Anomalous anatomical set members

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Alan Ruttenberg

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Dec 9, 2011, 2:32:56 AM12/9/11
to fma-owl-2009, Melissa Haendel, Bill Duncan, Carlo Torniai
In reviewing, and then attempting to debug, the representation of teeth, I came across a number of cases that seem to be in error.

The definition of Anatomical set is:

material anatomical entity which has as its members the maximal number of anatomical structures of the same type.
While some of anatomical sets could be regarded as an organ system subvision, e.g set of lumbar nerves, others do not satisfy one or two defining attributes of organ system subdivision. E.g. thoracic viscera consists of organs but not belonging to one organ system, dental arcade consists of similar organs but they are not connected.

I ran a function to find cases (~350) where anatomical set members are not anatomical structures. The cases are listed at http://svn.neurocommons.org/svn/trunk/convert/fma/reports/anatomical-sets-with-not-structure-members.txt

I'd also like to test my understanding of the member versus part relationships.

member_of => part_of
part_of: transitive
member_of: not transitive
member_of o part_of => member_of

The last one is the one to check - it says that if a set has a part, and the part has members, then the set has those members. 

If that is accepted, then some of the above cases might be recast using part_of. However I suspect that they should all be checked, given the situation described below.

In the specific case of dentition, the issue is that an uncareful interpretation of the current fma is that the primary dentition include secondary teeth.

That arises because 

'Dentition'(FMA_75150) has member 'Mandibular dentition'(FMA_269584) which is not anatomical structure
'Dentition'(FMA_75150) has member 'Maxillary dentition'(FMA_269582) which is not anatomical structure
 
and 'Primary dentition' is_a 'Dentition'

and the members of 'Maxillary dentition' are all secondary teeth.

On the reading of member as has_part we get the unintended inference.

There are a number of possible fixes, but before offering them I thought I would first check in about the above. I need to sort this out for a prototype I am currently working on.

Other cases of the anatomical set issue in that area of anatomy

'Dental arcade'(FMA_59415) has member 'Set of periodontia'(FMA_269567) which is not anatomical structure
'Dental arcade'(FMA_59415) has member 'Dentition'(FMA_75150) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Set of mandibular periodontia'(FMA_269572) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Mandibular dentition'(FMA_269584) which is not anatomical structure
'Dental arcade'(FMA_59415) has member 'Set of periodontia'(FMA_269567) which is not anatomical structure
'Dental arcade'(FMA_59415) has member 'Dentition'(FMA_75150) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Set of mandibular periodontia'(FMA_269572) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Mandibular dentition'(FMA_269584) which is not anatomical structure

Some clerical errors that need fixing are a number of orphan tooth surfaces and parts where there is no asserted relation to the corresponding tooth:

Distolingual cusp of right upper first molar tooth 
Occlusal surface of left lower first molar tooth 
Crown proper of left upper first molar tooth 
Incisal surface of right upper canine tooth 
Lingual surface of left upper second molar tooth 
Distal surface of right lower second premolar tooth 
Mesial surface of right upper third molar tooth 
Occlusal surface of right lower third molar tooth 

Finally, I note that the relation of the surfaces of the teeth are related by part_of to the teeth, but should instead be related by  bounded_by, as is documented in the papers and as occurs elsewhere in FMA. 

Best,
Alan

mej...@comcast.net

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Dec 9, 2011, 4:25:16 AM12/9/11
to fma-ow...@googlegroups.com, Melissa Haendel, Bill Duncan, Carlo Torniai
Alan,

My comments in-line  below.

Onard


From: "Alan Ruttenberg" <alanrut...@gmail.com>
To: "fma-owl-2009" <fma-ow...@googlegroups.com>
Cc: "Melissa Haendel" <hae...@ohsu.edu>, "Bill Duncan" <wddu...@gmail.com>, "Carlo Torniai" <tor...@ohsu.edu>
Sent: Thursday, December 8, 2011 11:32:56 PM
Subject: Anomalous anatomical set members


In reviewing, and then attempting to debug, the representation of teeth, I came across a number of cases that seem to be in error.

The definition of Anatomical set is:

material anatomical entity which has as its members the maximal number of anatomical structures of the same type.
While some of anatomical sets could be regarded as an organ system subvision, e.g set of lumbar nerves, others do not satisfy one or two defining attributes of organ system subdivision. E.g. thoracic viscera consists of organs but not belonging to one organ system, dental arcade consists of similar organs but they are not connected.

OM: In the FMA no anatomical set is regarded as an organ system subdivision and vice versa. The latter is an anatomical structures consisting of continuous parts as opposed to the former which consists of discontinuous members.


I ran a function to find cases (~350) where anatomical set members are not anatomical structures. The cases are listed at http://svn.neurocommons.org/svn/trunk/convert/fma/reports/anatomical-sets-with-not-structure-members.txt

I'd also like to test my understanding of the member versus part relationships.

member_of => part_of
part_of: transitive
member_of: not transitive
member_of o part_of => member_of

OM: We consider membership as a kind of parthood relation in the FMA, hence it has transitivity property. Member_of is a subproperty of part_of.

The last one is the one to check - it says that if a set has a part, and the part has members, then the set has those members. 

If that is accepted, then some of the above cases might be recast using part_of. However I suspect that they should all be checked, given the situation described below.

In the specific case of dentition, the issue is that an uncareful interpretation of the current fma is that the primary dentition include secondary teeth.

That arises because 

'Dentition'(FMA_75150) has member 'Mandibular dentition'(FMA_269584) which is not anatomical structure
'Dentition'(FMA_75150) has member 'Maxillary dentition'(FMA_269582) which is not anatomical structure
 
and 'Primary dentition' is_a 'Dentition'

and the members of 'Maxillary dentition' are all secondary teeth.

OM: Using the frame-based system and the "single inheritance" principle posed some limitations to the representation. Dentition is a good example.

Ideally we would like to declare in is_a hierarchy:

Dentition
      Primary dentition
           Primary maxillary dentition
           Primary mandibular dention
      Secondary dentition
           Secondary maxillary dentition
           Secondary mandibular dentition

As well as...

Maxillary dentition
     Primary maxillary dentition
     Secondary maxillary dentition

Mandibular dentition
     Primary mandibular dention
     Secondary mandibular dentition

And then declare the appropriate primary and secondary teeth to the corresponding maxillary and mandibular sets. We hope to achieve this in the OWL format. In the current version the maxillary and mandibular dentitions have secondary teeth members but that will change as soon as we move to OWL.


On the reading of member as has_part we get the unintended inference.

There are a number of possible fixes, but before offering them I thought I would first check in about the above. I need to sort this out for a prototype I am currently working on.

Other cases of the anatomical set issue in that area of anatomy

'Dental arcade'(FMA_59415) has member 'Set of periodontia'(FMA_269567) which is not anatomical structure
'Dental arcade'(FMA_59415) has member 'Dentition'(FMA_75150) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Set of mandibular periodontia'(FMA_269572) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Mandibular dentition'(FMA_269584) which is not anatomical structure
'Dental arcade'(FMA_59415) has member 'Set of periodontia'(FMA_269567) which is not anatomical structure
'Dental arcade'(FMA_59415) has member 'Dentition'(FMA_75150) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Set of mandibular periodontia'(FMA_269572) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Mandibular dentition'(FMA_269584) which is not anatomical structure

OM: What is missing in the definition is the inclusion of subsets as members (parts) of a the bigger set.


