Another HCLS blog

For those who didn't see this blog, there's possibly some material of
interest here:

http://www.w3.org/blog/hcls/2011/01/31/2010_a_good_year
2010 - A good year.

2010 was a good year for the Semantic Web, which has especially gained
momentum in health care and life sciences. I will just mention a few of the
reasons it was a good year. Semantic Web and Linked Data have become a clear
choice for projects that have a special interest in interoperability and
data sharing across enterprises and between project partners. This includes
the European Innovative Medicine Initiatives (IMI), in which a number of
projects that will want to share results and information across several
domains including drug discovery, electronic patient records, clinical
trials, tissue banking, etc. The Pistoia Alliance SESL project has also
moved things forward, showing how to add value to data through linking
microarray data with claims in literature and other public domain resources.
Great news: With another 5 years of NIH funding, NCBO is well-positioned to
contribute to collaborative science and translational research.

Biobanking provides Semantic Web with an ideal resource sharing application
- one that makes the added value of linked data more concrete for bench
scientists, who understand the immediate need of sharing tissue libraries in
order to move certain types of research forward. A keynote speaker at BBMRI
meetings in the Netherlands and the Life Sciences Momentum 2010
conference<http://www.momentum2010.nl/>
, David Cox <http://www.momentum2010.nl/speaker_cox.html> (Pfizer) provides
a business case for biobanking, couched in a solid research strategy that is
mutually beneficial to pharmaceutical companies and their academic partners.
In the strategy outlined by Cox, a transparent policy of public domain
knowledge and intellectual property is key to make biobanking and drug
development work well for academic and pharmaceutical partners. Although
David Cox does not focus on data sharing in his presentation, it plays an
implicit central role in biobanking and matching biobanking resources with
drug development goals. Please see the interview with David Cox “Collaborate
in order to understand the
biology”<http://www.bbmri.nl/images/stories/hub2_web.pdf>
.

In the HCLS Interest Group, we have progressed on several fronts: an
approach to creating semantic views on distributed data sources, including
both relational databases and triplestores (see the SWObjects federated
query tutorial <http://precedings.nature.com/documents/5538/> at SWAT4LS),
published about how we applied the Translational Medicine Ontology to
patient records in Indivo format and were able to pose cross-domain queries
on the results, demonstrated  <http://purl.org/net/biordfmicroarray/demo>and
published about a federated approach to microarray study results in
RDF<http://people.csail.mit.edu/pcm/tempISWC/workshops/SWPM2010/InvitedPaper_6.pdf>
at
the Provenance Workshop <http://wiki.knoesis.org/index.php/SWPM-2010> at
ISWC, further defined several ontologies for describing discourse and
annotations, in the process of documenting best practices for linked
data, checking
correspondence of radiology and pathology reports for breast
cancer<http://esw.w3.org/HCLSIG/Terminology/PathRadCorrelation>,
with more publications, demonstrations, and W3C notes on the way. Look for a
Best Practices document from the Linked Open Drug Data task force and a
specification of microarray RDF practices from BioRDF / Scientific Discourse
task forces in the coming months.

Did I mention being impressed by TripleMap <http://triplemap.com/>? It makes
it possible to create maps of interest using Linked Open Drug Data in a very
nice user interface geared toward essential concerns such as compounds,
disease, genes, etc.

-------------------------------------------

Another blog from this year here:

http://www.w3.org/blog/hcls/2011/02/22/c_shals_2011
Cheers,
Scott

-- 
M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
http://staff.science.uva.nl/~marshall