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User Guide

This user guide aims to help you through the different steps to register your own entry to bio.tools.

Note

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

Create an account

Creating an account on bio.tools is very quick and simple. Just click on the sign up button at the top-right corner of the page. Then you just need to give a username, your email address and a password to get your account done.

Add content

Every user is welcome to register its own resource to bio.tools. Once your account is created, you can start adding your content by clicking on add content.

The registration of an new entry is splitted in different parts that are described below.

Note

The minimum information required is marked with a red asterix asterix.

At every moment, you can check the validity of your information by clicking on Validate and save it by clicking on Save validate_save.

Note

Saving the entry makes it directly available online. If you want to save what you have done without publishing it, the only way is to go to the :ref:`json` part and save the .json file locally.

Summary

For this first part, you give the main descriptors of your entry. This includess the name of your resource with a description, its version and a homepage URL. A unique ID is automatically generated from the name but it is still possible to change it.

Note

A unique URL on bio.tools will be generated for the entry with the following format: http://bio.tools/tool/ID/version/version_number.

Function

This is where you describe the functionnality of your entry based on the EDAM ontology [1]. The description is built on the following diagram:

biotool_function

In each box, you can add as many fields as you want. You can also add a general comment about the function (this is particularly useful when your entry has several functions).

Note

It can be difficult to find the right ontology to describe your function(s), input(s) or output(s). Please visit OLS EDAM and BioPortal EDAM websites to find more information about the different ontologies and help you finding the best description.

Labels

In this part, you can tell more about your tool:

  • What type of tool it is (command line tool, library...).
  • In which topic(s) the tool belongs to (based on EDAM ontology [1]).
  • In which operating system it is possible to use it.
  • The language used to develop the tool, its license and maturity.
  • The accessibility of your tool and its cost.

Contact

At least one contact is required to register a tool but you can add as many contact as you want.

Note

If you wish to mention people that participated in the development of the tool, you can use the :ref:`credits` part.

Links

It is the place where your share links that do not belong to the other parts. For instance, it can be link to a mailing list, mirror or repository.

Download

You can here share all the different download links you want. It can be many different kind such as binaries, source code, biological data, test data (full list available on the drop down menu of Download type).

Documentation

Make your different documentations for your tool available here.

Publications

Share the different publications of the tool which can be the primary publication but also review or secondary references that are relevant to this tool. You can use either the PubMed Central ID (PMCID), the PubMed ID (PMID) or the Digital Object ID (DOI).

Credits

Credits represent all type of entities that participated in the tool. It can be a people, but also an institution or a consortium.

JSON

This is all the information you gave about your tool, formatted in JSON format.

Permissions

You can decide to make the entry either editable only by yourself, a list of users or anyone.

Update a resource

There is two way to update a resource from its tool card: update

  • Click on update this record if it concerns minor changes
  • Click on create a new version to register a new version. This allows to keep all the information concerning the previous version

Remove a resource

From the tool card, click on update this record. Then you can remove the entry by clicking on the remove button remove.

Warning

Removing an entry is definitive.

Search for a tool

Coming soon...

References

[1](1, 2) Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S. and Rice, P. (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 29(10): 1325-1332.