Re: [Obo-anatomy] Fwd: Representation of pelvic girdles

[Terry Hayamizu]

Thanks so much, Melissa and Chris, for this information.


With regards to:

The term "hip bone" (MA:0000655) is confusing . Usually "hip bone" is

synonymous with the Innominate, i.e. the fused structure. MA doesn't

include definitions, but we can surmise from the partonomy below that

MA uses MA:0000655 as synonymous with something like "bone of hip

region":

----is_a MA:0000655 ! hip bone

--------is_a MA:0001336 ! ilium

--------is_a MA:0001337 ! ischium

--------is_a MA:0001338 ! pubis

--------is_a MA:0001359 ! femur ***

I would recommend this be renamed in MA.

I agree, although I will probably go with "hip region bone" for nomenclature consistency, unless we can identify a reason to do otherwise. For a number of reasons, we have tried to avoid term names of the form, e.g., "Y of X", except in cases such as "loop of Henle". That said, we did feel that "joint of rib" would be better than "rib joint." Please feel free to comment.

Terry

--

Terry Hayamizu, M.D., Ph.D.
Scientific Curator
Gene Expression Database
Mouse Genome Informatics
http://www.informatics.jax.org/
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
tel: 207-288-6661
email: ter...@informatics.jax.org

[Melissa Haendel]

Hi all, 

We've been discussing girdles in the vertebrate working group at the Phenotype RCN workshop. Chris put together this nice treatise on the state of affairs regarding girdles that we thought would be relevant to 

to all of you.

Cheers,

Melissa

I'm trying to sort through various inconsistencies in how terms like

"pelvic girdle" and "pectoral girdle" are used.

I've put together a strawman list of recommendations:

1. Both pelvic and pectoral girdles come in pairs; i.e. there is a

   left girdle and a right gridle (consistent with FMA). Each girdle

   is thus part of a single limb (or fin). When referring to the

   mereological sum, a term like "pair of pelvic girdles" or "pelvic

   girdle ring" should be used.

ALTERNATIVE: it may be more intuitive to have "girdle" refer to the

 pair, especially for pelvic girdle (consistent with AAO); but then

 we need an intuitive term for each half (e.g. "pelvic girdle

 lateral half").

2. The term "limb girdle" should denote a subdivision of the limb or

   fin (i.e. it *includes* fleshy parts). When referring to the

   skeletal elements, the term "limb girdle skeleton" or similar

   should be used. For full precision, we could follow the FMA and

   distinguish between the skeletal system (including joints) and

   skeleton.

ALTERNATIVE: we follow ZFA, AAO and TAO and use "girdle" to denote

 the skeletal structure. Here we would need a term like "girdle

 segment" for demarcating the corresponding part of the limb.

3. The girdle skeleton is entirely part of the appendicular

   skeleton, and there are no parts in common with the axial

   skeleton. If there is need to name a structure that overlaps

   both, then another term should be used.

4. We need a term that encompasses both individual bones and the

   zones of fused bones that correspond to individual bones, such as

   the ilium.

5. The term "hip bone" should be synonymous with "innominate

   bone". This should be the mereological sum of the pelvic girdle

   skeleton plus some part of the axial skeleton (e.g. sacrum and

   coccyx in humans).

This is partially just a strawman - comparative anatomists should

weigh in here. Currently there is some possibly confusing

inconsistency in how these terms are used and how the corresponding

ontologies are structured.

I've attached an analysis of how the girdles are represented in some

AOs, focusing on the pelvic girdle and mammals. There are enough

prosaic issues in defining terms here before we get to more

interesting issues regarding limb evolution.

