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kgea_api.yaml
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kgea_api.yaml
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openapi: 3.0.1
info:
version: 1.5.0
title: >-
OpenAPI for the Biomedical Translator Knowledge Graph EXchange Archive.
Although this API is SmartAPI compliant, it will not normally be visible
in the Translator SmartAPI Registry since it is mainly meant to be
accessed through Registry indexed KGE File Sets, which will have
distinct entries in the Registry.
description: >-
OpenAPI for the NCATS Biomedical Translator
Knowledge Graph Exchange Archive
license:
name: MIT 2.0
url: https://en.wikipedia.org/wiki/MIT_License
termsOfService: https://ncats.nih.gov/translator
contact:
name: "Richard Bruskiewich"
x-role: "responsible developer"
email: "richard.bruskiewich@delphinai.com"
x-id: "https://github.com/RichardBruskiewich"
x-translator:
component: "SRI service"
team:
- "SRI"
servers:
- url: "http://localhost:8080/archive"
description: "Localhost URL for server, to be proxied to the real internet"
externalDocs:
description: >-
Documentation for the NCATS Biomedical Translator
Knowledge Graph Exchange (KGE) Archive
url: "https://github.com/NCATSTranslator/Knowledge_Graph_Exchange_Registry"
tags:
- name: translator
description: Designates a NCATS Biomedical Data Translator component API
- name: kge
description: Designates a Translator Knowledge Graph eXchange (KGE) Archive API
- name: catalog
description: Endpoints to access catalog of KGE file sets
- name: upload
description: Endpoints for KGE file set upload
- name: content
description: Endpoints to access version specific KGE file set content (meta-)data.
paths:
/catalog:
get:
tags:
- catalog
summary: Returns the catalog of available KGE File Sets
operationId: get_knowledge_graph_catalog
responses:
'200':
description: >-
Catalog of available KGE File Sets, their name and their versions.
content:
application/json:
schema:
description: >-
Dictionary of available KGE File Sets, with a list of
(at least one) version. The keys of the dictionary are the
internal normalized identifiers ('kg_id') of the file sets.
type: object
additionalProperties:
$ref: '#/components/schemas/KgeFileSetEntry'
/register/graph:
post:
description: >-
Register core metadata for a new KGE persisted Knowledge Graph. Since
this endpoint assumes assumes a web session authenticated user, this
user is automatically designated as the 'owner' of the new KGE graph.
tags:
- catalog
summary: Register core metadata for a distinct KGE Knowledge Graph
operationId: register_knowledge_graph
requestBody:
$ref: '#/components/requestBodies/RegisterGraphRequestBody'
responses:
'201':
description: New knowledge graph registration operation successfully completed.
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this OpenAPI
schema OR a specific parameter is believed to be invalid somehow
(or not just recognized).
content:
application/json:
schema:
type: string
/register/fileset:
post:
description: >-
Register core metadata for a newly persisted file set version of a
KGE persisted Knowledge Graph. Since this endpoint assumes a web
session authenticated session user, this user is automatically
designated as the 'owner' of the new versioned file set.
tags:
- catalog
summary: Register core metadata for a distinctly versioned file set of a KGE Knowledge Graph
operationId: register_file_set
requestBody:
$ref: '#/components/requestBodies/RegisterFileSetRequestBody'
responses:
'201':
description: New file set registration operation successfully completed.
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this OpenAPI
schema OR a specific parameter is believed to be invalid
somehow (or not just recognized).
content:
application/json:
schema:
type: string
/publish/{kg_id}/{fileset_version}:
get:
parameters:
- name: kg_id
in: path
description: >-
KGE Knowledge Graph identifier for the knowledge graph
for which data files are being accessed.
required: true
schema:
type: string
- name: fileset_version
in: path
description: >-
KGE File Set version identifier for the knowledge graph
for which data files are being accessed.
required: true
schema:
type: string
tags:
- catalog
summary: Publish a registered File Set
operationId: publish_file_set
responses:
'302':
description: >-
After KGE File Set publication is triggered, user gets redirected to /home.
/upload:
get:
description: >-
Uploading of (meta-)data files to a specific KGE File Set version,
belonging to a specified Knowledge Graph. The files are assumed to
be html form file "blob" objects. The 'get' only sets up the file
uploading (with progress indications). A follow-up HTTP POST call
to the /upload endpoint is expected, with the 'upload token' returned
from this call and an 'uploaded_file' parameter set to the file to be
uploaded. The 'content_name' should be set either to the file name.
