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Re: SenseLab Ontology

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Fri, 6 Apr 2007 00:14:29 -0400
Message-Id: <AB17B40A-6972-420F-A21A-6A38245D6C5D@gmail.com>
Cc: public-semweb-lifesci@w3.org
To: kc28 Cheung <kei.cheung@yale.edu>, Matthias Samwald <samwald@gmx.at>

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.

  - 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 Friday, 6 April 2007 04:15:13 GMT

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