W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > March 2007

RE: cell types, brain regions mentioned in gensat

From: Donald Doherty <donald.doherty@brainstage.com>
Date: Fri, 2 Mar 2007 11:13:55 -0500
To: "'Alan Ruttenberg'" <alanruttenberg@gmail.com>
Cc: <public-semweb-lifesci@w3.org>
Message-ID: <003101c75ce5$c8c1aab0$2f01a8c0@Brainstage>

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 16:08:52 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:30 UTC