RE: cell types, brain regions mentioned in gensat

Bill, Too bad but I suspected as much. I've also looked at the OBO
NeuroNames files and I'm daunted by the task to make it useful for us
(perhaps I'm wrong here?).

 

Don

 

-----Original Message-----
From: William Bug [mailto:William.Bug@DrexelMed.edu] 
Sent: Friday, March 02, 2007 1:54 PM
To: donald.doherty@brainstage.com
Cc: 'Alan Ruttenberg'; public-semweb-lifesci@w3.org
Subject: Re: cell types, brain regions mentioned in gensat

 

I hate to say it, but based on our attempts to use MeSH for this purpose in
BIRN, I would suggest this is not really going to work.

 

UMLS does contain NeuroNames - but given the deliberate process that must go
into UMLS curation, it is an older version of NN and not one that includes
any of the work the NN group has done to integrate rodent terminologies in
with those for primate.

 

Cheers,

Bill

 

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