Initialize a GitHub repo for managing your ontology the OBO Library way!
For more details, see
Any Linux or OS X command line environment should work. You will minimally need the following installed:
The kit will also try to make an initial ontology release, unless you tell it not to. It will attempt to download the following dependencies:
Download this starter package
It's recommended you get a release version: https://github.com/INCATools/ontology-starter-kit/releases
First you must be in the root level of the starter kit
seed-my-ontology-repo.pl command does everything you need. For help:
./seed-my-ontology-repo.pl -d po ro pato -u cmungall -t "Triffid Behavior ontology" triffo
You can list any set of dependencies you like after "-d". However, these must be the official OBO ontology IDs. See http://obofoundry.org for details.
This will create your starter files in
target/triffid-behavior-ontology. It will also prepare an initial
release and initialize a local repository (not yet pushed to GitHub).
You can customize at this stage, or (recommended) after making an initial push to github
Push to GitHub
The starter kit will automatically initialize a git project, add all files and commit.
You will need to create a project on GitHub.
- Go to: https://github.com/new
- The owner MUST be the org you selected with the
-uoption. The MUST be the one you set with
- Do not initialize with a README (you already have one)
- Click Create
- See the section under "…or push an existing repository from the command line"
Follow the instructions there. E.g.
cd target/triffid-behavior-ontology git remote add origin email@example.com:cmungall/triffid-behavior-ontology.git git push -u origin master
Note: you can now mv
target/triffid-behavior-ontology to anywhere you like in your home directory. Or you can do a fresh checkout from github
Edit and release cycle
In your repo you will see a README-editors.md file that has been customized for your project. Follow these instructions.
Generally the cycle is to:
- the edit the edit.owl file
- make test
- git commit
- git push
To make a release
Note that any make step can be preceded by run.sh if you have Docker installed
OBO Library metadata
The assumption here is that you are ahdering to OBO principles and want to eventually submit to OBO. Your repo will contain stub metadata files to help you do this.
You can create pull requests for your ontology on the OBO Foundry. See the
src/metadata file for more details.
For more documentation, see http://obofoundry.org
You will want to also:
- enable travis
- enable zenodo (optional)
See the README-editors.md file that has been generated for your project.
If you have issues, file them here: https://github.com/INCATools/ontology-starter-kit/issues
Some things to check:
- if something goes wrong you can try again. You may want to remove the
targetdir, or use the
- make sure your ontid has no spaces
- if your title has spaces, enclose it in quotes
You will likely want to customize the build process, and of course to edit the ontology.
The main thing you will want to do is to modify the seeds that are used to build the imports. The ones that are there are just examples, edit them as you like. See the ROBOT docs and the OBO Tutorial for more info.
Adapting an existing ontology repo
The OSK is designed for creating a new repo for a new ontology. It can still be used to help figure out how to migrate an existing github repository to the OSK structure. There are different ways to do this.
- Manually compare your ontology against the template folder and make necessary adjustments
- Run osk as if creating a new repo. Manually compare this with your existing repo and use
git mvto rearrange, and adding any missing files by copying them across and doing a
- Create a new repo de novo and abandon your existing one, using github issue mover to move tickets across.
Obviously the second method is not ideal as you lose your github history. Note even with
git mv history tracking becomes harder
You will find additional documentation in the src/ontology/README-editors.md file in your repo