SenseLab Ontology

Hi,

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 under developing.  The new version of the NeuronDB OWL
ontology 
and the mapping file is available at:

http://neurowe
b.med.yale.edu/senselab/

Best,

-Kei

(PS: Matthias Samwald just joined our SenseLab team for a
3-month 
internship.)

Hi Alan,

Thanks for your comments, many of the things you mentioned
are already on my to-do list. Of course, some things (like
drastic changes in nomenclature) have to be coordinated with
the core SenseLab working group. Furthermore, some of the
constructs are the result of an automated export. We don't
want to make transient changes to the ontology that will be
lost when the next automated export is made -- we will make
these changes, but need some more time to implement them.

It seems the version that was online until now was not the
very latest version of NeuronDB OWL. I have corrected that,
and some of the things you pointed out are already corrected
in the version that is now online.

>     - Similarly Transmittors. Ions > CO

CO is commonly seen as a gaseous transmitter, not an ion.


>   - 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.

With CL you mean the OBO Celltype ontology?


>   - Some of the Brain Regions, don't seem to be, e.g.
retina,

This is a bit controversial. Many people see the retina and
the optical tract as parts of the brain because of their
ontogenesis. On the other hand, braininfo/neuronames makes
the clear statement that the retina is not part of the
brain.

> 
>    - Neuron can be below CARO_0000013 (cell)
> 
>    - Cell compartment can be below CARO_0000014 (cell
component)

I will include this into the mapping file for now. Maybe we
can integrate some selected classes of CARO into the
SenseLab OWL file (without importing the whole ontology).
Needs discussion.

 
>     - Don't believe you want or need the class
"neuron  
> property" (neuron receptor is a neuron property.
not)

This is also on my todo list, but again, it requires
discussion. I would really prefer to see this as a parthood
relation, but there might be arguments for viewing this as a
'property' or a 'quality' of a neuron. Of course, in this
case it would be problematic to represent the 'receptors' as
physical structures.

 
>     - I think it would be better  to use OBO RO for the
relations,  
> rather than the unofficial ifomis version.

I hope there will be an agreement on a single namespace
soon. For example, Birnlex uses the ifomis namespace, while
John's OWL representation of the Allan Brain Atlas uses the
OBO namespace.
As the meaning of the properties are not confined to the
biological domain in any way, I would prefer a namespace
that does not have biological connotations (for
psychological reasons). Therefore, I prefer the ifomis
namespace at the moment. I guess it would be best for the
Relation ontology (and probably also the BFO ontology) to
use a PURL namespace that is as neutral as possible.
However, this should probably be discussed on other mailing
lists.

cheers,
Matthias Samwald







.
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On 4/6/07, Alan Ruttenberg <alanruttenberggmail.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://neurowe
b.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
>
>
>

On Apr 7, 2007, at 10:17 PM, Huajun Chen  Zhejiang
University wrote:

>>  - 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?

I don't know. I guess I am first concerned about mistakes
here. The  
two things that seemed odd were that the page would show
structure  
the database doesn't have (I assumed that the pages were
generated  
from the database), and that the page didn't agree with the
database  
(at least as reflected by the OWL) wrt which neuron cells
were which,  
which would seem to indicate that there is an error on the
page, or  
in the database.

If the distinction between principal and interneuron isn't
important  
then perhaps it shouldn't appear in the ontology.

-Alan

On 4/7/07, Alan Ruttenberg <alanruttenberggmail.com> wrote:
> On Apr 7, 2007, at 10:17 PM, Huajun Chen  Zhejiang
University wrote:
>
> >>  - 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?
>
> I don't know. I guess I am first concerned about
mistakes here. The
> two things that seemed odd were that the page would
show structure
> the database doesn't have (I assumed that the pages
were generated
> from the database), and that the page didn't agree with
the database
> (at least as reflected by the OWL) wrt which neuron
cells were which,
> which would seem to indicate that there is an error on
the page, or
> in the database.

Oh, that's a fault of my program, it does not recognize
interneuron
and pricipal neuron when translating. Since the total number
of
interneuron is very small, I manually modify this part after
the
transformation.  That's gonna be ok in the next version.

>
> If the distinction between principal and interneuron
isn't important
> then perhaps it shouldn't appear in the ontology.
>
> -Alan
>
>