API endpoints

This is a lightweight web service with a REST interface, which provides an easy way to access the bio.tools database. An API (Application programming interface) is a protocol intended to be used as an interface by software components to communicate with each other.

If you find a bug, have any questions or suggestions, please get in touch with us.

List resources

List and search through all the available resources. Can sort, filter, and search the results.

HTTP GET

https://bio.tools/api/tool/
https://bio.tools/api/t/

Endpoint Parameters

Parameter	Required	Type	Default	Description
page	No	Integer	1	Result page number
format	No	String(json, xml, api)	json	Response media type
q	No	String		Query term, used for searching, matches all attributes
sort	No	String(lastUpdate, additionDate, name, affiliation, score)	lastUpdate	Sorts the results by choosen value (score only available when there is a query)
ord	No	String(desc, asc)	desc	Orders the results by either Ascending or Descending order
<attribute>	No	String		Filter by <attribute>. List of supported attributes below.

Filtering

To filter the results by attribute name, the attribute name has to be added as a parameter to the URL, with the value being the desired search term, e.g. ?name=signalp

Attributes

These are attributes supported by bio.tools

id, name, topic, function, operation, input,
inputDataFormat, inputDataType, output, outputDataFormat,
outputDataType, homepage, description, version,
accessibility, toolType, collection, contact,
elixirInfo, maturity, operatingSystem, language,
cost, license, documentation, link, download, publication,
credit, owner

Example

curl -X GET "https://bio.tools/api/tool/?page=1&format=json&name=signalp&sort=name&ord=asc&q=protein-signal-peptide-detection"

Response data

Key Name	Description	Example
count	The total resource count results for your query	2313
previous	Link to the previous page	?page=4
next	Link to the next page	?page=6
list	An array with multiple resources and their relative information	ARRAY

Resource detail

Obtain information about a single resource.

HTTP GET

https://bio.tools/api/tool/:id/
https://bio.tools/api/t/:id/

Endpoint Parameters

Parameter	Required	Type	Default	Description
id	Yes	String		Resource unique ID
format	No	String(json, xml, api)	json	Response media type

Example

curl -X GET "https://bio.tools/api/tool/signalp/?format=json"

List resource versions

Obtain information about avaliable versions of a single resource.

HTTP GET

https://bio.tools/api/tool/:id/version/
https://bio.tools/api/t/:id/version/

Endpoint Parameters

Parameter	Required	Type	Default	Description
id	Yes	String		Resource unique ID
format	No	String(json, xml, api)	json	Response media type

Example

curl -X GET "https://bio.tools/api/t/signalp/version/"

Resource version detail

Obtain information about a specified version of a single resource.

HTTP GET

https://bio.tools/api/tool/:id/version/:version_id
https://bio.tools/api/t/:id/version/:version_id

Endpoint Parameters

Parameter	Required	Type	Default	Description
id	Yes	String		Resource unique ID
format	No	String(json, xml, api)	json	Response media type
version_id	Yes	String		Resource version unique ID

Example

curl -X GET "https://bio.tools/api/tool/signalp/version/4.1?format=json"

Register a resource

Note

This method requires the user to be authenticated. Learn how to :ref:`Token`.

HTTP POST

https://bio.tools/api/tool/
https://bio.tools/api/t/

Endpoint Parameters

Parameter	Required	Type	Description
data	Yes	Resource	Resource you wish to register. See an example resource.

Note

It is possible to specify editing permissions for resources. Learn how to manage :ref:`Editing_permissions`.

Note

It is possible to create multiple versions of the same resource. Learn how to use :ref:`Resource_versioning`.

Headers

Parameter	Required	Allowed values	Description
Content-Type	Yes	String(application/json, application/xml)	Resource media type
Authorization	Yes	String('Token <authorization token>')	Authorization header. Learn how to :ref:`Token`.

Example

curl -X POST -H "Content-Type: application/json" \
-H "Authorization: Token 028595d682541e7e1a5dcf2306eccb720dadafd7" \
-d '<resource>' "https://bio.tools/api/tool/"

Validate registering a resource

Test registering a resource without it actually being saved into the database.

Note

This method requires the user to be authenticated. Learn how to :ref:`Token`.

HTTP POST

https://bio.tools/api/tool/validate/
https://bio.tools/api/t/validate/

Endpoint Parameters

Parameter	Required	Type	Description
data	Yes	Resource	Resource you wish to validate. See an example resource.

Headers

Parameter	Required	Allowed values	Description
Content-Type	Yes	String(application/json, application/xml)	Resource media type
Authorization	Yes	String('Token <authorization token>')	Authorization header. Learn how to :ref:`Token`.

Example

curl -X POST -H "Content-Type: application/json" \
-H "Authorization: Token 028595d682541e7e1a5dcf2306eccb720dadafd7" \
-d '<resource>' "https://bio.tools/api/tool/validate/"

Update a resource

Update a resource description.

Note

This method requires the user to be authenticated. Learn how to :ref:`Token`.

