Fixes #2049 add has soma location 'retinal bipolar neuron'

[aleixpuigb]

Fixes #2049 add soma location OFF-bipolar cell

[aleixpuigb]

#gogoeditdiff

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontologies are identical

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

ON-bipolar cell http://purl.obolibrary.org/obo/CL_0000749

Removed

• ON-bipolar cell SubClassOf has soma location some inner nuclear layer of retina

retinal bipolar neuron http://purl.obolibrary.org/obo/CL_0000748

Removed

• retinal bipolar neuron EquivalentTo bipolar neuron and (has soma location some retina)

Added

• retinal bipolar neuron EquivalentTo bipolar neuron and (has soma location some inner nuclear layer of retina)

[ghost]

Consider if it is more appropriate to place this axiom at the level of the parent class, CL:0000748 'retinal bipolar neuron'.

[aleixpuigb]

Consider if it is more appropriate to place this axiom at the level of the parent class, CL:0000748 'retinal bipolar neuron'.

Thank you for the suggestion, I will add this axiom to 'retinal bipolar neuron' and remove from ON-bipolar cell.

As 'retinal neuron layer' had the EA 'bipolar neuron' and ('has soma location' some retina), all bipolar cells with soma in the retina would be classified under this class and therefore inherit 'has soma location' some 'inner nuclear layer of retina'. Therefore, it makes sense to substitute the EA to 'bipolar neuron' and ('has soma location' some 'inner nuclear layer of retina').

[aleixpuigb]

#gogoeditdiff

[dosumis]

I think moving the soma location axiom to the more general term makes sense from what I know of the biology. For a broader review of the biology - I've found this useful:

Euler, T., Haverkamp, S., Schubert, T., & Baden, T. (2014). Retinal bipolar cells: elementary building blocks of vision. Nature Reviews Neuroscience, 15(8), 507–519. https://doi.org/10.1038/nrn3783