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openapi_full.yml
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openapi: 3.0.3
info:
contact:
email: help@myvariant.info
name: Chunlei Wu
x-id: https://github.com/newgene
x-role: responsible developer
description: Documentation of the MyVariant.info genetic variant query web services. Learn
more about [MyVariant.info](https://docs.myvariant.info/en/latest/index.html)
termsOfService: http://myvariant.info/terms/
title: MyVariant.info API
version: '1.0'
x-translator:
infores: "infores:myvariant-info"
component: KP
team:
- Service Provider
biolink-version: "3.5.0"
servers:
- description: Encrypted Production server
url: https://myvariant.info/v1
x-maturity: production
- description: Production server
url: http://myvariant.info/v1
x-maturity: production
tags:
- name: variant
- name: query
- name: metadata
- name: translator
- name: biothings
paths:
"/variant/{id}":
get:
description: >-
By default, this will return the complete variant annotation object in JSON format.
See [here](https://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#returned-object)
for an example and [here](https://docs.myvariant.info/en/latest/doc/data.html#variant-object)
for more details. If the input variant 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 object. Multiple attributes should be separated by commas. If an attribute is not
available for a specific variant object, it will be ignored. Note that the attribute names are
case-sensitive.
Just like the variant query service, you can also pass a "callback" parameter to make a JSONP call.
parameters:
## these are provided in the docs https://docs.myvariant.info/en/latest/doc/variant_annotation_service.html
- name: id
description: >-
Retrieve chemical data based on ID - currently the
HGVS-based id using genomic location based on hg19 human genome assembly
in: path
required: true
example: "chr6:g.152708291G>A"
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 https://myvariant.info/v1/spec endpoint; commenting out for now
## assembly is unique to MyVariant
# - "$ref": "#/components/parameters/assembly"
# - "$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 from https://docs.myvariant.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:
# $ref: '#/components/schemas/Chem'
# '404':
# description: A response indicating an unknown chemical ID
tags:
- variant
"/variant":
post:
description: >-
Although making simple GET requests above to our variant query service is sufficient in most use cases,
there are some times you might find it easier to batch query (e.g., retrieving variant annotations for
multiple variants). Fortunately, you can also make batch queries via POST requests when you need to.
parameters:
## these are provided in the docs https://docs.myvariant.info/en/latest/doc/variant_annotation_service.html
- name: ids
description: >-
Required. Accepts multiple HGVS variant ids separated by comma,
e.g., "ids=chr6:g.152708291G>A,chr7:g.55241707G>T,chr16:g.28883241A>G".
Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted.
The request body can also be used to provide these ids.
in: query
## setting to false since putting this info in the request body seems to work as well
required: false
schema:
type: string
- "$ref": "#/components/parameters/fields"
- "$ref": "#/components/parameters/email"
## this is useful even when it's not noted in the docs
- "$ref": "#/components/parameters/size"
## these are noted in the https://myvariant.info/v1/spec endpoint; commenting out for now
## assembly is unique to MyVariant
# - "$ref": "#/components/parameters/assembly"
# - "$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:
- "chr6:g.152708291G>A"
- "chr7:g.55241707G>T"
schema:
type: object
properties:
ids:
description: >-
Accepts multiple variant 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:
- variant
"/metadata":
get:
description: Get metadata about the data available from the API
## these are noted in the hhttps://myvariant.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 hhttps://myvariant.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: >-
MyChem.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.myvariant.info/en/latest/doc/variant_query_service.html#query-syntax
description: >-
Required, passing user query. The detailed query syntax for parameter is explained
[here](https://docs.myvariant.info/en/latest/doc/variant_query_service.html#query-syntax).
in: query
required: true
example: "rs58991260"
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"
- "$ref": "#/components/parameters/email"
## these are noted in the https://myvariant.info/v1/spec endpoint; commenting out for now
## assembly is unique to MyVariant
# - "$ref": "#/components/parameters/assembly"
# - "$ref": "#/components/parameters/aggs"
# - "$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:
# "$ref": "#/components/schemas/ErrorResult"
# description: A response indicating an improperly formatted query
# description: Make queries and return matching gene hits. Supports JSONP and CORS
# as well.
tags:
- query
post:
description: >-
Although making simple GET requests above to our variant query service is sufficient for most use cases,
there are times you might find it more efficient to make batch queries (e.g., retrieving variant annotation
for multiple variants). Fortunately, you can also make batch queries via POST requests when you need to.
