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Re: cell types, brain regions mentioned in gensat

From: Chris Mungall <cjm@fruitfly.org>
Date: Fri, 2 Mar 2007 08:47:51 -0800
Message-Id: <862CB0DB-6C77-45C8-BDD7-2632C2BD154C@fruitfly.org>
Cc: "'Alan Ruttenberg'" <alanruttenberg@gmail.com>, <public-semweb-lifesci@w3.org>
To: <donald.doherty@brainstage.com>


Umm, the OBO Cell ontology? There are a few ontological issues with  
OBO-Cell right now, but these are currently being addressed. There  
are also efforts within OBO to link cells with the brain regions they  
are part of, although these are currently focused on model organisms.

On Mar 2, 2007, at 8:13 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 16:48:08 UTC

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