Editors’ Guide for CRO developers

Creating a new branch

Edits to the CRO should be done on a branch via a Pull Request. For guidance on creating a branch and creating a pull request, go here.

1. Open the file cro-edit.owl in Protege. On the bottom left, you should see your branch name (not Git: master)

2. Switch on the Elk reasoner: Reasoner->Start Reasoner. If you are making changes, be sure to synchronize the reasoner.

Edit the ontology in Protege:

1. Find parent term in Protege by searching in the search box (at top of screen)
2. Double check that term is not already there
3. Add subclass
4. Add label (URI should be auto-generated)
5. Under annotations, add definition, click OK
6. Annotation on definition as ‘definition source’
7. hasDBxef, if applicable
8. Under annotations, add synonyms, if necessary as an ‘alternative term’.

Save

do not edit any other files!!!

Commit your changes

  git diff
  git status
  git commit -a -m "COMMIT MESSAGE"
  git push

CREATING NEW TERMS (Checklist)

• In general, the term should be announced on the GitHub tracker prior to creation of new term
• Make sure the Protege reasoner (Elk) is active to investigate any unforeseen and unintended logical inferences
• Most terms should have the following items added:
  • Label
  • Definition: This should be extended by definitioin source (e.g., a PubMed ID (PMID), another unique identifer to another source, a URL, or a reference to a paper. Note, there should be no spaces in the PMID.)
  • Comment: Optional. A comment can be used to provide additional information about the term.
  • hasDBxref: Indicate an item in another database that is equivalent to this CRO term. For instance, 8b73531f-db56-4914-9502-4cc4d4d8ed73.
  • alternative term: If possible, add relevant alternative terms/synonyms.
  • dc:creator: This should automatically add your ORCID if your Protege is configured properly.
  • dc:date This should be automatically added if your Protege is configured properly.

Closing Issues with Commit Messages

This is the preferred way to commit a new term.
See the GitHub help pages for this. To close and commit terms that relate to issue #68, for instance, create the terms and save them to file.

git add -u .
git commit -m "This closes #68"  
git push

Checklist

Always synchronize the reasoner before committing. Did your changes introduce unsatisfiable classes? If so, investigate them.

For any classes you have created, are they in your ID range? Did you add text definitions, adding provenance information? Is the reasoner finding unintended inferred equivalent classes? Subclasses?

Check the Travis report after your commits. This should alert you to any of the following:

• consistency problems with anatomy ontologies
• consistency problems with other ontologies
• violation of obo-format (e.g. two labels for a class; two text definitions; etc)

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