Re: [biotop] A new release of BioTop domain top ontology for Biomedicine
Chris Mungall
On Feb 15, 2007, at 5:11 AM, Robert Hoehndorf wrote:
>
>>>>>> "SS" == Stefan Schulz <ste...@gmail.com> writes:
>
> Hi,
>
> SS> a new OWL-DL version of the Biomedical Domain Top Ontology
> SS> ** BioTop **
> SS> is available for download at
> SS> http://www.ifomis.uni-saarland.de/biotop/
>
> I have some questions and remarks.
> You use the class Atom, with six specific subclass. Why choose these
> six?
It seems fine for illustrative purposes; but it may be a good idea to
separate out the illustrative part from the ontology that is intended
to be imported in real settings
> Would it not make more sense to import a period table OWL-file at
> this point, like http://www.daml.org/2003/01/periodictable/ ?
> The same could be done for amino acids, importing
> http://www.co-ode.org/ontologies/amino-acid/2005/10/11/amino-acid.owl
Or CHEBI (though CHEBI is a bit problematic here, I'm sure they'd be
willing to work towards a common solution)
> For Tissue, the definition may be extended. The cells within the
> tissue are probably connected, and somehow have the same function.
> Why do you need the hasGrain only EntireMolecularEntity in the
> definition?
Note CARO has just been released
http://www.bioontology.org/wiki/index.php/CARO:Main_Page#CARO
CARO is an upper level ontology for anatomical entities, a
collaboration between model organism developmental biologists, the
FMA and formal ontologists
> Having a Virus as a sublcass of Organism seems arguable, at least. I
> am certain there are many biologists who do not agree with this
> definition.
biotop should be bold and define organism. I think having at least
one cell would be sensible. If viruses are organisms, how about
transposons?
> I do not like the fact that almost every class is modelled twice,
> i.e., the whole hierarchy is mirrored under ObjectAggregate. It seems
> unnecessary, because whenever needed, it is simple to define these
> specific aggregates. And it increases classification time a lot.
there is a case for some pre-coordination here, eg bacterial
colonies, but it's hard to say where to draw the line. duplicating
all the ncbi taxonomy inside biotop would be a little mad
> What is an Object? And why are Atoms not a subclass of Object?
>
> Biological process could need a definition. Text-definition is a
> process specific for biological systems. Maybe introducing a
> biological system could help in defining these processes.
>
> CellInVivo is defined as subclass of Cell and subclass of (Organism or
> hasProperPart some Organism). It should probably be properPartOf some
> Organism.
cell in vivo seems like a relic of the obo cell ontology, which is
being revised anyway
> My last remark is related to Sequences, but you should probably
> consult Chris Mungall for more specific information. Defining it as
> something which consists of some and only Deoxyribonucleotides seems
> to ignore the "sequence" of the sequence. After all, it could be a
> collection of these molecules that satisfies this definition.
yep
> I also
> believe that the fact that a sequence is a subclass of a molecule is
> not agreed upon. There are biological sequences without
> instances.
not sure about this.
> There may be properties that the sequences have, that
> cannot be derived from the molecules alone. There may be two different
> molecules that have the same sequence.
> I think that with a lot of care all these properties of sequences may
> at some point be reduced to properties of molecules. But it requires
> some effort, esp. for a bioinformatician, who is used to work with
> abstract sequences, to make all this explicit.
we should have a better handle on these issues post-March
> Rob.
>
> >
>