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 is 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:[EMAIL PROTECTED] *On Behalf Of *Matthew
Cockerill
*Sent:* Monday, June 05, 2006 6:05 PM
*To:* public-semweb-lifesci@w3.org
*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-lifesci@w3.org>
*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' <public-semweb-lifesci@w3.org
<mailto:public-semweb-lifesci@w3.org>>
*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.