HTTP PUT

https://bio.tools/api/tool/:id/
https://bio.tools/api/t/:id/

Endpoint Parameters

Parameter	Required	Type	Description
id	Yes	String	Resource unique ID
data	Yes	Resource	Description with which you wish to update the resource See an example resource.

Note

It is possible to specify editing permissions for resources. Learn how to manage :ref:`Editing_permissions`.

Note

It is possible to create multiple versions of the same resource. Learn how to use :ref:`Resource_versioning`.

Headers

Parameter	Required	Allowed values	Description
Content-Type	Yes	String(application/json, application/xml)	Resource media type
Authorization	Yes	String('Token <authorization token>')	Authorization header. Learn how to :ref:`Token`.

Example

curl -X PUT -H "Content-Type: application/json" \
-H "Authorization: Token 028595d682541e7e1a5dcf2306eccb720dadafd7" \
-d '<resource>' "https://bio.tools/api/tool/SignalP"

Validate updating a resource

Test updating a resource without it actually being saved into the database.

Note

This method requires the user to be authenticated. Learn how to :ref:`Token`.

HTTP PUT

https://bio.tools/api/tool/:id/validate/
https://bio.tools/api/t/:id/validate/

Endpoint Parameters

Parameter	Required	Type	Description
id	Yes	String	Resource unique ID
data	Yes	Resource	Description with which you wish to update the resource for validation See an example resource.

Headers

Parameter	Required	Allowed values	Description
Content-Type	Yes	String(application/json, application/xml)	Resource media type
Authorization	Yes	String('Token <authorization token>')	Authorization header. Learn how to :ref:`Token`.

Example

curl -X PUT -H "Content-Type: application/json" \
-H "Authorization: Token 028595d682541e7e1a5dcf2306eccb720dadafd7" \
-d '<resource>' "https://bio.tools/api/tool/SignalP/validate/"

Resource versioning

All resources can have a specified version assigned to them. This allows for example new versions of resources to be registered while keeping an older version of the resource intact. In order to create a new version of a given resource, the following parameters need to be added to the resource data:

Parameter	Type	Description
versionId	String	ID of a new resource version to be created. Once created, the version id becomes permanent and is used to uniquely identify a specific version. See :ref:`Resource_version_detail` for more information.
latest	1 or 0	Specify if the created resource version is the latest. All previous resources marked as 'latest' will no longer be considered that after a new version gets marked as 'latest'.

Editing permissions

It is possible to manage editing permissions for the registered resources. There are currently three types of editing permissions supported by the system:

Private

A private resource can only be edited by the creator of the resource. This is the default option. In order to set this kind of permission, add the following info into the resource data:

"editPermission": {
    "type": "private"
}

Public

Public resource can be modified by any user registered in the system. In order to set this kind of permission, add the following info into the resource data:

"editPermission": {
    "type": "public"
}

Group

Specify a list of users in the system that can edit the resource. In order to set this kind of permission, add the following info into the resource data:

"editPermission": {
    "type": "private",
    "authors": [
        "registered_user_1", "registered_user_2"
    ]
}

Delete a resource

Removes a resource from the registry.

Note

This method requires the user to be authenticated. Learn how to :ref:`Token`.

HTTP DELETE

https://bio.tools/api/tool/:id/
https://bio.tools/api/t/:id/

Endpoint Parameters

Parameter	Required	Type	Description
id	Yes	String	Resource unique ID

Headers

Parameter	Required	Allowed values	Description
Authorization	Yes	String('Token <authorization token>')	Authorization header. Learn how to :ref:`Token`.

Example

curl -X DELETE \
-H "Authorization: Token 028595d682541e7e1a5dcf2306eccb720dadafd7" \
"https://bio.tools/api/tool/SignalP"

List used terms

Obtain a list of terms registered with tools for some attributes, e.g. a list of names of all tools.

HTTP GET

https://bio.tools/api/used-terms/:attribute

Endpoint Parameters

Parameter	Required	Type	Default	Description
attribute	Yes	String(name, topic, functionName, input, output, credits, all)		Attribute for which a list of used terms will be returned
format	No	String(json, xml, api)	json	Response media type

Example

curl -X GET "https://bio.tools/api/used-terms/name/?format=json"

Response data

Key Name	Description
data	A list of used terms

Create a user account

Creates a user account and emails a verification email.

HTTP POST

https://bio.tools/api/rest-auth/registration/

POST data

Key Name	Required	Type	Description	Example
username	Yes	String	Account username	username
password1	Yes	String	Password	password
password2	Yes	String	Repeated password	password
email	Yes	String	Account email. The verification email will be sent to this address	example@example.org

Headers

Parameter	Required	Allowed values	Description
Content-Type	Yes	String(application/json, application/xml)	POST data media type

Example

curl -X POST -H "Content-Type: application/json" \
-d '{"username":"username", "password1":"password", \
"password2":"password", "email":"example@example.org"}' \
"https://bio.tools/api/rest-auth/registration/"

Verify a user account

Verifies a user account based on the emailed verification key.

