long bones - not always appendicular?

cmungall commented 10 years ago

See http://www.ncbi.nlm.nih.gov/pubmed/8167393

cmungall commented 10 years ago

There is a problem if we want to add vertebral epiphysis:

UBERON:0000064 ! organ part
- UBERON:0005913 ! zone of bone organ
- UBERON:0005055 ! zone of long bone
  - UBERON:0001437 ! epiphysis

If long bone is part of appendicular skeleton, causes spatial disjointness violation

there appears to be no appendicular assumption in HPO:

HP:0000924 ! Abnormality of the skeletal system
- HP:0011842 ! Abnormality of skeletal morphology
- HP:0009121 ! Abnormal axial skeleton morphology
  - HP:0000925 ! Abnormality of the vertebral column
  - HP:0003468 ! Abnormality of the vertebrae
    - HP:0100734 ! Abnormality of the vertebral epiphyses
- HP:0011314 ! Abnormality of long bone morphology
  - HP:0005930 ! Abnormality of the epiphyses
  - HP:0100734 ! Abnormality of the vertebral epiphyses

cmungall commented 10 years ago

Currently we have:

[Term]
id: UBERON:0002495
name: long bone
def: "Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd]." [VSAO:wd, Wikipedia:Long_bone]
comment: Endochondral_ossification is an essential process during the rudimentary formation of long bones, with the exception of the clavicle[Wikipedia:Endochondral_ossification]. The medial and and lateral ends undergo EO, the mid-portion is formed by a process with features of EO & IO (the process is shared by the mandible)[ISBN:9780397517251]
subset: uberon_slim
xref: FMA:7474 ! Long bone
xref: MA:0002802 ! long bone
xref: OpenCyc:Mx4rv6axr5wpEbGdrcN5Y29ycA
xref: ncithesaurus:Long_Bone ! Long Bone
xref: galen:LongBone ! long bone
xref: OpenCyc:Mx4rv6axr5wpEbGdrcN5Y29ycA ! long bone
xref: BTO:0004256 ! long bone
is_a: UBERON:0001474 ! bone element
relationship: part_of UBERON:0002091 ! appendicular skeleton
xref: SCTID:332709000 ! Entire long bone
xref: UMLS:C0222647 {source="ncithesaurus:Long_Bone"}
synonym: "os longum" RELATED [BTO:0004256]

ie, always part of appendicular, both logically and in the text def

This came from VSAO, so requesting @wdahdul to make a change here

We also have:

[Term]
id: UBERON:0003606
name: limb long bone
def: "A long bone that is part of a limb [Automatically generated definition]." [OBOL:automatic]
synonym: "long bone of limb" EXACT [OBOL:automatic]
xref: MA:0000298 ! limb long bone
intersection_of: UBERON:0002495 ! long bone
intersection_of: part_of UBERON:0002101 ! limb

This extra term isn't doing much work - if long bones are necessarily appendicular, then they are either limb or fin.

It seems there are two useful concepts - a broader one, one a bone that has an epiphysis and hence develops in a certain way; and a narrower one, which has the same properties, but is in the appendicular skeleton (and is typically more elongated??)

What are the appropriate names for these two concepts?

once we have decided on this we have 3 options for refactoring:

Option 1 - broaden existing 'long bone'

We generalize the existing 'long bone' so there is no appendicular requirement. We can then repurpose the existing 'limb long bone' to be a broader 'appendicular long bone'

This may end up in some xrefs migrating downwards - e.g. the FMA concept appears appendicular

Option 2 - introduce new broader class

We keep the existing 'long bone' as appendicular, create a new broader concept.

We probably obsolete 'limb long bone' as being no longer useful, and the MA xrefs shift up by one (i.e. the MA "long bone" which is not appendicularly restricted matches our newer broader concept)

Option 3 - obsolete

obsolete both classes and generate new unambiguous classes: at least the broader concept, and possibly a subclass for the appendicular subtype

gouttegd commented 3 years ago

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.

obophenotype / uberon