for the record - bit of FMA documentation
Alan Ruttenberg
---------- Forwarded message ----------
From: mej...@u.washington.edu <mej...@u.washington.edu>
Date: Tue, Jun 7, 2011 at 11:59 AM
Subject: Re: [Obo-anatomy] Fwd: Representation of pelvic girdles
To: Melissa Haendel <hae...@ohsu.edu>
Cc: Terry Hayamizu <ter...@informatics.jax.org>,
"rcn-vertebrate...@googlegroups.com"
<rcn-vertebrate...@googlegroups.com>, Chris Mungall
<cjmu...@lbl.gov>, "obo-a...@lists.sourceforge.net"
<obo-a...@lists.sourceforge.net>, Onard Mejino <mej...@comcast.net>
Hi Melissa,
Thanks for the feedback! I have included below some explanations for
the FMA representation of "bony pelvic girdle" and "hipbone".
On Fri, 3 Jun 2011, Melissa Haendel wrote:
>
> == FMA ==
>
>
> The FMA names a lot more entities than the MA. Many of these are
>
> undefined, requiring us to figure things out from the ontology edges
>
> or terminology alone.
>
>
> The first thing to note is that in FMA the term "pelvic girdle"
>
> doesn't refer to a bony structure, but rather to a subdivision of the
>
> whole limb. E.g.:
>
>
> ----is_a FMA:9661 ! Limb segment
>
> --------is_a FMA:24874 ! Limb girdle
>
> ------------is_a FMA:16581 ! Pelvic girdle
>
> --------is_a FMA:24960 ! Subdivision of pelvic girdle
>
> ------------is_a FMA:24964 ! Hip
>
> ------------is_a FMA:25245 ! Buttock
>
>
> This is in contrast to ontologies like the ZFA, which treats "pelvic
>
> girdle" as a bony structure. The AAO (which has a skeletal focus) uses
>
> "pelvic girdle" as the combination of "pelvic girdle skeleton" plus
>
> holes.
>
>
> For the corresponding bony structures, the FMA has the partonomy:
>
>
> FMA:61412 ! Bony pelvic girdle
>
> spo FMA:16585 ! Hip bone
>
> rpo FMA:16589 ! Ilium
>
> rpo FMA:16592 ! Ischium
>
> rpo FMA:16595 ! Pubis
>
> rpo FMA:43533 ! Ischiopubic ramus
>
>
> (I have omitted some sub-parts, e.g. vasculature). The 4 parts are
>
> individually subtypes of "zone of hip bone".
>
>
> The distinction between "hip bone" and "bony pelvic girdle" is not
>
> immediately clear, they both share the same parts. One interpretation
>
> might be that the bony pelvic girdle is the mereological sum of left
>
> and right hip bones. However, this doesn't appear to be the case, as
>
> there is both a left and right bony pelvic girdle in FMA.
OM: We have not yet completed the parthood relationships for "bony
pelvic girdle". It is a transitive subclass of "Subdivision of
skeletal system". By definition the skeletal system includes both the
skeleton and the articular system (among other things) and therefore
"bony pelvic girdle" would include "skeleton of pelvic girdle" and
"set of joints of pelvic girdle" (e.g. pubic symphysis, sacro-iliac
joint).
>
>
> "hip bone" is classified as a bone, whereas "bony pelvic girdle" is a
>
> skeletal subdivision. This still doesn't quite explain the difference
>
> to me. Isn't a skeletal subdivision whose contents is a single bone
>
> identical to that bone?
Yes, this is a problem when data entry has not yet been completed. The
FMA is huge and we do rely on feedbacks, such as yours, to identify
gaps.
Perhaps the goal here is to mirror pectoral
>
> girdle, where the bones are not fused?
>
>
> FMA also includes a class "Skeleton of pelvic girdle" (FMA:87592),
>
> which appears to be unconnected in the ontology to either hip bone or
>
> bony pelvic girdle, which confuses matters. I'm not sure how this term
>
> differs from bony pelvic girdle or hip bone.
See above.
>
>
> I would recommend that FMA include definitions of these terms, because
>
> annotators may have difficulties selecting the correct term.
Agreed.
>
>
> The FMA also has the class "bony pelvis" which includes the sacum and
>
> coccyx bones. Note also that in the FMA, the bony pelvis is
>
> considered part of the axial skeletal system - this is despite
>
> including appendicular skeletal system parts, such as the Ilium. From
>
> this we must surmise that appendicular and axial skeletons overlap,
>
> which seems undesirable.
There are shared parts in the FMA such as blood vessels which are
parts of the blood vessel tree but also part of the structures they
supply.
>
>
> == HPO ==
>
>
> HPO often uses the terms bony pelvis, pelvis, pelvic girdle and hip
>
> girdle interchangeably; e.g.:
>
>
> HP:0002644 ! Abnormality of the pelvis *** [DEF: "An abnormality of the bony pelvis (pelvic girdle); which is a ring of bones connecting the vertebral column to
> the femurs."]
>
>
> The definition would appear to exclude parts of the vertebral column,
>
> but the children of this include "abnormality of the coccyx" (but not
>
> abnormality of the sacrum). HP also uses the term "hip-girdle" in
>
> places, which appears non-standard.
>
>
> == MPO ==
>
>
> Largely follows MA, but doesn't distinguish between the innominate bones and pelvic girdle bones - the LCS of abormal sacrum/coccyx and ilium is abnormal
> skeleton:
>
>
> is_a MP:0009250 ! abnormal appendicular skeleton morphology [SYNONYM: "appendicular skeletion dysplasia" (exact)]
>
> is_a MP:0004509 ! abnormal pelvic girdle bone morphology *** [SYNONYM: "abnormal coxal bones" (exact)] [SYNONYM: "abnormal innominate bones" (exact)]
> [SYNONYM: "abnormal pelvic bone morphology" (exact)] [SYNONYM: "abnormal pelvis bones" (exact)] [SYNONYM: "pelvic girdle bone dysplasia" (exact)]
>
> is_a MP:0004506 ! abnormal pubis morphology [SYNONYM: "abnormal pubic bone morphology" (exact)] [SYNONYM: "abnormal pubis morphology" (exact)]
>
> is_a MP:0004507 ! abnormal ischium morphology
>
> is_a MP:0005354 ! abnormal ilium morphology [SYNONYM: "abnormal iliac bone" (exact)] [SYNONYM: "abnormal ilium" (exact)]
>
>
> is_a MP:0002114 ! abnormal axial skeleton morphology
>
> is_a MP:0004703 ! abnormal vertebral column
>
> is_a MP:0010113 ! abnormal sacrum morphology ***
>
> is_a MP:0010114 ! abnormal coccyx morphology ***
>
>
>
> Dr. Melissa Haendel
>
>
> eagle-i Networking Research Resources
>
> OHSU Library
>
> Department of Medical Informatics and Epidemiology
>
> Oregon Health & Science University
>
> hae...@ohsu.edu
>
> skype: melissa.haendel
>
> 503-407-5970
>
>
>
>
>
> Dr. Melissa Haendel
>
> eagle-i Networking Research Resources
> OHSU Library
> Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> hae...@ohsu.edu
> skype: melissa.haendel503-407-5970
>
>
>
> Dr. Melissa Haendel
>
> eagle-i Networking Research Resources
> OHSU Library
> Department of Medical Informatics and Epidemiology
> Oregon Health & Science University
> hae...@ohsu.edu
> skype: melissa.haendel503-407-5970
>
>
>
>
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