The specific KGX file content of the current upload file is
set by the `kgx_file_content' for KGX data files uploaded as set
by the selected 'metadata', 'nodes' or 'edges' radio button.
parameters:
- name: kg_id
in: query
description: >-
KGE File Set identifier for the knowledge graph
for which data file metadata are being accessed
required: true
schema:
type: string
- name: fileset_version
in: query
description: >-
Specific version of KGE File Set for the knowledge graph
for which data file metadata are being accessed
required: true
schema:
type: string
- name: kgx_file_content
in: query
description: >-
Tags the upload as either 'metadata', 'nodes', 'edges' or 'archive'.
required: true
schema:
type: string
- name: content_name
in: query
description: >-
The file name of the data set to be uploaded.
required: true
schema:
type: string
tags:
- upload
summary: Configure form upload context for a specific file of a KGE File Set.
operationId: setup_upload_context
responses:
'200':
description: >-
Upload configuration successful, returning associated object key.
content:
application/json:
schema:
$ref: '#/components/schemas/UploadTokenObject'
'404':
description: >-
Knowledge graph or KGE File Set version is unknown (not registered).
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this
OpenAPI schema OR a specific parameter is believed
to be invalid somehow (or just not recognized).
content:
application/json:
schema:
type: string
post:
tags:
- upload
summary: Uploading of a specified file from a local computer.
operationId: upload_file
requestBody:
$ref: '#/components/requestBodies/UploadRequestBody'
responses:
'201':
description: Upload successfully completed.
content:
application/json:
schema:
type: string
'404':
description: >-
Knowledge graph or requested KGE File Set version is unknown.
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this
OpenAPI schema OR a specific parameter is believed
to be invalid somehow (or just not recognized).
content:
application/json:
schema:
type: string
/upload/url:
get:
description: >-
Direct file from URL transfer of (meta-)data files to a specific
KGE File Set version, belonging to a specific Knowledge Graph. The
'content_url' parameter is taken as a REST endpoint of a file to be
transferred into the Archive (http authentication not yet supported,
therefore, the URL should provide for unauthenticated access). The
'content_name' is set the file name to be assigned to the file within
the KGE Archive. The specific KGX file content of the current upload
file is set by the `kgx_file_content' for KGX data files uploaded as
set by the selected 'metadata', 'nodes' or 'edges' radio button.
parameters:
- name: kg_id
in: query
description: >-
KGE File Set identifier for the knowledge graph
for which data file metadata are being accessed
required: true
schema:
type: string
- name: fileset_version
in: query
description: >-
Specific version of KGE File Set for the knowledge graph
for which data file metadata are being accessed
required: true
schema:
type: string
- name: kgx_file_content
in: query
description: >-
Tags the upload as either 'metadata', 'nodes', 'edges' or 'archive'.
required: true
schema:
type: string
- name: content_url
in: query
description: >-
(Optional) URL to a web based file resource to be
directly uploaded to the KGE Archive from it's server.
required: true
schema:
type: string
- name: content_name
in: query
description: >-
The file name of the data set to be uploaded.
required: true
schema:
type: string
tags:
- upload
summary: Trigger direct URL file transfer of a specific file of a KGE File Set.
operationId: transfer_from_url
responses:
'200':
description: >-
Transfer initiated successfully, returning associated object key.
Note that the transfer itself may not yet be completed (especially
if it is a huge file) so the associated archive may not yet be
accessible for downloading.
content:
application/json:
schema:
$ref: '#/components/schemas/UploadTokenObject'
'404':
description: >-
Knowledge graph or KGE File Set version is unknown (not registered).
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this
OpenAPI schema OR a specific parameter is believed
to be invalid somehow (or just not recognized).
content:
application/json:
schema:
type: string
/upload/progress:
get:
description: >-
Poll the status of a given upload process.
parameters:
- name: upload_token
in: query
description: >-
Upload token associated with a given file for uploading to
the Archive as specified by a preceding /upload GET call.
required: true
schema:
type: string
tags:
- upload
summary: Get the progress of uploading for a specific file of a KGE File Set.
operationId: get_upload_status
responses:
'200':
description: Details about the status of a file upload operation.
content:
application/json:
schema:
$ref: '#/components/schemas/UploadProgressToken'
'404':
description: >-
Specified upload token is unknown.
