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

Forwarded message 1

  • From: Kei Cheung <kei.cheung@yale.edu>
  • Date: Fri, 02 Mar 2007 13:56:53 -0500
  • Subject: Re: cell types, brain regions mentioned in gensat
  • To: June Kinoshita <junekino@media.mit.edu>
  • CC: donald.doherty@brainstage.com, Alan Ruttenberg <alanruttenberg@gmail.com>, Gwen Wong <wonglabow@verizon.net>
  • Message-ID: <45E87375.8040003@yale.edu>
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
>>
>>
>>
>>
>

Received on Friday, 2 March 2007 18:59:55 UTC