Enterobase-API
API for EnteroBase (https://enterobase
COMMUNITYAPI KEY0 INSTALLS
OpenAPI Specificationv3.0
{
"openapi": "3.0.0",
"info": {
"contact": {
"email": "enterobase@warwick.ac.uk",
"name": "Nabil-Fareed Alikhan"
},
"description": "\nAPI for EnteroBase (https://enterobase.warwick.ac.uk) \n\nEnteroBase is a user-friendly online resource, where users can upload their \nown sequencing data for de novo assembly by a stream-lined pipeline. The assemblies \nare used for calling MLST and wgMLST patterns, allowing users to compare their strains \nto publically available genotyping data from other EnteroBase users, GenBank and classical MLST databases.\n\nClick here to find how to get and use an API token: http://bit.ly/1TKlaOU\n",
"title": "Enterobase-API",
"version": "v2.0",
"x-apisguru-categories": [
"open_data"
],
"x-logo": {
"backgroundColor": "#FFFFFF",
"url": "https://api.apis.guru/v2/cache/logo/https_twitter.com_warwickuni_profile_image.jpeg"
},
"x-origin": [
{
"format": "openapi",
"url": "http://enterobase.warwick.ac.uk/api/v2.0/swagger",
"version": "3.0"
}
],
"x-providerName": "warwick.ac.uk",
"x-serviceName": "enterobase"
},
"tags": [],
"paths": {
"/api/v2.0": {
"get": {
"description": "Top level information about EnteroBase databases",
"parameters": [
{
"description": "Database prefix, e.g. SAL for Salmonella",
"in": "query",
"name": "prefix",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "query",
"name": "name",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Database description",
"in": "query",
"name": "description",
"required": false,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "A info object"
},
"403": {
"description": "Unauthorised access for this specific resource or data"
}
},
"tags": [
"Info"
]
}
},
"/api/v2.0/login": {
"get": {
"description": "Login endpoint, refresh your API token",
"parameters": [
{
"description": "EnteroBase username",
"in": "query",
"name": "username",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "EnteroBase Password",
"in": "query",
"name": "password",
"required": false,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "A login object"
},
"403": {
"description": "Unauthorised access for this specific resource or data"
}
},
"tags": [
"Login"
]
}
},
"/api/v2.0/lookup": {
"get": {
"description": "Generic endpoint for lookup list of barcodes",
"parameters": [
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_<Table code> e.g. SAL_AA0001AA_ST",
"in": "query",
"name": "barcode",
"required": false,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "List of lookup objects"
},
"403": {
"description": "Unauthorised access for this specific resource or data"
},
"408": {
"description": "Connection timeout, please try again later."
}
},
"tags": [
"Lookup"
]
}
},
"/api/v2.0/lookup/{barcode}": {
"get": {
"description": "Generic endpoint for lookup of barcodes",
"parameters": [
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_<Table code> e.g. SAL_AA0001AA_ST",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "A lookup object"
},
"403": {
"description": "Unauthorised access for this specific resource or data"
}
},
"tags": [
"Lookup"
]
},
"post": {
"description": "Generic endpoint for lookup of barcodes",
"parameters": [
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_<Table code> e.g. SAL_AA0001AA_ST",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"content": {
"application/json": {
"schema": {
"properties": {
"barcode": {
"type": "string"
}
},
"type": "object"
}
}
}
},
"responses": {
"200": {
"description": "A lookup object"
},
"403": {
"description": "Unauthorised access for this specific resource or data"
}
},
"tags": [
"Lookup"
]
}
},
"/api/v2.0/{database}/assemblies": {
"get": {
"description": "Genome assemblies",
"parameters": [
{
"description": "Field to order by. Default: barcode",
"in": "query",
"name": "orderby",
"required": false,
"schema": {
"default": "barcode",
"type": "string"
}
},
{
"description": "",
"explode": true,
"in": "query",
"name": "only_fields",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_AS e.g. SAL_AA0001AA_AS",
"explode": true,
"in": "query",
"name": "barcode",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "n50",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "top_species",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "uberstrain",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "version",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "Number of results per page",
"in": "query",
"name": "limit",
"required": false,
"schema": {
"default": 50,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "reldate",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "Cursor position in results",
"in": "query",
"name": "offset",
"required": false,
"schema": {
"default": 0,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "assembly_status",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Order of search results: asc or desc",
"in": "query",
"name": "sortorder",
"required": false,
"schema": {
"default": "asc",
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "List of assemblies objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Assemblies"
]
}
},
"/api/v2.0/{database}/assemblies/{barcode}": {
"get": {
"description": "Genome assemblies",
"parameters": [
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_AS e.g. SAL_AA0001AA_AS",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body3"
},
"responses": {
"200": {
"description": "List of assemblies objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Assemblies"
]
},
"post": {
"description": "Genome assemblies",
"parameters": [
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_AS e.g. SAL_AA0001AA_AS",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body3"
},
"responses": {
"200": {
