Major fixes to visual areas in the brain#2450
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1) Created term cortical visual area 2) Broaden primary visual cortex by removing human specific stuff 3) Create a new term Broadmann area 17 by splitting out human specific stuff in visual cortex 4) added capable of part of some visual perception to all visual areas in brain
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PS: if you wait an hourish, there should be an easier to review ROBOT diff on this that will have more human readable change log that includes reasoned changes. |
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error: whoops - my bad, will fix |
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huh, didnt know uberon didnt allow equiv + subclass, moved subclass up to equiv, not a big deal |
Here's a diff of how these changes impact the classified ontology (on -simple file):Ontology comparisonLeft
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Ontology importsOntology annotationsUBERON_8440010
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsUBERON_8440010
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Here's a diff of your human-view# Ontology comparisonLeft
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Ontology importsOntology annotationsUBERON_8440010
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This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so. |
](http://upload.wikimedia.org/wikipedia/commons/7/70/Brodmann_areas_17_18_19.png%22%5E%5E%5BanyURI%5D(http://www.w3.org/2001/XMLSchema#anyURI)){kind=link}
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@shawntanzk would you like to schedule some time to discuss? |
Happy to sometime next week if need be, though if @stevevanhooser, @daniscafidi, & @cmungall are happy with this, also happy to just merge this in (if not do let me know when a good time for everyone is) thanks! |
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@stevevanhooser, @daniscafidi, & @cmungall - could I get a thumbs up on this if you are good with this solution? want to make sure the template you all curated doesn't slip through the cracks but I think it requires this to be agreed upon first. |
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Hi @shawntanzk , is there a way to preview what was done? Sorry to be clueless... Thanks! |
Yes! you can look at the automated diff comment (github-actions comments) above to see a human-readable (sort of) version of what we changed. The edit file diff is what I made changes to, and the classified ontology one is how it affects the reasoned ontology. If you want to view it graphically, I guess the only way is to check out the branch and open the edit file in something like protege. Though given uberon is obo format, I personally find looking at the diff directly easier, but it might be just me. |
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This looks good to me @shawntanzk , thanks! |
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Looks good. I worry a bit that occiptal lobe is meant to apply in species where there is not a distinct occipital lobe (did I get that right?) but OK with it if @stevevanhooser considers a good/non-confusing compromise. One other question, do we get any automated classification to 'cortical visual area'? Expected to see that as superclass to PVC and new areas coming from @stevevanhooser (although perhaps those new areas still to be added?) |
new areas are not added yet (see googlesheets) - I'm waiting for this PR to go through to get to it, would rather see how the new terms fall after merging template in so i can make edits needed immediately. |
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@dosumis I think the occipital lobe comment is well put..even in species where there is no agreed occipital lobe division, sometimes people still use the term. So I think it is the right comment. |
4 participants
Fixes #2412
@dosumis, @stevevanhooser, @cmungall, @daniscafidi - could you take a look at this PR and make sure you agree with the changes? thanks :)