Creating a new Ontology using the ODK

We will walk you though the steps to make a new ontology project

1. Install and Start Docker

See below for an alternative protocol where you install the software yourself rather than use Docker

2. Download the wrapper script and pull latest ODK version

  • Linux/Mac: seed-via-docker.sh

  • PC: seed-via-docker.bat

  • First, make sure you have Docker running (you will see the Docker whale in your toolbar on a Mac)

  • To make sure you have the latest version of the ODK installed, run in the command line

    docker pull obolibrary/odkfull

NOTE The very first time you run this it may be slow, while docker downloads necessary images. Don’t worry, subsequent runs should be much faster!

3. Run the wrapper script

You can either pass in a project.yaml file that specifies your ontology project setup, or you can pass arguments on the command line.

Passing arguments on the command line:

./seed-via-docker.sh -d po -d ro -d pato -u cmungall -t "Triffid Behavior ontology" triffo

Using a the predefined examples/triffo/project.yaml file:

./seed-via-docker.sh -C examples/triffo/project.yaml

You can add a -c (lowercase) just before the -C (capital c) in the command to first delete any previous attempt to generate your ontology with the ODK, and then replaces it with a completely new one.

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 your Git host site such as GitHub or GitLab).

You can customize at this stage, or (recommended) after making an initial push to your git host.

4. Push to Git hosting website

The development kit will automatically initialize a git project, add all files and commit.

You will need to create a project on you Git hosting site.

For GitHub:

  1. Go to: https://github.com/new
  2. The owner MUST be the org you selected with the -u option. The name MUST be the one you set with -t.
  3. Do not initialize with a README (you already have one)
  4. Click Create
  5. See the section under “…or push an existing repository from the command line”

For GitLab:

  1. Go to: https://gitlab.com/projects/new
  2. The owner MUST be the org you selected with the -u option. The name MUST be the one you set with -t.
  3. Do not initialize with a README (you already have one)
  4. Click ‘Create project’
  5. See the section under “Push an existing Git repository”

Follow the instructions there. E.g.

cd target/triffid-behavior-ontology
git remote add origin git@github.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.