NeuroNames [was: slides for the UMLS presentation]

Some of the NeuroNames developers have embraced the Foundational Model
of Anatomy (FMA).  Much of the content from NeuroNames has been
re-tooled as part of the FMA, which is slated (as I understand it) for
open release as part of OBO.

Peter Mork

>-----Original Message-----
>From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-
>request@w3.org] On Behalf Of Donald Doherty
>Sent: Monday, June 05, 2006 9:29 PM
>To: 'kc28'
>Cc: 'Matthew Cockerill'; public-semweb-lifesci@w3.org;
>wilbanks@creativecommons.org; 'Daniel Rubin'
>Subject: RE: BioRDF [Telcon]: slides for the UMLS presentation
>
>
>
>
>I wouldn't suggest an open neural anatomy ontology be built without
the
>neuroscience community. Such an animal would need to be like a large
open
>source software effort (think Linux, for example) but with both
>informaticists and neuroscientists rather than traditional coders.
>
>Don
>
>-----Original Message-----
>From: kc28 [mailto:kei.cheung@yale.edu]
>Sent: Monday, June 05, 2006 9:16 PM
>To: donald.doherty@brainstage.com
>Cc: 'Matthew Cockerill'; public-semweb-lifesci@w3.org;
>wilbanks@creativecommons.org; 'Daniel Rubin'
>Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
>
>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/>
>>
>> donald.doherty@brainstage.com <mailto:donald.doherty@brainstage.com>
>>
>> 412-478-4552
>>
>> -----Original Message-----
>> *From:* public-semweb-lifesci-request@w3.org
>> [mailto:public-semweb-lifesci-request@w3.org] *On Behalf Of *Matthew
>> Cockerill
>> *Sent:* Monday, June 05, 2006 6:05 PM
>> *To:* public-semweb-lifesci@w3.org
>> *Cc:* wilbanks@creativecommons.org; 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: *public-semweb-lifesci@w3.org
>> <mailto:public-semweb-lifesci@w3.org>
>>
>> *From: *Olivier Bodenreider <olivier@nlm.nih.gov
>> <mailto:olivier@nlm.nih.gov>>
>>
>> *Date: *5 June 2006 22:54:01 BDT
>>
>> *To: *kei cheung <kei.cheung@yale.edu <mailto:kei.cheung@yale.edu>>
>>
>> *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: *olivier@nlm.nih.gov <mailto:olivier@nlm.nih.gov>
>>
>> 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_
>u
>ids=9410576&dopt=Abstract
>>>
><http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&
list_
>u
>ids=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.
>>
>
>
>
>

Received on Tuesday, 6 June 2006 10:40:06 UTC