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:[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
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 - [EMAIL PROTECTED]