Some clerical errors that need fixing are a number of orphan tooth surfaces and parts where there is no asserted relation to the corresponding tooth:

Distolingual cusp of right upper first molar tooth 
Occlusal surface of left lower first molar tooth 
Crown proper of left upper first molar tooth 
Incisal surface of right upper canine tooth 
Lingual surface of left upper second molar tooth 
Distal surface of right lower second premolar tooth 
Mesial surface of right upper third molar tooth 
Occlusal surface of right lower third molar tooth

OM: Thank you for the list. I will add the links to the corresponding teeth.

Finally, I note that the relation of the surfaces of the teeth are related by part_of to the teeth, but should instead be related by  bounded_by, as is documented in the papers and as occurs elsewhere in FMA.

OM: That indeed is not right. I think the original intent was to represent the surface layer (3-D structure) but in the process they were classified as surfaces (2-D). I will look into this and apply the corrections.

Again, many thanks for the heads up.
Onard

Best,
Alan

Alan Ruttenberg

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Dec 9, 2011, 10:37:31 AM12/9/11
to fma-ow...@googlegroups.com, Melissa Haendel, Bill Duncan, Carlo Torniai
On Fri, Dec 9, 2011 at 4:25 AM, <mej...@comcast.net> wrote:
Alan,

My comments in-line  below.

Onard


From: "Alan Ruttenberg" <alanrut...@gmail.com>
To: "fma-owl-2009" <fma-ow...@googlegroups.com>
Cc: "Melissa Haendel" <hae...@ohsu.edu>, "Bill Duncan" <wddu...@gmail.com>, "Carlo Torniai" <tor...@ohsu.edu>
Sent: Thursday, December 8, 2011 11:32:56 PM
Subject: Anomalous anatomical set members


In reviewing, and then attempting to debug, the representation of teeth, I came across a number of cases that seem to be in error.

The definition of Anatomical set is:

material anatomical entity which has as its members the maximal number of anatomical structures of the same type.
While some of anatomical sets could be regarded as an organ system subvision, e.g set of lumbar nerves, others do not satisfy one or two defining attributes of organ system subdivision. E.g. thoracic viscera consists of organs but not belonging to one organ system, dental arcade consists of similar organs but they are not connected.

OM: In the FMA no anatomical set is regarded as an organ system subdivision and vice versa. The latter is an anatomical structures consisting of continuous parts as opposed to the former which consists of discontinuous members.

Right. My point is that the definitions disallows members of anatomical sets being other anatomical sets(many of the cases listed) or things that are not anatomical structures, such as blood:
 
'Hematopoietic system'(FMA_9667) has member 'Portion of blood'(FMA_9670) which is not anatomical structure


I ran a function to find cases (~350) where anatomical set members are not anatomical structures. The cases are listed at http://svn.neurocommons.org/svn/trunk/convert/fma/reports/anatomical-sets-with-not-structure-members.txt

I'd also like to test my understanding of the member versus part relationships.

member_of => part_of
part_of: transitive
member_of: not transitive
member_of o part_of => member_of

OM: We consider membership as a kind of parthood relation in the FMA, hence it has transitivity property. Member_of is a subproperty of part_of.

It makes sense that member_of be a kind of parthood relation. However member_of is generally not considered to be transitive, and it doesn't become transitive solely by being a subproperty of another transitive property.  Suppose you have a set (call it "coin set set") whose members are sets of coins, one generally doesn't consider the coins to also be members of "coin set set". Also, since anatomical structure and anatomical set are disjoint, there shouldn't ever be an opportunity for transitivity to be exercised, since member_of isn't an appropriate relation to relate anatomical structures to other things. 

(1) Anatomical set -- has_member --> (2) Anatomical structure --- // has member (not!) // --> (3) anything else.

For has_member to be meaningfully transitive, it would need to be the case that member_of was a valid relation for (2).
 
The last one is the one to check - it says that if a set has a part, and the part has members, then the set has those members. 

If that is accepted, then some of the above cases might be recast using part_of. However I suspect that they should all be checked, given the situation described below.

In the specific case of dentition, the issue is that an uncareful interpretation of the current fma is that the primary dentition include secondary teeth.

That arises because 

'Dentition'(FMA_75150) has member 'Mandibular dentition'(FMA_269584) which is not anatomical structure
'Dentition'(FMA_75150) has member 'Maxillary dentition'(FMA_269582) which is not anatomical structure
 
and 'Primary dentition' is_a 'Dentition'

and the members of 'Maxillary dentition' are all secondary teeth.

OM: Using the frame-based system and the "single inheritance" principle posed some limitations to the representation. Dentition is a good example.

It's potentially the single inheritance, not the frame system.
 
Ideally we would like to declare in is_a hierarchy:

Dentition
      Primary dentition
           Primary maxillary dentition
           Primary mandibular dention
      Secondary dentition
           Secondary maxillary dentition
           Secondary mandibular dentition

As well as...

Maxillary dentition
     Primary maxillary dentition
     Secondary maxillary dentition

Mandibular dentition
     Primary mandibular dentition

     Secondary mandibular dentition

And then declare the appropriate primary and secondary teeth to the corresponding maxillary and mandibular sets. We hope to achieve this in the OWL format. In the current version the maxillary and mandibular dentitions have secondary teeth members but that will change as soon as we move to OWL.

Right, since that's what I thought you were trying to accomplish. But consider this, which may be more than adequate (parentheses show parent class)

Dentition (anatomical set)
      has_part Primary dentition (anatomical set)
             has_part Primary maxillary dentition (anatomical set)
             has_part Primary mandibular dentition (anatomical set)
      has_part Secondary dentition (anatomical set)
            has_part Secondary maxillary dentition (anatomical set)
            has_part Secondary mandibular dentition (anatomical set)

Maxillary dentition (anatomical set)
     has_part Primary maxillary dentition (anatomical set)
     has_part Secondary maxillary dentition (anatomical set)

Mandibular dentition (anatomical set)
     has_part Primary mandibular dentition (anatomical set)
     has_part Secondary mandibular dentition 
(anatomical set)

In this view, the hierarchy is completely a partonomy, and all the terms are is_a anatomical set, so no multiple inheritance is triggered.

If you wanted to pull out as a type primary versus secondary and a add a bit more is_a structure
(that would be my guess as to the sensible thing) then you would have:

Primary tooth (type)
Secondary tooth (type)
set of teeth =def anatomical set whose members are tooth
set of primary teeth =def set of teeth whose members are primary tooth
set of secondary teeth =def set of teeth whose members are secondary tooth

Dentition (set of teeth)
  has_part Maxillary dentition (
set of teeth)
  has_part Mandibular dentition (set of teeth)

Maxillary dentition (set of teeth)
     has_part Primary maxillary dentition (
set of primary teeth)
     has_part Secondary maxillary dentition (
set of secondary teeth)

Mandibular dentition (set of teeth)
     has_part Primary mandibular dentition (
set of primary teeth)
     has_part Secondary mandibular dentition 
(set of secondary teeth)

Primary dentition (set of primary teeth)
Secondary dentition (set of secondary teeth)

The have each tooth be 
is_a either primary or secondary tooth, 
and member either primary or secondary dentition
and member one of Primary mandibular dentition, or Primary maxillary dentition, Secondary mandibular dentition, or Secondary maxillary dentition

Assuming I have confused myself, I believe this captures all the anatomical sets you want, and avoids multiple inheritance.
  


On the reading of member as has_part we get the unintended inference.

There are a number of possible fixes, but before offering them I thought I would first check in about the above. I need to sort this out for a prototype I am currently working on.

