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CONTRIBUTING.md

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How to contribute to EDAM

Your pull requests, issues, comments and suggestions are warmly welcome! 🙏🏽🙇🏽‍♂️

Note: If you don't want to edit an OWL file (RDF/XML) or deal with Git, please skip to the bottom of this file to find other very welcome ways to contribute. 🎈🙌🏽

Source code

The "source code" of EDAM is in the file EDAM_dev.owl (see main). The format of the source file is RDF/XML. EDAM_dev.owl can be editted locally (e.g. in a text editor), or online on Gitpod. The file is too big to be editted directly on GitHub.

New to Git?

Some neat efficient learning resources are:

Git setup on your local machine

Please make sure to read the following when you are cloning this repo:

There is a pre-commit hook set up, to validate that the source code of EDAM is in the right format. To make it work, please use one of the following 2 options:

😮 Wait a second! Is this too fast? Do you need a slightly more step-by-step guide? Then you are welcome to follow issue #616.

Option 1

This is the preferred option. Your git version needs to be 2.9.0 or higher for the hook to work.

Please make sure to have set up the correct path to the hooks directory, globally or locally:

  • Run git config --list from inside of your cloned edamontology repo, and see if core.hooksPath has value .githooks
  • To set it locally for your edamontology repo: git config core.hooksPath .githooks
  • To set it globally for your git: git config --global core.hooksPath .githooks
  • To see your git config with where the variables are stored, run git config --list --show-origin from inside of your edamontology repo

Test option 1:

  1. Make a dummy change in EDAM_dev.owl using a text editor (best if you create an experimental Git branch for that), and try to commit it. The commit should work.
  2. Now replace all owl:Class in the EDAM_dev.owl file with for example wol:Class 🦉, and try to commit that change. The commit should fail now (returning 0), not allowing you to commit.

Option 2

If you want to continue using an older version of git than 2.9.0, please run the pre-commit script manually: r Inside the edamontology repo, run: .githooks/pre-commit or sh .githooks/pre-commit (whichever works for you).

If the pre-commit script fails (i.e. non-zero exit code), the source code is invalid (i.e. not containing any owl:Class string).

Test option 2:

  1. Make a dummy change in EDAM_dev.owl using a text editor (best if you create an experimental Git branch for that), and run the .githooks/pre-commit. It should succeed, that is return a non-zero number.
  2. Now replace all owl:Class in the EDAM_dev.owl file with for example wol:Class 🦉, and run the script again. It should fail now, returning 0.

Using Gitpod

TODO

How to add a new concept

TODO

Other contributions

Not wanting to edit an OWL file yourself? Also your ideas and requests are highly appreciated!

We'll welcome your comments and suggestions in WebProtégé (free registration required to view and comment) or in the NCBO BioPortal (free registration required to add notes and suggestions). You are also welcome to request a new concept to be added to EDAM, using an issue template.

Please see Getting involved for more ways to contribute to EDAM.

Note: There is a separate repository for EDAM-bioimaging 🔬 (including concepts for Bioimage informatics and Machine learning), where contributions are very warmly welcome! 🙌🏽 EDAM-bioimaging is abundantly commented in WebProtégé (free registration required to view and comment), and there is a possiblity to add notes and suggestions also in the NCBO BioPortal (free registration required to add notes and suggestions). 🚀 EDAM-bioimaging can also be editted directly on GitHub, and confirmed eager contributors will get edit rights directly on WebProtégé. Contribution details here. 🛰