"description": "List of assemblies objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Assemblies"
]
},
"put": {
"description": "Genome assemblies",
"parameters": [
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_AS e.g. SAL_AA0001AA_AS",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body3"
},
"responses": {
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Assemblies"
]
}
},
"/api/v2.0/{database}/schemes": {
"get": {
"description": "Genotyping schemes",
"parameters": [
{
"description": "Field to order by. Default: barcode",
"in": "query",
"name": "orderby",
"required": false,
"schema": {
"default": "barcode",
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "scheme_name",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "created",
"required": false,
"schema": {
"format": "date-time",
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "lastmodified",
"required": false,
"schema": {
"format": "date-time",
"type": "string"
}
},
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"explode": true,
"in": "query",
"name": "barcode",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "label",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"explode": true,
"in": "query",
"name": "only_fields",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "version",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "Number of results per page",
"in": "query",
"name": "limit",
"required": false,
"schema": {
"default": 50,
"format": "int32",
"type": "integer"
}
},
{
"description": "Order of search results: asc or desc",
"in": "query",
"name": "sortorder",
"required": false,
"schema": {
"default": "asc",
"type": "string"
}
},
{
"description": "Cursor position in results",
"in": "query",
"name": "offset",
"required": false,
"schema": {
"default": 0,
"format": "int32",
"type": "integer"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "List of schemes objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Schemes"
]
}
},
"/api/v2.0/{database}/schemes/{barcode}": {
"get": {
"description": "Genotyping schemes",
"parameters": [
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body2"
},
"responses": {
"200": {
"description": "List of schemes objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Schemes"
]
},
"post": {
"description": "Genotyping schemes",
"parameters": [
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body2"
},
"responses": {
"200": {
"description": "List of schemes objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Schemes"
]
},
"put": {
"description": "Genotyping schemes",
"parameters": [
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body2"
},
"responses": {
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Schemes"
]
}
},
"/api/v2.0/{database}/straindata": {
"get": {
"description": "Strain data",
"parameters": [
{
"description": "",
"in": "query",
"name": "comment",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "secondary_sample_accession",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "my_strains",
"required": false,
"schema": {
"type": "boolean"
}
},
{
"description": "Cursor position in results",
"in": "query",
"name": "offset",
"required": false,
"schema": {
"default": 0,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "serotype",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "n50",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "county",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"explode": true,
"in": "query",
"name": "only_fields",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "postcode",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "lab_contact",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "substrains",
"required": false,
"schema": {
"type": "boolean"
}
},
{
"description": "",
"in": "query",
"name": "custom_fields",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "city",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "strain_name",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "collection_date",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "collection_month",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "reldate",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "continent",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "source_details",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "version",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "latitude",
"required": false,
"schema": {
"format": "float",
"type": "number"
}
},
{
"description": "",
"in": "query",
"name": "email",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "source_niche",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_AS e.g. SAL_AA0001AA_AS",
"explode": true,
"in": "query",
"name": "barcode",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "uberstrain",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Order of search results: asc or desc",
"in": "query",
"name": "sortorder",
"required": false,
"schema": {
"default": "asc",
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "collection_year",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "Field to order by. Default: strain barcode",
"in": "query",
"name": "orderby",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "assembly_status",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "source_type",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "country",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "region",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "longitude",
"required": false,
"schema": {
"format": "float",
"type": "number"
}
},
{
"description": "",
"in": "query",
"name": "sample_accession",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Number of results per page",
"in": "query",
"name": "limit",
"required": false,
"schema": {
