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smartapi.yaml
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openapi: 3.0.1
info:
contact:
name: Ma'ayan Lab
url: http://labs.icahn.mssm.edu/maayanlab/contact/
x-id: http://labs.icahn.mssm.edu/maayanlab/
x-role: responsible organization
description: 'Harmonizome is a web-based tool that allows users to search for genes
or
proteins and their functional terms, extracted and organized from over a
hundred publicly available resources.
'
license:
name: Apache 2.0
url: http://www.apache.org/licenses/LICENSE-2.0.html
termsOfService: http://amp.pharm.mssm.edu/Harmonizome/terms
title: Harmonizome
version: 1.0.0
servers:
- url: http://amp.pharm.mssm.edu/Harmonizome
tags:
- name: Maayanlab
- name: NIHdatacommons
paths:
/api/1.0:
get:
operationId: getEntities
responses:
'200':
content:
application/octet-stream:
schema:
example:
entities:
- entity: attribute
href: /api/1.0/attribute
- entity: gene
href: /api/1.0/gene
version: 1.0
properties:
entities:
items:
properties:
entity:
type: string
href:
type: string
type: object
type: array
version:
format: float
type: number
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns a list of available data entities
/api/1.0/attribute:
get:
operationId: attribute
parameters:
- $ref: '#/components/parameters/cursor'
responses:
'200':
content:
application/octet-stream:
schema:
example:
count: 295496
entities:
- href: /api/1.0/attribute/%26alpha%3B-bungarotoxin
name: \u0026alpha;-bungarotoxin
- href: /api/1.0/attribute/%26alpha%3B%26beta%3B-meATP
name: \u0026alpha;\u0026beta;-meATP
next: /api/1.0/attribute?cursor\u003d100
selection:
- 0
- 100
properties:
count:
type: integer
entities:
items:
$ref: '#/components/schemas/names'
type: array
next:
type: string
selection:
$ref: '#/components/schemas/selection'
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns information on attributes
/api/1.0/attribute/{endpoint}:
get:
operationId: attribute_data
parameters:
- description: Endpoint of an attribute href
example: '%26alpha%3B-bungarotoxin'
in: path
name: endpoint
required: true
schema:
type: string
responses:
'200':
content:
application/octet-stream:
schema:
example:
descriptionFromNamingAuthority: ''
geneSets:
- href: /api/1.0/gene_set/%26alpha%3B-bungarotoxin/Guide
name: \u0026alpha;-bungarotoxin/Guide
idFromNamingAuthority: ''
name: \u0026alpha;-bungarotoxin
nameFromDataset: \u0026alpha;-bungarotoxin
nameFromNamingAuthority: \u0026alpha;-bungarotoxin
namingAuthority:
href: /api/1.0/naming_authority/Guide+to+Pharmacology
name: Guide to Pharmacology
urlFromNamingAuthority: ''
properties:
descriptionFromNamingAuthority:
type: string
geneSets:
items:
$ref: '#/components/schemas/names'
type: array
idFromNamingAuthority:
type: string
name:
type: string
nameFromNamingAuthority:
type: string
namingAuthority:
$ref: '#/components/schemas/names'
urlFromNamingAuthority:
type: string
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns data from a specified attribute
/api/1.0/dataset:
get:
operationId: dataset
parameters:
- $ref: '#/components/parameters/cursor'
responses:
'200':
content:
application/octet-stream:
schema:
example:
count: 114
entities:
- href: /api/1.0/dataset/Biocarta+Pathways
name: Biocarta Pathways
- href: /api/1.0/dataset/CTD+Gene-Disease+Associations
name: CTD Gene-Disease Associations
next: /api/1.0/dataset?cursor\u003d100
selection:
- 0
- 100
properties:
count:
type: integer
entities:
items:
$ref: '#/components/schemas/names'
type: array
next:
type: string
selection:
