API Reference

Attention

The bio.tools Web API provides an easy way to access the bio.tools database.

List tools

List and search through all the available tools. 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 the attributes supported by bio.tools:

Parameter Search behaviour
biotoolsID

Search for bio.tools tool ID (usually quoted - to get exact match)

biotoolsID=”signalp”

name

Search for tool name (quoted as needed)

name=signalp

homepage

Exact search for tool homepage URL (must be quoted)

homepage=”http://cbs.dtu.dk/services/SignalP/”

description

Search over tool description (quoted as needed)

description=”peptide cleavage”

version

Exact search for tool version (must be quoted)

version=”4.1”

topic

Search for EDAM Topic (term) (quoted as needed)

topic=”Proteomics”

topicID

Exact search for EDAM Topic (URI): must be quoted

topicID=”topic_3510”

function

Fuzzy search over function (input, operation, output, note and command)

function=”Sequence analysis”

operation

Fuzzy search for EDAM Operation (term) (quoted as needed)

operation=”Sequence analysis”

operationID

Exact search for EDAM Operation (ID) (must be quoted)

operationID=”operation_2403”

dataType

Fuzzy search over input and output for EDAM Data (term) (quoted as needed)

dataType=”Protein sequence”

dataTypeID

Exact search over input and output for EDAM Data (ID) (must be quoted)

dataTypeID=”data_2976”

dataFormat

Fuzzy search over input and output for EDAM Format (term) (quoted as needed)

dataFormat=”FASTA”

dataFormatID

Exact search over input and output for EDAM Format (ID) (must be quoted)

dataFormatID=”format_1929”

input

Fuzzy search over input for EDAM Data and Format (term) (quoted as needed)

input=”Protein sequence”

inputID

Exact search over input for EDAM Data and Format (ID) (must be quoted)

inputID=”data_2976”

inputDataType

Fuzzy search over input for EDAM Data (term) (quoted as needed)

inputDataType=”Protein sequence”

inputDataTypeID

Exact search over input for EDAM Data (ID) (must be quoted)

inputDataTypeID=”data_2976”

inputDataFormat

Fuzzy search over input for EDAM Format (term) (quoted as needed)

inputDataFormat=”FASTA”

inputDataFormatID

Exact search over input for EDAM Format (ID) (must be quoted)

inputDataFormatID=”format_1929”

output

Fuzzy search over output for EDAM Data and Format (term) (quoted as needed)

output=”Sequence alignment”

outputID

Exact search over output for EDAM Data and Format (ID) (must be quoted)

outputID=”data_0863”

outputDataType

Fuzzy search over output for EDAM Data (term) (quoted as needed)

outputDataType=”Sequence alignment”

outputDataTypeID

Exact search over output for EDAM Data (ID) (must be quoted)

outputDataTypeID=”data_0863”

outputDataFormat

Fuzzy search over output for EDAM Format (term) (quoted as needed)

outputDataFormat=”ClustalW format”

outputDataFormatID

Exact search over output for EDAM Format (ID) (must be quoted)

outputDataFormatID=”format_1982”

toolType

Exact search for tool type

toolType=”Command-line tool”

collectionID

Exact search for tool collection (normally quoted)

collectionID=”Rare Disease”

maturity

Exact search for tool maturity

maturity=Mature

operatingSystem

Exact search for tool operating system

operatingSystem=Linux

language

Exact search for programming language

language=Java

cost

Exact search for cost

cost=”Free of charge”

license

Exact search for software or data usage license (quoted as needed)

license=”GPL-3.0”

accessibility

Exact search for tool accessibility

accessibility=”Open access”

credit

Fuzzy search over credit (name, email, URL, ORCID iD, type of entity, type of role and note)

credit=”Henrik Nielsen”

creditName

Exact search for name of credited entity

creditName=”Henrik Nielsen”

creditTypeRole

Exact search for role of credited entity

creditTypeRole=Developer

creditTypeEntity

Exact search for type of credited entity

creditTypeEntity=”Funding agency”

creditOrcidID

Exact search for ORCID iD of credited entity (must be quoted)

creditOrcidID=”0000-0001-5121-2036”

publication

Fuzzy search over publication (DOI, PMID, PMCID, publication type and tool version) (quoted as needed)

publication=10.12688/f1000research.12974.1

publicationID

Exact search for publication ID (DOI, PMID or PMCID) (must be quoted)

publicationID=”10.12688/f1000research.12974.1”

publicationType

Exact search for publication type

publicationType=Primary

publicationVersion

Exact search for tool version associated with a publication (must be quoted)

publicationVersion=”1.0”

link

Fuzzy search over general link (URL, type and note) (quote as needed)

link=”Issue tracker”

linkType

Exact search for type of information found at a link

linkType=”Issue tracker”

documentation

Fuzzy search over documentation link (URL, type and note) (quote as needed)

documentation=Manual

documentationType

Exact search for type of documentation

documentationType=Manual

download

Fuzzy search over download link (URL, type, version and note) (quote as needed)

download=Binaries

downloadType

Exact search for type of download

downloadType=Binaries

downloadVersion

Exact search for tool version associated with a download (must be quoted)

downloadVersion=”1.0”

otherID

Fuzzy search over alternate tool IDs (ID value, type of ID and version)

otherID=”rrid:SCR_015644”

otherIDValue

Exact search for value of alternate tool ID (must be quoted)

otherIDValue=”rrid:SCR_015644”

otherIDType

Exact search for type of alternate tool ID

otherIDType=RRID

otherIDVersion

Exact search for tool version associated with an alternate ID (must be quoted)

otherIDVersion=”1.0”

