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Re: SenseLab Ontology

From: Huajun Chen @ Zhejiang University <@>
Date: Sat, 7 Apr 2007 22:17:22 -0400
Message-ID: <cd02451e0704071917o104cbft82a7953119cf9708@mail.gmail.com>
To: "Alan Ruttenberg" <alanruttenberg@gmail.com>
Cc: "Luis Marenco" <luis.marenco@yale.edu>, ernest.llim@yale.edu, public-semweb-lifesci@w3.org

On 4/6/07, Alan Ruttenberg <alanruttenberg@gmail.com> wrote:
>
> On Apr 5, 2007, at 11:59 PM, kc28 wrote:
> > We just finished a round of revision of NeuronDB OWL ontology based
> > on the feedback from people like Matthias, Alan, Bill, ... (thanks
> > to them). We also established mapping to other ontologies like
> > BAMS, Birnlex, BFO, OBI, etc. (thanks to Don for helping to
> > establish mapping of some of the terms). Our ontology development
> > and mapping effort is still underway.  The new version of the
> > NeuronDB OWL ontology and the mapping file is available at: http://
> > neuroweb.med.yale.edu/senselab/
>
> Hi Kei, Matthias,
>
> Great to see the progress on NeuronDB!
>
> Some comments:
>
>    - Review receptor hierarchy. E.g. Zn2+ receptor is an ion
> receptor. Also naming: Zn2+ is easily confused with the ion. In this
> case you mean the receptor. You don't need to change the url if you
> don't want, but and RDF label would be helpful. Another example:
> Muscarinic (receptors) superclass of  M1-M5 receptors. These
> relations are listed as "Receptor" versus "subtype" on e.g. http://
> senselab.med.yale.edu/senselab/NeuronDB/receptors.asp?
> select_receptor=Acetylcholine
>
>    - Similarly Transmittors. Ions > CO
>
>    - Following some other ontologies, you might consider using the
> senselab id to form the URI and use the name in the RDF label. e.g
> http://neuroweb.med.yale.edu/senselab/
> neuron_ontology.owl#Olfactory_bulb_granule_cell
> -> http://neuroweb.med.yale.edu/senselab#NDB_3979
> Depends on which you think will be less subject to revision.
>
>    - At least the currents and the compartments are too difficult to
> understand without a better label or comment.
>    - Some existing labels have superfluous space e.g.
> "               I Na,t
> "
>
>   - It would be nice to be able to link the receptors to their
> proteins and what they sense. Half of this can be done,
> at least for a subset of the terms, by using go terminology; e.g.
> GABA receptor activity GO:0016917. The other half
> by reference to at least the transmitters in NeuronDB, and then those
> to CHEBI, e.g 4-aminobutanoate [CHEBI:30566].
> I'm guessing that this is a couple of hours work. [I notice that the
> genes are at least mentioned on the web pages]
>
>  - similarly it would be nice to link the currents to the ions they
> are currents of. Are the currents hierarchical as well? e.g. is "I A,
> slow" subclass of "I A"
>
>  - Cell types could be linked to/ replaced with CL terms. If the
> terms are not yet in CL, we have an offer from the CL curators to add
> them. I'll send them the list.
>
>  - Dentrite subclass naming: Apical_Dentritic subclas of Dentrite.
> The former sounds like an adjective, the latter a noun. Perhaps
> rename Apical_Dendrite.
>
>  - The layout of http://senselab.med.yale.edu/senselab/NeuronDB/
> ndbRegions.asp?sr=0 suggests that there is some relation between
> principal neurons and interneurons. I don't know the biology here -
> is there? Also, some of the interneurons in that table are principal
> neurons in the ontology.
NeuronDB does contain such kind of information, my programs just did
not retrieve these data.  Is this information essential?


>  - Some of the Brain Regions, don't seem to be, e.g. retina, spinal
> cord, cochlea. A simple solution to this might be to get rid of the
> BrainRegion class, and instead root them below CARO_0000003 (material
> anatomical entity) or below if you feel like expending more effort.
> Rooting below CARO will help with integration efforts, in any case.
>
>   - Neuron can be below CARO_0000013 (cell)
>
>   - Cell compartment can be below CARO_0000014 (cell component)
>
>    - Don't believe you want or need the class "neuron
> property" (neuron receptor is a neuron property. not)
>
>    - Common practice is to use singular for in names of classes
>
>    - I think it would be better  to use OBO RO for the relations,
> rather than the unofficial ifomis version.
>
> Regards,
> Alan
>
>
>
Received on Sunday, 8 April 2007 02:17:25 GMT

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