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:[EMAIL PROTECTED]
Sent: Friday, March 02, 2007 1:54 PM
To: [EMAIL PROTECTED]
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:[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]
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]
