Re: cell types, brain regions mentioned in gensat

The CRITICAL issue here given the current BioRDF data sources is:
	can you align what you are doing with GENSAT cell types with:
		- BrainPharm/SenseLab
		- CCDB (which I'll help you to specify this weekend - as I've been  
doing with ABA & GENSAT)

CL ontology and MeSH for that matter  covers many of these cell types  
(MeSH at a coarse level) though their underlying graph doesn't  
necessarily match to that of GENSAT, BrainPharm, or Cell-Centered  
Dtb, because of differing application requirements.

Of the other data sets listed on the BioRDF data page:
	http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Data

those likely to include important cell level info are:
	- GO (will have pre-composed references to many neuronal cell types)
	- BioCyc (will have pre-composed references to many neuronal cell  
types)
	- Reactome (will have pre-composed references to many neuronal cell  
types)
	- KEGG (depending on the subset that has been converted)
	- OMIM  (depending on the subset that has been converted)
	- PubMed (PubMed XML instances are filled with MeSH terms - many  
"coarse" neuronal types will be there - THOUGH - whether a term-based  
matching will create TRUE assertions in your triplets is anyone's  
guess - really would need to be manually reviewed - as would most  
neuronal cell type bridging we do de novo for this demo)
	- BioZen (http://neuroscientific.net/bio-zen.owl)

Is this page still accurate and comprehensive?  We certainly will  
need to add GENSAT, ABA, and CCDB (once that's been mapped).
	
BioZen has a cell type "concept", but I'm not certain whether  
Matthias has mapped specific cell types in as sub-types:
OWL-Class: bio-zen:cell-type-concept

Annotations:
rdfs:label (Datatype http://www.w3.org/2001/XMLSchema#string) :  
Celltype concept
rdfs:comment (Datatype http://www.w3.org/2001/XMLSchema#string) :  
Concept describing a cell type (e.g. "hepatocyte", "neuron", "HeLa  
cell").

Subclass of:
bio-zen:cell-concept

Cheers,
Bill

On Mar 2, 2007, at 12:50 PM, Alan Ruttenberg wrote:

>
> 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
>>>
>>>
>>>
>>>
>>>
>>
>
>

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