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.
In ONTIE we use ROBOT templates to convert spreadsheets to OWL. Edit the relevant
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
README.mdthis overview document
ontie.owlthe latest release of ONTIE
Makefilescripts for building ONTIE
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 testbuild ONTIE and run tests (this is run on every push to GitHub)
make sortsort templates, and fix quoting and line endings, see more in Keeping Things Tidy section
make ONTIE.owlbuild the release file
make allrun all build tasks
make cleanremove temporary files
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:
- Sign up for a GitHub account
- Install the Git command line tool, the GitHub Desktop app, or another Git client of your choosing
- Configure Git with your name and email
- Clone the ONTIE repository
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.
git fetchmake sure your local copy is up-to-date
git checkout masterstart on the
git checkout -b your-branch-namecreate a new branch named for the change you're making
- make your changes
git diffinspect your changes
git add --update src/add all updated files in the
src/directory to staging
git commit --message "Description, issue #123"commit staged changes with a message; it's good to include an issue number
git push --set-upstream origin your-branch-namepush your commit to GitHub
- 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.
make sort command will fix line endings and sorting by running all the templates through a Python script.