Other cases of the anatomical set issue in that area of anatomy

'Dental arcade'(FMA_59415) has member 'Set of periodontia'(FMA_269567) which is not anatomical structure
'Dental arcade'(FMA_59415) has member 'Dentition'(FMA_75150) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Set of mandibular periodontia'(FMA_269572) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Mandibular dentition'(FMA_269584) which is not anatomical structure
'Dental arcade'(FMA_59415) has member 'Set of periodontia'(FMA_269567) which is not anatomical structure
'Dental arcade'(FMA_59415) has member 'Dentition'(FMA_75150) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Set of mandibular periodontia'(FMA_269572) which is not anatomical structure
'Mandibular dental arcade'(FMA_55635) has member 'Mandibular dentition'(FMA_269584) which is not anatomical structure

OM: What is missing in the definition is the inclusion of subsets as members (parts) of a the bigger set.

Right, that was my point earlier about: member_of o part_of => member_of.
If you have subsets be part of sets, then with the above rule (which can be expressed in OWL 2) you will get the intended behavior.
 
Some clerical errors that need fixing are a number of orphan tooth surfaces and parts where there is no asserted relation to the corresponding tooth:

Distolingual cusp of right upper first molar tooth 
Occlusal surface of left lower first molar tooth 
Crown proper of left upper first molar tooth 
Incisal surface of right upper canine tooth 
Lingual surface of left upper second molar tooth 
Distal surface of right lower second premolar tooth 
Mesial surface of right upper third molar tooth 
Occlusal surface of right lower third molar tooth

OM: Thank you for the list. I will add the links to the corresponding teeth.

Finally, I note that the relation of the surfaces of the teeth are related by part_of to the teeth, but should instead be related by  bounded_by, as is documented in the papers and as occurs elsewhere in FMA.

OM: That indeed is not right. I think the original intent was to represent the surface layer (3-D structure) but in the process they were classified as surfaces (2-D). I will look into this and apply the corrections.

Again, many thanks for the heads up.

Welcome. If you plan to do this in the near future, could you let me know and I'll wait to pick up your changes, which would save me a bit of time.
 
Onard

Best,
Alan

Alan Ruttenberg

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Dec 9, 2011, 10:45:58 AM12/9/11
to fma-ow...@googlegroups.com, Melissa Haendel, Bill Duncan, Carlo Torniai
One more thing ;-)

The sets of teeth are unlike some other sets as they gather members that do not necessarily exist at the same time. I wonder if there is precedent elsewhere in the FMA for that, or whether it might make more sense to stay away from that and not create as sets dentition (meaning set of all primary and secondary teeth), mandibular dention (also mixes primary and secondary teeth) or maxilliary dentition (also mixes primary and secondary teeth).

-Alan

On Fri, Dec 9, 2011 at 4:25 AM, <mej...@comcast.net> wrote:

ro...@u.washington.edu

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Dec 9, 2011, 12:41:36 PM12/9/11
to fma-ow...@googlegroups.com, Melissa Haendel, Bill Duncan, Carlo Torniai, Cornelius Rosse, Onard Mejino
Alan, it is true for sets of anatomical entities in the fully developed vertebral body that their members do not exist at the same time. For example, members of sets vertebrae, sets of muscles, etc appear during ontogeny at separate times. Hence adding a time element to the definitions is always necessary. I realize that FMA definitions do not do this, because the FMA takes account of a canonical, fully developed human body. I realize that there are arguments for and against the justification of such a strategy.

Cornelius

On Fri, 9 Dec 2011, Alan Ruttenberg wrote:

> One more thing ;-)
> The sets of teeth are unlike some other sets as they gather members that do not necessarily exist at the same time. I wonder
> if there is precedent elsewhere in the FMA for that, or whether it might make more sense to stay away from that and not create
> as sets dentition (meaning set of all primary and secondary teeth), mandibular dention (also mixes primary and secondary
> teeth) or maxilliary dentition (also mixes primary and secondary teeth).
>
> -Alan
>
> On Fri, Dec 9, 2011 at 4:25 AM, <mej...@comcast.net> wrote:
> Alan,
>
> My comments in-line below.
>
> Onard
>

> ______________________________________________________________________________________________________________________________

Alan Ruttenberg

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Dec 9, 2011, 1:19:57 PM12/9/11
to fma-ow...@googlegroups.com, Melissa Haendel, Bill Duncan, Carlo Torniai, Cornelius Rosse, Onard Mejino
On Fri, Dec 9, 2011 at 12:41 PM, <ro...@u.washington.edu> wrote:
Alan, it is true for sets of anatomical entities in the fully developed vertebral body that their members do not exist at the same time. For example, members of sets vertebrae, sets of muscles, etc appear during ontogeny at separate times. Hence adding a time element to the definitions is always necessary. I realize that FMA definitions do not do this, because the FMA takes account of a canonical, fully developed human body. I realize that there are arguments for and against the justification of such a strategy.

Hi Cornelius,

Thanks for the response (happy to hear your virtual voice :) . 

Dentition is one of those in-between cases which slightly stretches the model to allow for two canonical cases - childhood and adulthood, with reasonably clear delineation between the immature and mature forms. My inclination would therefore be to only use Anatomical set for each of these separately, with the same caveats you mention earlier applicable, and not to name sets that include members of both as, given the current FMA, the members of Anatomical sets seem to generally be more approximately contemporaneous than is the case with primary and secondary teeth.

Would you concur, or do you see benefit in having Anatomical sets that have both as members?

Regards,
Alan

ps. Barry and I frequently argue about what you would say about this or that issue. It would be great fun to find a time again when we could all sit together and have it out :)

mej...@comcast.net

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Dec 9, 2011, 1:36:17 PM12/9/11
to fma-ow...@googlegroups.com, Melissa Haendel, Bill Duncan, Carlo Torniai, Cornelius Rosse, Onard Mejino
Alan,

The class "Dentition" does not have both primary and secondary teeth as members but rather it has subtypes primary and secondary. The members of class "Dentition" are maxillary dentition and mandibular dentition, and the subtype of "Dentition", "Primary dentition", has members primary maxillary and primary mandibular sets (same rationale for the secondary dentition). Currently in the FMA, you will find that "Primary dentition" has as members only the primary teeth.

Temporal property is of great interest to me and one I would like to explore for the FMA. As Cornelius mentioned, not all members exist at the same time but remember we are dealing with a continuant, one that takes into account its canonical completeness over a period of time, not at a one specific stage.

Onard



From: "Alan Ruttenberg" <alanrut...@gmail.com>
To: fma-ow...@googlegroups.com
Cc: "Melissa Haendel" <hae...@ohsu.edu>, "Bill Duncan" <wddu...@gmail.com>, "Carlo Torniai" <tor...@ohsu.edu>, "Cornelius Rosse" <ro...@u.washington.edu>, "Onard Mejino" <mej...@u.washington.edu>
Sent: Friday, December 9, 2011 10:19:57 AM
Subject: Re: Anomalous anatomical set members

Alan Ruttenberg

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Dec 9, 2011, 1:40:37 PM12/9/11
to mej...@u.washington.edu, fma-ow...@googlegroups.com, Melissa Haendel, Bill Duncan, Carlo Torniai, Cornelius Rosse
On Fri, Dec 9, 2011 at 1:32 PM, mej...@u.washington.edu <mej...@u.washington.edu> wrote:
Alan,

The class "Dentition" does not have both primary and secondary teeth as members but rather it has subtypes primary and secondary. The members of class "Dentition" are maxillary dentition and mandibular dentition, and the subtype of "Dentition", "Primary dentition", has members primary maxillary and primary mandibular sets (same rationale for the secondary dentition).

Yes. But I think that's wrong. If Dentition has members and subclasses, then instances of the subclasses also have those members= by inheritance. As maxillary dentition would include both primary and secondary teeth, the inheritance would lead to an incorrect membership for Primary dentition (and secondary dentition).

