Nanopublications

[excerpted from another discussion list, been meaning to bring this to
your attention]

The nice thing about nanopublications, see DOI link below, is that
they lead very nicely to
RDF. I would describe them as an assertion with prescribed provenance.
If we want to share assertions about SNPs, then we need to be
able to programmatically consume and assess them. In order to do so,
they should use common vocabularies and meet provenance requirements.
The handiest way to do this is with RDF and SPARQL. Of course, each
different type of assertion, has special provenance requirements in
order for consumers to decide if it meets their criteria. The SNP
assertion (nanopublication) should refer to a reference sequence, a
population/ethnicity, etc. A differentially expressed gene assertion
(from an expression study) should refer to the experimental
conditions, as well as a p or q-value, etc. As each of the different
assertion types gets an RDF rendering, we can nanopublish it as linked
data. And a new era of publishing is born.

It is very encouraging to see what appears to be a mass movement to
SPARQL endpoints taking place. At least, to my eyes, the movement
appears relatively massive :) . NCBO has had a SPARQL endpoint since
the beginning of last year. ArrayExpress is working towards it, with
initial production of RDF for the Gene Expression Atlas. Uniprot is preparing
one and it sounds like others such as EMBL are interested as well. I am also
aware that the European Innovative Medicine Initiative (IMI) called
OpenPhacts has started a demo project by getting participants to
create SPARQL endpoints to their online resources. BTW, OpenPhacts was
put together by the same Barend Mons as the one who instigated the
nanopublications mentioned in the Nature Genetics article and the
Concept Web Alliance.

Cheers,
Scott

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

On Fri, Jun 24, 2011 at 12:43 PM, Rutger Vos <R.A.Vos@reading.ac.uk> wrote:
> On a slightly different note, but not irrelevant for us scientists &
> semantic web aficionados, everyone seen this? It's about
> micro-attribution to incentivize semantic annotation:
>
> Crowdsourcing human mutations
> Nature Genetics, Vol. 43, No. 4. (29 April 2011), pp. 279-279
> http://dx.doi.org/10.1038/ng0411-279
>
> --
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading, RG6 6BX, United Kingdom
> Tel: +44 (0) 118 378 7535
> http://rutgervos.blogspot.com

Received on Friday, 24 June 2011 11:13:05 UTC