The "query" field in the returned object indicates the matching query term. If a query term has no match,
it will return with a "notfound" field with the value "true".
parameters:
## these are provided in the docs https://docs.myvariant.info/en/latest/doc/variant_query_service.html#id2
- name: q
description: >-
Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000
maximum, the rest will be omitted.
The request body can also be used to provide these ids.
in: query
## setting to false since putting this info in the request body seems to work as well
required: false
schema:
type: array
items:
type: string
- name: scopes
description: >-
Optional, specify one or more fields (separated by commas) to search, e.g., "scopes=dbsnp.rsid".
The available "fields" can be passed to "scopes" parameter are listed
[here](https://docs.myvariant.info/en/latest/doc/data.html#available-fields). Default: _id
The request body can also be used to provide this information.
in: query
## setting to false since putting this info in the request body seems to work as well
required: false
schema:
type: string
- "$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"
- "$ref": "#/components/parameters/scroll_id"
## these are noted in the https://myvariant.info/v1/spec endpoint; commenting out for now
## assembly is unique to MyVariant
## others haven't been written down here: with_total, analyzer
# - "$ref": "#/components/parameters/assembly"
# - "$ref": "#/components/parameters/sort"
# - "$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:
- "rs58991260"
- "rs928128624"
scopes:
- "dbsnp.rsid"
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, e.g., "scopes=dbsnp.rsid".
The available "fields" can be passed to "scopes" parameter are listed
[here](https://docs.myvariant.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
## 16 operations (8 sets)
x-bte-kgs-operations:
- "$ref": "#/components/x-bte-kgs-operations/civic-geneDisease"
- "$ref": "#/components/x-bte-kgs-operations/civic-geneDisease-rev"
- "$ref": "#/components/x-bte-kgs-operations/civic-variantDisease"
- "$ref": "#/components/x-bte-kgs-operations/civic-variantDisease-rev"
- "$ref": "#/components/x-bte-kgs-operations/dbsnp-variantGene"
- "$ref": "#/components/x-bte-kgs-operations/dbsnp-variantGene-rev"
- "$ref": "#/components/x-bte-kgs-operations/clinvar-variantGene"
- "$ref": "#/components/x-bte-kgs-operations/clinvar-variantGene-rev"
- "$ref": "#/components/x-bte-kgs-operations/clinvar-geneDisease"
- "$ref": "#/components/x-bte-kgs-operations/clinvar-geneDisease-rev"
- "$ref": "#/components/x-bte-kgs-operations/clinvar-variantDisease"
- "$ref": "#/components/x-bte-kgs-operations/clinvar-variantDisease-rev"
- "$ref": "#/components/x-bte-kgs-operations/docm-geneDisease"
- "$ref": "#/components/x-bte-kgs-operations/docm-geneDisease-rev"
- "$ref": "#/components/x-bte-kgs-operations/docm-variantDisease"
- "$ref": "#/components/x-bte-kgs-operations/docm-variantDisease-rev"
components:
parameters:
## assembly is specific to MyVariant
assembly:
name: assembly
in: query
required: false
schema:
type: string
default: hg19
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
## commenting out schemas and other status codes for now
# 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-response-mapping:
civic-geneDisease:
DOID: civic.evidence_items.disease.doid
ref_pmid: civic.evidence_items.source.pubmed ## no prefix
ref_clinicaltrials: civic.evidence_items.source.clinical_trials.nct_id ## no prefix (ID starts with "NCT")
