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Hi June et al.,
I just got back to my office from a meeting, trying to catch up with the
emails. Before I go to another meeting, I'd like to suggest the
following URL for people to look at:
http://senselab.med.yale.edu/senselab/NeuronDB/ndbRegions.asp?sr=1
Although they are not a comprehensive lists of brain regions and neuron
cell types for vetebrates, it could be a start (with mappings between
the two lists).
By reading the AD/PD use case, one of the questions has to do with what
genes are expressed in what regions of the brain (if such gene
expressions are localized to certain brain regions). I wonder what
Alan's currently working on can help address this type of question (even
though the kind of gene expression data is for the mouse -- perhaps we
can find homologous genes for human). Also, I'd encourage people to take
look at what Bill Bug's Wiki page:
http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology/SeedOntologyDetailedFollowup#preview
On that page, it describes the following OWL axiom example:
*EquivalentClass*(CerebellarPurkinjeCell
*intersectionOf*(PurkinjeNeuron, *Restriction*(locatedInBrainRegion
*allValuesFrom*(Cerebellum)))
We can use a similar axiom to define the localization of a certain type
of neuron cell type (CA1 pyramidal neuron) in a particular brain region
(e.g., hippocampus). Due to my limited knowledge of OWL, can this type
of axioms/rules be parameterized (e.g., cell type and brain region can
be treated as variables)?
Finally, due to the lack of annotation or lack of standard annotation,
it's difficult for users/neuroscientists or web agents to find relevant
sources (e.g., microarray databases, brain altases, ...) that may
contain the type of data they want (e.g., what genes are significantly
expressed in what brain regions). The type of shallow annotation (Alan
mentioned in a previous email) could at least help users identify
potentially relevant resources even the the data provided by those
sources are not in RDF/OWL format yet. For annotation, it might be
helpful to include a little bit more description of the experiment such
as species of the subject(s) (e.g., mouse), an indication of whether it
is a disease study, drug study, ...
I need to go now. Hope it helps. Maybe more later.
Cheers,
-Kei
June Kinoshita wrote:
Hi everyone,
I think NeuronDB might be able to provide the mapping between
anatomical regions and cell types. Kei, what do you think?
June
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:[EMAIL PROTECTED]
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
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