API Reference¶

Attention

reference docs for the bio.tools API
to make suggestions about these guidelines please add comments via GitHub
if you find a bug, have any questions or suggestions, please get in touch with us.
see also the API Usage Guide

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, 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.

https://bio.tools/api/tool?topicID=”topic_3510”

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.

https://bio.tools/api/tool?biotoolsID=”blast” returns the tool with biotoolsID of “blast” (the “canonical” blast)
https://bio.tools/api/tool?biotoolsID=blast returns all tools with “blast” in their biotoolsID (all blast flavours)

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"

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"

Caution

bio.tools supports upload/download of data in XML format compliant to biotoolsScheme v3.0.0. If you want to download in XML format you should use these endpoints (see Tool detail below):

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

e.g. https://bio.tools/api/tool/signalp

Were you to try to get XML format returned from a search over bio.tools

e.g. https://bio.tools/api/tool?toolid=signalp&format=xml

currently you’d get garbled / invalid XML (don’t use it!) - we’re looking at a fix.

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"