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

Hi Bill,

You really can write faster than I can read :-).  Actually, we have 
discussed in a previous telconf about how to outreach to  the 
neuroscience community. I think this represents a good opportunity to 
try to get people like Doug Bowden involved, as we are interested in 
converting Neuronames into RDF/OWL. I wonder if it's possible to invite 
neuroscientists like Doug Bowden and Gordon Shepherd (and possibly more) 
to talk about their work in our future BioRDF/Ontology telconf. This 
will foster more interaction between the semantic web community and 
neuroscience community. I wonder how this sounds to other semantic web 
folks.

Cheers,

-Kei

William Bug wrote:

>
> 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 23:47:31 UTC