== MA ==

The core representation in MA is fairly straightforward:

----is_a MA:0000532 ! pelvis bone ***

--------is_a MA:0000293 ! pelvic girdle bone

------------is_a MA:0001335 ! acetabulum

------------is_a MA:0001336 ! ilium

------------is_a MA:0001337 ! ischium

------------is_a MA:0001338 ! pubis

--------is_a MA:0000310 ! caudal vertebra

------------is_a MA:0001420 ! coccygeal vertebra

--------is_a MA:0000313 ! sacral vertebra

------------is_a MA:0001434 ! sacral vertebra 1

------------is_a MA:0001435 ! sacral vertebra 2

------------is_a MA:0001436 ! sacral vertebra 3

------------is_a MA:0001437 ! sacral vertebra 4

This is for the adult mouse - in adult humans the sacral vertebrae

would be fused. (I'll sometimes use "sacrum" and "coccyx" here for

brevity, or just "S" and "C", on the understanding that this is

applicable to the homologous collection of vertebrae).

Here we can see a subdivision of the pelvis bones into appendicular

skeletal components (A+Il+Is+P - ie the girdle) and (postcranial)

axial skeleton components (S+C). Whilst the girdle is exclusively

appendicular, the set of pelvis bones overlaps both appendicular and

axial skeletons. This seems fairly standard.

Note also that the ilium, ischium, pubis and acetabulum are treated as

individual bones. Leaving the acetabulum aside for now, this seems

reasonable, as these can be considered fused bones. The MA does not

name the unit that is the mereological sum of these fused bones. The

treatment of these structures is different from the FMA, where these

are subclasses of "zone of hip bone". The FMA treatment is more

rigorous, but we perhaps lose something in that it's useful capturing

the fact that these are fused bones.

The term "hip bone" (MA:0000655) is confusing . Usually "hip bone" is

synonymous with the Innominate, i.e. the fused structure. MA doesn't

include definitions, but we can surmise from the partonomy below that

MA uses MA:0000655 as synonymous with something like "bone of hip

region":

----is_a MA:0000655 ! hip bone

--------is_a MA:0001336 ! ilium

--------is_a MA:0001337 ! ischium

--------is_a MA:0001338 ! pubis

--------is_a MA:0001359 ! femur ***

I would recommend this be renamed in MA.

== 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.

"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? 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.

I would recommend that FMA include definitions of these terms, because

annotators may have difficulties selecting the correct term.

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.

== 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.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.haendel

503-407-5970

[mej...@u.washington.edu]

Hi Melissa,

Thanks for the feedback! I have included below some explanations for the FMA representation of "bony pelvic girdle" and "hipbone".

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.

[Chris Mungall]

On Jun 8, 2011, at 1:58 PM, Dahdul, Wasila wrote:

>>>>>> I'm trying to sort through various inconsistencies in how terms like
>>>>>> "pelvic girdle" and "pectoral girdle" are used.
>>>>>>
>>>>>> I've put together a strawman list of recommendations:
>>>>>>
>>>>>> 1. Both pelvic and pectoral girdles come in pairs; i.e. there is a
>>>>>> left girdle and a right gridle (consistent with FMA). Each girdle
>>>>>> is thus part of a single limb (or fin). When referring to the
>>>>>> mereological sum, a term like "pair of pelvic girdles" or "pelvic
>>>>>> girdle ring" should be used.
>>>>>>
>>>>>> ALTERNATIVE: it may be more intuitive to have "girdle" refer to the
>>>>>> pair, especially for pelvic girdle (consistent with AAO); but then
>>>>>> we need an intuitive term for each half (e.g. "pelvic girdle
>>>>>> lateral half").
>

> We agreed with the alternative recommendation of "pelvic girdle" referring to the pair, and using "pelvic girdle lateral half" for each half. This falls in line with common usage in comparative anatomy.

OK. Would pectoral girdle be treated in the same way?

It's unfortunate that this conflicts with the FMA usage, but I suspect there are many areas where human anatomy terminology conflicts with comparative anatomy. The best we can do is provide definitions, synonyms and a documentation trail.

>>>>>> 2. The term "limb girdle" should denote a subdivision of the limb or
>>>>>> fin (i.e. it *includes* fleshy parts). When referring to the
>>>>>> skeletal elements, the term "limb girdle skeleton" or similar
>>>>>> should be used. For full precision, we could follow the FMA and
>>>>>> distinguish between the skeletal system (including joints) and
>>>>>> skeleton.
>>>>>>
>>>>>> ALTERNATIVE: we follow ZFA, AAO and TAO and use "girdle" to denote
>>>>>> the skeletal structure. Here we would need a term like "girdle
>>>>>> segment" for demarcating the corresponding part of the limb.
>

> Yes, using "pelvic girdle skeleton" for the skeletal structure, and "pelvic girdle" for the structure including soft parts, made sense to us.