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this
OpenAPI schema OR a specific parameter is believed
to be invalid somehow (or just not recognized).
content:
application/json:
schema:
type: string
/upload/cancel:
delete:
description: >-
Cancel a given upload process identified by upload token.
parameters:
- name: upload_token
in: query
description: >-
Upload token associated with a given file whose uploading is to be cancelled.
required: true
schema:
type: string
tags:
- upload
summary: Cancel uploading of a specific file of a KGE File Set.
operationId: cancel_upload
responses:
'204':
description: Success of the upload cancellation (nothing returned)
'404':
description: >-
Specified upload token is unknown.
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this
OpenAPI schema OR a specific parameter is believed
to be invalid somehow (or just not recognized).
content:
application/json:
schema:
type: string
/{kg_id}/{fileset_version}/metadata:
get:
parameters:
- name: kg_id
in: path
description: >-
KGE File Set identifier for the knowledge graph
for which data file metadata are being accessed
required: true
schema:
type: string
- name: fileset_version
in: path
description: >-
Specific version of KGE File Set for the knowledge graph
for which data file metadata are being accessed
required: true
schema:
type: string
tags:
- content
summary: Get provider and content metadata for a specified KGE File Set version.
operationId: get_file_set_metadata
responses:
'200':
description: >-
Provider and content metadata relating to the given version of a specified KGE File Set.
content:
application/json:
schema:
$ref: '#/components/schemas/KgeMetadata'
'404':
description: >-
Knowledge graph or requested KGE File Set version is unknown.
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this
OpenAPI schema OR a specific parameter is believed
to be invalid somehow (or just not recognized).
content:
application/json:
schema:
type: string
/{kg_id}/{fileset_version}/meta_knowledge_graph:
get:
parameters:
- name: kg_id
in: path
description: >-
KGE File Set identifier for the knowledge graph
for which graph metadata is being accessed.
required: true
schema:
type: string
- name: fileset_version
in: path
description: >-
Version of KGE File Set for a given knowledge graph.
required: true
schema:
type: string
- name: downloading
in: query
description: >-
Boolean flag indicating whether data is to be downloaded as an
attachment or rather if a signed URL (string) is to be returned
to the caller, for direct access to the data file (default: true).
required: false
schema:
type: boolean
tags:
- content
summary: Meta knowledge graph representation of this KGX knowledge graph.
operationId: meta_knowledge_graph
responses:
'200':
description: >-
Returns meta knowledge graph representation
of this KGX knowledge graph.
content:
application/json:
schema:
$ref: '#/components/schemas/MetaKnowledgeGraph'
'404':
description: >-
Knowledge graph or requested KGE File Set version is unknown.
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this
OpenAPI schema OR a specific parameter is believed
to be invalid somehow (or just not recognized).
content:
application/json:
schema:
type: string
/{kg_id}/{fileset_version}/download:
get:
parameters:
- name: kg_id
in: path
description: >-
Identifier of the knowledge graph of the KGE File Set a file set version for which is being accessed.
required: true
schema:
type: string
- name: fileset_version
in: path
description: >-
Version of file set of the knowledge graph being accessed.
required: true
schema:
type: string
tags:
- content
summary: Returns specified KGE File Set as a gzip compressed tar archive
operationId: download_file_set_archive
responses:
'200':
description: >-
A KGE File Set as a gzip compressed tar archive of
KGX compliant files plus an associated metadata json file
content:
application/gzip:
schema:
type: string
format: binary
'404':
description: >-
Knowledge graph or requested KGE File Set version is unknown.
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this
OpenAPI schema OR a specific parameter is believed
to be invalid somehow (or just not recognized).
content:
application/json:
schema:
type: string
/{kg_id}/{fileset_version}/sha1hash:
get:
parameters:
- name: kg_id
in: path
description: >-
Identifier of the knowledge graph of the KGE File Set a file set version for which is being accessed.
required: true
schema:
type: string
- name: fileset_version
in: path
description: >-
Version of file set of the knowledge graph being accessed.
required: true
schema:
type: string
tags:
- content
summary: Returns SHA1 hash of the current KGE File Set as a small text file.
operationId: download_file_set_archive_sha1hash
responses:
'200':
description: >-
A small text file containing the SHA1 hash of its associated
KGE File Set gzip compressed tar archive.
content:
application/gzip:
schema:
type: string
format: binary
'404':
description: >-
Knowledge graph or requested KGE File Set version is unknown.
content:
application/json:
schema:
type: string
'400':
description: >-
Bad request. Request is invalid according to this
OpenAPI schema OR a specific parameter is believed
to be invalid somehow (or just not recognized).
