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Re: aTag and conclusion sections from PubMed

From: Matthias Samwald <matthias.samwald@meduniwien.ac.at>
Date: Fri, 22 Jun 2012 22:36:03 +0200
Message-ID: <F0742362A5B2468092002DDF4894E72C@zetsu>
To: <rdb20@pitt.edu>, <public-semweb-lifesci@w3.org>
Hi Richard,

Thanks for digging this up. As a reminder:  aTags = a convention for using 
the SIOC vocabulary for the simple representation of scientific assertions 
annotated with terms from controlled vocabularies.

The aTag website fell in disrepair when I left DERI (a fate of so many 
research-driven projects...), but I will now work with Lena to bring at 
least parts of it back online. So far, aTags were adopted in the context of 
some research projects, but not on any broader scale or independent from 
this group (at least I am not aware of it).

However, I will revisit aTags in the context of ongoing work (e.g., 
summarizing biomedical articles quickly to make research findings easier to 
consume in time-constrained clinical settings). It might be interesting to 
switch from the SIOC vocabulary to a very simple extension of Schema.org... 
so far, Schema.org does not really cover this, but extending it would be 
very simple.

aTags should be very simple to create, integrate and consume (you don't have 
the problem of different ontology design patterns), so I can encourage you 
to expose some of the data you are working on in this format!


From: "Richard Boyce" <rdb20@pitt.edu>
Sent: Friday, June 22, 2012 9:05 PM
To: <public-semweb-lifesci@w3.org>
Subject: aTag and conclusion sections from PubMed

> A few years ago Matthias and others did some interesting work on aTags 
> <http://www.jbiomedsem.com/content/1/S1/S5#B28> and an initial extraction 
> of conclusions from PubMed abstracts still queryable in the HCLS knowledge 
> base. Does anyone know what the status of the atag approach is? Did it 
> gain traction in the SW community or is has work progressed in some way?
> Also, I would be interested to expand the conclusions section demo, any 
> way that could be accomplished?
> I see that most of the related links seem to be dead on the HCLS site: 
> <http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/aTags/datasets>. The 
> science commons still provides a text annotation service that embeds atags 
> <http://whatizit.neurocommons.org/>.
> Since I didn't start working with this group until 2010 I am still 
> discovering work done by members of the group several years ago!
> -Rich
> -- 
> Richard Boyce, PhD
> Assistant Professor of Biomedical Informatics
> Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research 
> and Training Program
> Scholar, Comparative Effectiveness Research Program
> University of Pittsburgh
> rdb20@pitt.edu
> 412-648-9219 (W), 206-371-6186 (C)
> Twitter: @bhaapgh
Received on Friday, 22 June 2012 20:36:36 UTC

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