[DOCS] Clarify the Contributing UpdateImports documentation with CL-specific examples.

[lubianat]

Motivated by some discussions on Slack, including these key comments (registered here for future reference:

By @rays22
The SOP could use an update by tailoring it to commonly used OBO ontology ODK workflows, so that if you know how to update a typical OBO/ODK ontology then the process should be very similar and not divergent for a specific ontology like CL.
Have you tried

cd [PATH_TO]/cell-ontology/src/ontology
sh run.sh make refresh-merged

to update the imports? The steps prior to this (i.e. prior to the ‘Using the Base Module approach’ section of the SOP) depend on how you declare the terms (e.g. adding a new term to cell-ontology/src/ontology/imports/uberon_terms.txt) you want to be imported.

@aleixpuigb
The fastest and easiest way to import terms is the protege-based declaration. You can then use the term without refreshing. I normally import by adding the terms in the specific file and then refresh.

and by myself:

The guidelines for imports in CL
https://obophenotype.github.io/cell-ontology/odk-workflows/UpdateImports/
seem to be mostly copied and pasted from
https://oboacademy.github.io/obook/howto/update-import/
Maybe it needs some revision to show the proceedings done by cl editors + have a link to the general OBO workflow?

• conversation with @gouttegd at

#1853

[anitacaron]

Here's the documentation specific to CL https://obophenotype.github.io/cell-ontology/Adding_classes_from_another_ontology/

[lubianat]

@anitacaron oh thanks!!! I only saw that now. Maybe we need to link that in "contributing".