Publishing a tool in bio.tools#

bio.tools is an ELIXIR repository of software metadata that serves two main purposes:

• collecting systematic and reasonable statistics about the available software for many purposes, including data science and performance reports
• dissemination of your tools to other researchers

To get your software visible, you will need to register to create a bio.tools account. Once logged-in, the process of adding a tool record is as follows:

• you click Add content in the Menu on the top right on the main page of bio.tools site
• in there, you go through around 10 tabs that allow you to fill lots of interesting information about your tool
• once you submit the information, your tool becomes immediately visible at the bio.tools site.

General tips#

What to do if you do not know what to write into a field#

• Use search and consult the curation guide to resolve ambiguities. bio.tools maintain a specialized curation guide to help you with your tool submission. It includes helpful and authoritative guidelines for almost all fields that you can fill, including examples.

• Look at what others did. As the last resort, when you do not know what to do with a field, you can use the search suggestions in the structured search box in the top of the page, and try to be at least consistent with the rest of the bio.tools entries. In the search box, you can type in a single letter of your desired annotation category, wait a moment until the autocomplete starts (or press the down arrow button), and then use the suggestions for inspiration.

Add a “backup” maintainer to your tool’s entry#

This may remove a lot of unnecessary workload from you, and will help everyone at times when you are not available. (Or, at least, reduce the stress levels.)

Add many links to all types of documentation#

Adding links to documentation helps at least in 2 ways:

• The search engines will be able to categorize and index your contents better, possibly giving more helpful links to your tools.
• Users of bio.tools will be able to explore the most relevant parts of your documentation very quickly, helping them to make a faster decision about using your tool. For example, it is often a relief to quickly see that a bioinformatics tool has an explicit step-by-step tutorial, and that a web visualization framework has a complete useful API reference.

Generally, each tool should have at least one dedicated link to a complete “reference” documentation, and one link to a “quick start” guide.

Similarly, include the (interesting) relations to other tools. This gives a little more data to both search engines and statisticians who process bio.tools content, and gives a documentation of possible “use-cases”.

Proper labeling#

Choose a suitable bio.tools ID#

As the name says, the Persistent biotoolsID cannot be changed. It will be permanently displayed as an identifier in almost all content that is autogenerated from bio.tools. For users, that concerns mainly the URLs, so you may want to apply similar formatting guidelines as for URLs (use hyphens - instead of underscores _, do not use capital letters, …).

Add your tool to proper collections#

Collections group the results of various larger cooperated (or loosely organized) efforts, such as “Galaxy tools”, “Parkinson disease research”, and “3D BioInfo”.

If your tool is related to ELIXIR, you should fill in the correct ELIXIR node, platform, community and collection. Remember to:

• Add all involved ELIXIR nodes.
• Add your tool to the node-specific ELIXIR collections. For LCSB, that is usually ELIXIR-LU. This is counter-intuitive and seems duplicate to the categorization by ELIXIR nodes, but:
  • at least 2 nodes use collections labels instead of node labels to scrape data about their tools.
  • there is search support only for the collections; currently (March 2021) it seems that you cannot easily search for tools by ELIXIR nodes.

On top of that (but also if the tool is not related to ELIXIR) you add further collections:

Fill in the tool “Function” very verbosely#

The main reason for categorizing tool functions is to provide a systematic way for listing the tools in topic-based catalogues that can be browsed by users.

The categories and data formats available for describing your tool function rarely give a precise match. That is okay, you can choose a broader category.

Use all categories that match even a small part of your tool; it will potentially help bio.tools users to find your tool even if they do not know what precisely they are searching for.

Selecting a very specific category (“deeper” in the topic tree) also implies all “parent” categories, so you do not have to be afraid of over-specification. bio.tools search box will automatically include your tool in searches for the broader categories.

References and publications#

Be comprehensive about publications#

Add all publications where you described, showcased, and benchmarked the tool. Also add preprints.

There are several purposes for the precise publication tracking:

• the users may (and often will) sort the tools by the citation count, likely trying the most tested approach first
• the publications provide an additional form of documentation (often more colorful than the API docs)
• the links and citation counts provide a nice, easily available statistic about the real-world performance of your software development

Use the Credit tab#

The purpose of the “Credit” tab is not immediately obvious – basically, you can credit anything that has helped you with creating the tool. This is currently used for at least 3 purposes:

• systematic tracking of non-ELIXIR collaborators (add their ORCIDs)
• listing of any industrial partners
• listing affiliations to particular research institutions (remember to add LCSB as an affiliation)