Dear Matthias,
I would strongly recommend you contact Doug Bowden and colleagues at
NeuroNames before you undertake this task - or at least take a look
at the NeuroNames specifics I list in my previous email. I'd be glad
to answer any questions you may have about statements I made. Doug
and his collaborators are extremely collegial and make a very sincere
effort to work with those interested in making effective - or novel -
use of NN.
The other person you should contact is Daniel Rubin at NCBO, who, for
all I know, is lurking on this thread. Others in the thread appeared
to be addressing Daniel. This is a topic actively under
investigation both by NCBO and by the BIRN.
As I mentioned in my post to this thread, Doug & colleagues have been
working for the last year with Jack Park of SRI to express NN in XTM
format. A lot of effort needs to go into vetting this "remapping" to
make certain none of the assertions in the hierarchy - explicit or
implicit - are invalidated - as well as ensuring no new assertions
are unwittingly introduced. You may want to work from this version
of NN to create an RDF/OWL version. As I mentioned in the previous
post, there has been some substantive effort to examine the
differences and similarities between XTM & RDF - and there may even
be translators or XSL instances that can get you most of the way.
Doug also distributes the entirety of NN on CD with all of the latest
work they've done in the past year to incorporate rat & mouse
neuroanatomical terminologies - an added dimension absolutely
critical to those of us interested in collating microarray, in situ &
IHC expression studies in mouse brain with neuroimaging data sets and
3D digital brain atlases.
There is definitely a need for an open source, RDF/OWL version of
NeuroNames (and the neuroanatomical portion of RadLex for that matter
- http://www.rsna.org/RadLex/ - if you are interested in human,
radiological imaging of the brain).
I believe we must do our best to work with the curators/developers on
these various knowledge resource projects, given the biological
complexity embedded in these resources.
As far as the licensing goes, Doug realizes this is a thorny issue.
The initial license was merely put in place to avoid others
downloading this highly curated knowledge resource, modifying it,
then repackaging it as "NeuroNames." As I mentioned, this was not a
paranoid fear. The license was imposed in response to someone
actually having done this with NN. Knowledge resources like this -
even when they are just terminologies - require careful curation, and
uncontrolled dissemination and modification can ultimately degrade
the usefulness of the resource.
Of course, closed, proprietary licensing can also degrade its
usefulness, so there is a delicate balance that must be struck.
This is an issue I believe NCBO can help us all to resolve. They
won't have all the answers, but may be able to sponsor a means to
derive an effective solution to this problem.
My recommendation is a statement be sent by the W3CSW HCLSIG - maybe
the BioRDF & BIOONT groups collectively - informing Doug of the need
as they see it. He will not be surprised by the nature of your
request, but will be very surprised and pleased to see this need
emerging from the semantic web community. I don't believe he reads
this list. I know he will be happy to work with participants on the
W3CSW HCLSIG to get us what we have all identified as essential - an
open source, unified neuroanatomical terminological (and in
association with FMA - as Neuro-FMA - ontological) resource all
formal annotation efforts can make shared and productive use of.
Just my $0.02 on the topic.
Cheers,
Bill
On Jun 6, 2006, at 3:38 PM, Matthias Samwald wrote:
Hi Kei,
I am under the impression that the neuronames ontology available on
their website (as an Excel file...) is different from the version
that is licensed as part of the UMLS. I guess the version that is
online is a newer version of the one incorporated in UMLS. However,
this might be seen as a derivative work, so it might still be
restricted. In that case, it would seem like people of the
neuronames group are violating the licence restrictions themselves
(by making it available on the internet). I will write them and ask
about that.
kind regards,
Matthias
Hi Matthias,
Thanks for doing that, but do we still have the licensing issue as
stated by Olivier?
Cheers,
-Kei
Matthias Samwald wrote:
I will convert the neuronames - ontology to SKOS (an OWL ontology
used for the representation of taxonomies / theasauri). It will
be added to the extension of the bio-zen ontologies framework
[1]. I will keep you updated.
kind regards,
Matthias Samwald
[1] http://neuroscientific.net/index.php?id=download
On Mon, 05 Jun 2006 21:17:55 -0400, 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?).
Bill Bug
Senior 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)
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