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README.md

Ontology for Biomedical Investigations

Build Status

The Ontology for Biomedical Investigations (OBI) helps you communicate clearly about scientific investigations by defining more than 2500 terms for assays, devices, objectives, and more.

This is the developer repository for OBI. You can download the most up-to-date OBI products here and learn more about OBI through our documentation.

Editing

Our ontology terms come in three groups. Depending on what type of term you want to edit or add, you have to go through different routes:

  1. external terms (from other ontologies): We use OntoFox for imports. Edit the corresponding src/ontology/OntoFox_inputs/ file.
  2. template terms: We use ROBOT templates to convert spreadsheets to OWL. Edit the relevant src/ontology/templates/ file:
  3. other terms: Edit src/ontology/obi-edit.owl in Protege.

See below for a full list of files, build instructions, and instructions on using Git and GitHub for OBI.

Files

Building

The Makefile contains scripts for building OBI. 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 merge and run SPARQL tests (this is run on every push to GitHub)
  • make sort sort templates, and fix quoting and line endings
  • make imports update OntoFox imports
  • make modules update ROBOT templates
  • make obi.owl build the release file; reasoning can take about 10 minutes
  • make views update ROBOT templates
  • make all prepare for a release, runs imports, modules, test, obi.owl, and views
  • make build/obi_merged.owl merge obi-edit.owl into a single file, don't reason
  • make clean remove temporary files

Development

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

Initial Set Up

Before you can start developing with OBI, 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 OBI repository

  5. if you're using macOS and Excel, set up a pre-commit hook (see below for details):

    ln -s ../../src/scripts/check-line-endings.sh .git/hooks/pre-commit
    

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 OBI repository. Make sure your local copy is up-to-date. Make your changes on a new branch. Please use the OBI Term ID Reservations sheet to manage new IDs.

When you're ready, push your branch to the OBI 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/obi-ontology/obi in your browser and click the "Make Pull Request" button

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.

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