/dotfield"
- "$ref": "#/components/parameters/email"
## this is useful even when it's not noted in the docs
- "$ref": "#/components/parameters/size"
## these are noted in the https://mygene.info/v3/spec endpoint; commenting out for now
# - "$ref": "#/components/parameters/species_facet_filter"
# - "$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 from https://docs.mygene.info/en/latest/doc/response_status_codes.html
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:
# $ref: '#/components/schemas/Chem'
# '404':
# description: A response indicating an unknown chemical ID
tags:
- gene
"/gene":
post:
description: >-
Although making simple GET requests above to our gene query service is sufficient in most use cases,
there are some times you might find it easier to batch query (e.g., retrieving gene annotations for
multiple genes). Fortunately, you can also make batch queries via POST requests when you need to.
parameters:
## these are provided in the docs https://docs.mygene.info/en/latest/doc/chem_annotation_service.html
- name: ids
description: >-
Accept multiple geneids (either Entrez or Ensembl gene ids) seperated by comma, e.g.,
"ids=1017,1018" or "ids=695,ENSG00000123374".
Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.
The request body can also be used to provide these ids.
in: query
## setting to false since putting this info in the request body seems to work as well
required: false
schema:
type: string
- "$ref": "#/components/parameters/fields"
- "$ref": "#/components/parameters/species"
- "$ref": "#/components/parameters/dotfield"
- "$ref": "#/components/parameters/email"
## this is useful even when it's not noted in the docs
- "$ref": "#/components/parameters/size"
## these are noted in the https://mygene.info/v3/spec endpoint; commenting out for now
# - "$ref": "#/components/parameters/species_facet_filter"
# - "$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:
- "1017"
- "1018"
schema:
type: object
properties:
ids:
description: >-
Accepts multiple gene 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:
- gene
"/metadata":
get:
description: Get metadata about the data available from the API
## these are noted in the https://mygene.info/v3/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://mygene.info/v3/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: >-
MyGene.info chemical query web 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 partially from https://docs.mygene.info/en/latest/doc/query_service.html#query-syntax
description: >-
Required, passing user query. The detailed query syntax for parameter is explained
[here](https://docs.mygene.info/en/latest/doc/query_service.html#query-syntax).
in: query
required: true
example: CDK2
schema:
type: string
## species, species_facet_filter, entrezonly, ensemblonly,
## exists, missing, post_filter, include_tax_tree
## are special parameters for MyGene
- "$ref": "#/components/parameters/fields"
- "$ref": "#/components/parameters/species"
- "$ref": "#/components/parameters/size"
- "$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/species_facet_filter"
- "$ref": "#/components/parameters/entrezonly"
- "$ref": "#/components/parameters/ensemblonly"
- "$ref": "#/components/parameters/callback"
- "$ref": "#/components/parameters/dotfield"
- "$ref": "#/components/parameters/email"
## these are noted in the https://mygene.info/v3/spec endpoint; commenting out for now
# - "$ref": "#/components/parameters/exists"
# - "$ref": "#/components/parameters/missing"
# - "$ref": "#/components/parameters/post_filter"
# - "$ref": "#/components/parameters/include_tax_tree"
# - "$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
# description: 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 chemical query service is sufficient for most use cases,
there are times you might find it more efficient to make batch queries (e.g., retrieving gene annotation
for multiple genes). 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:
## these are provided in the docs https://docs.mygene.info/en/latest/doc/query_service.html#batch-queries-via-post
- 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.
The available "fields" can be passed to "scopes" parameter are listed
[here](https://docs.mygene.info/en/latest/doc/data.html#available-fields). 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
## species, species_facet_filter, entrezonly, ensemblonly,
## exists, missing, post_filter, include_tax_tree
## are special parameters for MyGene
- "$ref": "#/components/parameters/species"
- "$ref": "#/components/parameters/fields"
- "$ref": "#/components/parameters/dotfield"
- "$ref": "#/components/parameters/email"
## these aren't noted in the docs for POST, but they are in GET or are useful
- "$ref": "#/components/parameters/size"
- "$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/species_facet_filter"
- "$ref": "#/components/parameters/entrezonly"
- "$ref": "#/components/parameters/ensemblonly"
- "$ref": "#/components/parameters/callback"
## these are noted in the https://mygene.info/v3/spec endpoint; commenting out for now
## others haven't been written down here: with_total, analyzer
# - "$ref": "#/components/parameters/exists"
# - "$ref": "#/components/parameters/missing"
# - "$ref": "#/components/parameters/post_filter"
# - "$ref": "#/components/parameters/include_tax_tree"
# - "$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
requestBody:
content:
application/json:
example:
q:
- "1017"
- "1018"
scopes:
- "entrezgene"
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.
