Download Anatomical structure - Structural Informatics Group

To:
Members of the SOFG-Definitions Group
From:
Cornelius
Subject:
Definition of Anatomical Structure
Date:
January 24, 2005
Comments: February 7, 2005 [cjm]
Comments: February 15, 2005 [mah]
Comments: February 15, 2005 [sel]
The validity of all the FMA definitions relating to cell and cell parts depends on the
definition of the genus of Cell: Anatomical structure. All the entities we have to define in
our working group fall into subclasses of Anatomical structure; i.e., they are all
anatomical structures. This term is used with many different meanings in traditional and
in silico source; e.g., some of these sources regard a space such as the pleural cavity, as
an anatomical structure. Therefore, I feel it is important that we should be clear at the
outset about what we mean by this term and we should be in agreement. The FMA
definition is:
Anatomical structure
Material physical anatomical entity which has inherent 3D shape; is generated by coordinated
expression of the organism's own structural genes; its parts are spatially related to one another in
patterns determined by coordinated gene expression. Examples: heart, right ventricle, mitral
valve, myocardium, endothelium, lymphocyte, fibroblast, thorax, cardiovascular system,
hemoglobin, T cell receptor, gene.
I don’t think gene is an example of anatomical structure! Perhaps a gene product such a protein
or RNA molecule. I completely agree with Chris on this one. There are certainly regions on a
chromosome that are inherited, and are associated with certain physical products in the cell
(transcripts and proteins). The extent of these regions however is not clear-cut however, and I
think it better to stay with concrete physical entities for which the boundaries are inarguable.
One of the tenets of FMA is the strict organizing relationships. It would be good to state that here.
I’m also wondering if you might want to (somewhere) mention the cell ontology. At least to
provide the rationale for including everything from the gross morphological level to the molecular.
Comment:
1. Let us disregard the genus [Material physical anatomical entity, which means that
the entities in this class have volume and mass, unlike spaces, which have volume but no
mass] and deal with each of the differentia:
a. has inherent 3D shape. Unlike liquids [blood, urine], which also have
volume and mass, anatomical structures are solid/semisolid [gel] objects,
which have their own shape, unlike liquids, which adapt to the shape of
their container.
I’m not quite sure why you have excluded liquids though, Plasma consists of many proteins;
blood contains cells. Surely these are things we would want to include. The biologists I ask here
consider blood, plasma, milk, semen, etc. all as tissues.
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b. is generated by coordinated expression of the organism's own structural
genes. This differentia distinguishes anatomical structures from inanimate
objects [bullets, prostheses] and foreign organisms and their parts
[parasite, transplant] located in an organism. This should lead us to
consider what is the smallest or most primitive object that qualifies as an
anatomical structure, but let us defer that.
Can you define “structural” in the context of genes?
Would we want to exclude a transplanted organ?
Barry has (quite rightly) always argued against circular definitions. The definition above for
“Anatomical structure” includes the adjective “anatomical”. It would be nice to remove this. If we
do, then the definition has to carefully limit the scope, so that things like a bird’s nest, or the by
products of sugar metabolism aren’t included (they are 3-D and physical and the organism
produced them)
c. its parts are spatially related to one another in patterns determined by
coordinated gene expression. This differentia excludes from the class
Anatomical structure a sediment of blood cells, a rouleau, or the “buffy
coat”.
These properties (a-c) are shared by a biological macromolecule, a
mitochondrion, a cell, a tissue, and the other things we have to define. These
entities inherited these properties from their superclass in the taxonomy.
This definition includes molecules, even small molecules, because these
are generated by coordinated gene expression (maybe we have to define
coordinated gene expression?). Is this problematic? Most people would
not think of “arginine” as an anatomical stucture; I don’t see how [c]
would exclude this. Should there be a “minimal granularity” beyond
which it is no longer anatomical?
This definition is dependent on the definition of “gene”. This is
notoriously problematic. Is there a different way to word the definition?
Maybe just changing it to “gene products”. Even then, it seems
problematic. Many structures are formed from a combination of genes and
environment. It would seem odd to include “termite nest” as an anatomical
structure, but I’m not sure what is to stop a machine reasoning otherwise!
(ha-ha, Chris and I were thinking the same thing)
The “own” is problematic in “coordinated expression of the organism’s
own structural genes”. What about maternal effect genes? Yes, I agree.
We must account for maternal effect genes. The egg is a big thing
(usually) and the products from the mother that are in the cytoplasm have
to be accounted for. There are other situations as well
I agree, I think we need to avoid the use of the term “gene.” Let’s think
about our purpose here, which I understand is to generate cross species
definitions for anatomical terms. Do we really want our ontologies to be
populated with genes, proteins, and protein complexes? I too do not think
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of these things as anatomical structures, though they are certainly required
for anatomical structures to develop and be maintained. Perhaps a
definition that limits anatomical structures to be comprised of one or more
cells would work?
2. Such inheritance of attributes [characteristics, properties and differentia] is a
critical requirement that definitions have to meet, if the intent is to construct a
taxonomy or ontology [ultimately]. A dictionary, such as Stedman’s, is not
constrained by such requirements. Unlike dictionary definitions, each of the FMA
definitions on its own is incomplete. It is competed by the definition of each of
the ancestors of any given class in the taxonomy.
3. I realize that you may not want to set such aims for the definitions we have to
generate, since our immediate objective seems to be to reach consensus among
ourselves about the meaning of given terms. I suggest that it would be a mistake
to limit our task in such a way. We should be able to have our cake and eat it.
Yes, let’s have both dictionary and formal defs, but we should be careful to separate
them.
4. Finally, note that Anatomical structure may be a better genus for Cell than “The
smallest unit of living structure”. We may argue about what that smallest structure
might be. But even if we agree, where would we put smallest unit of living structure
in an ontology or taxonomy? Would other classes of the ontology subsume petite,
M, L, XL, XXL sizes of anatomical entities?
What about keeping the def structural; eg “Material physical entity which has inherent
3D shape and is part of (or the whole of) an organism” . Would obviously require precise
definition of organism. (One that takes into account unusual organisms like
dictostelium….).
Anatomy comes from the latin anatomia, meaning dissection; ana=up and tome=a
cutting; cutting up of the body. With this in mind, a definition of anatomical structure
would imply that one could isolate that structure physically on a gross level. Perhaps
subcellular structures, including genes and their products, could be described by
“microscopic anatomical structures” or “subcellular anatomical structures,” which really
comprise a different subject.
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