$ref: '#/components/schemas/selection'
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns information on datasets
/api/1.0/dataset/{endpoint}:
get:
operationId: dataset_data
parameters:
- description: Endpoint of a dataset href
example: Biocarta+Pathways
in: path
name: endpoint
required: true
schema:
type: string
responses:
'200':
content:
application/octet-stream:
schema:
example:
association: protein-pathway associations
attributeGroup: functional term, phrase or reference
attributeType: pathway
datasetGroup: structural or functional annotations
description: sets of proteins participating in pathways
geneSets:
- href: /api/1.0/gene_set/acetylation+and+deacetylation
name: acetylation and deacetylation of rela
- href: /api/1.0/gene_set/actions+of+nitric+oxide
name: actions of nitric oxide
measurement: association by literature curation
name: Biocarta Pathways
pubMedIds: []
resource:
href: /api/1.0/resource/Biocarta
name: Biocarta
properties:
association:
type: string
attributeGroup:
type: string
attributeType:
type: string
datasetGroup:
type: string
geneSets:
items:
$ref: '#/components/schemas/names'
type: array
measurement:
type: string
name:
type: string
resource:
$ref: '#/components/schemas/names'
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns data from a specified dataset
/api/1.0/gene:
get:
operationId: gene
parameters:
- $ref: '#/components/parameters/cursor'
responses:
'200':
content:
application/octet-stream:
schema:
example:
count: 56720
entities:
- href: /api/1.0/gene/ITGA8
symbol: ITGA8
- href: /api/1.0/gene/ITGA9
symbol: ITGA9
next: /api/1.0/gene?cursor\u003d100
selection:
- 0
- 100
properties:
count:
type: integer
entities:
$ref: '#/components/schemas/symbols'
next:
type: string
selection:
$ref: '#/components/schemas/selection'
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns information on genes
/api/1.0/gene/{endpoint}:
get:
operationId: gene_data
parameters:
- description: Endpoint of a gene href
example: ITGA9
in: path
name: endpoint
required: true
schema:
type: string
- description: Display functional associations for a gene
in: query
name: showAssociations
schema:
default: false
type: boolean
responses:
'200':
content:
application/octet-stream:
schema:
example:
description: This gene encodes an alpha integrin
hgncRootFamilies:
- href: /api/1.0/gene_family/Integrins+%28ITG%29
name: Integrins (ITG)
name: integrin, alpha 9
ncbiEntrezGeneId: 3680
proteins:
- href: /api/1.0/protein/ITA9_HUMAN
symbol: ITA9_HUMAN
symbol: ITGA9
synonyms:
- ALPHA-RLC
- RLC
- ITGA4L
properties:
description:
type: string
hgncRootFamilies:
items:
$ref: '#/components/schemas/names'
type: array
name:
type: string
ncbiEntrezGeneId:
type: integer
ncbiEntrezGeneUrl:
type: string
proteins:
items:
$ref: '#/components/schemas/symbols'
type: array
symbol:
type: string
synonyms:
items:
type: string
type: array
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns data from a specified gene
x-bte-kgs-operations:
- $ref: '#/components/x-bte-kgs-operations/gene-annotation'
/api/1.0/gene_family:
get:
operationId: gene_family
parameters:
- $ref: '#/components/parameters/cursor'
responses:
'200':
content:
application/octet-stream:
schema:
example:
count: 309
entities:
- href: /api/1.0/gene_family/Annexins+%28ANXA%29
name: Annexins (ANXA)
- href: /api/1.0/gene_family/Butyrophilins+%28BTN%29
name: Butyrophilins (BTN)
next: /api/1.0/gene_family?cursor\u003d100
selection:
- 0
- 100
properties:
count:
type: integer
entities:
items:
$ref: '#/components/schemas/names'
type: array
next:
type: string
