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cartilaginous radials #334
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Sounds like you're going to want to automate this so I added "tech" to the labels for this item. Before heading down this route, this is definitely the way you want to go: a trad of classes for every element? (we might extend this to a quad to be consistent with how we've done things in tetrapods, with an additional pre-cartilage element). The other option is to consolidate on "element" What is your timeline? I can help with automation but this may have to wait til 2nd week of Oct. |
We (Paula, Alex, and I) think it's better to have the quad of classes for each element, otherwise we lose information on composition by having only a single 'element' for each class. Would be great if you could automate creating the classes, and second week of October is fine. |
Shall we treat the existing radial classes as elements? |
We would end up mapping the ZFA classes (which are bones) to elements, but I think this is fine |
I think it's better to keep the existing radial classes as types of endochondral bone. For phenoscape, most of our exisitng annotations would refer to the bone class. |
By the way, 'pelvic radial cartilage' and its children are already in uberon. Not sure if there are more cartilage classes though. |
OK, so this will prove a little harder to automate than I thought. First, all the existing textual definitions would be moved to the new element class. The element should be treated as the primitive. The existing bone and new cartilage classes would have compositional defs of the form "A that is composed of {cartilage, bone tissue}". Would you agree? It means that people coming in from outside might first land on the bone term and be one step away from the more lovingly crafted element definition. However, this is the only way we can keep the approach scalable and maintainable, we can't be maintaining defs in 3 places at once. Just want to be sure we're aware of the implications of going down this route. This would eventually apply to femur, etc as well. |
Just want to make sure we're on the same page; when you say: it's not clear you would lose anything. You could have high level rules such that "(skeletal element and part_of some appendicular skeleton and part_of some Taxon:x) SubClassOf bone". Even without this axiom, the only information you effectively lose is about the ossification state. |
*all the existing textual definitions would be moved to the new element class. |
*You could have high level rules such that "(skeletal element and part_of some appendicular skeleton and part_of some Taxon:x) SubClassOf bone". I think adding taxon restrictions for element composition would require a lot of research, and there may not be sufficient information in the literature to adequately document this in Uberon. WIth the triad of element classes, it isn't difficult for curators to choose the appropriate class, given information in the paper they are curating. |
Ok, we'll have to be careful. 7 defs reference bones explicitly. So the I will start with the cloning step. On Fri, Nov 8, 2013 at 7:30 AM, wdahdul notifications@github.com wrote:
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Some notes: Not as straightforward as thought. For example, this was lifted from TAO when ext was created:
The relationship says bone, but the text def says cartilage. There are no logical axioms telling us this is cartilage, so we must check using the text. This has since been classified as a pect fin prox radial, hence its relevance here. What do you want to be done with these? May be safest to obsolete? |
Committed fix to r4011 in phenoscape-ext. Requires review. |
still working on this. reconciling original cartilage radials:
is this all of them? |
@wdahdul - you'll have to do the pelvic radial {1,2,3} cartilage. Their relationship to the bones is not clear to me. Can you also review basipterygium. The rest follow a standard pattern. Take a look and confirm it's OK Remember, look in the inferred hierarchy with Elk on |
Still to fix:
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Thanks for this work, Chris! All looks fine. A few notes: *we need the triad represented for propterygium, metapterygium, and mesopterygium. Can you add these? It's fine to obsolete 'propterygium' because it's been inconsistently used in our annotations.
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WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues. |
Classes for cartilaginous radials are needed. Also need radial element classes to group the bone radial classes (In uberon, 'radial' and its children are subclasses of 'endochondral bone').
Note, Uberon already has classes for cartilaginous pelvic radials ('pelvic radial cartilage and three children: 'pelvic radial 1 cartilage', pelvic radial 2 cartilage, pelvic radial 3 cartilage)
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