I would strongly recommend using the neuroanatomy community's
ontologies if at all possible. People I work with at MGH use that
for doing structural morphometry, the results of which you would want
to integrate with experimental results from other modalities as well
as organized research findings related to particular structures.
Tim
On Jun 5, 2006, at 9:17 PM, kc28 wrote:
For more up-to-date information about neuronames and related tools,
please visit: http://braininfo.rprc.washington.edu/. While building
our own open neural anatomy is one option, getting the
neuroscientist (e.g., braininfo people) involved if possible may be
another option (outreach to the neuroscience community?).
Speaking of moving the neuroscience semantic web forward, another
major type of neuroscience data seems to be microarray data. In
addition to public microarray data repositories like NCBI GEO which
may contain neuroscience microarray data, there is an NIH-funded
neuroscience microarray consortium (http://arrayconsortium.tgen.org/
np2/home.do) which allows public access. It might be time to think
about how to convert mged ontology or mage-ml into RDF/OWL. The
following are two related articles:
http://www.nature.com/msb/journal/v2/n1/full/msb4100052.html
http://www.nature.com/nbt/journal/v23/n9/full/nbt0905-1095.html
Cheers,
-Kei
Donald Doherty wrote:
Matthew’s statement is a truism.
Even though I’m in private enterprise I feel the patent/copyright/
etc. system is broken and a huge liability for where IP needs to
go during the 21^st century. Worse, the problem has been
exacerbated by the Bayh-Dole Patent act.
Enough rant…
Anyone want to get together and build a totally open, freely
available, Neural Anatomy Ontology?
Kei is absolutely correct that it is needed and it’s an
embarrassment that the anatomy ontologies that are out there are
locked up behind licensing. We will move the neuroscience semantic
web massively forward…
Don
Donald Doherty, Ph.D.
Brainstage Research, Inc.
www.brainstage.com <http://www.brainstage.com/>
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
412-478-4552
-----Original Message-----
*From:* [EMAIL PROTECTED] [mailto:public-semweb-
[EMAIL PROTECTED] *On Behalf Of *Matthew Cockerill
*Sent:* Monday, June 05, 2006 6:05 PM
*To:* [email protected]
*Cc:* [EMAIL PROTECTED]; Daniel Rubin
*Subject:* Fwd: BioRDF [Telcon]: slides for the UMLS presentation
Seems like rights restrictions on standard ontologies (within UMLS
for example) could be a significant hindrance to semantic web
efforts.
John, Daniel,
I wonder if this may be an area where Science Commons (and the
NCBO) can help?
i.e. By encouraging the rights owners for ontologies to open them
up to allow the semantic web to make full and flexible use of
them, and by drafting standard terms on which this might be done...
[And by identifying/prioritizing problem areas where there may be
a need for the creation of alternate non-rights-encumbered
ontologies?]
Matt
Begin forwarded message:
*Resent-From: [EMAIL PROTECTED] <mailto:public-semweb-
[EMAIL PROTECTED]>
*From: *Olivier Bodenreider <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
*Date: *5 June 2006 22:54:01 BDT
*To: *kei cheung <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
*Cc: *'public-semweb-lifesci' <[email protected]
<mailto:[email protected]>>
*Subject: **Re: BioRDF [Telcon]: slides for the UMLS presentation*
*Reply-To: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
kei cheung wrote:
Hi Olivier,
Sorry, I missed part of your talk (the beginning part and the
ending part) as I needed to be at other meetings. Is Neuronames
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
cmd=Retrieve&db=PubMed&list_uids=9410576&dopt=Abstract <http://
www.ncbi.nlm.nih.gov/entrez/query.fcgi?
cmd=Retrieve&db=PubMed&list_uids=9410576&dopt=Abstract>) part of
UMLS now? If so, does it make sense to convert (all or a portion
of) the Neuronames Brain Hierarchy into RDF/OWL instead of
converting the entire UMLS into RDF? It might be helfpul to our
RDF conversion efforts if they share the same neuroanatomical
terminology.
Some version of Neuronames (1999) is integrated in the UMLS.
Converting one single vocabulary to RDF/OWL is likely to be much
simpler than converting the whole UMLS.
I don't know enough the specifics of Neuronames to be able to
estimate the difficulty of converting it to to RDF. At first
glance, all relations seem to be parent/child relations and it
should be pretty trivial.
Attached below is the list of restrictions for "Category 3"
vocabularies in the UMLS. My understanding is that it wouldn't be
possible to make the RDFized version of Neuronames publicly
available or even part of a production system.
-- Olivier
From: http://www.nlm.nih.gov/research/umls/license_appendix.html
12. 3. Category 3:
LICENSEE's right to use material from the source vocabulary is
restricted to internal use at the LICENSEE's site(s) for research,
product development, and statistical analysis only. Internal use
includes use by employees, faculty, and students of a single
institution at multiple sites. Notwithstanding the foregoing, use
by students is limited to doing research under the direct
supervision of faculty. Internal research, product development,
and statistical analysis use expressly excludes: use of material
from these copyrighted sources in routine patient data creation;
incorporation of material from these copyrighted sources in any
publicly accessible computer-based information system or public
electronic bulletin board including the Internet; publishing or
translating or creating derivative works from material from these
copyrighted sources; selling, leasing, licensing, or otherwise
making available material from these copyrighted works to any
unauthorized party; and copying for any purpose except for back up
or archival purposes.
LICENSEE may be required to display special copyright, patent and/
or trademark notices before displaying content from the vocabulary
source. Applicable notices are included in the list of UMLS
Metathesaurus Vocabulary sources, that is part of this Agreement.