content:
application/json:
schema:
type: string
components:
requestBodies:
RegisterGraphRequestBody:
content:
application/x-www-form-urlencoded:
schema:
$ref: '#/components/schemas/RegisterGraphRequestBody'
required: true
RegisterFileSetRequestBody:
content:
application/x-www-form-urlencoded:
schema:
$ref: '#/components/schemas/RegisterFileSetRequestBody'
required: true
UploadRequestBody:
description: KGE File Set metadata or data file submitted
content:
multipart/form-data:
schema:
$ref: '#/components/schemas/UploadRequestBody'
required: true
schemas:
KgeFileSetEntry:
description: >-
Basic KGE Archive catalog entry indexing a KGE File Set.
type: object
properties:
name:
description: Human readable KGE File Set name ('kg_name')
type: string
example: "Semantic Medline Database"
versions:
description: List of versions ('fileset_version') of a KGE File Set
type: array
items:
type: string
minItems: 1
example: ["4.1", "4.2", "4.3"]
KgeMetadata:
description: >-
KGE File Set provider and content metadata,
including the inventory of associated files.
type: object
properties:
provider:
$ref: '#/components/schemas/KgeProviderMetadata'
fileset:
$ref: '#/components/schemas/KgeFileSetMetadata'
KgeProviderMetadata:
description: >-
KGE File Set provider and content metadata,
including the inventory of associated files.
type: object
properties:
kg_id:
description: >-
Identifier of the knowledge graph that the metadata describes.
type: string
example: "semantic_medline_database"
kg_name:
description: >-
Semantic Medline Database.
type: string
example: "Semantic Medline Database"
kg_description:
description: >-
Identifier of the knowledge graph that the metadata describes.
type: string
example: "Curated Biolink Model-compliant knowledge graph subset of the Semantic Medline Database"
translator_component:
description: >-
Type of Translator component generating the knowledge graph (i.e. KP, ARA, SRI).
type: string
example: "KP"
translator_team:
description: >-
Translator team providing the knowledge graph data.
type: string
example: "RENCI"
submitter_name:
description: >-
Name of the submitter/owner of the knowledge graph provider
type: string
example: "John Smith"
submitter_email:
description: >-
Email address for the submitter/owner of the knowledge graph provider.
type: string
example: "jsmith@knowledge.org"
license_name:
description: >-
Name of Knowledge Graph data use license.
type: string
example: "Creative-Commons-4.0"
license_url:
description: >-
URL to Knowledge Graph license data use description.
type: string
example: "https://creativecommons.org/licenses/by/4.0/legalcode"
terms_of_service:
description: >-
URL to Knowledge Graph data use "terms of service".
type: string
example: "https://ncats.nih.gov/translator"
KgeFileSetMetadata:
description: >-
Metadata including content metadata and the inventory of
associated files, for a specific version of KGE File Set.
type: object
properties:
biolink_model_release:
description: >-
Biolink Model released associated with the file set.
type: string
example: "2.0.2"
fileset_version:
description: >-
Version identifier of the file set.
type: string
example: "1.0"
date_stamp:
description: >-
Date stamp of the file set.
type: string
format: date
submitter_name:
description: >-
Name of the submitter of the KGE FileSet
type: string
example: "John Smith"
submitter_email:
description: >-
Email address for the submitter.
type: string
example: "jsmith@knowledge.org"
status:
$ref: '#/components/schemas/KgeFileSetStatusCode'
files:
description: >-
Annotated list of files within a given file set.
type: array
items:
$ref: '#/components/schemas/KgeFile'
size:
description: approximate aggregate size of data files in the file set (megabytes)
type: number
format: float
contents:
$ref: '#/components/schemas/MetaKnowledgeGraph'
KgeUploadProgressStatusCode:
description: >-
Code for status of upload or direct URL
transfer progress for a given file.
type: string
enum:
- Ongoing
- Completed
- Error
KgeFileSetStatusCode:
description: >-
Code for status of processing for a KGE File Set.
type: string
enum:
- Created
- Loaded
- Processing
- Validated
- Error
KgeFile:
description: >-
Annotated file in a KGE File Set.
type: object
properties:
original_name:
description: original name of file (as uploaded)
type: string
assigned_name:
description: assigned name of file (by archive, for export)
type: string
file_type:
description: >-
Designates if the file is (content or file set) meta-, node or edge data
type: string
file_size:
description: size of file in megabytes
type: number
format: float
kgx_compliance_status:
$ref: '#/components/schemas/KgxCompliance'
errors:
description: if 'non-compliant' file, list of error messags
type: array
items:
type: string
required:
- original_name
- assigned_name
- file_type
- file_size
- kgx_compliance_status
additionalProperties: false
KgxCompliance:
description: >-
KGX compliance status of a specific KGE File.