OK

>>>>>>
>>>>>> 3. The girdle skeleton is entirely part of the appendicular
>>>>>> skeleton, and there are no parts in common with the axial
>>>>>> skeleton. If there is need to name a structure that overlaps
>>>>>> both, then another term should be used.
>

> Agreed.

>
>>>>>>
>>>>>> 4. We need a term that encompasses both individual bones and the
>>>>>> zones of fused bones that correspond to individual bones, such as
>>>>>> the ilium.
>

> We didn't get to this, but perhaps others can chime in here. My sense is that the ilium is referred to as "ilium" whether or not it's fused, at least in the comparative context.

That's fine. The request was for a generic grouping class. In FMA and other ontologies have "bone" (aka "bone organ") as well as "zone of bone organ". Currently ilium is classified under the latter, which seems fine. However, it might be useful to have a more specific subclass of "zone of bone organ" that means something like "zone of bone organ that corresponds to what is a distinct bone earlier in development". I can see this being useful in a comparative context too (e.g. tibiafibila and friends).

>>>>>>
>>>>>> 5. The term "hip bone" should be synonymous with "innominate
>>>>>> bone". This should be the mereological sum of the pelvic girdle
>>>>>> skeleton plus some part of the axial skeleton (e.g. sacrum and
>>>>>> coccyx in humans).

> "Innominate bone" and "hip bone" are not commonly used in comparative anatomy although we did see at least innominate bone used in some text book figures. We decided to use pelvic bone and pelvic bone skeleton for the multispecies context.

OK

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[Dahdul, Wasila]

Hi all,

Comments below from our discussion at the Phenotype RCN.  We didn't get to all points, but I'll refer back to these items as the vertebrate and amniote ontologies are being developed and reviewed.

Wasila

---

On Jun 3, 2011, at 11:24 AM, Melissa Haendel wrote:

Hi all, 

We've been discussing girdles in the vertebrate working group at the Phenotype RCN workshop. Chris put together this nice treatise on the state of affairs regarding girdles that we thought would be relevant to 

to all of you.

Cheers,

Melissa

I'm trying to sort through various inconsistencies in how terms like

"pelvic girdle" and "pectoral girdle" are used.

I've put together a strawman list of recommendations:

1. Both pelvic and pectoral girdles come in pairs; i.e. there is a

   left girdle and a right gridle (consistent with FMA). Each girdle

   is thus part of a single limb (or fin). When referring to the

   mereological sum, a term like "pair of pelvic girdles" or "pelvic

   girdle ring" should be used.

ALTERNATIVE: it may be more intuitive to have "girdle" refer to the

 pair, especially for pelvic girdle (consistent with AAO); but then

 we need an intuitive term for each half (e.g. "pelvic girdle

 lateral half").

We agreed with the alternative recommendation of "pelvic girdle" referring to the pair, and using "pelvic girdle lateral half" for each half.  This falls in line with common usage in comparative anatomy.

2. The term "limb girdle" should denote a subdivision of the limb or

   fin (i.e. it *includes* fleshy parts). When referring to the

   skeletal elements, the term "limb girdle skeleton" or similar

   should be used. For full precision, we could follow the FMA and

   distinguish between the skeletal system (including joints) and

   skeleton.

ALTERNATIVE: we follow ZFA, AAO and TAO and use "girdle" to denote

 the skeletal structure. Here we would need a term like "girdle

 segment" for demarcating the corresponding part of the limb.

Yes, using "pelvic girdle skeleton" for the skeletal structure, and "pelvic girdle" for the structure including soft parts, made sense to us. 

3. The girdle skeleton is entirely part of the appendicular

   skeleton, and there are no parts in common with the axial

   skeleton. If there is need to name a structure that overlaps

   both, then another term should be used.

