Re: cell types, brain regions mentioned in gensat

Hi Don,

One of the problems here is there IS no OBO NeuroNames.  There is an  
TMRM expression of NeuroNames created by Jack Park at SRI, and he's  
been working to have some of this be representable in RDF.

In OBO, where anatomy is concerned, there are currently many  
anatomical ontologies - those relevant to us are:
	MGI Mouse adult gross anatomy (http://www.berkeleybop.org/ontologies/ 
obo-all/adult_mouse_anatomy/adult_mouse_anatomy.owl)
	EMAP mouse gross anatomy & development (http://www.berkeleybop.org/ 
ontologies/obo-all/emap/emap.owl)
	FMA "light" for adult human anatomy (http://www.berkeleybop.org/ 
ontologies/obo-all/fma_lite/fma_lite.owl)
	Human developmental anatomy - both:
		abstract (http://www.berkeleybop.org/ontologies/obo-all/human-dev- 
anat-abstract/human-dev-anat-abstract.owl)
		time-based (http://www.berkeleybop.org/ontologies/obo-all/human-dev- 
anat-staged/human-dev-anat-staged.owl)
	MeSH (http://www.berkeleybop.org/ontologies/obo-all/mesh/mesh.owl)
	NCI Thesaurus (http://www.berkeleybop.org/ontologies/obo-all/ 
ncithesaurus/ncithesaurus.owl)

None of them have quite met our needs in BIRN - yet - so we've been  
working more directly to represent NN in OWL within our context.  I  
fully hope and expect we'll be able to pass this on to one of the  
above authorities, once we have it working for our applications  
(cross-species, multi-resolution neuroanatomical semantic integration  
in the context of neurodegenerative disease).
	
I can see wanting to bring in worm (C. elegans) and Zebrafish (D.  
rerio), given how critical these two model organisms have been to  
basic research in nervous system development and disease, but I think  
that's out-of-scope for the upcoming demo deadline.

Cheers,
Bill
	
On Mar 2, 2007, at 2:04 PM, Donald Doherty wrote:

> 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
>
>
>
>
>
>
>
>

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