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Updating the tool and resource list

How to add a tool or resource to Infectious Diseases Toolkit

Way of working

The tools or resources you will find on pages are a filtered set from a bigger list. This filtering is done using page_id. If a tool or resource is tagged with, for example, the page_id metadata, it will be automatically listed on the corresponding page. The page_id can be found in the Website overview page.

The all_tools_and_resources list is based on the csv file in the _data directory of the Infectious Diseases Toolkit repository. Tools and resources can be manually linked to FAIRsharing.org, Bio.tools and TeSS, but every week we also run a fully automatic check that links tools and resources with the corresponding registries. A GitHub Bot will generate a Pull Request (PR) with the new links added to the main data file of the website (a yaml file).

The main table

The main table is based on this google spreadsheet.

The table consists of 5 columns:

  • name: the name of the tool or resource
  • url: URL to the main page of the tool or resource, make sure to let the URL start with https://
  • description: A short description of the tool or resource. Try to not use the characters " or '
  • registry: 3 registries are supported: Bio.tools, FAIRsharing.org and TeSS. The keywords you can use respectively are: biotools, fairsharing, fairsharing-coll and tess, specifying the id or query with a colon). FAIRsharing collections have an ID that follows the pattern bsg-s000XXX. List multiple registries using a comma , between the keywords to separate the key:value pairs. The values that are given in the table will always overrule the automatic links. If no FAIRsharing ID, Bio.tools ID or TeSS Query is available for a source, you can overwrite the automatic linking by adding ‘NA’ as registry.
  • related_pages: This is used to tag the tools so that they can be listed on the correct page. We only allow page_id that are linked to a page. To find out what the page_id of a page is, please check its metadata attribute page_id at the top of the markdown file or the Website overview page. List multiple page_id’s by using a comma , between them.
name url description registry related_pages
Beacon https://beacon-project.io/ The Beacon protocol defines an open standard for genomics data discovery.   researcher, data manager, IT support, human data
Bioconda https://bioconda.github.io/ Bioconda is a bioinformatics channel for the Conda package manager biotools:bioconda IT support, data analysis
BrAPI https://www.brapi.org Specification for a standard API for plant data: plant material, plant phenotyping data   IT support, plants
Conda https://docs.conda.io/en/latest/ Open source package management system   IT support, data analysis
COPO https://copo-project.org/ Portal for scientists to broker more easily rich metadata alongside data to public repos. biotools:copo, fairsharing-coll:bsg-d001247 metadata, researcher, plants

What tool or resource can be added to the table

Tools and resources specifically mentioned in the text of the pages should be present in the main table. If necessary, tools and resources equivalent to the one mentioned in the text could also be added to the table.

Making changes

Since the csv file is not user-friendly and prone to mistakes because of potential empty fields and use of commas, we do not recommend making changes using the GitHub website itself, instead we point people to the Google spreadsheet.

The editors will do the work on Git for you. All you need to do is:

  • Check if a tool or resource is already listed.
  • Add or edit tools and resources as described above.
  • Done! The editors will update the “tool and resource list” in GitHub regularly. In case your change is urgent, ping an editor in an issue or pull request.

Let the editor and GitHub bot do the rest

If the PR of the editor containing the changes to the .csv table is merged, a PR will be opened by github-actions. Please check that the changes this PR proposes to the yaml file are in line with what you want to have changed.