type: string
enum:
- Assessing
- Compliant
- Non-Compliant
UploadTokenObject:
description: >-
Upload token associated with a file for uploading into a KGE File Set.
type: object
properties:
upload_token:
description: >-
Upload object key returned, for use in a local file
upload and/or in in progress monitoring of a local
upload or a URL-specified file transfer.
type: string
required:
- upload_token
additionalProperties: false
UploadProgressToken:
description: >-
Token tracking the upload progress of a file into a KGE File Set.
type: object
properties:
upload_token:
description: >-
Upload token associated with a given uploading file.
type: string
status:
description: >-
Code for status of upload or direct URL
transfer progress for a given file.
$ref: '#/components/schemas/KgeUploadProgressStatusCode'
current_position:
description: >-
Number of bytes uploaded so far.
type: integer
end_position:
description: >-
Total expected bytes to be uploaded.
type: integer
required:
- upload_token
- status
- current_position
- end_position
additionalProperties: false
BiolinkEntity:
description: >-
Compact URI (CURIE) for a Biolink class, biolink:NamedThing
or a child thereof. The CURIE must use the prefix 'biolink:'
followed by the PascalCase class name.
type: string
pattern: ^biolink:[A-Z][a-zA-Z]*$
externalDocs:
description: Biolink model entities
url: https://biolink.github.io/biolink-model/docs/NamedThing.html
example: biolink:PhenotypicFeature
BiolinkPredicate:
description: >-
CURIE for a Biolink 'predicate' slot, taken from the Biolink slot
('is_a') hierarchy rooted in biolink:related_to (snake_case). This
predicate defines the Biolink relationship between the subject and
object nodes of a biolink:Association defining a knowledge graph edge.
type: string
pattern: ^biolink:[a-z][a-z_]*$
externalDocs:
description: Biolink model predicates
url: https://biolink.github.io/biolink-model/docs/related_to.html
example: biolink:interacts_with
MetaKnowledgeGraph:
type: object
description: >-
Knowledge-map representation of this KGX knowledge graph.
properties:
nodes:
type: object
description: >-
Collection of node categories provided by this KGX knowledge graph,
indexed by Biolink class CURIEs.
additionalProperties:
$ref: '#/components/schemas/MetaNode'
edges:
type: array
description: >-
List of edges/predicates provided by this KGX knowledge graph.
items:
$ref: '#/components/schemas/MetaEdge'
minItems: 1
MetaNode:
type: object
description: >-
Description of a node category provided by this KGX knowledge graph.
properties:
id_prefixes:
type: array
description: >-
List of CURIE prefixes for the node category that this TRAPI web
service understands and accepts on the input.
items:
type: string
minItems: 1
example: [CHEMBL.COMPOUND, INCHIKEY]
count:
type: integer
description: >-
Total number of node instances of this node category known to this
KGX knowledge graph, or -1 if the number is not known.
count_by_source:
type: object
description: >-
Number of node instances by their source
additionalProperties:
type: integer
example:
ChEMBL: 1234
required:
- id_prefixes
additionalProperties: false
MetaEdge:
type: object
description: >-
Edge in a meta knowledge map describing relationship between a subject
Biolink class and an object Biolink class.
properties:
subject:
$ref: '#/components/schemas/BiolinkEntity'
description: >-
Subject node category of this relationship edge.
example: biolink:ChemicalSubstance
predicate:
$ref: '#/components/schemas/BiolinkPredicate'
description: >-
Biolink relationship between the subject and object categories.
example: biolink:affects
object:
$ref: '#/components/schemas/BiolinkEntity'
description: >-
Object node category of this relationship edge.
example: biolink:Protein
relations:
type: array
description: >-
Low-level relations from the underlying source.
items:
type: string
example: [inhibits, activates]
count:
type: integer
description: >-
Total number of edge instances of this (subject, predicate,
object) triple known to this KGX knowledge graph, or -1 if the
number is not known.
count_by_source:
type: object
description: >-
Number of edge instances by their source.
additionalProperties:
type: integer
example:
ChEMBL: 1234
required:
- subject
- predicate
- object
additionalProperties: false
RegisterGraphRequestBody:
type: object
description: >-
KGE Knowledge Graph registration metadata.
properties:
translator_component:
type: string
translator_team:
type: string
kg_name:
type: string
kg_description:
type: string
license_name:
type: string
license_url:
type: string
terms_of_service:
type: string
required:
- translator_component
- translator_team
- kg_name
RegisterFileSetRequestBody:
type: object