"default": 50,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "top_species",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "collection_time",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "List of straindata objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Straindata"
]
}
},
"/api/v2.0/{database}/strains": {
"get": {
"description": "Strain metadata",
"parameters": [
{
"description": "",
"in": "query",
"name": "comment",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "secondary_sample_accession",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "antigenic_formulas",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "my_strains",
"required": false,
"schema": {
"type": "boolean"
}
},
{
"description": "",
"in": "query",
"name": "serotype",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "county",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"explode": true,
"in": "query",
"name": "only_fields",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "postcode",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "lab_contact",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "substrains",
"required": false,
"schema": {
"type": "boolean"
}
},
{
"description": "",
"in": "query",
"name": "city",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "strain_name",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "collection_date",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "collection_month",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "reldate",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "continent",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "source_details",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "version",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "latitude",
"required": false,
"schema": {
"format": "float",
"type": "number"
}
},
{
"description": "",
"in": "query",
"name": "assembly_barcode",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "source_niche",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"explode": true,
"in": "query",
"name": "barcode",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "uberstrain",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Order of search results: asc or desc",
"in": "query",
"name": "sortorder",
"required": false,
"schema": {
"default": "asc",
"type": "string"
}
},
{
"description": "Cursor position in results",
"in": "query",
"name": "offset",
"required": false,
"schema": {
"default": 0,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "collection_year",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "Field to order by. Default: barcode",
"in": "query",
"name": "orderby",
"required": false,
"schema": {
"default": "barcode",
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "return_all",
"required": false,
"schema": {
"type": "boolean"
}
},
{
"description": "",
"in": "query",
"name": "source_type",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "country",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "region",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "longitude",
"required": false,
"schema": {
"format": "float",
"type": "number"
}
},
{
"description": "",
"in": "query",
"name": "sample_accession",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Number of results per page",
"in": "query",
"name": "limit",
"required": false,
"schema": {
"default": 50,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "collection_time",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "List of strains objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Strains"
]
}
},
"/api/v2.0/{database}/strains/{barcode}": {
"get": {
"description": "Strain metadata",
"parameters": [
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body"
},
"responses": {
"200": {
"description": "List of strains objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Strains"
]
},
"post": {
"description": "Strain metadata",
"parameters": [
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body"
},
"responses": {
"200": {
"description": "List of strains objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Strains"
]
},
"put": {
"description": "Strain metadata",
"parameters": [
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body"
},
"responses": {
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Strains"
]
}
},
"/api/v2.0/{database}/strainsversion": {
"get": {
"description": "Strain previous metadata",
"parameters": [
{
"description": "",
"in": "query",
"name": "comment",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "secondary_sample_accession",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "antigenic_formulas",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "my_strains",
"required": false,
"schema": {
"type": "boolean"
}
},
{
"description": "",
"in": "query",
"name": "serotype",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "county",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"explode": true,
"in": "query",
"name": "only_fields",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "postcode",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "lab_contact",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "substrains",
"required": false,
"schema": {
"type": "boolean"
}
},
{
"description": "",
"in": "query",
"name": "city",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "strain_name",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "collection_date",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "collection_month",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "reldate",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "continent",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "source_details",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "version",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "latitude",
"required": false,
"schema": {
"format": "float",