selection:
$ref: '#/components/schemas/selection'
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns information on gene families
/api/1.0/gene_family/{endpoint}:
get:
operationId: gene_family_data
parameters:
- description: Endpoint of a gene family href
example: Annexins+%28ANXA%29
in: path
name: endpoint
required: true
schema:
type: string
responses:
'200':
content:
application/octet-stream:
schema:
example:
familyId: 404
genes:
- href: /api/1.0/gene/ANXA8L1
symbol: ANXA8L1
- href: /api/1.0/gene/ANXA1
symbol: ANXA1
name: Annexins (ANXA)
url: http://www.genenames.org/cgi-bin/genefamilies/set/404
properties:
familyId:
type: integer
genes:
items:
$ref: '#/components/schemas/symbols'
type: array
name:
type: string
url:
type: string
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns data from a specified gene family
/api/1.0/gene_set:
get:
operationId: gene_set
parameters:
- $ref: '#/components/parameters/cursor'
responses:
'200':
content:
application/octet-stream:
schema:
example:
count: 332715
entities:
- href: /api/1.0/gene_set/HS683/Achilles+Cell+Line
name: HS683/Achilles Cell Line
- href: /api/1.0/gene_set/OV7/Achilles+Cell+Line
name: OV7/Achilles Cell Line
next: /api/1.0/gene_set?cursor\u003d100
selection:
- 0
- 100
properties:
count:
type: integer
entities:
items:
$ref: '#/components/schemas/names'
type: array
next:
type: string
selection:
$ref: '#/components/schemas/selection'
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns information on gene sets
/api/1.0/gene_set/{endpoint}:
get:
operationId: gene_set_data
parameters:
- description: Endpoint of a gene set href
example: HS683/Achilles+Cell+Line+Gene+Essentiality+Profiles
in: path
name: endpoint
required: true
schema:
type: string
responses:
'200':
content:
application/octet-stream:
schema:
example:
associations:
- gene:
href: /api/1.0/gene/CD36
symbol: CD36
standardizedValue: 1.00344
thresholdValue: 1.0
- gene:
href: /api/1.0/gene/RBM10
symbol: RBM10
standardizedValue: 1.24312
thresholdValue: 1.0
attribute:
href: /api/1.0/attribute/HS-683+cell
name: HS-683 cell
dataset:
href: /api/1.0/dataset/Achilles+Cell+Line
name: Achilles Cell Line Gene Essentiality Profiles
properties:
associations:
items:
properties:
gene:
$ref: '#/components/schemas/symbols'
standardizedValue:
type: number
thresholdValue:
type: number
type: object
type: array
attribute:
$ref: '#/components/schemas/names'
dataset:
$ref: '#/components/schemas/names'
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns data from a specified gene set
/api/1.0/naming_authority:
get:
operationId: naming_authority
parameters:
- $ref: '#/components/parameters/cursor'
responses:
'200':
content:
application/octet-stream:
schema:
example:
count: 89
entities:
- href: /api/1.0/naming_authority/Cell+Ontology
name: Cell Ontology
- href: /api/1.0/naming_authority/Gene+Ontology
name: Gene Ontology
next: ''
selection:
- 0
- 89
properties:
count:
type: integer
entities:
items:
$ref: '#/components/schemas/names'
type: array
next:
type: string
selection:
$ref: '#/components/schemas/selection'
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns information on naming authorities
/api/1.0/naming_authority/{endpoint}:
get:
operationId: naming_authority_data
parameters:
- description: Endpoint of a resource href
example: Cell+Ontology
in: path
name: endpoint
required: true
schema:
type: string
responses:
'200':
content:
application/octet-stream:
schema:
example:
acronym: CL
description: The Cell Ontology is designed as a structured controlled
vocabulary for cell types.