## commenting out because data-processing / biolink-modeling issues
# ## categorical var / relation
# civic_clinical_significance: civic.evidence_items.clinical_significance
# ## free text
# civic_description: civic.evidence_items.description
# ## context: drugs involved
# civic_drug_interaction: civic.evidence_items.drug_interaction_type
# civic_drugs_involved: civic.evidence_items.drugs.name
# ## categorical vars
# civic_evidence_direction: civic.evidence_items.evidence_direction
# civic_evidence_level: civic.evidence_items.evidence_level
# civic_evidence_type: civic.evidence_items.evidence_type
# ## context: variant involved, could use "biolink:sequence_variant_qualifier"
# ## but then ID-namespace would be unclear (this ID doesn't have a prefix)
# civic_variant_id: civic.evidence_items.variant_id
# ## context: variant involved was Somatic, unknown...
# civic_variant_origin: civic.evidence_items.variant_origin
civic-geneOnly:
NCBIGene: civic.entrez_id
civic-variantDisease:
DOID: civic.evidence_items.disease.doid
## variant name
input_name: _id
ref_pmid: civic.evidence_items.source.pubmed ## no prefix
ref_clinicaltrials: civic.evidence_items.source.clinical_trials.nct_id ## no prefix (ID starts with "NCT")
## commenting out because data-processing / biolink-modeling issues
# ## categorical var / relation
# civic_clinical_significance: civic.evidence_items.clinical_significance
# ## free text
# civic_description: civic.evidence_items.description
# ## context: gene involved
# civic_variant_in_gene: civic.entrez_name
# ## context: drugs involved
# civic_drug_interaction: civic.evidence_items.drug_interaction_type
# civic_drugs_involved: civic.evidence_items.drugs.name
# ## categorical vars
# civic_evidence_direction: civic.evidence_items.evidence_direction
# civic_evidence_level: civic.evidence_items.evidence_level
# civic_evidence_type: civic.evidence_items.evidence_type
# ## context: variant involved was Somatic, unknown...
# civic_variant_origin: civic.evidence_items.variant_origin
dbsnp-rsid:
DBSNP: dbsnp.rsid ## no prefix
output_name: _id ## variant name
dbsnp-gene:
NCBIGene: dbsnp.gene.geneid ## no prefix
input_name: _id ## variant name
clinvar-rsid:
DBSNP: clinvar.rsid ## no prefix
output_name: _id ## variant name
clinvar-geneDisease:
OMIM: clinvar.rcv.conditions.identifiers.omim ## no prefix
## commenting out because data-processing / biolink-modeling issues
# ## edge attributes
# clinvar_clinical_significance: clinvar.rcv.clinical_significance ## similar to relation
# variant_rsid: dbsnp.rsid ## no prefix
# clinvar_submission_last_evaluated: clinvar.rcv.last_evaluated ## gives a date yyyy-mm-dd
# clinvar_num_submitters: clinvar.rcv.number_submitters
# clinvar_variant_origin: clinvar.rcv.origin
# clinvar_review_status: clinvar.rcv.review_status
clinvar-gene-variant-start:
NCBIGene: clinvar.gene.id ## no prefix
input_name: _id ## variant name
clinvar-variantDisease:
OMIM: clinvar.rcv.conditions.identifiers.omim ## no prefix
input_name: _id ## variant name
## commenting out because data-processing / biolink-modeling issues
# ## edge attributes
# clinvar_clinical_significance: clinvar.rcv.clinical_significance ## similar to relation
# clinvar_variant_in_gene: clinvar.gene.symbol ## context: gene
# clinvar_submission_last_evaluated: clinvar.rcv.last_evaluated ## gives a date yyyy-mm-dd
# clinvar_num_submitters: clinvar.rcv.number_submitters
# clinvar_variant_origin: clinvar.rcv.origin
# clinvar_review_status: clinvar.rcv.review_status
clinvar-gene:
NCBIGene: clinvar.gene.id ## no prefix
docm-disease-only:
DOID: docm.doid
docm-gene:
ENSEMBL: docm.ensembl_gene_id
docm-disease-variant-start:
DOID: docm.doid
input_name: _id ## variant name
ref_url: docm.url ## only MyCancerGenome urls? Also, an issue: sometimes it's just `null`
