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.
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
- template terms: We use ROBOT templates to convert spreadsheets to OWL. Edit the relevant
- other terms: Edit
See below for a full list of files, build instructions, and instructions on using Git and GitHub for OBI.
Editing Templates in Excel
If you wish to edit a template or templates in Excel, rather than copy & pasting the template, we ask that you follow this workflow to preserve quoting. Going back and forth with Excel can cause some unintentional changes to double quotes within templates.
First, install the python requirements:
python3 -m pip install -r requirements.txt
Then, make the Excel sheet. In your local OBI git directory, run the following command to create a file called
obi.xlsx in Excel (or whatever editor you prefer). This spreadsheet contains a tab for each OBI template (e.g., "study-design", "assays", etc.). Find the tab that corresponds to the template you need to edit, make your changes, and save the Excel spreadsheet to the same location (
obi.xlsx). Finally, run the following to update the TSV versions of the templates:
This will convert the tabs in
obi.xlsx back to TSVs and overwrite the existing TSVs in the
src/ontology/templates/ directory with your changes. Review your changes (
git diff) and make your pull request.
To find where a term lives, you can use
Then you can run the script to find terms by ID or label by passing them as a space-separated list, for example:
src/scripts/locate.py OBI:0000070 CHMO:0000087 GO:0000785
Labels should be enclosed in double quotes:
src/scripts/locate.py "assay" "fluorescence microscopy" "chromatin"
Editing Utility Scripts
The OBI repo includes some Python scripts to help developers efficiently edit both
obi-edit.owl and OBI templates. These scripts require Python 3.
The scripts also require that you first to build two databases (one from OBI edit, and one from a merged version of OBI):
Since labels are used in templates, manually finding and replacing all usages of a term can be difficult and tedious. Instead, you can use
src/scripts/relabel.py to automatically update a term's label and its usages.
You can run this by passing the term you want to update and the new label:
src/scripts/relabel.py CHMO:0000087 "microscopy with fluorescence"
You can also pass the old label as the first argument, as long as it is enclosed in double quotes:
src/scripts/relabel.py "fluorescence microscopy" "microscopy with fluorescence"
Make sure to commit all changed files to ensure that all usages are updated.
README.mdthis overview document
obi.owlthe latest release of OBI
Makefilescripts for building OBI
views/various specialized views of OBI
ontology/source files for OBI
obi-edit.owlthe main OBI OWL file
core.txtthe list of OBI Core terms
external-byhand.owlsome custom imports from other ontologies
catalog-v001.xmlan 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
views/configuration for views
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 testmerge and run SPARQL tests (this is run on every push to GitHub)
make sortsort templates, and fix quoting and line endings
make importsupdate OntoFox imports
make modulesupdate ROBOT templates
make obi.owlbuild the release file; reasoning can take about 10 minutes
make viewsupdate ROBOT templates
make allprepare for a release, runs
obi-edit.owlinto a single file, don't reason
make cleanremove temporary files
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:
sign up for a GitHub account
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
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 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
make sortsort and normalize tables, for cleaner diffs
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/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 will be reviewed by OBI developers. When that review is complete, a senior OBI developer will merge the PR. Rinse and repeat!
Keeping Things Tidy
The easiest way to edit our
src/ontology/template/ files is with Excel. Unfortunately Excel has some idiosyncratic rules for quoting cell values, and on macOS uses old line endings. Both these things make our diffs messy and confusing.
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.