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 may be 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_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.
>

Received on Tuesday, 6 June 2006 01:22:49 UTC