The available "fields" can be passed to "scopes" parameter are listed
[here](https://docs.mygene.info/en/latest/doc/data.html#available-fields). 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
# description: Make batch gene queries and return matching gene hits
tags:
- query
## 18 operations (9 sets)
x-bte-kgs-operations:
- $ref: "#/components/x-bte-kgs-operations/PathwayHasGene1"
- $ref: "#/components/x-bte-kgs-operations/PathwayHasGene2"
- $ref: "#/components/x-bte-kgs-operations/PathwayHasGene3"
- $ref: "#/components/x-bte-kgs-operations/PathwayHasGene4"
- $ref: "#/components/x-bte-kgs-operations/involvedInPathway1"
- $ref: "#/components/x-bte-kgs-operations/involvedInPathway2"
- $ref: "#/components/x-bte-kgs-operations/involvedInPathway3"
- $ref: "#/components/x-bte-kgs-operations/involvedInPathway4"
- $ref: "#/components/x-bte-kgs-operations/involvedInBP"
- $ref: "#/components/x-bte-kgs-operations/BPToGene"
- $ref: "#/components/x-bte-kgs-operations/enablesMF"
- $ref: "#/components/x-bte-kgs-operations/MFToGene"
- $ref: "#/components/x-bte-kgs-operations/involvedInCC"
- $ref: "#/components/x-bte-kgs-operations/CCToGene"
- $ref: "#/components/x-bte-kgs-operations/geneToDisease"
- $ref: "#/components/x-bte-kgs-operations/diseaseToGene"
- $ref: "#/components/x-bte-kgs-operations/hasHomolog-MGI"
- $ref: "#/components/x-bte-kgs-operations/hasHomolog-MGI-rev"
components:
parameters:
## these are specific to MyGene
ensemblonly:
name: ensemblonly
description: >-
Optional. When passed as “true” or “1”, the query returns only the hits with valid Ensembl gene ids. Default: false.
in: query
schema:
type: boolean
default: false
entrezonly:
name: entrezonly
description: >-
Optional. When passed as “true” or “1”, the query returns only the hits with valid Entrez gene ids. Default: false.
in: query
schema:
type: boolean
default: false
species:
name: species
description: >-
Optional, can be used to limit the gene hits from given species.
You can use "common names" for nine common species (human, mouse,
rat, fruitfly, nematode, zebrafish, thale-cress, frog and pig).
All other species, you can provide their taxonomy ids from
[NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy). See more details
[here](https://docs.mygene.info/en/latest/doc/data.html#species).
Multiple species can be passed using comma as a separator. Passing "all" will
query against all available species. Default: all.
in: query
required: false
schema:
type: array
items:
type: string
default: all
species_facet_filter:
name: species_facet_filter
description: >-
Optional, relevant when faceting on species (i.e., "facets=taxid" are passed).
It's used to pass species filter without changing the scope of faceting,
so that the returned facet counts won't change. Either species name or taxonomy id
can be used, just like "species" parameter above. See examples of faceted queries
[here](https://docs.mygene.info/en/latest/doc/query_service.html#faceted-queries).
in: query
required: false
schema:
type: array
items:
type: string
## these are specific to MyGene, but only noted in the https://mychem.info/v1/spec endpoint; commenting out for now
# exists:
# name: exists
# in: query
# required: false
# schema:
# type: array
# items:
# type: string
# include_tax_tree:
# name: include_tax_tree
# in: query
# required: false
# schema:
# type: boolean
# missing:
# name: missing
# in: query
# required: false
# schema:
# type: array
# items:
# type: string
# post_filter:
# name: post_filter
# in: query
# required: false
# schema:
# type: string
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
here](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
here](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. Look
[here](https://docs.mychem.info/en/latest/doc/data.html#available-fields) for a list of available fields.
