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obophenotype / mouse-anatomy-ontology

Ontologies for mouse anatomy and development
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axial skeleton #43

Closed cmungall closed 9 years ago

cmungall commented 14 years ago

See this item in the FMA tracker: https://sourceforge.net/tracker/?func=detail&aid=2983975&group\_id=76834&atid=974957

MA appears to agree with FMA, but disagree with classic use which includes the skull

e.g. http://en.wikipedia.org/wiki/Axial\_skeleton

Original comment by: cmungall

Original Ticket: obo/mouse-anatomy-requests/27

cmungall commented 14 years ago

Original comment by: tfhayamizu

cmungall commented 14 years ago

For the MA, I followed the Edinburgh anatomy for mouse development in only including vertebral column-related components in the "axial skeleton." In addition, a quick perusal of at least the mouse and humanl literature indicates that, in general, it appears that this is how the term "axial skeleton" is commonly used. However, certainly this does not mean that this is correct. In fact, as you mention, most anatomy resources I found, including Gray's Anatomy, also include the cranium (skull) as part of the axial skeleton.

Interestingly, while FMA term "Axial skeleton" (FMAID:71221) does not list "Cranium" as one of its parts, subclasses of "Subdivision of axial skeleton" (78585) include: "Skeleton of the head" (71223) and "Set of bones of cranium" (71325). Note, also, that the FMA has an additional term "Axial skeletal system" (7483) which does not include any cranial component, but also includes: "Bony pelvis" (16580) and "Set of axial joints" (71278),

So, it appears that the axial skeleton SHOULD include the cranium/skull, but the term "axial skeleton" is often used synonymously with "post-cranial axial skeleton." In is interesting that the anatomy ontologies that I have looked at include one or the other, but not both, as terms.

How then to proceed? Among the possibilities: (1) add ""post-cranial axial skeleton" as a synonym for the existing "axial skeleton" term; (2) rename the current MA term "post-cranial axial skeleton" (+/- synonym: "axial skeleton"); or (3) create a new sub-term for "axial skeleton" called "post-cranial axial skeleton" (moving the former's children to the latter), and moving "cranium" as a child of the former.

If we decide on #3, then perhaps this should be applied by all of the vertebrate anatomy ontologies. This is something to certainly something to consider with regards to mapping between the ontologies. An issue for the skeletal anatomy workshop participants to ponder?

Original comment by: tfhayamizu

cmungall commented 14 years ago

anatomy ontology comparison

Original comment by: tfhayamizu

cmungall commented 14 years ago

For a comparison of high-level skeletal anatomy hierarchies in the different anatomy ontologies, see attached pdf.

Original comment by: tfhayamizu

cmungall commented 14 years ago

Original comment by: tfhayamizu

cmungall commented 14 years ago

This Tracker item was closed automatically by the system. It was previously set to a Pending status, and the original submitter did not respond within 14 days (the time period specified by the administrator of this Tracker).

Original comment by: sf-robot

cmungall commented 14 years ago

Original comment by: sf-robot