In general, having a set type that has both members and subtypes seems to me to be a recipe for confusion and error, and while it might work in certain cases, it seems best avoided.
  
Currently in the FMA, you will find that "Primary dentition" has as members only the primary teeth.

Plus the ones inherited from dentition, which include secondary teeth.
 
Temporal property is of great interest to me and one I would like to explore for the FMA. As Cornelius mentioned, not all members exist at the same time but remember we are dealing with a continuant, one that takes into account its canonical completeness over a period of time, not at a one specific stage.

Agreed. What did you think of the analysis in my response with regard to primary and secondary teeth, where the temporal separation is more clear?

Best,
Alan

Onard

Alan Ruttenberg

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Dec 9, 2011, 1:45:56 PM12/9/11
to mej...@u.washington.edu, fma-ow...@googlegroups.com, Melissa Haendel, Bill Duncan, Carlo Torniai, Cornelius Rosse
Onard wrote:
Temporal property is of great interest to me and one I would like to explore for the FMA.

For starters I think it would help to simply clarify the status of Anatomical set as it is used in the FMA and augment the definition with the resulting clarification.

Is an anatomical set instantiated at any time any of its members develops, perhaps having changing membership over time, until none are present? Or is it the intention that the term denote the full set of entities only during the time that they are all present. These are different from an ontological point of view, though in both cases continuant.

-Alan

mej...@comcast.net

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Dec 9, 2011, 1:47:26 PM12/9/11
to fma-ow...@googlegroups.com, Melissa Haendel, Bill Duncan, Carlo Torniai, Cornelius Rosse, mej...@u.washington.edu
Can I ask you a favor? Can you include my UW address, mej...@uw.edu, to the email group? I'd rather respond using the UW mail than this comcast service.

Thanks.
Onard



From: "Alan Ruttenberg" <alanrut...@gmail.com>
To: mej...@u.washington.edu
Cc: fma-ow...@googlegroups.com, "Melissa Haendel" <hae...@ohsu.edu>, "Bill Duncan" <wddu...@gmail.com>, "Carlo Torniai" <tor...@ohsu.edu>, "Cornelius Rosse" <ro...@u.washington.edu>
Sent: Friday, December 9, 2011 10:40:37 AM

Subject: Re: Anomalous anatomical set members



mej...@comcast.net

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Dec 9, 2011, 2:22:16 PM12/9/11
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From: "Alan Ruttenberg" <alanrut...@gmail.com>
To: mej...@u.washington.edu
Cc: fma-ow...@googlegroups.com, "Melissa Haendel" <hae...@ohsu.edu>, "Bill Duncan" <wddu...@gmail.com>, "Carlo Torniai" <tor...@ohsu.edu>, "Cornelius Rosse" <ro...@u.washington.edu>
Sent: Friday, December 9, 2011 10:40:37 AM
Subject: Re: Anomalous anatomical set members



On Fri, Dec 9, 2011 at 1:32 PM, mej...@u.washington.edu <mej...@u.washington.edu> wrote:
Alan,

The class "Dentition" does not have both primary and secondary teeth as members but rather it has subtypes primary and secondary. The members of class "Dentition" are maxillary dentition and mandibular dentition, and the subtype of "Dentition", "Primary dentition", has members primary maxillary and primary mandibular sets (same rationale for the secondary dentition).

Yes. But I think that's wrong. If Dentition has members and subclasses, then instances of the subclasses also have those members= by inheritance. As maxillary dentition would include both primary and secondary teeth, the inheritance would lead to an incorrect membership for Primary dentition (and secondary dentition).

OM: I'm not quite sure I follow you but consider these:

Dentition is  a class whose members consist only of teeth, without specifying which particular set of teeth.
Entire dentition is a class whose members include all kinds of teeth, primary and secondary.
Primary dentition is a subclass of 'dentition' which specifies the membership only to include primary teeth.
Maxillary dentition is a subclass of 'dentition' which specifies the membership only to include all kinds of teeth attached to the maxillae, whether they are primary or secondary.
Entire maxillary dentition is a subclass of 'maxillary dentition' which specifies the membership only to include all kinds of teeth attached to the maxillae, whether they are primary or secondary.
Primary maxillary dentition is a subclass of 'maxillary dentition' which specifies the membership only to include primary teeth attached to the maxillae.

And the instances of each class are those which satisfy the properties of that particular class.

Onard

mej...@comcast.net

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From: "Alan Ruttenberg" <alanrut...@gmail.com>

Cc: "Melissa Haendel" <hae...@ohsu.edu>, "Bill Duncan" <wddu...@gmail.com>, "Carlo Torniai" <tor...@ohsu.edu>
Sent: Friday, December 9, 2011 7:37:31 AM

Subject: Re: Anomalous anatomical set members

On Fri, Dec 9, 2011 at 4:25 AM, <mej...@comcast.net> wrote:
Alan,

My comments in-line  below.

Onard


From: "Alan Ruttenberg" <alanrut...@gmail.com>
To: "fma-owl-2009" <fma-ow...@googlegroups.com>
Cc: "Melissa Haendel" <hae...@ohsu.edu>, "Bill Duncan" <wddu...@gmail.com>, "Carlo Torniai" <tor...@ohsu.edu>
Sent: Thursday, December 8, 2011 11:32:56 PM
Subject: Anomalous anatomical set members


In reviewing, and then attempting to debug, the representation of teeth, I came across a number of cases that seem to be in error.

The definition of Anatomical set is:

material anatomical entity which has as its members the maximal number of anatomical structures of the same type.
While some of anatomical sets could be regarded as an organ system subvision, e.g set of lumbar nerves, others do not satisfy one or two defining attributes of organ system subdivision. E.g. thoracic viscera consists of organs but not belonging to one organ system, dental arcade consists of similar organs but they are not connected.

OM: In the FMA no anatomical set is regarded as an organ system subdivision and vice versa. The latter is an anatomical structures consisting of continuous parts as opposed to the former which consists of discontinuous members.

Right. My point is that the definitions disallows members of anatomical sets being other anatomical sets(many of the cases listed) or things that are not anatomical structures, such as blood:
 
'Hematopoietic system'(FMA_9667) has member 'Portion of blood'(FMA_9670) which is not anatomical structure


OM: The definition of anatomical set does not disallow body substances, that why we have the class "Hematopoietic system".
We also have sets of immaterial anatomical entities, such as "Set of subarachnoid sulci" and "Set of external nares".



I ran a function to find cases (~350) where anatomical set members are not anatomical structures. The cases are listed at http://svn.neurocommons.org/svn/trunk/convert/fma/reports/anatomical-sets-with-not-structure-members.txt

I'd also like to test my understanding of the member versus part relationships.

member_of => part_of
part_of: transitive
member_of: not transitive
member_of o part_of => member_of

OM: We consider membership as a kind of parthood relation in the FMA, hence it has transitivity property. Member_of is a subproperty of part_of.

It makes sense that member_of be a kind of parthood relation. However member_of is generally not considered to be transitive, and it doesn't become transitive solely by being a subproperty of another transitive property.  Suppose you have a set (call it "coin set set") whose members are sets of coins, one generally doesn't consider the coins to also be members of "coin set set". Also, since anatomical structure and anatomical set are disjoint, there shouldn't ever be an opportunity for transitivity to be exercised, since member_of isn't an appropriate relation to relate anatomical structures to other things.

