Ontology for Immune Epitopes

The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes.

This is the developer repository for ONTIE. You can learn more about ONTIE through our documentation.

Editing

In ONTIE we use ROBOT templates to convert spreadsheets to OWL. Edit the relevant src/ontology/templates/ file:

• assays.tsv for assays related to immune epitopes
• complex.tsv for protein complexes
• disease.tsv for diseases
• external.tsv external terms from Chemical Entities of Biological Interest (CHEBI), NCBI Taxon, Gene Ontology (GO), NCBI Taxon database, and other sources
• index.tsv list of ONTIE terms
• other.tsv all miscellaneous ontology terms
• predicate.tsv top level terms
• protein.tsv all protein related terms in ONTIE
• taxon.tsv NCBI Taxon, biological tax

Files

• README.md this overview document
• ontie.owl the latest release of ONTIE
• Makefile scripts for building ONTIE
• src/
  • ontology/ source files for ONTIE
  • obsolete/ contains obsolete code files
  • scripts utility scripts

Building

The Makefile contains scripts for building ONTIE. On macOS or Linux, you should just be able to run make or one of the specific tasks below. On Windows consider using some sort of Linux virtual machine such as Docker or Vagrant. Most results will be in the build/ directory. If you have trouble, contact James.

• make test build ONTIE and run tests (this is run on every push to GitHub)
• make sort sort templates, and fix quoting and line endings, see more in Keeping Things Tidy section
• make ONTIE.owl build the release file
• make all run all build tasks
• make clean remove temporary files

Development

We use git and GitHub to develop ONTIE. There's a lot of good documentation on both:

• git website with files and documentation
• GitHub Help and Flow
• git command-line overview

Initial Set Up

Before you can start developing with ONTIE, you will need to do some initial setup:

1. Sign up for a GitHub account
2. Install the Git command line tool, the GitHub Desktop app, or another Git client of your choosing
3. Configure Git with your name and email
4. Clone the ONTIE repository

Making Changes

Changes should be made in manageable pieces, e.g. add one term or edit a few related terms. Most changes should correspond to a single issue on the tracker.

Start from a local copy of the master branch of the ONTIE repository. Make sure your local copy is up-to-date. Make your changes on a new branch.

When you're ready, push your branch to the ONTIE repository and make a Pull Request (PR) on the GitHub website. Your PR is a request to merge your branch back into master. Your PR will be tested, discussed, adjusted if necessary, then merged. Then the cycle can repeat for the next change that you or another developer will make.

These are the steps with their CLI commands. When using a GUI application the steps will be the same.

1. git fetch make sure your local copy is up-to-date
2. git checkout master start on the master branch
3. git checkout -b your-branch-name create a new branch named for the change you're making
4. make your changes
5. git status and git diff inspect your changes
6. git add --update src/ add all updated files in the src/ directory to staging
7. git commit --message "Description, issue #123" commit staged changes with a message; it's good to include an issue number
8. git push --set-upstream origin your-branch-name push your commit to GitHub
9. open https://github.com/IEDB/ONTIE in your browser and click the "Make Pull Request" button. Enter the details of the changes you intend to contribute.

Your Pull Request will be automatically tested. If there are problems, we will update your branch. When all tests have passed, your PR can be merged into master. Rinse and repeat!

Keeping Things Tidy

The easiest way to edit our src/ontology/template/ files is with Excel. Unfortunately Excel on macOS uses old line endings, and this messes up our diffs.

For clean diffs, we also like to keep out templates sorted by ID.

The make sort command will fix line endings and sorting by running all the templates through a Python script.