Re: cell types, brain regions mentioned in gensat

Hi Chris,

A reasonable suggestion.

I'm kind of fishing for a volunteer to verify that whatever source we  
choose has the appropriate coverage, and then to the mapping do the  
mapping :)

Regarding ontological questions, the usual thing I see in these sorts  
of hierarchies is that derivation is confused with is_a.
I might use the URIs someone else coined for the specific classes of  
cells and then then arrange the ontology properly.

-Alan

On Mar 2, 2007, at 11:47 AM, Chris Mungall wrote:

>
> 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 17:51:15 UTC