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RE: NeuronDB RDF and OWL

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Tue, 13 Mar 2007 09:39:09 -0400
Message-ID: <2BF18EC866AF0448816CDB62ADF653810660E8C6@PHSXMB11.partners.org>
To: <samwald@gmx.at>, "Kei Cheung" <kei.cheung@yale.edu>
Cc: <public-semweb-lifesci@w3.org>


Matthias,

These are great suggestions below. I have the following questions/suggestions.

Are the naming suggestions based on aligning to a particular (upper) ontology,
e.g., OBO/BFO/DOLCE?  The reason, I bring this up is that once we start
converting our data sets into RDF, it will be great that we choose node types
and labels from edges in consistently, preferably from the same ontology?

Is it possible that you can start a wiki page, just enumerating these
suggestions? I have a feeling they will become critical when we start merging
the RDF datasets.

Cheers,

---Vipul

=======================================
Vipul Kashyap, Ph.D.
Senior Medical Informatician
Clinical Informatics R&D, Partners HealthCare System
Phone: (781)416-9254
Cell: (617)943-7120
http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik
 
To keep up you need the right answers; to get ahead you need the right questions
---John Browning and Spencer Reiss, Wired 6.04.95
> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-
> request@w3.org] On Behalf Of samwald@gmx.at
> Sent: Tuesday, March 13, 2007 8:48 AM
> To: Kei Cheung; public-semweb-lifesci@w3.org
> Subject: Re: NeuronDB RDF and OWL
> 
> 
> 
> > We just finished exporting the NeuronDB of Senselab into RDF and OWL.
> >
> > http://neuroweb.med.yale.edu/senselab/
> 
> 
> Great!
> 
> Here are some thoughts I had while browsing through the OWL version (I
> post them in public so others do not give you redundant feedback):
> 
> According to the Pellet reasoner, the ontology is fully consistent.
> 
> I guess you plan to change this in the final release anyways, but all the
> classes need to have a value for the rdfs:label property. The URIs are not
> intended to be read by humans, so none of the classes has an actual name
> in the current version of the ontology.
> 
> Assuming that the class names will be identical with the current URIs:
> 
> "Forebrain" should be renamed to "Prosencephalon", to be consistent with
> the naming of the other major brain regions (e.g. "mesencephalon",
> "metencephalon"). Of course, you could also rename the other classes to
> the English trivial names ("midbrain" etc.).
> 
> With the current names of the classes, many of the class-subclass
> relations are in fact whole-part relations (e.g. the ontology states that
> "Vestibular_Organ" is a subclass of "Cochlea", but in fact it is a part of
> the cochlea). If you want to preserve the current class structure, but be
> ontologically consistent, I would suggest to rename such classes from "X"
> to "X or part of X". For example, "Vestibular_Organ" would become
> "Vestibular_Organ_or_part_of_Vestibular_Organ". Now it would be correct to
> state that "Cochlea" is a subclass of
> "Vestibular_Organ_or_part_of_Vestibular_Organ", because the superclass
> includes parts.
> 
> The IDs/names of the subclasses of "Dendritic Compartment" and "Axon"
> could be a little clearer (I assume that d, m and p stand for distal,
> medial and proximal, AH is axon hillock and T is terminal?).
> 
> Some of the subclasses of "Neuron_Receptor" and "Neuron_Transmitter"
> (Neurotransmitter) have names in the plural form (e.g. "Ion_Receptors").
> This should be changed to singular to be consistent with the rest of the
> ontology.
> 
> Using Protege 3.2, I have troubles view the annotations that relate facts
> to individuals belonging to the "Notes" class. Looking at the source, I
> see that rdfs:seeAlso and blank nodes were used. I guess it is Protege's
> fault that these relations are not displayed.
> 
> 
> cheers,
> Matthias Samwald
> 
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Received on Tuesday, 13 March 2007 13:45:01 UTC

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