- From: Tim Clark <tim_clark@harvard.edu>
- Date: Mon, 5 Jun 2006 22:53:38 -0400
- To: kc28 <kei.cheung@yale.edu>
- Cc: donald.doherty@brainstage.com, "'Matthew Cockerill'" <matt@biomedcentral.com>, public-semweb-lifesci@w3.org, wilbanks@creativecommons.org, "'Daniel Rubin'" <dlrubin@stanford.edu>
I would strongly recommend using the neuroanatomy community's ontologies if at all possible. People I work with at MGH use that for doing structural morphometry, the results of which you would want to integrate with experimental results from other modalities as well as organized research findings related to particular structures. Tim On Jun 5, 2006, at 9:17 PM, 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?). > > 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 03:15:43 UTC