OM:
Set of C1, C2 and C3 vertebrae is a set of Cervical vertebrae
Set of Cervical vertebrae is a set of vertebrae
Set of C1, C2 and C3 vertebrae is a set of vertebrae
Set of vertebrae is a set of axial bones
Set of axial bones is a set of bones
Set of C1, C2 and C3 vertebrae is a set of bones

And yes, there is a relationship between an anatomical structure and a set of anatomical structures:

Hand has constitutional_part
      Skin of hand
      Superficial fascia of hand
      Musculature of hand (Anatomical set)
      Skeleton of hand (Anatomical set)
      Neural network of hand
      Vasculature of hand
  


(1) Anatomical set -- has_member --> (2) Anatomical structure --- // has member (not!) // --> (3) anything else.

For has_member to be meaningfully transitive, it would need to be the case that member_of was a valid relation for (2).
 
The last one is the one to check - it says that if a set has a part, and the part has members, then the set has those members. 

If that is accepted, then some of the above cases might be recast using part_of. However I suspect that they should all be checked, given the situation described below.

In the specific case of dentition, the issue is that an uncareful interpretation of the current fma is that the primary dentition include secondary teeth.

That arises because 

'Dentition'(FMA_75150) has member 'Mandibular dentition'(FMA_269584) which is not anatomical structure
'Dentition'(FMA_75150) has member 'Maxillary dentition'(FMA_269582) which is not anatomical structure
 
and 'Primary dentition' is_a 'Dentition'

and the members of 'Maxillary dentition' are all secondary teeth.

OM: Using the frame-based system and the "single inheritance" principle posed some limitations to the representation. Dentition is a good example.

It's potentially the single inheritance, not the frame system.

You're right, I can have multiple inheritance in frames.

OM: I addressed this in the previous message.


mej...@comcast.net

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Dec 9, 2011, 2:45:22 PM12/9/11
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Corrections, I meant:

Maxillary dentition is a subclass of 'dentition' which specifies the membership only to include teeth attached to the maxillae, without specifying whether they are primary or secondary.
Entire maxillary dentition is a subclass of 'maxillary dentition' which specifies the membership to include all kinds of teeth attached to the maxillae.



From: mej...@comcast.net
To: fma-ow...@googlegroups.com
Cc: "Melissa Haendel" <hae...@ohsu.edu>, "Bill Duncan" <wddu...@gmail.com>, "Carlo Torniai" <tor...@ohsu.edu>, "Cornelius Rosse" <ro...@u.washington.edu>, mej...@u.washington.edu
Sent: Friday, December 9, 2011 11:22:16 AM

ro...@u.washington.edu

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Dec 9, 2011, 7:07:05 PM12/9/11
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Alan,

Yes; an eminently sensible proposition.

Cornelius

On Fri, 9 Dec 2011, Alan Ruttenberg wrote:

>
>
> On Fri, Dec 9, 2011 at 12:41 PM, <ro...@u.washington.edu> wrote:
> Alan, it is true for sets of anatomical entities in the fully developed vertebral body that their members do not
> exist at the same time. For example, members of sets vertebrae, sets of muscles, etc appear during ontogeny at
> separate times. Hence adding a time element to the definitions is always necessary. I realize that FMA definitions
> do not do this, because the FMA takes account of a canonical, fully developed human body. I realize that there are
> arguments for and against the justification of such a strategy.
>
>
> Hi Cornelius,
>

> Thanks for the response (happy to hear your virtual voice :) .ᅵ


>
> Dentition is one of those in-between cases which slightly stretches the model to allow for two canonical cases - childhood and
> adulthood, with reasonably clear delineation between the immature and mature forms. My inclination would therefore be to only
> use Anatomical set for each of these separately, with the same caveats you mention earlier applicable, and not to name sets
> that include members of both as, given the current FMA, the members of Anatomical sets seem to generally be more approximately
> contemporaneous than is the case with primary and secondary teeth.
>
> Would you concur, or do you see benefit in having Anatomical sets that have both as members?
>
> Regards,
> Alan
>
> ps. Barry and I frequently argue about what you would say about this or that issue. It would be great fun to find a time again
> when we could all sit together and have it out :)

> ᅵ


>
>
> Cornelius
>
> On Fri, 9 Dec 2011, Alan Ruttenberg wrote:
>
> One more thing ;-)
> The sets of teeth are unlike some other sets as they gather members that do not necessarily exist at the
> same time. I wonder
> if there is precedent elsewhere in the FMA for that, or whether it might make more sense to stay away from
> that and not create
> as sets dentition (meaning set of all primary and secondary teeth), mandibular dention (also mixes primary
> and secondary
> teeth) or maxilliary dentition (also mixes primary and secondary teeth).
>
> -Alan
>
> On Fri, Dec 9, 2011 at 4:25 AM, <mej...@comcast.net> wrote:

> ᅵ ᅵ ᅵAlan,
>
> ᅵ ᅵ ᅵMy comments in-line ᅵbelow.
>
> ᅵ ᅵ ᅵOnard
>
> _____________________________________________________________________________________________________________________________
> _
> ᅵ ᅵ ᅵFrom: "Alan Ruttenberg" <alanrut...@gmail.com>
> ᅵ ᅵ ᅵTo: "fma-owl-2009" <fma-ow...@googlegroups.com>
> ᅵ ᅵ ᅵCc: "Melissa Haendel" <hae...@ohsu.edu>, "Bill Duncan" <wddu...@gmail.com>, "Carlo Torniai"
> <tor...@ohsu.edu>
> ᅵ ᅵ ᅵSent: Thursday, December 8, 2011 11:32:56 PM
> ᅵ ᅵ ᅵSubject: Anomalous anatomical set members
>
> ᅵ ᅵ ᅵIn reviewing, and then attempting to debug, the representation of teeth, I came across a number of cases that
> seem
> ᅵ ᅵ ᅵto be in error.
>
> ᅵ ᅵ ᅵThe definition of Anatomical set is:
>
> ᅵ ᅵ ᅵ ᅵ ᅵ ᅵmaterial anatomical entity which has as its members the maximal number of anatomical structures of the
> ᅵ ᅵ ᅵ ᅵ ᅵ ᅵsame type.
> ᅵ ᅵ ᅵ ᅵ ᅵ ᅵWhile some of anatomical sets could be regarded as an organ system subvision, e.g set of lumbar
> ᅵ ᅵ ᅵ ᅵ ᅵ ᅵnerves, others do not satisfy one or two defining attributes of organ system subdivision. E.g.
> ᅵ ᅵ ᅵ ᅵ ᅵ ᅵthoracic viscera consists of organs but not belonging to one organ system, dental arcade consists of
> ᅵ ᅵ ᅵ ᅵ ᅵ ᅵsimilar organs but they are not connected.

> ï¿œand 'Primary dentition' is_a 'Dentition'


>
> and the members of 'Maxillary dentition' are all secondary teeth.
>
> OM: Using the frame-based system and the "single inheritance" principle posed some limitations to the
> representation.
> Dentition is a good example.
>
> Ideally we would like to declare in is_a hierarchy:
>
> Dentition

> ᅵ ᅵ ᅵPrimary dentition
> ᅵ ᅵ ᅵ ᅵ ᅵ Primary maxillary dentition
> ᅵ ᅵ ᅵ ᅵ ᅵ Primary mandibular dention
> ᅵ ᅵ ᅵSecondary dentition
> ᅵ ᅵ ᅵ ᅵ ᅵ Secondary maxillary dentition
> ᅵ ᅵ ᅵ ᅵ ᅵ Secondary mandibular dentition


>
> As well as...
>
> Maxillary dentition

> ᅵ ᅵ Primary maxillary dentition
> ᅵ ᅵ Secondary maxillary dentition
>
> Mandibular dentition
> ᅵ ᅵ Primary mandibular dention
> ᅵ ᅵ Secondary mandibular dentition

> be related by ï¿œbounded_by, as is documented in the papers and as occurs elsewhere in FMA.

