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:

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:

   • obsolete.tsv for obsolete terms
   • assays.tsv for general assays
   • epitope-assays.tsv specifically for immune epitope assays
   • value-specifications.tsv
   • specimens.tsv for specimens
   • medical-history.tsv for medical history classifications and related selection criteria
   • study-designs.tsv for study designs
   • data-sets.tsv for data sets

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.

Importing from a New Ontology

If you wish to import terms from an ontology for which OBI does not currently have an OntoFox import file (src/ontology/OntoFox_inputs/), follow these steps:

1. Write the import file for the new ontology (see existing import files for reference).
2. Update catalog-v001.xml to list the new import file like it lists the existing import files.
3. Add an import statement to obi-edit.owl.
4. Create a blank file for the output module in src/ontology/OntoFox_outputs/, e.g., to make phony output for foo.owl imports:

touch src/ontology/OntoFox_outputs/foo_imports.owl

5. Build the module & obi.owl.

make imports
make obi.owl

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:

make obi.xlsx

Next, open 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:

make update-tsv

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.

Finding Terms

To find where a term lives, you can use src/scripts/locate.py.

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):

make obi-dbs

Relabeling Terms

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.

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

Initial Set Up

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

1. # 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. make sort sort and normalize tables, for cleaner diffs
6. git status and git diff inspect your changes
7. git add --update src/ add all updated files in the src/ directory to staging
8. git commit --message "Description, issue #123" commit staged changes with a message; it's good to include an issue number
9. git push --set-upstream origin your-branch-name push your commit to GitHub
10. 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.