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
here](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
# schemas:
# Chem:
# properties:
# _id:
# type: string
# required:
# - _id
# type: object
# ErrorResult:
# properties:
# message:
# type: string
# success:
# type: boolean
# type: object
# QueryPOSTResult:
# items:
# allOf:
# - "$ref": "#/components/schemas/Chem"
# - properties:
# _score:
# format: float
# type: number
# query:
# type: string
# type: object
# type: array
# QueryResult:
# properties:
# hits:
# items:
# "$ref": "#/components/schemas/Chem"
# 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:
## Not including Gene <-> Transcript <-> Protein or Gene <-> Protein due to conflation, lack of use in Translator right now
## Pathway <-> Gene data notes:
## - for ConsensusPathDB, look at "content information" tab at http://cpdb.molgen.mpg.de/CPDB to see versions of the pathway databases they used
## - pathway info includes Reactome, KEGG.PATHWAY, Wikipathways, Biocarta
## However, SRI ID resolver only accepts SMPDB, REACT, GO, PANTHER.PATHWAY right now
## not included: humancyc, mousecyc, netpath, pharmgkb, pid, yeastcyc
## - Gene ID: all genes with pathway info have entrezgene field (NCBIGene namespace) https://mygene.info/v3/query?q=_exists_:pathway%20AND%20NOT%20_exists_:entrezgene
## - knowledge_level / agent_type
## - reactome: manually curated by experts https://reactome.org/what-is-reactome
## - kegg pathway: manually drawn https://www.genome.jp/kegg/pathway.html
## - wikipathways: manually curated by community https://www.wikipathways.org/about.html
## - biocarta: curated, assuming manually https://maayanlab.cloud/Harmonizome/dataset/Biocarta%20Pathways
PathwayHasGene1: ## using Reactome, KEGG, Wikipathways, Biocarta
- supportBatch: true
useTemplating: true
inputs:
- id: REACT
semantic: Pathway
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: pathway.reactome.id
outputs:
- id: NCBIGene
semantic: Gene
parameters:
## all records with pathway.reactome.id field also have entrezgene field
fields: entrezgene
species: human
size: 1000 ## note the size limit
predicate: has_participant
source: "infores:reactome"
knowledge_level: knowledge_assertion
agent_type: manual_agent
response_mapping:
$ref: "#/components/x-bte-response-mapping/entrezgene"
testExamples:
- qInput: "REACT:R-HSA-70895" ## Branched-chain amino acid catabolism
oneOutput: "NCBIGene:10295" ## BCKDK
PathwayHasGene2:
- supportBatch: true
useTemplating: true
inputs:
- id: "KEGG.PATHWAY"
semantic: Pathway
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: pathway.kegg.id
outputs:
- id: NCBIGene
semantic: Gene
parameters:
## all records with pathway.kegg field also have entrezgene field
fields: entrezgene,pathway.kegg.name
species: human
size: 1000 ## note the size limit
predicate: has_participant
source: "infores:cpdb" ## ConsensusPathDB
knowledge_level: knowledge_assertion
agent_type: manual_agent
response_mapping:
$ref: "#/components/x-bte-response-mapping/entrezgene-keggname"
testExamples:
- qInput: "KEGG.PATHWAY:hsa00120" ## Primary bile acid biosynthesis - Homo sapiens (human)
oneOutput: "NCBIGene:8309" ## ACOX2
PathwayHasGene3:
- supportBatch: true
useTemplating: true
inputs:
- id: WIKIPATHWAYS
semantic: Pathway
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: pathway.wikipathways.id
outputs:
- id: NCBIGene
semantic: Gene
parameters:
## all records with pathway.wikipathways field also have entrezgene field
fields: entrezgene,pathway.wikipathways.name
species: human
size: 1000 ## note the size limit
predicate: has_participant
source: "infores:cpdb" ## ConsensusPathDB
knowledge_level: knowledge_assertion
agent_type: manual_agent
response_mapping:
$ref: "#/components/x-bte-response-mapping/entrezgene-wikiname"
testExamples:
- qInput: "WIKIPATHWAYS:WP2034" ## Leptin signaling pathway
oneOutput: "NCBIGene:3953" ## LEPR
PathwayHasGene4:
- supportBatch: true
useTemplating: true
inputs:
- id: BIOCARTA
semantic: Pathway
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: pathway.biocarta.id
outputs:
- id: NCBIGene
semantic: Gene
parameters:
## all records with pathway.biocarta field also have entrezgene field
fields: entrezgene,pathway.biocarta.name
species: human
size: 1000 ## note the size limit
predicate: has_participant
source: "infores:cpdb" ## ConsensusPathDB
knowledge_level: knowledge_assertion
agent_type: manual_agent