Agreed.

4. We need a term that encompasses both individual bones and the

   zones of fused bones that correspond to individual bones, such as

   the ilium.

We didn't get to this, but perhaps others can chime in here. My sense is that the ilium is referred to as "ilium" whether or not it's fused, at least in the comparative context. 

5. The term "hip bone" should be synonymous with "innominate

   bone". This should be the mereological sum of the pelvic girdle

   skeleton plus some part of the axial skeleton (e.g. sacrum and

   coccyx in humans).

"Innominate bone" and "hip bone" are not commonly used in comparative anatomy although we did see at least innominate bone used in some text book figures.  We decided to use pelvic bone and pelvic bone skeleton for the multispecies context.

<ATT00001..txt><ATT00002..txt>

[mej...@u.washington.edu]

On Wed, 8 Jun 2011, Chris Mungall wrote:

>
> On Jun 8, 2011, at 1:58 PM, Dahdul, Wasila wrote:
>
>>>>>>> I'm trying to sort through various inconsistencies in how terms like
>>>>>>> "pelvic girdle" and "pectoral girdle" are used.
>>>>>>>
>>>>>>> I've put together a strawman list of recommendations:
>>>>>>>
>>>>>>> 1. Both pelvic and pectoral girdles come in pairs; i.e. there is a
>>>>>>> left girdle and a right gridle (consistent with FMA). Each girdle
>>>>>>> is thus part of a single limb (or fin). When referring to the
>>>>>>> mereological sum, a term like "pair of pelvic girdles" or "pelvic
>>>>>>> girdle ring" should be used.
>>>>>>>
>>>>>>> ALTERNATIVE: it may be more intuitive to have "girdle" refer to the
>>>>>>> pair, especially for pelvic girdle (consistent with AAO); but then
>>>>>>> we need an intuitive term for each half (e.g. "pelvic girdle
>>>>>>> lateral half").
>>
>> We agreed with the alternative recommendation of "pelvic girdle" referring to the pair, and using "pelvic girdle lateral half" for each half. This falls in line with common usage in comparative anatomy.
>
> OK. Would pectoral girdle be treated in the same way?
>
> It's unfortunate that this conflicts with the FMA usage, but I suspect there are many areas where human anatomy terminology conflicts with comparative anatomy. The best we can do is provide definitions, synonyms and a documentation trail.

This is an interesting and important issue. I understand that the word "girdle" is defined as a "belt or sash around the waist" and therefore combining the pair makes a lot of sense but in human anatomy most sources apply the term to only one side of the limb. I think it's a misnomer but nonetheless it is represented as such in most reputable sources (Gray's, Morris, Terminologia Anatomica, Hollinshead). The alternative recommendation for pelvic girdle sounds reasonable because both sides are joined anteriorly via the symphysis pubis but the pectoral girdles are not connected (well, except by a small interclavicular ligament). This approach entails new partitions: "lower appendicular limb system" consists of the pelvic girdle, the right free lower limb and the left free lower limb as one kind of partition and another kind, into right lower limb and left lower limb (each lower limb consists
of one side of pelvic girdle and a free lower limb). I will consult with the anatomy gods and see what they think.

