Re: BioRDF [Telcon]: slides for the UMLS presentation

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)


Please Note: I now have a new email - William.Bug@DrexelMed.edu







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Received on Tuesday, 6 June 2006 21:20:16 UTC