Re: cell types, brain regions mentioned in gensat

	+++++++=========== 	NEURONAL CELL TYPES 	===========+++++++

Chris is correct - the MOST LIKELY shared community ontology to  
address the issue of cells would be the Cell Ontology, though in its  
currently distributed form - see (http://www.berkeleybop.org/ 
ontologies/#mappings) - it's very problematically both ontologically  
and in terms of what a neuroanatomist and cellular neurobiologist  
would want.

This brings us to a particular problem with the GENSAT AND the  
BrainPharm/SenseLab cell types - relating to shared cell type  
ontologies.  It's POSSIBLE the GENSAT folks started with the Cell  
Ontology.  Some of their cell terms are in there.  It's even more  
likely this is something they grew themselves.  This is most  
definitely true for many of the cell "sub types".

The Cell-Centered Database (CCDB) has done A LOT of work on this  
issue.  It would really be a terrible waste if this is not being  
included in whatever work is going on amongst the CL Ontology folks  
and GMOD folks - at least in the domain of neuronal cells.  It's  
quite likely some form of the CCDB work is available in OWL.  I've  
cc'd Maryann & Stephen who've been working on CCDB ontologies.  They  
could answer that question.

With BrainPharm - at least as I understand it (Luis Marenco and/or  
Kei of Yale would be best suited to answer this) the "cell types"  
they create have been based both on the wealth of knowledge Gordon  
Shepherd brings to this issue of neuronal cell types (at least as a  
core organizing principle).  This - possibly with input from some  
shared, distilled knowledge resources such as MeSH (as Don says) has  
then been built out by the 1000s of cellular neurobiologists who've  
contributed to the the SenseLab database - very empirically.  To my  
knowledge (Kei & Luis?), they have not tied this into any current,  
shared community ontology for cell types - and I'm certain there are  
real reasons why this is the case.


	+++++++=========== 	RODENT BRAIN ATLASES and BRAIN REGION  
SPECIFICATION 	===========+++++++

As for brain regions, this TOO is problematic.  What Gwen states is  
colloquially correct - you will find brain regions specified in  
atlases.  However, primate atlases and rodent atlases do not  
correspond in many areas (this is an ACTIVE area of research and a  
major task for us in BIRN given our mandate to integrate across  
animal models and human clinical neuroimages related to the diagnosis  
and study of neurodegenerative disease).

Limiting just one sub-species - say the Mus musculus musculus x Mus  
musculus domesticus hybrids that gave rise to most of the inbred  
strains (C57Bl/6, DBA/2, etc.) commonly used to create mouse models  
of disease - recombinant inbred, transgenics, congenics, etc. - there  
are AT LEAST 3 MRI/MRM atlases of the C57Bl/6 brain:
	LONI - http://www.loni.ucla.edu/MAP/Atlas/
	Ma et al. - http://www.bnl.gov/ctn/mouse/
	Mouse Imaging Center (Toronto) - http://www.mouseimaging.ca/research/ 
var_brain_atlas.html

and AT LEAST 2 histological atlases of the C57Bl/6 brain:
	LONI - http://www.loni.ucla.edu/MAP/Atlas/Atlas_Archive.html
	NeuroTerrain - http://fireball.drexelmed.edu/neuroterrain/tools.shtml

MRI/MRM atlases are just starting to get under 100 microns in  
resolution (compared to histologic resolution generally 20 - 50  
microns 3D isotropic) and don't have nearly comparable contrast (yet)  
to histological atlases required to perform highly granular region  
segmentation.  This contrast issue is especially true in the deep  
regions of the diencephalon where many regions important to  
neurodegenerative disease reside (s. nigra, n. basalis, striatum, etc.).

And - guess what - they don't all share the same "terminology" for  
naming those regions they do delineate (see BAMS links below) NOR are  
the regions (the 3D objects) they delineate for a given region -  
e.g., "hippocampal formation" -  geometrically equivalent - NOR do  
they place these geometries in the same 3D coordinate system.

I realize it must seem I'm getting into too much technical detail  
here - BUT- IF the goal is to make MEANINGFUL connections via SPARQL  
queries, this sort of behind the scenes "sausage making" issues are  
very important issues.

For primate brain regions, the SMARTEST source for a shared  
"terminology" is NeuroNames.  As I've mentioned before, this MIGHT be  
available in RDF or OWL based on work the BrainInfo/NN PI - Doug  
Bowden has done with Jack Park at SRI (I've cc'd Jack on this  
email).  Many names from other species are in there (though not in  
the downloadable versions of NN which are CIRCA 2002).  There is a  
knowledgeable - the Brain Architecture Managment System (BAMS) from  
Larry Swanson's lab which is curated by Mihail Bota - which makes  
available in XML format (don't know what the XSD is) the brain region  
specifications for several STANDARD rodent brain atlases.  You'll  
find these by navigating from the BAMS home page (http:// 
brancusi.usc.edu/bkms/) to the 'XML' link:
	http://brancusi.usc.edu/bkms/bamsxml.html

I would note the ABA uses the Franklin & Paxinos altas (2001).

HOWEVER - there are many regions in your spread sheet that are not in  
the BAMS Franklin&Paxinos download - for instance "CNU" - which may  
actually be a home-grown term for "CNS - unspecified".  Isn't that  
special.  Here's why that might be.  Go to the NN/Braininfo page for  
one of the regions the ABA classifies as "CNU" such as striatum:
	http://braininfo.rprc.washington.edu/Scripts/ 
hiercentraldirectory.aspx?ID=207
Click on the "Where is it in the brain?" link.
You will note Striatum, Globus Pallidus, and Amygdala are listed as  
being in the "Basal Ganglia".  Leaving the Amygdala aside, certainly  
in humans, the Striatum & Globus Pallidus (two regions critical to  
the PD Use case, BTW) are considered to be in the Basal Ganglia.
In rodents - especially in mice - this classification is very  
problematic.  You won't get any two mouse neuroanatomists to TRULY  
agree on all the details, however, there is a generally accepted  
region that sort of subsumes the same entity (based on various  
histological means of defining structural boundaries as well as other  
means such as structure-function, phylogenetic, and ontogenic  
relations) called the "caudoputamen" by most (if you drill into  
Striatum on BrainInfo, you'll find the Striatum has_part Caudate  
Nucleus.  Caudoputamen IS NOT equivalent to the "Basal Ganglia", but  
it is probably correct to say it is ANALOGOUS to what in a primate  
would be the Putamen and the Caudate Nucleus.
ABA may just have thrown up there hands and said - given their high- 
throughput directive - no one seems to agree on this issue, so lets  
be careful not to make an assertion that entails committing to an  
issue where there is disagreement.  Let's just call Striatum "CNS  
Unspecified".
Having said this, there is a Caudoputamen in ABA and it's classified  
as "Striatum dorsal Region (STRd).

I would guess Mihail, Maryann, and others would be able to give you a  
better explanation of the how to address these difficult issues of  
anatomical region correspondence between rodent brain image sets  
(GENSAT, ABA) and atlases (Franklin & Paxinos, NeuroTerrain, Ma et  
al., etc.).

Hope this helps some.

Cheers,
Bill


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