"type": "number"
}
},
{
"description": "",
"in": "query",
"name": "assembly_barcode",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "source_niche",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"explode": true,
"in": "query",
"name": "barcode",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "uberstrain",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Order of search results: asc or desc",
"in": "query",
"name": "sortorder",
"required": false,
"schema": {
"default": "asc",
"type": "string"
}
},
{
"description": "Cursor position in results",
"in": "query",
"name": "offset",
"required": false,
"schema": {
"default": 0,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "collection_year",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "Field to order by. Default: barcode",
"in": "query",
"name": "orderby",
"required": false,
"schema": {
"default": "barcode",
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "return_all",
"required": false,
"schema": {
"type": "boolean"
}
},
{
"description": "",
"in": "query",
"name": "source_type",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "country",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "region",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "longitude",
"required": false,
"schema": {
"format": "float",
"type": "number"
}
},
{
"description": "",
"in": "query",
"name": "sample_accession",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Number of results per page",
"in": "query",
"name": "limit",
"required": false,
"schema": {
"default": 50,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "collection_time",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "List of strainsversion objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Strainsversion"
]
}
},
"/api/v2.0/{database}/traces": {
"get": {
"description": "Traces (sequence-reads) metadata",
"parameters": [
{
"description": "Field to order by. Default: barcode",
"in": "query",
"name": "orderby",
"required": false,
"schema": {
"default": "barcode",
"type": "string"
}
},
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_TR e.g. SAL_AA0001AA_TR",
"explode": true,
"in": "query",
"name": "barcode",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"explode": true,
"in": "query",
"name": "only_fields",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "Number of results per page",
"in": "query",
"name": "limit",
"required": false,
"schema": {
"default": 50,
"format": "int32",
"type": "integer"
}
},
{
"description": "Order of search results: asc or desc",
"in": "query",
"name": "sortorder",
"required": false,
"schema": {
"default": "asc",
"type": "string"
}
},
{
"description": "Cursor position in results",
"in": "query",
"name": "offset",
"required": false,
"schema": {
"default": 0,
"format": "int32",
"type": "integer"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "List of traces objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Traces"
]
}
},
"/api/v2.0/{database}/traces/{barcode}": {
"get": {
"description": "Traces (sequence-reads) metadata",
"parameters": [
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_TR e.g. SAL_AA0001AA_TR",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body4"
},
"responses": {
"200": {
"description": "List of traces objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Traces"
]
},
"post": {
"description": "Traces (sequence-reads) metadata",
"parameters": [
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_TR e.g. SAL_AA0001AA_TR",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body4"
},
"responses": {
"200": {
"description": "List of traces objects"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Traces"
]
},
"put": {
"description": "Traces (sequence-reads) metadata",
"parameters": [
{
"description": "Unique barcode for Traces records, <database prefix>_<ID code>_TR e.g. SAL_AA0001AA_TR",
"in": "path",
"name": "barcode",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"requestBody": {
"$ref": "#/components/requestBodies/Body4"
},
"responses": {
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Traces"
]
}
},
"/api/v2.0/{database}/{scheme}/alleles": {
"get": {
"description": "Alleles data ",
"parameters": [
{
"description": "",
"in": "query",
"name": "allele_id",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "seq",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"explode": true,
"in": "query",
"name": "barcode",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "reldate",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "locus",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "",
"explode": true,
"in": "query",
"name": "only_fields",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "limit",
"required": false,
"schema": {
"default": 50,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "offset",
"required": false,
"schema": {
"default": 0,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "path",
"name": "scheme",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "List of alleles objects"
},
"400": {
"description": "Malformed request, contains an error"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Alleles"
]
}
},
"/api/v2.0/{database}/{scheme}/loci": {
"get": {
"description": "Loci ",
"parameters": [
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"explode": true,
"in": "query",
"name": "barcode",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "locus",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"explode": true,
"in": "query",
"name": "only_fields",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "create_time",
"required": false,
"schema": {
"format": "date-time",
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "limit",
"required": false,
"schema": {
"default": 50,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "offset",