response_mapping:
$ref: "#/components/x-bte-response-mapping/entrezgene-biocartaname"
testExamples:
- qInput: "BIOCARTA:raspathway"
oneOutput: "NCBIGene:3265" ## HRAS
involvedInPathway1: ## using Reactome, KEGG, Wikipathways, Biocarta
- supportBatch: true
useTemplating: true
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: entrezgene
outputs:
- id: REACT
semantic: Pathway
parameters:
## not including name since BTE isn't ingesting properly right now
fields: >-
pathway.reactome.id
species: human
size: 1000
predicate: participates_in
source: "infores:reactome"
knowledge_level: knowledge_assertion
agent_type: manual_agent
response_mapping:
$ref: "#/components/x-bte-response-mapping/reactomePathway"
testExamples:
- qInput: "NCBIGene:1629" ## DBT
oneOutput: "REACT:R-HSA-70895" ## Branched-chain amino acid catabolism
involvedInPathway2:
- supportBatch: true
useTemplating: true
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: entrezgene
outputs:
- id: "KEGG.PATHWAY"
semantic: Pathway
parameters:
## not including name since BTE isn't ingesting properly right now
fields: >-
pathway.kegg.id,pathway.kegg.name
species: human
size: 1000
predicate: participates_in
source: "infores:cpdb" ## ConsensusPathDB
knowledge_level: knowledge_assertion
agent_type: manual_agent
response_mapping:
$ref: "#/components/x-bte-response-mapping/keggPathway"
testExamples:
- qInput: "NCBIGene:1629" ## DBT
oneOutput: "KEGG.PATHWAY:hsa00280" ## Valine, leucine and isoleucine degradation - Homo sapiens (human)
involvedInPathway3:
- supportBatch: true
useTemplating: true
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: entrezgene
outputs:
- id: WIKIPATHWAYS
semantic: Pathway
parameters:
## not including name since BTE isn't ingesting properly right now
fields: >-
pathway.wikipathways.id,pathway.wikipathways.name
species: human
size: 1000
predicate: participates_in
source: "infores:cpdb" ## ConsensusPathDB
knowledge_level: knowledge_assertion
agent_type: manual_agent
response_mapping:
$ref: "#/components/x-bte-response-mapping/wikipathway"
testExamples:
- qInput: "NCBIGene:8309" ## ACOX2
oneOutput: "WIKIPATHWAYS:WP3942" ## PPAR signaling pathway
involvedInPathway4:
- supportBatch: true
useTemplating: true
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: entrezgene
outputs:
- id: BIOCARTA
semantic: Pathway
parameters:
## not including name since BTE isn't ingesting properly right now
fields: >-
pathway.biocarta.id,pathway.biocarta.name
species: human
size: 1000
predicate: participates_in
source: "infores:cpdb" ## ConsensusPathDB
knowledge_level: knowledge_assertion
agent_type: manual_agent
response_mapping:
$ref: "#/components/x-bte-response-mapping/biocarta"
testExamples:
- qInput: "NCBIGene:5608" ## MAP2K6
oneOutput: "BIOCARTA:p38mapkpathway" ## p38 mapk signaling pathway
## knowledge_level / agent_type for ncbi-gene: need separation by evidence code for more-specific settings
## has info on how it gets go-annotation data https://www.ncbi.nlm.nih.gov/books/NBK3840/#genefaq.GO_terms
involvedInBP:
- supportBatch: true
useTemplating: true
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: entrezgene
outputs:
- id: GO
semantic: BiologicalProcess
parameters:
## all records with go.BP field also have entrezgene field
## not including: name, category/gocategory (not needed)
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# go.BP.id,
# go.BP.evidence,
# go.BP.pubmed,
# go.BP.qualifier
fields: go.BP.id,go.BP.pubmed
species: human
size: 1000
predicate: participates_in
source: "infores:ncbi-gene" ## which got from GO Annotations...
knowledge_level: knowledge_assertion
agent_type: not_provided
response_mapping:
$ref: "#/components/x-bte-response-mapping/biologicalProcess"
testExamples:
- qInput: "NCBIGene:632" ## BGLAP
oneOutput: "GO:0001501" ## skeletal system development
BPToGene:
- supportBatch: true
useTemplating: true
inputs:
- id: GO
semantic: BiologicalProcess
requestBody:
body:
q: "{{ queryInputs | replPrefix('GO') }}" ## HAS PREFIX (GO)
scopes: go.BP.id
outputs:
- id: NCBIGene
semantic: Gene
parameters:
## all records with go.BP field also have entrezgene field
fields: entrezgene
species: human
size: 1000 ## note size limit
predicate: has_participant
source: "infores:ncbi-gene" ## which got from GO Annotations...
knowledge_level: knowledge_assertion
agent_type: not_provided
response_mapping:
$ref: "#/components/x-bte-response-mapping/entrezgene"