>
>>>>>>> 2. The term "limb girdle" should denote a subdivision of the limb or
>>>>>>> fin (i.e. it *includes* fleshy parts). When referring to the
>>>>>>> skeletal elements, the term "limb girdle skeleton" or similar
>>>>>>> should be used. For full precision, we could follow the FMA and
>>>>>>> distinguish between the skeletal system (including joints) and
>>>>>>> skeleton.
>>>>>>>
>>>>>>> ALTERNATIVE: we follow ZFA, AAO and TAO and use "girdle" to denote
>>>>>>> the skeletal structure. Here we would need a term like "girdle
>>>>>>> segment" for demarcating the corresponding part of the limb.
>>
>> Yes, using "pelvic girdle skeleton" for the skeletal structure, and "pelvic girdle" for the structure including soft parts, made sense to us.
>
> OK
>
>>>>>>>
>>>>>>> 3. The girdle skeleton is entirely part of the appendicular
>>>>>>> skeleton, and there are no parts in common with the axial
>>>>>>> skeleton. If there is need to name a structure that overlaps
>>>>>>> both, then another term should be used.
>>
>> Agreed.
>>
>>>>>>>
>>>>>>> 4. We need a term that encompasses both individual bones and the
>>>>>>> zones of fused bones that correspond to individual bones, such as
>>>>>>> the ilium.
>>
>> We didn't get to this, but perhaps others can chime in here. My sense is that the ilium is referred to as "ilium" whether or not it's fused, at least in the comparative context.
>
> That's fine. The request was for a generic grouping class. In FMA and other ontologies have "bone" (aka "bone organ") as well as "zone of bone organ". Currently ilium is classified under the latter, which seems fine. However, it might be useful to have a more specific subclass of "zone of bone organ" that means something like "zone of bone organ that corresponds to what is a distinct bone earlier in development". I can see this being useful in a comparative context too (e.g. tibiafibila and friends)

Hmm, zone of confluent bone organ? Or reserve the terms "ilium", "ischium" and "pubis" as bonafide bone organs that are present only in certain stages and use "iliac region", "ischial region" and "pubic region" as organ parts of hip bone. Some developmental properties will link them.

[Chris Mungall]

On Jun 8, 2011, at 4:11 PM, mej...@u.washington.edu wrote:

>
>
>
> On Wed, 8 Jun 2011, Chris Mungall wrote:
>
>>
>> On Jun 8, 2011, at 1:58 PM, Dahdul, Wasila wrote:
>>
>>>>>>>> I'm trying to sort through various inconsistencies in how terms like
>>>>>>>> "pelvic girdle" and "pectoral girdle" are used.
>>>>>>>>
>>>>>>>> I've put together a strawman list of recommendations:
>>>>>>>>
>>>>>>>> 1. Both pelvic and pectoral girdles come in pairs; i.e. there is a
>>>>>>>> left girdle and a right gridle (consistent with FMA). Each girdle
>>>>>>>> is thus part of a single limb (or fin). When referring to the
>>>>>>>> mereological sum, a term like "pair of pelvic girdles" or "pelvic
>>>>>>>> girdle ring" should be used.
>>>>>>>>
>>>>>>>> ALTERNATIVE: it may be more intuitive to have "girdle" refer to the
>>>>>>>> pair, especially for pelvic girdle (consistent with AAO); but then
>>>>>>>> we need an intuitive term for each half (e.g. "pelvic girdle
>>>>>>>> lateral half").
>>>
>>> We agreed with the alternative recommendation of "pelvic girdle" referring to the pair, and using "pelvic girdle lateral half" for each half. This falls in line with common usage in comparative anatomy.
>>
>> OK. Would pectoral girdle be treated in the same way?
>>
>> It's unfortunate that this conflicts with the FMA usage, but I suspect there are many areas where human anatomy terminology conflicts with comparative anatomy. The best we can do is provide definitions, synonyms and a documentation trail.
>
> This is an interesting and important issue. I understand that the word "girdle" is defined as a "belt or sash around the waist" and therefore combining the pair makes a lot of sense but in human anatomy most sources apply the term to only one side of the limb. I think it's a misnomer but nonetheless it is represented as such in most reputable sources (Gray's, Morris, Terminologia Anatomica, Hollinshead). The alternative recommendation for pelvic girdle sounds reasonable because both sides are joined anteriorly via the symphysis pubis but the pectoral girdles are not connected (well, except by a small interclavicular ligament). This approach entails new partitions: "lower appendicular limb system" consists of the pelvic girdle, the right free lower limb and the left free lower limb as one kind of partition and another kind, into right lower limb and left lower limb (each lower limb consists of one side of pelvic girdle and a free lower limb). I will consult with the anatomy gods and see what they think.

Thanks Onard, this is really useful.