"required": false,
"schema": {
"default": 0,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "scheme",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "path",
"name": "scheme",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "List of loci objects"
},
"400": {
"description": "Malformed request, contains an error"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Loci"
]
}
},
"/api/v2.0/{database}/{scheme}/sts": {
"get": {
"description": "ST profile data",
"parameters": [
{
"description": "",
"in": "query",
"name": "st_id",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "scheme",
"required": false,
"schema": {
"type": "string"
}
},
{
"description": "",
"in": "query",
"name": "show_alleles",
"required": false,
"schema": {
"type": "boolean"
}
},
{
"description": "Unique barcode for Strain records, <database prefix>_<ID code> e.g. SAL_AA0001AA",
"explode": true,
"in": "query",
"name": "barcode",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"explode": true,
"in": "query",
"name": "only_fields",
"required": false,
"schema": {
"items": {
"type": "string"
},
"type": "array"
}
},
{
"description": "",
"in": "query",
"name": "limit",
"required": false,
"schema": {
"default": 50,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "reldate",
"required": false,
"schema": {
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "query",
"name": "offset",
"required": false,
"schema": {
"default": 0,
"format": "int32",
"type": "integer"
}
},
{
"description": "",
"in": "path",
"name": "scheme",
"required": true,
"schema": {
"type": "string"
}
},
{
"description": "Species database name (senterica, ecoli, yersinia, mcatarrhalis) for Salmonella, Escherichia, Yersinia, Moraxella respectively",
"in": "path",
"name": "database",
"required": true,
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "List of sts objects"
},
"400": {
"description": "Malformed request, contains an error"
},
"403": {
"description": "Unauthorised access for this specific resource"
}
},
"tags": [
"Sts"
]
}
}
},
"components": {
"requestBodies": {
"Body": {
"content": {
"application/json": {
"schema": {
"properties": {
"antigenic_formulas": {
"type": "string"
},
"assembly_barcode": {
"type": "string"
},
"barcode": {
"items": {
"type": "string"
},
"type": "array"
},
"city": {
"type": "string"
},
"collection_date": {
"format": "int32",
"type": "integer"
},
"collection_month": {
"format": "int32",
"type": "integer"
},
"collection_time": {
"type": "string"
},
"collection_year": {
"format": "int32",
"type": "integer"
},
"comment": {
"type": "string"
},
"continent": {
"type": "string"
},
"country": {
"type": "string"
},
"county": {
"type": "string"
},
"lab_contact": {
"type": "string"
},
"latitude": {
"format": "float",
"type": "number"
},
"limit": {
"default": 50,
"format": "int32",
"type": "integer"
},
"longitude": {
"format": "float",
"type": "number"
},
"my_strains": {
"type": "boolean"
},
"offset": {
"default": 0,
"format": "int32",
"type": "integer"
},
"only_fields": {
"items": {
"type": "string"
},
"type": "array"
},
"orderby": {
"default": "barcode",
"type": "string"
},
"postcode": {
"type": "string"
},
"region": {
"type": "string"
},
"reldate": {
"format": "int32",
"type": "integer"
},
"return_all": {
"type": "boolean"
},
"sample_accession": {
"type": "string"
},
"secondary_sample_accession": {
"type": "string"
},
"serotype": {
"type": "string"
},
"sortorder": {
"default": "asc",
"type": "string"
},
"source_details": {
"type": "string"
},
"source_niche": {
"type": "string"
},
"source_type": {
"type": "string"
},
"strain_name": {
"type": "string"
},
"substrains": {
"type": "boolean"
},
"uberstrain": {
"type": "string"
},
"version": {
"format": "int32",
"type": "integer"
}
},
"type": "object"
}
}
}
},
"Body2": {
"content": {
"application/json": {
"schema": {
"properties": {
"barcode": {
"items": {
"type": "string"
},
"type": "array"
},
"created": {
"format": "date-time",
"type": "string"
},
"label": {
"type": "string"
},
"lastmodified": {
"format": "date-time",
"type": "string"
},
"limit": {
"default": 50,
"format": "int32",
"type": "integer"
},
"offset": {
"default": 0,
"format": "int32",
"type": "integer"
},
"only_fields": {
"items": {
"type": "string"
},
"type": "array"
},
"orderby": {
"default": "barcode",
"type": "string"
},
"scheme_name": {
"type": "string"
},
"sortorder": {
"default": "asc",
"type": "string"
},
"version": {
"format": "int32",
"type": "integer"
}
},
"type": "object"
}
}
}
},
"Body3": {
"content": {
"application/json": {
"schema": {
"properties": {
"assembly_status": {
"type": "string"
},
"barcode": {
"items": {
"type": "string"
},
"type": "array"
},
"limit": {
"default": 50,
"format": "int32",
"type": "integer"
},
"n50": {
"format": "int32",
"type": "integer"
},
"offset": {
"default": 0,
"format": "int32",
"type": "integer"
},
"only_fields": {
"items": {
"type": "string"
},
"type": "array"
},
"orderby": {
"default": "barcode",
"type": "string"
},
"reldate": {
"format": "int32",
"type": "integer"
},
"sortorder": {
"default": "asc",
"type": "string"
},
"top_species": {
"type": "string"
},
"uberstrain": {
"type": "string"
},
"version": {
"format": "int32",
"type": "integer"
}
},
"type": "object"
}
}
}
},
"Body4": {
"content": {
"application/json": {
"schema": {
"properties": {
"barcode": {
"items": {
"type": "string"
},
"type": "array"
},
"limit": {
"default": 50,
"format": "int32",
"type": "integer"
},
"offset": {
"default": 0,
"format": "int32",
"type": "integer"
},
"only_fields": {
"items": {
"type": "string"
},
"type": "array"
},
"orderby": {
"default": "barcode",
"type": "string"
},
"sortorder": {
"default": "asc",
"type": "string"
}
},
"type": "object"
}
}
}
}
},
"securitySchemes": {
"api_key": {
"description": "Basic Authentication is required for all requests ",
"scheme": "basic",
"type": "http"
}
}
}
}