Chris Mungall

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Dec 9, 2011, 6:07:02 PM12/9/11
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On Dec 9, 2011, at 7:37 AM, Alan Ruttenberg wrote:

OM: Using the frame-based system and the "single inheritance" principle posed some limitations to the representation. Dentition is a good example.

It's potentially the single inheritance, not the frame system.

Yes, and there are unfortunately many problem cases like this where SI has been adhered to in too rigid a fashion.

I think there's been a lot of confusion about SI vs MI. What we all generally agree on is that asserted SI plus inferred MI is a good thing.

I would go further - the _worst_ of all worlds is the combination of:

* pure SI
* large numbers of compositional classes
* no mechanism for inferring the full polyhierarchy

Unfortunately the FMA, in it's currently released forms, falls into this category. The consequence is that there are many is_a links missing in FMA between compositional classes. This confuses biologists and results in false negatives when FMA is used for querying.

The situation is easily fixed by having equivalence axioms for the compositional classes. However, as I understand this isn't possible in the legacy frame system that FMA uses. In my opinion moving away from this system (e.g. to something OWL-based) is high priority for the FMA.

An alternative solution would be to have the equivalence axions maintained in a separate OWL ontology that imports an automated OWL translation of the core FMA. Then the official releases of the FMA in OWL could be pre-reasoned and include the complete polyhierarchy.

However you choose to implement it, I would say it's high priority.

In the absence of any such solution, a way to mitigate the problem would be to release an FMA-core that has fewer pre-coordinated compositional classes. This will mitigate, though not solve the problem. I think a lot of your users might like to see this in any case.

Alan Ruttenberg

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Dec 13, 2011, 1:08:29 PM12/13/11
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On Fri, Dec 9, 2011 at 4:25 AM, <mej...@comcast.net> wrote:
> OM: That indeed is not right. I think the original intent was to represent
> the surface layer (3-D structure) but in the process they were classified as
> surfaces (2-D). I will look into this and apply the corrections.

I think that while the 2d surfaces may perhaps be useful in some
contexts, I anticipate the 3d surfaces (and in general the
constitutional parts) of each tooth will be helpful to have explicitly
represented, as dental information systems do refer to damage and
restorations to such parts of specific teeth.

It has been raised by a colleague at the dental school that in
addition it may be of benefit to represent those anatomical sites in
which the teeth place, as they are also referred to (as when there is
such a site without a tooth occupying it, and when work is done to
place a tooth in such a site).

Thanks,
Alan

Alan Ruttenberg

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Dec 13, 2011, 1:15:27 PM12/13/11
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On Fri, Dec 9, 2011 at 2:41 PM, <mej...@comcast.net> wrote:
> Right. My point is that the definitions disallows members of anatomical sets
> being other anatomical sets(many of the cases listed) or things that are not
> anatomical structures, such as blood:
>
> 'Hematopoietic system'(FMA_9667) has member 'Portion of blood'(FMA_9670)
> which is not anatomical structure
>
>
> OM: The definition of anatomical set does not disallow body substances, that
> why we have the class "Hematopoietic system".
> We also have sets of immaterial anatomical entities, such as "Set of
> subarachnoid sulci" and "Set of external nares".

The definition of Anatomical set as provided by the FMA is:

"material anatomical entity which has as its members the maximal
number of anatomical structures of the same type."

As I read the current FMA, portion of body substance, being a sibling
of Anatomical set, is disjoint from it. So the definition contradicts
the assertion. I am advocating that one of them be changed so that
there is no longer a contradiction.

I would also suggest that the definition be changed to not say
anything about the "maximal number", as this raises issues regarding
time. Instead, push any kind of such maximality down to the particular
terms. For example, the term "dentition" could be defined as being the
set of all the teeth that are present at any time, if desired.

-Alan

Alan Ruttenberg

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Dec 13, 2011, 1:38:36 PM12/13/11
to fma-ow...@googlegroups.com
> On Fri, Dec 9, 2011 at 1:32 PM, mej...@u.washington.edu
> <mej...@u.washington.edu> wrote:
>>
>> Alan,
>>
>> The class "Dentition" does not have both primary and secondary teeth as
>> members but rather it has subtypes primary and secondary. The members of
>> class "Dentition" are maxillary dentition and mandibular dentition, and the
>> subtype of "Dentition", "Primary dentition", has members primary maxillary
>> and primary mandibular sets (same rationale for the secondary dentition).
>
>
> Yes. But I think that's wrong. If Dentition has members and subclasses, then
> instances of the subclasses also have those members= by inheritance.
> As maxillary dentition would include both primary and secondary teeth, the
> inheritance would lead to an incorrect membership for Primary dentition (and
> secondary dentition).
>
> OM: I'm not quite sure I follow you but consider these:
>

Note we are going to stumble on words (and perhaps already have) by
using "members" to both name instances of the class, for members of a
set (a particular). In the following I will rename to "instance" uses
of "member" that I think you meant to mean instance of class. Please
check and see I got your sense correctly, or correct?

> Dentition is  a class whose members consist only of teeth, without specifying which particular set of teeth.

Dentition is an Anatomical set whose members are only teeth.

> Entire dentition is a class whose members include all kinds of teeth,

(see below re: discussion with Cornelius)

> primary and secondary.
> Primary dentition is a subclass of 'dentition' which specifies the
> membership only to include primary teeth.

Primary dentition is a dentition, all of whose members are all (all
extant?) primary teeth
Secondary dentition is a dentition, all of whose members are (all
extant?) secondary teeth

> Maxillary dentition is a subclass of 'dentition' which specifies the membership only to include teeth attached to the maxillae, without specifying whether they are primary or secondary.

Maxillary dentition is a dentition, all of whose members are attached
to the maxillae.

> Entire maxillary dentition is a subclass of 'maxillary dentition' which specifies the membership to include all kinds of teeth attached to the maxillae.

Given the discussion with Cornelius I don't think we should have this
set. It would make sense, however to have a class

You might want
Maxillary tooth - a tooth that is attached to the maxillae.
(in the site formulation it would be a tooth that occupies a site
hosted by the maxillae)

> Primary maxillary dentition is a subclass of 'maxillary dentition' which
> specifies the membership only to include primary teeth attached to the
> maxillae.

Primary maxillary dentition is a maxillary dentition all of whose
members are primary teeth.

I think we also want (looking at
http://en.wikipedia.org/wiki/Tooth_development for a reasonable
discriminator)
(but note this would raise multiple inheritance issues with maxillary
tooth, above)

Primary tooth
A tooth whose initial calcification is completed in-utero.

Secondary tooth
A tooth whose initial calcification is completed after birth.

There is a minor twist, also mentioned by my Dental School colleague.
It is occurs not so unoften that a developmentally primary tooth is
classified as a secondary tooth later in life if a corresponding
secondary tooth does not develop to push the primary tooth out. A
definition of primary and secondary based on site would be able to
avoid this problem. Instead we would define primary tooth sites and
secondary tooth sites, then primary and secondary teeth as those that
eventually occupy those sites. This would also require that primary
and secondary tooth not be disjoint (since some primary teeth could
transform (in the BFO relations sense) into secondary teeth.

-Alan

Todd Detwiler

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Dec 13, 2011, 1:38:30 PM12/13/11
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Alan, where are you getting this definition of Anatomical set? I have looked in the live FMA, the last release version of the FMA (v3.2) and the version before that (from early 2010, v3.1). All have the following definition for Anatomical set:

"Material anatomical entity which consists of the maximum number of discontinuous members of the same class. Examples: set of cranial nerves, ventral branches of aorta, set of mammary arteries, thoracic viscera, dental arcade."

It does not say that the members of the set must be from the class Anatomical structure.

Todd
Landon Todd Detwiler
Structural Informatics Group (SIG)
University of Washington

mej...@comcast.net

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From: "Alan Ruttenberg" <alanrut...@gmail.com>
To: fma-ow...@googlegroups.com
Sent: Tuesday, December 13, 2011 10:08:29 AM

Subject: Re: Anomalous anatomical set members

On Fri, Dec 9, 2011 at 4:25 AM,  <mej...@comcast.net> wrote:
> OM: That indeed is not right. I think the original intent was to represent
> the surface layer (3-D structure) but in the process they were classified as
> surfaces (2-D). I will look into this and apply the corrections.

I think that while the 2d surfaces may perhaps be useful in some
contexts, I anticipate the 3d surfaces (and in general the
constitutional parts) of each tooth will be helpful to have explicitly
represented, as dental information systems do refer to damage and
restorations to such parts of specific teeth.

OM: I agree. I will look into this.


It has been raised by a colleague at the dental school that in
addition it may be of benefit to represent those anatomical sites in
which the teeth place, as they are also referred to (as when there is
such a site without a tooth occupying it, and when work is done to
place a tooth in such a site).

OM: We do have "Alveolar compartment"  and representation is carried out to the specific tooth involved, such as "Alveolar compartment in tooth socket 9" (syn: Alveolar compartment in socket for left upper central secondary incisor tooth). The cavity or space that contains the compartment is called "Tooth socket" (e.g. Tooth socket 9 or Socket for left upper central secondary incisor tooth). The alveolar compartment has parts, root of tooth, periodontal ligament and associated neural and vascular networks. So if the tooth is missing, one can create a class called "Adental alveolar compartment 9" (I'm making up the "adental" term, the dental experts may have a better term) which consists of the same parts minus the tooth (root of tooth).




Thanks,
Alan

Chris Mungall

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Dec 13, 2011, 3:07:49 PM12/13/11
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Are these definitions being coordinated with CARO?

I don't remember the exact reasons we don't have anatomical set in CARO.

In the original CARO, which was based heavily on the FMA, we had:

  is_a CARO:0000006 ! material anatomical entity [DEF: "Anatomical entity that has mass."]
   is_a CARO:0000003 ! anatomical structure [DEF: "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome."]
    is_a CARO:0000054 ! anatomical group [DEF: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue."]
     is_a CARO:0000011 ! anatomical system [DEF: "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity."]
     is_a CARO:0000041 ! anatomical cluster  [DEF: "Anatomical group that has its parts adjacent to one another."]

Dentition would seem to fit 'anatomical cluster' - unless we consider a child who has a mixed dentition, consisting of a mixture of primary dentition, secondary dentition, and sets of unerupted teeth (maybe this isn't "canonical")

Chris Mungall

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Dec 13, 2011, 3:28:15 PM12/13/11
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The naming in the FMA is a little confusing:

 / FMA:62955 ! Anatomical entity
  is_a FMA:61775 ! Physical anatomical entity
   is_a FMA:67112 ! Immaterial anatomical entity
    is_a FMA:71917 ! Set of immaterial anatomical entities ***
     is_a FMA:71918 ! Set of anatomical spaces
      is_a FMA:76576 ! Set of cavities
   is_a FMA:67165 ! Material anatomical entity
    is_a FMA:55652 ! Anatomical set *** 
 
"anatomical set" should be renamed "set of material anatomical entities".

You could introduce "anatomical set" as a different class that is a set of material or immaterial entities, but this would go against the rigid SI principle in the FMA.

Alan Ruttenberg

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Dec 13, 2011, 3:47:07 PM12/13/11
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On Tue, Dec 13, 2011 at 1:38 PM, Todd Detwiler <d...@u.washington.edu> wrote:
> Alan, where are you getting this definition of Anatomical set? I have looked
> in the live FMA, the last release version of the FMA (v3.2) and the version
> before that (from early 2010, v3.1). All have the following definition for
> Anatomical set:
>
> "Material anatomical entity which consists of the maximum number of
> discontinuous members of the same class. Examples: set of cranial nerves,
> ventral branches of aorta, set of mammary arteries, thoracic viscera, dental
> arcade."

I'll check my version. I see that the FMAE has the version you cite,
which I'm happy to substitute.
It too is flawed, because the constraint "being members of the same
class" is effectively always true for anything, since everything is a
n instance of Anatomical entity. So you might as well leave that out.
Indeed I see that "Sets of parts of human body" is a subclass, which
makes the point.

-Alan

Alan Ruttenberg

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Dec 13, 2011, 3:53:32 PM12/13/11
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On Tue, Dec 13, 2011 at 3:07 PM, Chris Mungall <cjmu...@lbl.gov> wrote:
>
> Are these definitions being coordinated with CARO?
>
> I don't remember the exact reasons we don't have anatomical set in CARO.
> In the original CARO, which was based heavily on the FMA, we had:
>
>   is_a CARO:0000006 ! material anatomical entity [DEF: "Anatomical entity
> that has mass."]
>    is_a CARO:0000003 ! anatomical structure [DEF: "Material anatomical
> entity that has inherent 3D shape and is generated by coordinated expression
> of the organism's own genome."]
>     is_a CARO:0000054 ! anatomical group [DEF: "Anatomical structure
> consisting of at least two non-overlapping organs, multi-tissue aggregates
> or portion of tissues or cells of different types that does not constitute
> an organism, organ, multi-tissue aggregate, or portion of tissue."]

I'm not sure what case is covered by cells of different types as
opposed to tissues. Is there a collection of cells of different types
that is not an organ, multi-tissue aggregate or portion of tissue, and
yet still has "inherent 3D shape and is generated by coordinated
expression of the organism's own genome"?

>      is_a CARO:0000011 ! anatomical system [DEF: "Anatomical group that is
> has as its parts distinct anatomical structures interconnected by anatomical
> structures at a lower level of granularity."]
>      is_a CARO:0000041 ! anatomical cluster  [DEF: "Anatomical group that
> has its parts adjacent to one another."]
>
> Dentition would seem to fit 'anatomical cluster' - unless we consider a
> child who has a mixed dentition, consisting of a mixture of primary
> dentition, secondary dentition, and sets of unerupted teeth (maybe this
> isn't "canonical")

Teeth aren't necessarily adjacent (at least in the common sense),
though I see the RO sense is simply nearby "in spatial proximity".
Since the mouth can open quite wide it's not clear they would be
considered adjacent in even that sense.

FMA has both Anatomical Set as well as Anatomical Structure, BTW.

Ii haven't been coordinating with CARO but will make an effort to do
so in the subset of terms I extract to represent teeth.

-Alan

Alan Ruttenberg

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Dec 13, 2011, 6:33:21 PM12/13/11
to fma-ow...@googlegroups.com
OK, I tracked this down.

The definition is as you say. The "documentation" is:

"OM def (1.2.2007): material anatomical entity which has as


its members the maximal number of anatomical structures of the same

type.nn10.04.01: While some of anatomical sets could be regarded as an


organ system subvision, e.g set of lumbar nerves, others do not
satisfy one or two defining attributes of organ system subdivision.
E.g. thoracic viscera consists of organs but not belonging to one
organ system, dental arcade consists of similar organs but they are

not connected.")

So what is the status of the documentation slot value?

-Alan

On Tue, Dec 13, 2011 at 1:38 PM, Todd Detwiler <d...@u.washington.edu> wrote:

ro...@u.washington.edu

unread,
Dec 13, 2011, 8:17:45 PM12/13/11
to fma-ow...@googlegroups.com, Cornelius Rosse
I feel that if CARO adopts FMA definitions, those definitions in CARO should indicate that they are derived from the FMA, as is the case with SNOMED for example.

Cornelius

On Tue, 13 Dec 2011, Chris Mungall wrote:

>
> Are these definitions being coordinated with CARO?
>
> I don't remember the exact reasons we don't have anatomical set in CARO.
>
> In the original CARO, which was based heavily on the FMA, we had:
>

> ᅵ is_a CARO:0000006 ! material anatomical entity [DEF: "Anatomical entity that has mass."]
> ᅵ ᅵis_a CARO:0000003 ! anatomical structure [DEF: "Material anatomical entity that has inherent 3D shape and is generated by


> coordinated expression of the organism's own genome."]

> ᅵ ᅵ is_a CARO:0000054 ! anatomical group [DEF: "Anatomical structure consisting of at least two non-overlapping organs,


> multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ,
> multi-tissue aggregate, or portion of tissue."]

> ᅵ ᅵ ᅵis_a CARO:0000011 ! anatomical system [DEF: "Anatomical group that is has as its parts distinct anatomical structures


> interconnected by anatomical structures at a lower level of granularity."]

> ᅵ ᅵ ᅵis_a CARO:0000041 ! anatomical cluster ᅵ[DEF: "Anatomical group that has its parts adjacent to one another."]

Alan Ruttenberg

unread,
Dec 14, 2011, 9:56:27 AM12/14/11
to fma-ow...@googlegroups.com
Onard responds saying it is more about provenance and history and as
such I would map it to IAO's editor note.

On Tue, Dec 13, 2011 at 6:33 PM, Alan Ruttenberg
<alanrut...@gmail.com> wrote:
> OK, I tracked this down.
>
> The definition is as you say. The "documentation" is:
>
>           "OM def (1.2.2007): material anatomical entity which has as
> its members the maximal number of anatomical structures of the same
> type.nn10.04.01: While some of anatomical sets could be regarded as an
> organ system subvision, e.g set of lumbar nerves, others do not
> satisfy one or two defining attributes of organ system subdivision.
> E.g. thoracic viscera consists of organs but not belonging to one
> organ system, dental arcade consists of similar organs but they are
> not connected.")
>
> So what is the status of the documentation slot value?


Onard

Alan Ruttenberg

unread,
Dec 14, 2011, 10:00:43 AM12/14/11
to David Osumi-Sutherland, fma-ow...@googlegroups.com, Melissa Haendel
On Wed, Dec 14, 2011 at 4:50 AM, David Osumi-Sutherland
<dj...@gen.cam.ac.uk> wrote:
> Fabian and I both objected to 'anatomical set' in CARO1, as its main use seemed to be to duplicate classification as partonomy. Taken to the extreme, you could make such set terms for every class (type) in an ontology.

Yup. I think I vaguely get why in some cases these terms are
desirable, but it would be better to hear from Onard/Cornelius about
what their intent and goal was in introducing these terms. They also
seem to prone to these inheritance issues (I'll produce a list soon) -
general case

class A
class B
B subclass of A
member assertions on A that are false for B.

Anyways, I want to be faithful to FMA as much as I can where it makes
sense, so my preference is that we reach some consensus on how to
handle these terms and then all of us (FMA included) adopt it.

-Alan
-Alan


>
> I'm not sure why you would want to have:
> incisor is_a tooth
> AND
> incisor part_of some 'set of teeth'
>
> Bur if you do have both, you need some way to infer the second from the first or the two will go out a sync.
>
> 'anatomical group' is needed for cases where an anatomical entity is made up of disconnected parts of various classes.  The immune system is a good example.
>
> In some cases the parts are in close proximity. In those cases 'anatomical cluster' seems appropriate to me.
>
> CARO1 didn't do a good job of making these distinctions.
>
> Note, I have never been entirely comfortable with 'anatomical cluster' as a classification for joint as, AFAIK, the various parts of joints are connected to each other.

mej...@u.washington.edu

unread,
Dec 14, 2011, 11:21:27 AM12/14/11
to fma-ow...@googlegroups.com, David Osumi-Sutherland, Melissa Haendel


On Wed, 14 Dec 2011, Alan Ruttenberg wrote:

> On Wed, Dec 14, 2011 at 4:50 AM, David Osumi-Sutherland
> <dj...@gen.cam.ac.uk> wrote:
>> Fabian and I both objected to 'anatomical set' in CARO1, as its main use seemed to be to duplicate classification as partonomy. Taken to the extreme, you could make such set terms for every class (type) in an ontology.

I vaguely remember what Fabian objected to. I had a number of discussions with him but we never had a final agreement.


>
> Yup. I think I vaguely get why in some cases these terms are
> desirable, but it would be better to hear from Onard/Cornelius about
> what their intent and goal was in introducing these terms. They also
> seem to prone to these inheritance issues (I'll produce a list soon) -
> general case
>

There are references to groups of anatomical entities in anatomical discourse. Some other connected (anatomical cluster), e.g. root of lung and some are not (anatomical set), e.g. dentition (set of teeth and nothing else, ergo separate, independent structures taken as a set). The two groups are separated by the differentia/property "connectivity", hence are represented as separate classes/types. Cornelius may have other opinion.


> class A
> class B
> B subclass of A
> member assertions on A that are false for B.

What's the example?

>
> Anyways, I want to be faithful to FMA as much as I can where it makes
> sense, so my preference is that we reach some consensus on how to
> handle these terms and then all of us (FMA included) adopt it.
>
> -Alan
> -Alan
>
>
>>
>> I'm not sure why you would want to have:
>> incisor is_a tooth
>> AND
>> incisor part_of some 'set of teeth'

We don't have the latter relationship in the FMA unless Alan's program indirectly infers that. In the FMA the actual membership declared includes only the individual teeth (by transitivity). View the part hierarchy in the FME:

Dentition (part relation)
Maxillary dentition
Left upper third secondary molar tooth
Right upper third secondary molar tooth
etc.,
Mandibular dentition
Left lower third secondary molar tooth
Right lower third secondary molar tooth
etc.


>>
>> Bur if you do have both, you need some way to infer the second from the first or the two will go out a sync.
>>

>> 'anatomical group' is needed for cases where an anatomical entity is made up of disconnected parts of various classes. ï¿œThe immune system is a good example.

Exactly, the immune system is an anatomical set, with discontinuous parts.


>>
>> In some cases the parts are in close proximity. In those cases 'anatomical cluster' seems appropriate to me.

Proximity but not connected is also an anatomical set.

Anatomical cluster has parts connected, such as the joint.

>>
>> CARO1 didn't do a good job of making these distinctions.

We elaborated on the distinction in the FMA but I'm still not clear what the objection is. I would certainly entertain a better representation that captures the distinctions.

>>
>> Note, I have never been entirely comfortable with 'anatomical cluster' as a classification for joint as, AFAIK, the various parts of joints are connected to each other.


>>
>>
>> On 13 Dec 2011, at 20:53, Alan Ruttenberg <alanrut...@gmail.com> wrote:
>>
>>> On Tue, Dec 13, 2011 at 3:07 PM, Chris Mungall <cjmu...@lbl.gov> wrote:
>>>>
>>>> Are these definitions being coordinated with CARO?
>>>>
>>>> I don't remember the exact reasons we don't have anatomical set in CARO.
>>>> In the original CARO, which was based heavily on the FMA, we had:
>>>>

>>>> ᅵ is_a CARO:0000006 ! material anatomical entity [DEF: "Anatomical entity
>>>> that has mass."]
>>>> ᅵ ᅵis_a CARO:0000003 ! anatomical structure [DEF: "Material anatomical


>>>> entity that has inherent 3D shape and is generated by coordinated expression
>>>> of the organism's own genome.&