>>>>>>>> 4. We need a term that encompasses both individual bones and the
>>>>>>>> zones of fused bones that correspond to individual bones, such as
>>>>>>>> the ilium.
>>>
>>> We didn't get to this, but perhaps others can chime in here. My sense is that the ilium is referred to as "ilium" whether or not it's fused, at least in the comparative context.
>>
>> That's fine. The request was for a generic grouping class. In FMA and other ontologies have "bone" (aka "bone organ") as well as "zone of bone organ". Currently ilium is classified under the latter, which seems fine. However, it might be useful to have a more specific subclass of "zone of bone organ" that means something like "zone of bone organ that corresponds to what is a distinct bone earlier in development". I can see this being useful in a comparative context too (e.g. tibiafibila and friends)
>
> Hmm, zone of confluent bone organ? Or reserve the terms "ilium", "ischium" and "pubis" as bonafide bone organs that are present only in certain stages and use "iliac region", "ischial region" and "pubic region" as organ parts of hip bone. Some developmental properties will link them.

This seems reasonable, but I'm not sure how well this fits with current practice.

[Terry Hayamizu]

Certainly a lively discussion!

Onard - I'm trying to get a better handle on this and I was wondering if you could further explain how the FMA makes the distinction between: Pelvis, Pelvis proper, Pelvis wall, Bony pelvis, Pelvic skeleton, Pelvic girdle and Bony pelvic girdle. (See attached diagram, but please note that it is not complete.) From FMA definitions (using the FME which I realize may not be complete), the Pelvis is a subdivision of the abdomen, while the Pelvic girdle is a subdivision of the the free lower limb.

Although I cannot support my view with specific references, I have always thought of the pelvis (including the pelvic bones) a part of the "body" (Body proper in the FMA) rather than the limb. In contrast, it seems that what most people refer to as the "hip" is more of a (albeit inconsistently defined) region, which overlaps the pelvis and lower limb fields, but is not actually part of either. I can, however, see that it might be considered to be a part of the Appendicular skeletal system.

Finally, in the FMA partonomy, the Sacrum and Coccyx are represented (albeit indirectly) as part of the Lower limb. Do you feel that this is correct?

Much to ponder.

[mej...@u.washington.edu]

Hi Terry,

I have to go to a meeting but I'll come back to this as soon as I can.

Onard

[Chris Mungall]

Hi All

Returning to this thread from a year ago, as we never really reached a consensus on the appropriate terminology. One the one hand we have the RCN folks opting for "pectoral girdle" denote the mereological sum, and the FMA arguing for there being two pectoral girdles. a left and right, for each organism that has them.

I will combine both emails, see below:

On Jun 8, 2011, at 1:58 PM, Dahdul, Wasila wrote:

I'm trying to sort through various inconsistencies in how terms like

"pelvic girdle" and "pectoral girdle" are used.

I've put together a strawman list of recommendations:

1. Both pelvic and pectoral girdles come in pairs; i.e. there is a

   left girdle and a right gridle (consistent with FMA). Each girdle

   is thus part of a single limb (or fin). When referring to the

   mereological sum, a term like "pair of pelvic girdles" or "pelvic

   girdle ring" should be used.

ALTERNATIVE: it may be more intuitive to have "girdle" refer to the

 pair, especially for pelvic girdle (consistent with AAO); but then

 we need an intuitive term for each half (e.g. "pelvic girdle

 lateral half").

We agreed with the alternative recommendation of "pelvic girdle" referring to the pair, and using "pelvic girdle lateral half" for each half.  This falls in line with common usage in comparative anatomy.

And would this hold for "pectoral girdle" too? In organisms that lack a clavicle?

This is what Onard had to say:

This is an interesting and important issue. I understand that the word "girdle" is defined as a "belt or sash around the waist" and therefore combining the pair makes a lot of sense but in human anatomy most sources apply the term to only one side of the limb. I think it's a misnomer but nonetheless it is represented as such in most reputable sources (Gray's, Morris, Terminologia Anatomica, Hollinshead).  The alternative recommendation for pelvic girdle sounds reasonable because both sides are joined anteriorly via the symphysis pubis but the pectoral girdles are not connected (well, except by a small interclavicular ligament). This approach entails new partitions: "lower appendicular limb system" consists of the pelvic girdle, the right free lower limb and the left free lower limb as one kind of partition and another kind, into right lower limb and left lower limb (each lower limb consists of one side of pelvic girdle and a free lower limb). I will consult with the anatomy gods and see what they think.

