Apologies for the event spam post, but below is a related effort in terms of 
dealing with scholarly systems.  I plan on attending and just wondering if 
anyone else might be going?  Perhaps an opportunity for an informal chat about 
SWORD or rather all things 'beyond PDF'? /dff

> -----Original Message-----
Details are firming up for the ScholarlyHTML BtPDF hackfest in Cambridge on 
March12/13 and afterwards. For details follow the web page 
http://www-pmr.ch.cam.ac.uk/wiki/Scholarly_HTML  

One main thrust of the hackfest will be to create a "data journal" initially 
based on crystallography but extensible to other areas of science where objects 
can be created in semantic form. I have blogged this - see:
http://blogs.ch.cam.ac.uk/pmr/2011/03/04/scholarly-html-hackfest-and-visit-of-peter-sefton-and-martin-fenner/
 

Here is the gist:
The general plan is to CREATE something during the time that Peter Sefton is 
here. PS runs a world class team in University of Southern Queensland which has 
created a proven Open toolset based on WordPress for high quality scholarly 
documents (e.g. course materials, papers, theses). Martin has likewise 
pioneered many plugins for WordPress. 
We shall invite Peter and Martin to give presentations (but this will need to 
be on a weekday)

The theme is Scholarly HTML with particular emphasis on data publication.  It 
is to give authors the freedom to author as they wish, not as they are 
constrained but the recipient. A consequence is that all data should be 
semantic (i.e. understandable by machine). This means that bitmaps such as PNG 
should be replaced or augmented by - say - SVG or HTML5. Much of the impetus 
for the meeting came from "Beyond the PDF" run by Phil Bourne and Anita de 
Waard. 
In general we would like to be able to publish: 
*       Semantic (mainly rectangular) tables where columns have defined 
semantics 
*       Semantic graphs where axes are semantic and points, lines, bars etc are 
first-class objects 
*       Maths (MathML) 
*       Semantic bibliography (technically solved, but we'd like to include 
online OPEN resources (e.g. from Open Bibliography) 
*       Scalable diagrams (probably SVG) 
*       Chemistry/crystallography as CML 
There will be many ideas but as a focus we have come up with a unifying 
project. After discussion with Simon Hodson (JISC) and Brian McMahon (IUCr) we 
plan to implement the following idea in our JISCXYZ project and to start this 
during the hackfest. (Simon and Brian hope to be present for some of the time).

A data-journal for crystallography

Every week Crystaleye aggregates (automatically) a few hundred structures and 
creates fully semantic CML. These are currently published as HTML pages with 
embedded CML and PNGs (http://wwmm.ch.cam.ac.uk/crystaleye) . A typical page 
(there are ca 250,000) is 
http://wwmm.ch.cam.ac.uk/crystaleye/summary/acta/c/2008/01-00/data/av3113/av3113sup1_I/av3113sup1_I.cif.summary.html
 (you can twiddle the molecule and create the unit cell by clicking). We wish 
to create a "data publication" from this material. 
The proposed data journal will automatically select ca 10 interesting 
structures per week and publish these as a Scholarly HTML blog. The hackfest 
will educate us to the best ways of representing these as Scholarly HTML and 
allowing the best modes of presentation. Because we shall be using a blog 
readers can comment on these structures using the blog mechanism and also add 
their own ideas about interesting structures that we have not included. In this 
way we hope to build up a sense of publication and comment.
There is also the possibility for readers to submit their own structures which 
will be automatically validated during the submission process. We'll work very 
closely with the IUCr during this. We can add to the interest by having ranking 
tables for authors or contributors and having various "records" such as largest 
structure. 

All are welcome. It's hands-on. Let us know if you are interested.

P.

-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069

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This paper provides an overview of data connectivity, details
its effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d
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