Re: [Fwd: Re: cell types, brain regions mentioned in gensat]

The SenseLab cell type to region mapping will be a really good  
start.  Thank's Kei.

This at least can start to describe what SenseLab has done in this  
area.  This is a high value, expert vetted list.  I believe - however  
- they've done much more than this list - however - re: terms used to  
name cells.  This is why I include Luis Marenco on that email,  
because he knows what SenseLab has beyond what is presented on this  
page.  You will also note this page covers a much shorter list of  
neuronal cell types than what is used in GENSAT - and very very few  
brain regions.

I would also rather point to the other page I created:
	http://esw.w3.org/topic/HCLS/OntologyTaskForce/ 
OboPhenotypeSyntaxExperiment

in regards to expressing the relation between cell type and brain  
region.  It will be much more commensurable with the phenotype  
assertions we are working on - and take much less work to produce  
across a broader scope of brain regions & cell types.

Cheers,
Bill

On Mar 2, 2007, at 1:59 PM, Kei Cheung wrote:

>
>
> From: Kei Cheung <kei.cheung@yale.edu>
> Date: March 2, 2007 1:56:53 PM EST
> To: June Kinoshita <junekino@media.mit.edu>
> Cc: donald.doherty@brainstage.com,  Alan Ruttenberg  
> <alanruttenberg@gmail.com>, Gwen Wong <wonglabow@verizon.net>
> Subject: Re: cell types, brain regions mentioned in gensat
>
>
> Hi June et al.,
>
> I just got back to my office from a meeting, trying to catch up  
> with the emails. Before I go to another meeting, I'd like to  
> suggest the following URL for people to look at:
>
> http://senselab.med.yale.edu/senselab/NeuronDB/ndbRegions.asp?sr=1
>
> Although they are not a comprehensive lists of brain regions and  
> neuron cell types for vetebrates, it could be a start (with  
> mappings between the two lists).
>
> By reading the AD/PD use case, one of the questions has to do with  
> what genes are expressed in what regions of the brain (if such gene  
> expressions are localized to certain brain regions). I wonder what  
> Alan's currently working on can help address this type of question  
> (even though the kind of gene expression data is for the mouse --  
> perhaps we can find homologous genes for human). Also, I'd  
> encourage people to take look at what Bill Bug's Wiki page:
>
> http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology/ 
> SeedOntologyDetailedFollowup#preview
>
> On that page, it describes the following OWL axiom example:
>
> *EquivalentClass*(CerebellarPurkinjeCell *intersectionOf* 
> (PurkinjeNeuron, *Restriction*(locatedInBrainRegion *allValuesFrom* 
> (Cerebellum)))
>
> We can use a similar axiom to define the localization of a certain  
> type of neuron cell type (CA1 pyramidal neuron) in a particular  
> brain region (e.g., hippocampus). Due to my limited knowledge of  
> OWL, can this type of axioms/rules be parameterized (e.g., cell  
> type and brain region can be treated as variables)?
>
> Finally, due to the lack of annotation or lack of standard  
> annotation, it's difficult for users/neuroscientists or web agents  
> to find relevant sources (e.g., microarray databases, brain  
> altases, ...) that may contain the type of data they want (e.g.,  
> what genes are significantly expressed in what brain regions). The  
> type of shallow annotation (Alan mentioned in a previous email)  
> could at least help users identify potentially relevant resources  
> even the the data provided by those sources are not in RDF/OWL  
> format yet. For annotation, it might be helpful to include a little  
> bit more description of the experiment such as species of the  
> subject(s) (e.g., mouse), an indication of whether it is a disease  
> study, drug study,  ...
>
> I need to go now. Hope it helps. Maybe more later.
>
> Cheers,
>
> -Kei
>
> June Kinoshita wrote:
>> Hi everyone,
>>
>> I think NeuronDB might be able to provide the mapping between  
>> anatomical regions and cell types. Kei, what do you think?
>>
>> June
>>
>> On Mar 2, 2007, at 11:13 AM, Donald Doherty wrote:
>>
>>>
>>> Alan,
>>>
>>> The region names are all available in the MeSH...would that give  
>>> you the
>>> taxonomy you need? I don't know of a similar source for cell types.
>>>
>>> Don
>>>
>>> -----Original Message-----
>>> From: Alan Ruttenberg [mailto:alanruttenberg@gmail.com]
>>> Sent: Friday, March 02, 2007 3:21 AM
>>> To: Bill Bug; kc28 Cheung; June Kinoshita; Gwen Wong; Donald Doherty
>>> Cc: public-semweb-lifesci@w3.org
>>> Subject: cell types, brain regions mentioned in gensat
>>>
>>> I'm making progress in converting gensat to rdf.
>>>
>>> For mapping considerations, here is the list of cell types mentioned
>>> in gensat, followed by the list of brain regions. If we are going to
>>> do cross queries we will need to find standard names for these.  
>>> Bill,
>>> are these classes in birnlex? If not, we need to spawn a task to
>>> identify a vocabulary we will use for these.
>>>
>>> Note that we get a region<->neuron association via gensat where they
>>> annotation both a region and a cell type.
>>> Note also some amusements, like the presence of lung as region in an
>>> ostensibly CNS database.
>>>
>>> I've also attached the "ontology.csv" from the Allen Brain Explorer
>>> application, which I presume gives their hierarchy of brain regions/
>>> subregions. I've put labels on the first 3 columns which I think
>>> encode the hierarchy.
>>>
>>> The other interesting annotations, are the gene, the location,
>>> orientation, and size of the image, as well as some broad categories
>>> of qualitative expression, such as whether it is localized of widely
>>> expressed. There is also gender and a few categories of age.
>>>
>>> There are ~60K images in gensat.
>>>
>>> BTW, if someone has a theory of what the other number in  
>>> ontology.xls
>>> are, I'm all ears.
>>>
>>> -Alan
>>>
>>>
>>>
>>>
>>
>
>
>
>

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu