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[Deri.ie-research] Hackfest on Scholarly HTML - March 12-13 - Cambridge UK

From: Jodi Schneider <jodi.schneider@deri.org>
Date: Fri, 4 Mar 2011 13:05:04 +0000
Message-Id: <601E39DD-0D81-4C7F-B21A-B3064DD6CCAC@deri.org>
To: deri Research <deri.ie-research@lists.deri.org>
Cambridge UK hands-on scholarly communication hackfest Sat-Sun March 12-13, details below. -Jodi

---------- Forwarded message ----------
From: Peter Murray-Rust <pm286@cam.ac.uk>
Date: Fri, Mar 4, 2011 at 9:27 AM
Subject: Re: Continuing BtPDF - Hackfest on Scholarly HTML March Cambridge UK
To: beyond-the-pdf@googlegroups.com
Cc: Murray-Rust Group <chem-pmrgroup@lists.cam.ac.uk>, David FLANDERS <flandda@jisc.ac.uk>

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:

Here is the gist:
The general plan is to CREATE something during the time that PT is here. PT 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.


Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge

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