name: Cell Ontology
publication: dx.doi.org/10.1186/1471-2105-12-6
url: http://bioportal.bioontology.org/ontologies/CL
properties:
acronym:
type: string
description:
type: string
name:
type: string
publication:
type: string
url:
type: string
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns data from a specified resource
/api/1.0/protein:
get:
operationId: protein
parameters:
- $ref: '#/components/parameters/cursor'
responses:
'200':
content:
application/octet-stream:
schema:
example:
count: 19673
entities:
- href: /api/1.0/protein/A1BG_HUMAN
symbol: A1BG_HUMAN
- href: /api/1.0/protein/A1CF_HUMAN
symbol: A1CF_HUMAN
next: /api/1.0/protein?cursor\u003d100
selection:
- 0
- 100
properties:
count:
type: integer
entities:
$ref: '#/components/schemas/symbols'
next:
type: string
selection:
$ref: '#/components/schemas/selection'
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns information on proteins
/api/1.0/protein/{endpoint}:
get:
operationId: protein_data
parameters:
- description: Endpoint of a resource href
example: A1BG_HUMAN
in: path
name: endpoint
required: true
schema:
type: string
responses:
'200':
content:
application/octet-stream:
schema:
example:
description: This is a protein.
gene:
href: /api/1.0/gene/A1BG
symbol: A1BG
symbol: A1BG_HUMAN
uniprotId: P04217
uniprotUrl: http://www.uniprot.org/uniprot/P04217'
properties:
description:
type: string
gene:
$ref: '#/components/schemas/symbols'
name:
type: string
symbol:
type: string
uniprotId:
type: string
uniprotUrl:
type: string
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns data from a specified resource
/api/1.0/resource:
get:
operationId: resource
parameters:
- $ref: '#/components/parameters/cursor'
responses:
'200':
content:
application/octet-stream:
schema:
example:
count: 66
entities:
- href: /api/1.0/resource/Achilles
name: Achilles
- href: /api/1.0/resource/Biocarta
name: Biocarta
next: ''
selection:
- 0
- 66
properties:
count:
type: integer
entities:
items:
$ref: '#/components/schemas/names'
type: array
next:
type: string
selection:
$ref: '#/components/schemas/selection'
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns information on resources
/api/1.0/resource/{endpoint}:
get:
operationId: resource_data
parameters:
- description: Endpoint of a resource href
example: Achilles
in: path
name: endpoint
required: true
schema:
type: string
responses:
'200':
content:
application/octet-stream:
schema:
example:
acronym: ''
datasets:
- href: /api/1.0/dataset/Achilles+Cell+Line
name: Achilles Cell Line
description: This is a resource.
name: Achilles
pubMedIds:
- 25984343
- 20829323
- 21746896
url: http://www.broadinstitute.org/achilles
properties:
acronym:
type: string
datasets:
items:
$ref: '#/components/schemas/names'
type: array
description:
type: string
name:
type: string
pubMedIds:
items:
type: integer
type: array
url:
type: string
type: object
description: Successful response
'400':
$ref: '#/components/responses/400'
'404':
$ref: '#/components/responses/404'
5XX:
$ref: '#/components/responses/5XX'
summary: Returns data from a specified resource
components:
parameters:
cursor:
description: See the selection of data starting here
in: query
name: cursor
schema:
default: 0
type: integer
responses:
'400':
description: Bad request'
'404':
description: Page not found
5XX:
description: Unexpected error
schemas:
names:
properties:
href:
type: string
name:
type: string
type: object
selection:
items:
type: integer
type: array
symbols:
properties:
href:
type: string
symbol:
type: string
type: object
x-bte-kgs-operations:
gene-annotation:
- inputs:
- id: SYMBOL
semantic: Gene
method: get
outputs:
- id: NCBIGENE
semantic: Gene
parameters:
endpoint: '{inputs[0]}'
path: /query
predicate: equals
response_mapping:
$ref: '#/components/x-bte-response-mapping/gene-annotation'
source: Harmonizome
supportBatch: false
x-bte-response-mapping:
gene-annotation:
NCBIGENE: ncbiEntrezGeneId
x-externalResources:
- x-type: api documentation
x-url: https://github.com/MaayanLab/smartAPIs/blob/master/harmonizome_smartapi.yml
- x-description: "The harmonizome: a collection of processed datasets gathered to\
\ serve and \nmine knowledge about genes and proteins\n"
x-type: publication
x-url: https://academic.oup.com/database/article/doi/10.1093/database/baw100/2630482