Did the gods get back to you Onard?

I think both perspectives have equal merit. If there is genuinely no consensus, then perhaps the safest thing is to make the primary label unambiguous, and suffix it with "pair" or "half" - but this is really ugly and best avoided I think.

Onard's point brings up another points of possible difference in usage. In the FMA median structures such as the sternum are not considered part of the pectoral girdle - consistent with common reference sources such as Wikipedia.

However, VSAO considers the interclavicle as being part of the pectoral girdle (implicit in this relationship is the fact that the girdle is the mereological sum of both halves). In uberon there is the furcula, which is a pair of fused clavicles and possible the interclavicle. http://www.ncbi.nlm.nih.gov/pubmed/20422674 introduces the term "pectoral apparatus" for the sum of girdle halves plus sternum. Is this a widespread/intuitive term?

2. The term "limb girdle" should denote a subdivision of the limb or

   fin (i.e. it *includes* fleshy parts). When referring to the

   skeletal elements, the term "limb girdle skeleton" or similar

   should be used. For full precision, we could follow the FMA and

   distinguish between the skeletal system (including joints) and

   skeleton.

ALTERNATIVE: we follow ZFA, AAO and TAO and use "girdle" to denote

 the skeletal structure. Here we would need a term like "girdle

 segment" for demarcating the corresponding part of the limb.

Yes, using "pelvic girdle skeleton" for the skeletal structure, and "pelvic girdle" for the structure including soft parts, made sense to us. 

OK. I'm quite surprised by this as girdle has quite strong skeletal connotations.

Currently in Uberon the primary labels are suffixed to avoid ambiguity: "pelvic girdle skeleton" and "pelvic girdle region" (I don't like "region" so much, "subdivision" may be better).

However, I prefer to avoid such awkward names and would happily revert to using "girdle" for the organism subdivision, if other AOs will follow (FMA is already this way)

3. The girdle skeleton is entirely part of the appendicular

   skeleton, and there are no parts in common with the axial

   skeleton. If there is need to name a structure that overlaps

   both, then another term should be used.

Agreed.

OK

4. We need a term that encompasses both individual bones and the

   zones of fused bones that correspond to individual bones, such as

   the ilium.

We didn't get to this, but perhaps others can chime in here. My sense is that the ilium is referred to as "ilium" whether or not it's fused, at least in the comparative context. 

I agree.

5. The term "hip bone" should be synonymous with "innominate

   bone". This should be the mereological sum of the pelvic girdle

   skeleton plus some part of the axial skeleton (e.g. sacrum and

   coccyx in humans).

"Innominate bone" and "hip bone" are not commonly used in comparative anatomy although we did see at least innominate bone used in some text book figures.  We decided to use pelvic bone and pelvic bone skeleton for the multispecies context.

OK

I've removed the remainder of the discussion focusing on the hip bone - see the archives for details. I think the important thing now is to reach a consensus on halves vs pairs and median structures.

Some of these issues are also highlighted in the limb subdivisions document:

https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit?disco=AAAAAEVQBTI#

[mej...@u.washington.edu]

Comments in-line below.

Onard

On Wed, 20 Jun 2012, Chris Mungall wrote:

> Hi All
>
> Returning to this thread from a year ago, as we never really reached a consensus on the appropriate terminology. One the one hand we have the RCN folks opting for "pectoral girdle" denote the mereological sum,
> and the FMA arguing for there being two pectoral girdles. a left and right, for each organism that has them.
>
> I will combine both emails, see below:
>
> On Jun 8, 2011, at 1:58 PM, Dahdul, Wasila wrote:
>
>
>
> I'm trying to sort through various inconsistencies in how terms like
>
> "pelvic girdle" and "pectoral girdle" are used.
>
>
> I've put together a strawman list of recommendations:
>
>
> 1. Both pelvic and pectoral girdles come in pairs; i.e. there is a
>
>    left girdle and a right gridle (consistent with FMA). Each girdle
>
>    is thus part of a single limb (or fin). When referring to the
>
>    mereological sum, a term like "pair of pelvic girdles" or "pelvic
>
>    girdle ring" should be used.
>
>
> ALTERNATIVE: it may be more intuitive to have "girdle" refer to the
>
>  pair, especially for pelvic girdle (consistent with AAO); but then
>
>  we need an intuitive term for each half (e.g. "pelvic girdle
>
>  lateral half").
>
>
> We agreed with the alternative recommendation of "pelvic girdle" referring to the pair, and using "pelvic girdle lateral half" for each half.  This falls in line with common usage in comparative anatomy.
>
>
> And would this hold for "pectoral girdle" too? In organisms that lack a clavicle?

In the FMA, pectoral (or pelvic) girdle, is a subdivision of cardinal body part (organism subdivision is CARO?)and therefore does not refer only to bones. It includes skin, subcutaneous tissue, muscle, vasculature, neural network and bony (pectoral or pelvic) girdle. I suspect that the issue above is either about the bony girdle (bones and joints) or skeleton of girdle (just bones).

>
> This is what Onard had to say:
>
> This is an interesting and important issue. I understand that the word "girdle" is defined as a "belt or sash around the waist" and therefore combining the pair makes a lot of sense but
> in human anatomy most sources apply the term to only one side of the limb. I think it's a misnomer but nonetheless it is represented as such in most reputable sources (Gray's, Morris,
> Terminologia Anatomica, Hollinshead).  The alternative recommendation for pelvic girdle sounds reasonable because both sides are joined anteriorly via the symphysis pubis but the
> pectoral girdles are not connected (well, except by a small interclavicular ligament). This approach entails new partitions: "lower appendicular limb system" consists of the pelvic
> girdle, the right free lower limb and the left free lower limb as one kind of partition and another kind, into right lower limb and left lower limb (each lower limb consists of one side
> of pelvic girdle and a free lower limb). I will consult with the anatomy gods and see what they think.
>
>
> Did the gods get back to you Onard?

Yes, they want to maintain them as separate (pairs not halves).

>
> I think both perspectives have equal merit. If there is genuinely no consensus, then perhaps the safest thing is to make the primary label unambiguous, and suffix it with "pair" or "half" - but this is really
> ugly and best avoided I think.
>
> Onard's point brings up another points of possible difference in usage. In the FMA median structures such as the sternum are not considered part of the pectoral girdle - consistent with common reference sources
> such as Wikipedia.

Sternum and ribs are axial.

>
> However, VSAO considers the interclavicle as being part of the pectoral girdle (implicit in this relationship is the fact that the girdle is the mereological sum of both halves). In uberon there is the furcula,
> which is a pair of fused clavicles and possible the interclavicle. http://www.ncbi.nlm.nih.gov/pubmed/20422674 introduces the term "pectoral apparatus" for the sum of girdle halves plus sternum. Is this a
> widespread/intuitive term?
>
>
> 2. The term "limb girdle" should denote a subdivision of the limb or
>
>    fin (i.e. it *includes* fleshy parts). When referring to the
>
>    skeletal elements, the term "limb girdle skeleton" or similar
>
>    should be used. For full precision, we could follow the FMA and
>
>    distinguish between the skeletal system (including joints) and
>
>    skeleton.
>
>
> ALTERNATIVE: we follow ZFA, AAO and TAO and use "girdle" to denote
>
>  the skeletal structure. Here we would need a term like "girdle
>
>  segment" for demarcating the corresponding part of the limb.
>
>
> Yes, using "pelvic girdle skeleton" for the skeletal structure, and "pelvic girdle" for the structure including soft parts, made sense to us. 
>
>
> OK. I'm quite surprised by this as girdle has quite strong skeletal connotations.

That's true but in all major sources, the soft parts are always implied.