Multiple changes to disentangle epi and endothelial cells #2423
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Some sidetrack into work on fenestrated endothelial cells. Still to do - various kidney cells - where ellithelium vs endothelium may become ambigous?
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -simple file):Ontology comparisonLeft
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Ontology importsOntology annotationsRemoved
Added
alveolar capillary type 1 endothelial cell
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsRemoved
Added
blood vessel endothelial cell
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Also cleaned up 'squamous endothelial cell', which was used to refer only to the squamous endothelial cells of venules. There is now a new dedicated term for this. The definition of the existing term is now generic, as implied by the name.
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#gogoeditdiff |
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Update to pato import needed. |
UPdated imparts
Fixed some minor issues with synonyms and def text. Fixed some issues with endothelial cell classification.
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#gogoeditdiff |
deleted accidentally injected axiom on PATO term I'm trying to import.
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Seems that cl-edit file is broken! Not legal OWL. I'm not sure how that can happen when saving from Protege! Will roll back edits, but this might need to wait until tomorrow. |
Was Protege responsible?
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#gogoeditdiff |
OK. Now it's fixed? Quotes now *inside* brackets delimiting ofn clause. Doh!
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#gogoeditdiff |
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@aleixpuigb I think now good. Could you take a look through inference in the reasoned simple file to see if anything jumps out as obviously wrong? |
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Fixes #1492 |
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It is probably out of the scope of this PR, but I have detected one inconsistency in vasa recta cell, which is a 'kidney capillary endothelial cell' and a 'vein endothelial cell' at the same time. I will open a new ticket to solve that.
All the rest looks good to me.
@aleixpuigb vasa recta is both venous and arterial blood. It’s a place where the circulatory system meets. This is likely correct because of that. |
Yes, the problem is that not all cells are 'capillary endothelial cell' and 'vein endothelial cell'. We should probably have a disjoint so this doesn't happen. I might add that in ticket #2425. For now, I will solve it adding SubclassOf 'microvascular endothelial cell'. |
Some sidetrack into work on fenestrated endothelial cells.
Still to do - various kidney cells - where epi- vs endothelium may become ambiguous (?)
Fixes #2417