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

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
21st 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

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

From: Olivier Bodenreider <olivier@nlm.nih.gov>

Date: 5 June 2006 22:54:01 BDT

To: kei cheung <kei.cheung@yale.edu>

Cc: 'public-semweb-lifesci' <public-semweb-lifesci@w3.org>

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

Reply-To: 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
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_u
ids=9410576&dopt=Abstract> &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.