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:[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
