[openbiblio-dev] Bibliographic metadata from scientific publishers/publications

Sun Jun 27 10:29:37 UTC 2010

Part of #jiscobib concerns scientific publications and the extraction of
bibliographic data from them using either existing resources (e.g. TOCs) or
automatic extraction. [To avoid any rights issues all my examples come from
CC-BY publications].

So far I have discovered the following schemas/specs

* Dublin Core (http://en.wikipedia.org/wiki/Dublin_Core - IMO a better intro
than http://dublincore.org/ )
* NLMDTD (http://dtd.nlm.nih.gov/ "Journal Archiving and Interchange Tag
Suite")
* PRISM (
http://www.idealliance.org/industry_resources/intelligent_content_informed_workflow/prism)

are there others we need to know about?

Here are two examples from our collaborators in #jiscobib. I continue at the
end of the second:

DC + PRISM (IUCr)

PLoS (PLoS Biology)

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article
  PUBLIC "-//NLM//DTD Journal Publishing DTD v2.0 20040830//EN" "
http://dtd.nlm.nih.gov/publishing/2.0/journalpublishing.dtd">
<article xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="
http://www.w3.org/1998/Math/MathML" article-type="research-article"
dtd-version="2.0" xml:lang="EN">
<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="nlm-ta">PLoS Biol</journal-id>
<journal-id journal-id-type="pmc">plosbiol</journal-id>
<journal-title>PLoS Biology</journal-title>
<issn pub-type="ppub">1544-9173</issn>
<issn pub-type="epub">1545-7885</issn>
<publisher>
<publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc></publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">09-PLBI-RA-4846R2</article-id>
<article-id pub-id-type="doi">10.1371/journal.pbio.1000399</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research
Article</subject></subj-group></article-categories>
<title-group>
<article-title>Cortical Overexpression of Neuronal Calcium Sensor-1 Induces
Functional Plasticity in Spinal Cord Following Unilateral Pyramidal Tract
Injury in Rat</article-title>
<alt-title alt-title-type="running-head">Neuronal Calcium Sensor-1 Induces
Plasticity</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" xlink:type="simple"><name
name-style="western"><surname>Yip</surname><given-names>Ping
K.</given-names></name><xref ref-type="aff"
rid="aff1"><sup>1</sup></xref><xref ref-type="corresp"
rid="cor1"><sup>*</sup></xref></contrib>
<contrib contrib-type="author" xlink:type="simple"><name
name-style="western"><surname>Wong</surname><given-names>Liang-Fong</given-names></name><xref
ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib>
<contrib contrib-type="author" xlink:type="simple"><name
name-style="western"><surname>Sears</surname><given-names>Thomas
A.</given-names></name><xref ref-type="aff"
rid="aff1"><sup>1</sup></xref></contrib>
<contrib contrib-type="author" xlink:type="simple"><name
name-style="western"><surname>Yáñez-Muñoz</surname><given-names>Rafael
J.</given-names></name><xref ref-type="aff"
rid="aff3"><sup>3</sup></xref></contrib>
<contrib contrib-type="author" xlink:type="simple"><name
name-style="western"><surname>McMahon</surname><given-names>Stephen
B.</given-names></name><xref ref-type="aff"
rid="aff1"><sup>1</sup></xref></contrib>
</contrib-group>
<aff id="aff1"><label>1</label><addr-line>Neurorestoration Group, Wolfson
CARD, King's College London, Guy's Campus, London, United
Kingdom</addr-line>       </aff>
<aff id="aff2"><label>2</label><addr-line>Henry Wellcome LINE, Dorothy
Hodgkin Building, Bristol University, Bristol, United
Kingdom</addr-line>       </aff>
<aff id="aff3"><label>3</label><addr-line>School of Biological Sciences,
Royal Holloway-University of London, Egham, Surrey, United
Kingdom</addr-line>       </aff>
<contrib-group>
<contrib contrib-type="editor" xlink:type="simple"><name
name-style="western"><surname>Basbaum</surname><given-names>Allan
I.</given-names></name>
<role>Academic Editor</role>
<xref ref-type="aff" rid="edit1"/></contrib>
</contrib-group>
<aff id="edit1">University of California San Francisco, United States of
America</aff>
<author-notes>
<corresp id="cor1">* E-mail: <email xlink:type="simple">ping.yip at kcl.ac.uk
</email></corresp>
<fn fn-type="con"><p>The author(s) have made the following declarations
about their contributions: Conceived and designed the experiments: PKY.
Performed the experiments: PKY TAS. Analyzed the data: PKY TAS. Contributed
reagents/materials/analysis tools: PKY LFW RJYM. Wrote the paper: PKY TAS
SBM.</p></fn>
</author-notes>
<pub-date pub-type="collection"><month>6</month><year>2010</year></pub-date>
<pub-date
pub-type="epub"><day>22</day><month>6</month><year>2010</year></pub-date>
<volume>8</volume>
<issue>6</issue>
<elocation-id>e1000399</elocation-id>
<history>
<date
date-type="received"><day>10</day><month>11</month><year>2009</year></date>
<date
date-type="accepted"><day>12</day><month>5</month><year>2010</year></date>
</history>
<copyright-statement>Yip et al. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.</copyright-statement>
<copyright-year>2010</copyright-year>
<related-article id="RA1" related-article-type="companion"
ext-link-type="uri" vol="8" page="e1000400" xlink:type="simple"
xlink:href="info:doi/10.1371/journal.pbio.1000400"> <article-title>Healing
Spinal Cord Injuries</article-title></related-article>
<abstract abstract-type="toc">
<p>Overexpression of neuronal calcium sensor 1 in cortical neurons can help
restore axonal plasticity and regeneration following axonal injury in adult
rats, and can also improve behavioral function.</p>
</abstract>
<abstract>
<p>Following trauma  ... within the injured adult central nervous
system.</p>
</abstract>
<abstract abstract-type="summary"><title>Author Summary</title>
<p>Following trauma to the central nervous system  ...  and can help improve
behavioural function.</p>
</abstract>
<counts><page-count count="22"/></counts></article-meta>
</front>

So some questions:
* is the term "bibliographic entry" appropriate for these two specimens?
* can the OKF-RDF approach hold all the information in them?
* can a conversion to OKF-RDF be done automatically? [I appreciate we may
need to create a mapping].
* do we need to microparse any of the information? [I would like to do this
for the affiliations or to normalize this to a unique indentifier].

If the answers are YYY* then we should be able to convert a lot of Open
Access information immediately.

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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