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Open Access Publishing on the Semantic Web

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Richard Cave

Slideshow given at the San Francisco Meetup in August, 2009. A review of PLoS, the Ambra Open Source publishing platform, the Mulgara RDF triple store and future feature.

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Open Access Publishing on the Semantic Web
the Public Library of Science (PLoS) ,[object Object],[object Object],[object Object]
why Open Access? ,[object Object],[object Object],[object Object],[object Object]
PLoS Journals ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
state of STM publishing platforms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
big ideas for transforming journal publishing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],© by wales.nhs.uk
… embarked down the path ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Ambra / Topaz journal publishing platform Apache Ambra Fedora + Mulgara RDF Store Topaz OTM Topaz Files CAS Fedora is used to store digital objects (XML, PDF, images, etc.) article metadata, annotations (annotea) and user information (foaf) is stored as triples in Mulgara Topaz is used for storage and retrieval of the digital objects and triple stores through the Objects to Triples Mapping (OTM) Ambra (user interface) CAS single sign-on service Apache webhead
under the hood of Topaz (1) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
why Objects to Triples Mapping (OTM)? don’t walk a tree to retrieve objects (slow) instead, retrieve collections of objects with one query (fast) as an online-only publisher, we need fast
under the hood of Topaz (2) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Ambra ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Ambra features Ambra article ingestion search annotations discussions security mgmt ratings user profile/ preferences atom feeds multiple journals trackbacks SignOn Server article publication CrossRef registration DOI resolver Cache for web content and digital objects CAS single sign-on
Ambra <-> Mulgara interaction ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
article ingest (1) ,[object Object],<?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?> <!DOCTYPE article PUBLIC &quot;-//NLM//DTD Journal Publishing DTD v2.0 20040830//EN&quot; &quot;http://dtd.nlm.nih.gov/publishing/2.0/journalpublishing.dtd&quot;> <article xmlns:xlink=&quot;http://www.w3.org/1999/xlink&quot; xmlns:mml=&quot;http://www.w3.org/1998/Math/MathML&quot; article-type=&quot;research-article&quot; dtd-version=&quot;2.0&quot; xml:lang=&quot;EN&quot;> <front> <journal-meta> <journal-id journal-id-type=&quot;nlm-ta&quot;>PLoS ONE</journal-id> <journal-id journal-id-type=&quot;publisher-id&quot;>plos</journal-id> <journal-id journal-id-type=&quot;pmc&quot;>plosone</journal-id> <journal-title>PLoS ONE</journal-title> <issn pub-type=&quot;epub&quot;>1932-6203</issn>...
article ingest (2) ,[object Object],<info:doi/10.1371/journal.pone.0000000> <rdf:type> <http://rdf.plos.org/RDF/articleType/Research%20Article> <info:doi/10.1371/journal.pone.0000000> <rdf:type> <http://rdf.plos.org/RDF/articleType/research-article> <info:doi/10.1371/journal.pone.0000000> <rdf:type> <topaz:Article> <info:doi/10.1371/journal.pone.0000000> <rdf:type> <topaz:ObjectInfo> <info:doi/10.1371/journal.pone.0000000> <http://prismstandard.org/namespaces/1.2/basic/eIssn> '1932-6203' <info:doi/10.1371/journal.pone.0000000> <dc:creator> 'Bonnie Real' <info:doi/10.1371/journal.pone.0000000> <dc:creator> 'Richard Cave' <info:doi/10.1371/journal.pone.0000000> <dc:creator>...
Ambra – future development ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
semantic enhancement of content ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
© by David Shotton
 
system requirements ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
resources ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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Open Access Publishing on the Semantic Web

  • 1. Open Access Publishing on the Semantic Web
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  • 8. Ambra / Topaz journal publishing platform Apache Ambra Fedora + Mulgara RDF Store Topaz OTM Topaz Files CAS Fedora is used to store digital objects (XML, PDF, images, etc.) article metadata, annotations (annotea) and user information (foaf) is stored as triples in Mulgara Topaz is used for storage and retrieval of the digital objects and triple stores through the Objects to Triples Mapping (OTM) Ambra (user interface) CAS single sign-on service Apache webhead
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  • 10. why Objects to Triples Mapping (OTM)? don’t walk a tree to retrieve objects (slow) instead, retrieve collections of objects with one query (fast) as an online-only publisher, we need fast
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  • 13. Ambra features Ambra article ingestion search annotations discussions security mgmt ratings user profile/ preferences atom feeds multiple journals trackbacks SignOn Server article publication CrossRef registration DOI resolver Cache for web content and digital objects CAS single sign-on
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  • 19. © by David Shotton
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