HTTP POST

https://bio.tools/api/rest-auth/registration/verify-email/

POST data

Key Name	Required	Type	Description	Example
key	Yes	String	Verification key from account creation email	ndwowtbpmlk5zxdxfrwgu2822xynjidhizhwosycve7hro1of156hjwdsf1f6gbn

Headers

Parameter	Required	Allowed values	Description
Content-Type	Yes	String(application/json, application/xml)	POST data media type

Example

curl -X POST -H "Content-Type: application/json" \
-d '{"key":"ndwowtbpmlk5zxdxfrwgu2822xynjidhizhwosycve7hro1of156hjwdsf1f6gbn"}' \
"https://bio.tools/api/rest-auth/registration/verify-email/"

Log in / obtain token

Logs the user in and returns an authentication token.

HTTP POST

https://bio.tools/api/rest-auth/login/

POST data

Key Name	Required	Type	Description	Example
username	Yes	String	Account username	username
password	Yes	String	Password	password

Headers

Parameter	Required	Allowed values	Description
Content-Type	Yes	String(application/json, application/xml)	POST data media type

Example

curl -X POST -H "Content-Type: application/json" \
-d '{"username":"username","password":"password"}' \
"https://bio.tools/api/rest-auth/login/"

Response data

Key Name	Description
key	Authentication token

Get user information

Returns information about the logged in user account, including a list of registered resource (name, id, version, additionDate, lastUpdate)

Note

This method requires the user to be authenticated. Learn how to :ref:`Token`.

HTTP GET

https://bio.tools/api/rest-auth/user/

Endpoint Parameters

Parameter	Required	Type	Default	Description
format	No	String(json, xml, api)	json	Response media type

Headers

Parameter	Required	Allowed values	Description
Authorization	Yes	String('Token <authorization token>')	Authorization header. Learn how to :ref:`Token`.

Example

curl -X GET \
-H "Authorization: Token 028595d682541e7e1a5dcf2306eccb720dadafd7" \
"https://bio.tools/api/rest-auth/user/?format=json"

Response data

Key Name	Description
username	Account username
email	Account email
resources	List of registered resources (limited to name, id, version, additionDate, lastUpdate)

Log out

Note

This method requires the user to be authenticated. Learn how to :ref:`Token`.

HTTP POST

https://bio.tools/api/rest-auth/logout/

Headers

Parameter	Required	Allowed values	Description
Authorization	Yes	String('Token <authorization token>')	Authorization header. Learn how to :ref:`Token`.

Example

curl -X POST
-H "Authorization: Token 028595d682541e7e1a5dcf2306eccb720dadafd7" \
"https://bio.tools/api/rest-auth/logout/"

Reset user password

Sends a password reset email.

HTTP POST

https://bio.tools/api/rest-auth/password/reset/

POST data

Key Name	Required	Type	Description	Example
email	Yes	String	Account email	example@example.org

Headers

Parameter	Required	Allowed values	Description
Content-Type	Yes	String(application/json, application/xml)	POST data media type

Example

curl -X POST -H "Content-Type: application/json" \
-d '{"email":"example@example.org"}' \
"https://bio.tools/api/rest-auth/password/reset/"

Confirm password reset

Confirms a password reset using uid and token from a password reset email.

HTTP POST

https://bio.tools/api/rest-auth/password/reset/confirm/

POST data

Key Name	Required	Type	Description	Example
uid	Yes	String	UID from password reset email	MQ
token	Yes	String	Token from password reset email	4ct-67e90a1ab4f22fbb9b9f
password1	Yes	String	New password	new_password
password2	Yes	String	New password repeated	new_password

Headers

Parameter	Required	Allowed values	Description
Content-Type	Yes	String(application/json, application/xml)	POST data media type

Example

curl -X POST -H "Content-Type: application/json" \
-d '{"uid":"MQ", "token":"4ct-67e90a1ab4f22fbb9b9f", \
"password1":"new_password", "password2":"new_password"}' \
"https://bio.tools/api/rest-auth/password/reset/confirm/"

Stats

Compile stats about a the registry.

HTTP GET

https://bio.tools/api/stats

Example

curl -X GET "https://bio.tools/api/stats/?format=json"

Files

api_reference.rst

Latest commit

History

api_reference.rst

File metadata and controls

API endpoints

List resources

Endpoint Parameters

Filtering

Attributes

Example

Response data

Resource detail

Endpoint Parameters

Example

List resource versions

Endpoint Parameters

Example

Resource version detail

Endpoint Parameters

Example

Register a resource

Endpoint Parameters

Headers

Example

Validate registering a resource

Endpoint Parameters

Headers

Example

Update a resource

Endpoint Parameters

Headers

Example

Validate updating a resource

Endpoint Parameters

Headers

Example

Resource versioning

Editing permissions

Private

Public

Group

Delete a resource

Endpoint Parameters

Headers

Example

List used terms

Endpoint Parameters

Example

Response data

Create a user account

POST data

Headers

Example

Verify a user account

POST data

Headers

Example

Log in / obtain token

POST data

Headers

Example

Response data

Get user information

Endpoint Parameters

Headers

Example

Response data

Log out

Headers

Example

Reset user password

POST data

Headers

Example

Confirm password reset

POST data

Headers

Example