Anomalous anatomical set members (cc)

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Christine Golbreich

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Dec 15, 2011, 5:03:43 AM12/15/11
to fma-ow...@googlegroups.com
De : Christine Golbreich <chg...@wanadoo.fr>
Date : 15 décembre 2011 10:36:31 HNEC
À : mej...@u.washington.edu, ro...@u.washington.edu, Alan Ruttenberg
<alanrut...@gmail.com>
Cc : fma-ow...@googlegroups.com, Stefan DARMONI <Stefan....@chu-rouen.fr>
Objet : Rép : Anomalous anatomical set members

Hi Onard, Cornelius, Alan, Chris and all

First, for those who don't know, there is a FMA temptative ontology in
OWL 2 (cf.
The FMA in OWL 2, C. Golbreich , J. Grosjea, S. J. Darmoni
AIME'11 Proceedings of the 13th conference on Artificial intelligence
in medicine
Springer-Verlag Berlin, Heidelberg ©2011 ISBN: 978-3-642-22217-7
The presented version was achieved early 2010 and corresponds to FMA
3.0. It still needs work to be improved. But I don't have the fundings
and man power for it. Any suggestion is welcome.

Second, I have interrogations about "Anatomical set" and its
subclasses for a long time.

the definition of Anatomical set given in FMA 3.0 is:
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.

In " A reference ontology ...." Rosse & al. 2003 we have
Also problematic are such widely used concepts as viscera, or cranial
nerves, which represent a collection of anatomical structures that are
members of one class. We assign such collections to the class
Anatomical set. The FMA does not allow plural concepts and therefore
the singular concept Set of cranial nerves is en tered as a subclass
of Anatomical set. At the cellular level such a set is Myone, for
example, which is a set of skeletal muscle cells (muscle fibers)
innervated by a single alpha motor neuron. Anatomical sets have
members, rather than parts (e.g., Oculomotor nerve is a member of Set
of cranial nerves).
Members of an anatomical set, as defined in the FMA, are distinct from
elements of a mathematical set in at least two respects:
(1) indirect connections exist between the members, since all
anatomical structures of an organism are interconnected directly or
indirectly (except for those that are surrounded by body sub- stances;
e.g., blood cells afloat in plasma); (2) as a rule, the members are
ordered in accord with genetically determined patterns (e.g., the set
of cranial nerves associ- ated with the brain and the set of ribs
associated with the vertebral column are ordered and their members are
not interchangeable; whereas as far as we know, no such ordered
pattern exists for the disposition of members of a myone within a
muscle fasciculus); and (3) the mem- bers do not define an anatomical
set (which is a class), whereas a mathematical set is defined by its
members.

Despite the above explanation I have difficulties to get the "raison
d'etre" of the Anatomical set and its subclasses, such as the set of
cranial nerves

What is the fundamental difference for instance between the FMA class
'set of cranial nerves' and the class 'cranial nerves'?

I wonder if you would you like in fact to model the different species
of anatomical entities and assert some specific property attached to
such species ?

For example, would it be your intent to distinguish a) Cranial Nerves,
to be used as a class, the class of all cranial nerves and its
subclasses (see below), and b) an individual, the individual
representing the species 'Cranial Nerves' belonging to the
(meta)class of all the Anatomical entities species (currently named
'sets' ?)
If you would want to specify the individual Cranial nerves as species
and express for instance that it is the species of nerves that emerge
directly from the brain, it is possible to make it using OWL 2
metamodelling and attach a property to the individual.
see http://www.w3.org/TR/owl2-new-features/#Simple_metamodeling_capabilities
Eagle, to be used for both a class, the class of all Eagles, and an
individual, the individual representing the species Eagle belonging to
the (meta)class of all plant and animal species

Regards

--
Christine


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