Important

Values of the following parameters must be given in quotes to get sensible (or any) results:
  • homepage
  • version
  • topicID
  • operationID
  • dataTypeID
  • dataFormatID
  • inputID
  • inputDataTypeID
  • inputDataFormatID
  • outputID
  • outputDataTypeID
  • outputDataFormatID
  • creditOrcidID
  • publicationID
  • publicationVersion
  • downloadVersion
  • otherIDValue
  • otherIDVersion
e.g.
Values of other parameters can be quoted or unquoted:
  • Unquoted values invoke a fuzzy word search: it will search for fuzzy matches of words in the search phrase, to the target field
  • Quoted values invoke an exact phrase search; it will search for an exact match of the full-length of the search phrase, to the target field (matches to target substrings are allowed)
e.g.

Caution

The parameters are (currently) case-sensitive, e.g. you must use &biotoolsID= and not &biotoolsid

Example

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

Note

An EDAM concept ID can be specified as a concept URI or ID:
  • Concept URI e.g. http://edamontology.org/operation_2403
  • Concept ID e.g. operation_2403
In future we may add support for:
  • Concept CURIE e.g. EDAM:operation_2403
  • Numerical ID e.g. 2403

Note: URIs and IDs must be quoted, e.g. &topicID="operation_2403"

Caution

If querying by homepage you must quote the query value, e.g.

Response data

Key Name Description Example
count The total tool 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 tools and their relative information ARRAY

Tool detail

Obtain information about a single tool.

HTTP GET

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

Endpoint Parameters

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

Example

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

Register a tool

Register a new tool.

Important

This method requires the user to be authenticated. Learn how to Log in / obtain token.

HTTP POST

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

Endpoint Parameters

Parameter Required Type Description
data Yes Tool Tool you wish to register. See an example tool.

Note

It is possible to specify editing permissions for tools. Learn how to manage Editing permissions.

Headers

Parameter Required Allowed values Description
Content-Type Yes String(application/json, application/xml) Media type
Authorization Yes String(‘Token <authorization token>’) Authorization header. Learn how to Log in / obtain token.

Example

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

Validate registering a tool

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

Important

This method requires the user to be authenticated. Learn how to Log in / obtain token.

HTTP POST

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

Endpoint Parameters

Parameter Required Type Description
data Yes Tool Tool you wish to validate. See an example tool.

Headers

Parameter Required Allowed values Description
Content-Type Yes String(application/json, application/xml) Media type
Authorization Yes String(‘Token <authorization token>’) Authorization header. Learn how to Log in / obtain token.

Example

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

Update a tool

Update a tool description.

Important

This method requires the user to be authenticated. Learn how to Log in / obtain token.

HTTP PUT

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

Endpoint Parameters

Parameter Required Type Description
id Yes String biotoolsID
data Yes Tool Description with which you wish to update the tool See an example tool.

Note

It is possible to specify editing permissions for tools. Learn how to manage Editing permissions.

Headers

Parameter Required Allowed values Description
Content-Type Yes String(application/json, application/xml) Media type
Authorization Yes String(‘Token <authorization token>’) Authorization header. Learn how to Log in / obtain 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 tool

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

Important

This method requires the user to be authenticated. Learn how to Log in / obtain token.

HTTP PUT

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

Endpoint Parameters

Parameter Required Type Description
id Yes String biotoolsID
data Yes   Tool Description with which you wish to update the tool for validation See an example tool.

Headers

Parameter Required Allowed values Description
Content-Type Yes String(application/json, application/xml) Media type
Authorization Yes String(‘Token <authorization token>’) Authorization header. Learn how to Log in / obtain token.

Example

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

Editing permissions

Manage editing permissions for the registered tools.

There are currently three types of editing permissions supported by the system:

Private

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

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

Public

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

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

Group

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

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

Delete a tool

Removes a tool from the registry.

Important

This method requires the user to be authenticated. Learn how to Log in / obtain token.

HTTP DELETE

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

Endpoint Parameters

Parameter Required Type Description
id Yes String biotoolsID

Headers

Parameter Required Allowed values Description
Authorization Yes String(‘Token <authorization token>’) Authorization header. Learn how to Log in / obtain 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

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

Important

This method requires the user to be authenticated. Learn how to Log in / obtain 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 Log in / obtain 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 tools (limited to name, id, version, additionDate, lastUpdate)

Log out

Log out of the system.

Important

This method requires the user to be authenticated. Learn how to Log in / obtain 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 Log in / obtain token.

Example

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

Reset user password

Send 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

Confirm 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"