## commenting out because data-processing / biolink-modeling issues
## not taking notes on a bunch of fields about the gene and variant
# ref_pmid: docm.pubmed_id ## no prefix. issue: lists are ", "-delimited strings
# docm_source: docm.source ## issue: sometimes it's just the value "-" or `null`
# variant_consequence_type: docm.trv_type
# variant_type: docm.type
# docm_variant_in_gene: docm.genename
## not included:
## - cgi: only 323 records, doesn't have IDs for disease, gene, or drug ID...
## - cosmic: only seems to connect variants to tissue they were found in, but no IDs for the tissue...
## - dbnsfp.clinvar: overlap with clinvar section?
## missing indexing for omim, orphanet IDs have ORPHA000 format...
## - dbnsfp.ensembl.geneid: very repetitive for some reason...
## - dbnsfp.gtex.tissue: string, no IDs...
## - grasp.publication.phenotype: looks like curation of publications for variants / phenotypes. string, no IDs...
## - gwassnps.trait: looks like curation of publications for variants / phenotypes. string, no IDs...
x-bte-kgs-operations:
## CIVIC:
## data seems to be connecting variant-disease, sometimes with a drug (although that drug may not have an ID)
## having a drug means looking at drug response (given the disease...)
## However, the civic variant IDs don't seem to be easily mapped...
## The variants are mapped to their genes: 2648 records total, all have entrez_id field...
## - not including
## - civic assertions (only 30 variant records https://myvariant.info/v1/query?q=_exists_:%22civic.assertions%22)
## - civic evidence_items.phenotypes: 598 records, some seem to repeat the disease info
## - civic variant_groups: 129 records, not clear how to structure / what the relationship is
civic-geneDisease:
- supportBatch: true
useTemplating: true
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: civic.entrez_id
outputs:
- id: DOID
semantic: Disease
## out of 2648 civic records, most (2610) have the doid disease field...only some have dbsnp.rsid...
parameters:
## most fields below are categorical variables
## description is free text, Disease ID has prefix (DOID), variant ID is CIVIC (no prefix)
## only some records have drug information, and only some drugs have NCIT IDs
## commenting out because data-processing / biolink-modeling issues
# fields: civic.evidence_items
fields: >-
civic.evidence_items.disease.doid,
civic.evidence_items.source.pubmed,
civic.evidence_items.source.clinical_trials.nct_id
size: 1000 ## note size limit; added just in case
predicate: affects
source: "infores:civic"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/civic-geneDisease"
## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22
# testExamples:
# - qInput: "NCBIGene:1956" ## EGFR
# oneOutput: "DOID:3910" ## Lung Adenocarcinoma
civic-geneDisease-rev:
- supportBatch: true
useTemplating: true
inputs:
- id: DOID
semantic: Disease
requestBody:
body:
q: "{{ queryInputs }}" ## HAS PREFIX
scopes: civic.evidence_items.disease.doid
outputs:
- id: NCBIGene
semantic: Gene
parameters:
fields: civic.entrez_id ## no prefix
size: 1000
predicate: affected_by
source: "infores:civic"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/civic-geneOnly"
## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22
# testExamples:
# - qInput: "DOID:9256" ## Colorectal Cancer
# oneOutput: "NCBIGene:5290" ## PIK3CA
civic-variantDisease:
## out of 2648 civic records, only some (653) have the doid disease field...
- supportBatch: true
useTemplating: true
inputs:
- id: DBSNP
semantic: SequenceVariant
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: dbsnp.rsid
outputs:
- id: DOID
semantic: Disease
parameters:
## most fields below are categorical variables
## description is free text, Disease ID has prefix (DOID), variant ID is CIVIC (no prefix)
## only some records have drug information, and only some drugs have NCIT IDs
## using entrez gene name for now (human-readable) rather than id
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# civic.evidence_items,
# civic.entrez_name,
# _id
fields: >-
civic.evidence_items.disease.doid,
_id,
civic.evidence_items.source.pubmed,
civic.evidence_items.source.clinical_trials.nct_id
size: 1000 ## note size limit; added just in case
predicate: affects
source: "infores:civic"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/civic-variantDisease"
## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22%20AND%20_exists_:%22dbsnp.rsid%22
# testExamples:
# - qInput: "DBSNP:rs121913521" ## chr4:g.55593613T>G in KIT
# oneOutput: "DOID:9253" ## Gastrointestinal Stromal Tumor
civic-variantDisease-rev:
- supportBatch: true
useTemplating: true
inputs:
- id: DOID
semantic: Disease
requestBody:
body:
q: "{{ queryInputs }}" ## HAS PREFIX
scopes: civic.evidence_items.disease.doid
outputs:
- id: DBSNP
semantic: SequenceVariant
parameters:
fields: dbsnp.rsid,_id
size: 1000 ## note size limit; added just in case
predicate: affected_by
source: "infores:civic"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/dbsnp-rsid"
## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22%20AND%20_exists_:%22dbsnp.rsid%22
# testExamples:
# - qInput: "DOID:219" ## Colon Cancer
# oneOutput: "DBSNP:rs121913470" ## chr17:g.37880220T>C in ERBB2
dbsnp-variantGene:
## note: there may be redundant results in the response
## there are 446 million records
- supportBatch: true
useTemplating: true
inputs:
- id: DBSNP
semantic: SequenceVariant
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: dbsnp.rsid
outputs:
- id: NCBIGene
semantic: Gene
parameters:
fields: dbsnp.gene.geneid,_id ## no prefix
predicate: is_sequence_variant_of
source: "infores:dbsnp"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/dbsnp-gene"
## https://myvariant.info/v1/query?q=_exists_:%22dbsnp.rsid%22%20AND%20_exists_:%22dbsnp.gene.geneid%22
# testExamples:
# - qInput: "DBSNP:rs770112667" ## chr10:g.14260675G>A
# oneOutput: "NCBIGene:55691" ## FRMD4A
dbsnp-variantGene-rev:
- supportBatch: true
useTemplating: true
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: dbsnp.gene.geneid
outputs:
- id: DBSNP
semantic: SequenceVariant
parameters:
fields: dbsnp.rsid,_id
predicate: has_sequence_variant
source: "infores:dbsnp"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/dbsnp-rsid"
## https://myvariant.info/v1/query?q=_exists_:%22dbsnp.rsid%22%20AND%20_exists_:%22dbsnp.gene.geneid%22
# testExamples:
# - qInput: "NCBIGene:55691" ## FRMD4A
# oneOutput: "DBSNP:rs767038114" ## chr10:g.13693999G>A
clinvar-variantGene:
## there are 43k records with clinvar.rsid but no dbsnp
## https://myvariant.info/v1/query?q=_exists_:%22clinvar.rsid%22%20AND%20NOT%20_exists_:%22dbsnp.rsid%22
- supportBatch: true
useTemplating: true
inputs:
- id: DBSNP
semantic: SequenceVariant
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: clinvar.rsid
outputs:
- id: NCBIGene
semantic: Gene
parameters:
fields: clinvar.gene.id,_id ## no prefix
predicate: is_sequence_variant_of
source: "infores:clinvar"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/clinvar-gene-variant-start"
# testExamples:
# - qInput: "DBSNP:rs794727661" ## chrX:g.32361300dup
# oneOutput: "NCBIGene:1756" ## DMD
clinvar-variantGene-rev:
- supportBatch: true
useTemplating: true
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: clinvar.gene.id
outputs:
- id: DBSNP
semantic: SequenceVariant
parameters:
fields: clinvar.rsid,_id ## no prefix
predicate: has_sequence_variant
source: "infores:clinvar"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/clinvar-rsid"
# testExamples:
# - qInput: "NCBIGene:284098" ## PIGW
# oneOutput: "DBSNP:rs915498700" ## chr17:g.34893784T>C
clinvar-geneDisease:
## - conditions.identifiers can include multiple kinds
## some conditions have no IDs, some have multiple IDs (not all have OMIM).
## - omim: 497648 (no prefix)
## - orphanet: 416644 (no prefix)
## - human_phenotype_ontology: 74175
## - efo: 3637, has EFO_000 format (not ID or CURIE)
## - many medgen IDs but I don't think SRI ID resolver supports this...
## - not indexed: mesh, mondo
- supportBatch: true
useTemplating: true
inputs:
- id: NCBIGene
semantic: Gene
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: clinvar.gene.id
## out of >497,000 records with clinvar.rcv.conditions.identifiers.omim field, all have gene field...
outputs:
- id: OMIM
semantic: Disease
parameters:
## most should have dbsnp.rsid ID (see above)
## commenting out because data-processing / biolink-modeling issues
# fields: >-
# clinvar.rcv.conditions.identifiers.omim,
# clinvar.rcv.clinical_significance,
# dbsnp.rsid,
# clinvar.rcv.last_evaluated,
# clinvar.rcv.number_submitters,
# clinvar.rcv.origin,
# clinvar.rcv.review_status
fields: clinvar.rcv.conditions.identifiers.omim
size: 1000 ## note size limit; added just in case
predicate: related_to
## clinical significance is like a relation:
## Uncertain significance, Pathogenic, Likely pathogenic, other
source: "infores:clinvar"
response_mapping:
"$ref": "#/components/x-bte-response-mapping/clinvar-geneDisease"
# testExamples:
# - qInput: "NCBIGene:55806" ## HR
# oneOutput: "OMIM:209500" ## Atrichia with papular lesions (APL)
clinvar-geneDisease-rev:
- supportBatch: true
useTemplating: true
inputs:
- id: OMIM
semantic: Disease
requestBody:
body:
q: "{{ queryInputs }}" ## no prefix
scopes: clinvar.rcv.conditions.identifiers.omim
outputs:
- id: NCBIGene
semantic: Gene
parameters: