Re: BioTop
Chris Mungall
Looks good!
Some initial comments:
Peptide: We here use the term peptide in the most general sense, viz.
a oligo or polymer made out of amino acids.
How about: organic molecular entity made of two or more amino acids
DL: OrganicMolecularEntity THAT hasPart min 2 AminoAcid
AminoAcidSequence: subclassof Peptide
Question: what is an example of a peptide that is not an amino acid
sequence
More general question: is a sequence to be distinguished from the
overall molecule? If so, is the difference one of granulairty? Eg is
a sequence an AggregatedOfObjects with some kind of linear
topological relation R such that each member of the mereological sum
is connectedTo max 2 other members? biotop can't seem to make up it's
mind whether to append sequence to the end of labels. Not sure if
this is meaningful
is the division into peptide/oligopeptide/protein established
This definition is wrong
a UniCellularOrganism is a Organism that has a Cellular component and
that has a Cell Membrane component and has a Cytoplasm proper part
and causes YeastCell to be classified as a UniCellularOrganism
"Compound" does not seem like the best label for this:
n non-molecular object which has different parts and which changes
its ontological nature if sub divided
A lot of definitions depend on EntireMolecularEntity:
Separately distinguishable molecular structure, not part of another
molecular structure. Atoms are not considered molecular structures.
The hierarchy of entire entities mirrors the hierarchy of structures
Eg
Class (biotop:MoleculeComplex complete intersectionOf( restriction
(biotop:hasComponent allValuesFrom( biotop:EntireMolecularEntity))
restriction(biotop:hasComponent someValuesFrom
( biotop:EntireMolecularEntity)) ) )
I don't see a def for hasComponent but I presume it is non-reflexive
Chromosomes are molecule complexes (presumably because they are made
from EMEs like histones and DNA molecules.
DNA and RNA molecules are not. Why? are the nucleic acids and sugar
backbone not EMEs? Is it because they are part of the DNA molecule?
Could not the same be said for the components of a chromosome?
On Feb 14, 2007, at 5:03 AM, Stefan Schulz wrote:
>
> Dear colleagues,
>
> a new OWL-DL version of the Biomedical Domain Top Ontology
>
> ** BioTop **
>
> is available for download at
>
> http://www.ifomis.uni-saarland.de/biotop/
>
> If interested, subscribe to bio...@googlegroups.com
>
> Kind regards,
>
> Stefan Schulz, Freiburg University Hospital
> Holger Stenzhorn, Freiburg University Hospital & IFOMIS Saarbrücken
> Elena Beisswanger, Jena University Language & Information Engineering
> (JULIE) Lab
>
> >
>
waku
> a oligo or polymer made out of amino acids.
>
> How about: organic molecular entity made of two or more amino acids
> DL: OrganicMolecularEntity THAT hasPart min 2 AminoAcid
not just any molecular entity made of amino acids; peptide (amide)
bonds are essential.
> AminoAcidSequence: subclassof Peptide
>
> Question: what is an example of a peptide that is not an amino acid
> sequence
the question is what a sequence is. it does not seem correct to me to
say that a sequence of aminoacids is a peptide, or that a peptide is a
sequence of aminoacids.
a peptide is a molecule composed, in a particular way, of aminoacids;
a sequence of aminoacids (or whatever else) is a linear ordering of
those aminoacids (or whatever else).
two distinct peptides are built of distinct aminoacids; two distinct
peptides may have the same sequence of aminoacids. scientists find
the same sequences of nucleotides in the genes of different
indivduals, though they do not find the same nucleotides in those
individuals. (one might either say that they find the same gene in
distinct idividuals, or that they find distinct instances of the same
gene in distinct individuals, depending on how 'gene' is defined --
and this proves very problematic).
the point: neither a peptide is a sequence of aminoacids, nor vice
versa.
>
> More general question: is a sequence to be distinguished from the
> overall molecule? If so, is the difference one of granulairty?
no, it's not granularity. a sequence seems to be an abstract object.
i think sequence should be defined at the level of bfo. the term
'sequence' is very general, and it might be better to use another
term, such as 'biological sequence', with either narrower, or
different (that of an ordered aggregate rather than that of an order)
meaning.
> Eg is
> a sequence an AggregatedOfObjects with some kind of linear
> topological relation R such that each member of the mereological sum
> is connectedTo max 2 other members? biotop can't seem to make up it's
> mind whether to append sequence to the end of labels. Not sure if
> this is meaningful
>
> is the division into peptide/oligopeptide/protein established
only vaguely
>
> This definition is wrong
> a UniCellularOrganism is a Organism that has a Cellular component and
> that has a Cell Membrane component and has a Cytoplasm proper part
> and causes YeastCell to be classified as a UniCellularOrganism
wrong, of course.
there is a need for being able to say that some, but not all, yeast
organisms are unicellular organisms.
with the expressivity of owl, you could achieve this only if you were
more specific and said which yeasts are unicellular and which are not.
> "Compound" does not seem like the best label for this:
> n non-molecular object which has different parts and which changes
> its ontological nature if sub divided
especially that molecular entity is defined as a compound.
'molecular entity' is a misnomer. it seems that it is 'molecule' that
is meant here. i would think of a molecular entity as of an entity
composed of molecules.
this may not be easy, though. consider: "Molecular oxygen: A molecule
that is composed of two oxygen atoms, O2, that has no color, odor, or
taste." (can a single molecule have color?)
>
> A lot of definitions depend on EntireMolecularEntity:
>
> Separately distinguishable molecular structure, not part of another
> molecular structure. Atoms are not considered molecular structures.
> The hierarchy of entire entities mirrors the hierarchy of structures
atoms are not molecular. btw., particles are subatomic entities (in
physics, at least), molecules are superatomic entities; particles
cannot consist of molecules -- molecule complex in biotop is a
particle composed of molecules...
>
> Eg
>
> Class (biotop:MoleculeComplex complete intersectionOf( restriction
> (biotop:hasComponent allValuesFrom( biotop:EntireMolecularEntity))
> restriction(biotop:hasComponent someValuesFrom
> ( biotop:EntireMolecularEntity)) ) )
>
> I don't see a def for hasComponent but I presume it is non-reflexive
then a unicellular organism cannot have a cell as a component (under
the assumption, made in biotop, that a unicellular organism *is* a
cell). if so, there are cellular organisms of which do not have cells
as components.
>
> Chromosomes are molecule complexes (presumably because they are made
> from EMEs like histones and DNA molecules.
>
> DNA and RNA molecules are not. Why? are the nucleic acids and sugar
> backbone not EMEs? Is it because they are part of the DNA molecule?
> Could not the same be said for the components of a chromosome?
the hack is in how the molecules are connected. histones and dna in a
chromosome are not bound covalently.
and simply put: a molecule is not a molecule complex because it is
*one* molecule.