Ontology for Biomedical Investigations

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:

external terms (from other ontologies): We use OntoFox for imports. Edit the corresponding src/ontology/OntoFox_inputs/ file.
template terms: We use ROBOT templates to convert spreadsheets to OWL. Edit the relevant src/ontology/templates/ file:
- obsolete.tsv for obsolete terms
- assays.tsv for general assays
- epitope-assays.tsv specifically for immune epitope assays
- value-specifications.tsv
- biobank-specimens.tsv
- medical-history.tsv for medical history classifications and related selection criteria
- study-designs.tsv for study designs
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

README.md this overview document
obi.owl the latest release of OBI
Makefile scripts for building OBI
views/ various specialized views of OBI
- obi.obo the latest release of OBI in .obo file format
- obi_core.owl the latest release of OBI Core: ~100 key terms
src/
- ontology/ source files for OBI
  - obi-edit.owl the main OBI OWL file
  - core.txt the list of OBI Core terms
  - external-byhand.owl some custom imports from other ontologies
  - catalog-v001.xml an artisinal list of OWL import overrides
  - templates/ ROBOT template files for various branches of OBI
  - modules/ the results of the ROBOT templates
  - OntoFox_inputs/ OntoFox configuration files for importing from other ontologies
  - OntoFox_outputs/ OntoFox result files
- sparql/ SPARQL queries for building and validating OBI
- scripts/ utility scripts
- views/ configuration for views

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:

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

Initial Set Up

Before you can start developing with OBI, 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 OBI repository
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.

git fetch make sure your local copy is up-to-date
git checkout master start on the master branch
git checkout -b your-branch-name create a new branch named for the change you're making
make your changes
git status and git diff inspect 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-name push your commit to GitHub
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.

alisea47/obi