W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > September 2009

Re: [hcls] Extracting conclusion sections from PubMed abstracts and turning them into linked data

From: Susie Stephens <susie.stephens@gmail.com>
Date: Sun, 20 Sep 2009 12:35:04 -0400
Message-ID: <fcc499200909200935l78db3a16g8798401528c9d26b@mail.gmail.com>
To: Matthias Samwald <samwald@gmx.at>
Cc: public-semweb-lifesci <public-semweb-lifesci@w3.org>
Hi Matthias,
It's great to see that the aTag work is progressing so well.

It also nicely highlights the connection points between the work that is
ongoing within the BioRDF, LODD, and Scientific Discourse tasks.



On Thu, Sep 17, 2009 at 9:07 AM, Matthias Samwald <samwald@gmx.at> wrote:

> I did some preliminary work making use of conclusion sections in abstracts,
> representing them using Semantic Web / Linked Data technologies and aligning
> it with existing datasets produced by the HCLS IG. The e-mail became so long
> that I decided to turn it into a pre-print publication.
> Direct link to PDF:
> http://precedings.nature.com/documents/3775/version/1/files/npre20093775-1.pdf
> ======
> Extracting conclusion sections from PubMed abstracts for rapid key
> assertion integration in biomedical research
> Available from Nature Precedings
> <http://precedings.nature.com/documents/3775/version/1>
> Key assertions are extracted from "conclusions" sections of PubMed
> abstracts
> and converted into Semantic Web / Linked Data format. The results are made
> accessible via  files, a SPARQL endpoint, and a  faceted search interface.
> Conclusion sections are identified as valuable resources for
> machine-augmented key assertion identification and integration in the
> biomedical domain.  Results are discussed and opportunities for future work
> and cooperation are highlighted.
> ======
> If you just want to have a quick look at the outcome without bothering
> reading the paper, then:
> 1) have a look at http://hcls.deri.org/atag/explorer/
> (works in every browser except IE. This is just a rough prototype, it still
> does not link back to source / evidence etc.).
> 2) do a search for "Schizophrenia"
> 3) Further narrow down search results by entering additional search terms
> or selecting facet values on the left.
> I'm happy about feedback. I look forward to integrate this with other
> ongoing work in the HCLS IG. Together with Anja I will also look into making
> data from the LODD task available in the search interface above (a large
> part of SIDER has already been integrated, for example).
> Cheers,
> Matthias Samwald
> DERI Galway, Ireland
> http://deri.ie/
> Konrad Lorenz Institute for Evolution & Cognition Research, Austria
> http://kli.ac.at/
Received on Sunday, 20 September 2009 16:35:44 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 17:20:45 UTC