Open Access Publishing on the Semantic Web

the Public Library of Science (PLoS) non-profit, Open Access STM ( scientific, technical and medical) publisher focused on life-sciences mission: open the doors to the world's library of scientific knowledge by giving any scientist, physician, patient, or student - anywhere in the world - unlimited access to the latest scientific research all research articles are published under the Creative Commons Attribution License

non-profit, Open Access STM ( scientific, technical and medical) publisher focused on life-sciences

mission: open the doors to the world's library of scientific knowledge by giving any scientist, physician, patient, or student - anywhere in the world - unlimited access to the latest scientific research

all research articles are published under the Creative Commons Attribution License

why Open Access? taxpayers pay for research but print and online journals are available only to subscribers traditional publishers own the copyright to all the researchers published materials licensing is complex and restrictive libraries are struggling to provide access to all required journals because of subscription fees

taxpayers pay for research but print and online journals are available only to subscribers

traditional publishers own the copyright to all the researchers published materials

licensing is complex and restrictive

libraries are struggling to provide access to all required journals because of subscription fees

PLoS Journals publish seven peer-reviewed journals PLoS Biology, PLoS Medicine (flagship) PLoS Pathogens, PLoS Computational Biology, PLoS NTDs, PLoS Genetics (community) PLoS ONE (disruptive force) largest journal is PLoS ONE high volume, very efficient workflow ~6500 articles as of July 24, 2009 publish >400 articles a month (and growing) using semantic platform since December ‘06 PLoS ONE first journal on new platform all journals migrated to platform as of May 12, ‘09 ~13,000 articles published on semantic platform

publish seven peer-reviewed journals

PLoS Biology, PLoS Medicine (flagship)

PLoS Pathogens, PLoS Computational Biology, PLoS NTDs, PLoS Genetics (community)

PLoS ONE (disruptive force)

largest journal is PLoS ONE

high volume, very efficient workflow

~6500 articles as of July 24, 2009

publish >400 articles a month (and growing)

using semantic platform since December ‘06

PLoS ONE first journal on new platform

all journals migrated to platform as of May 12, ‘09

~13,000 articles published on semantic platform

state of STM publishing platforms publishing platforms are proprietary or hosted by a third party (PLoS) most publishers treat online journals as digital repositories for research articles “ end of the road” for research articles online backseat to print journals ($$) the internet changes everything cheap and fast global quick search and retrieval open source solutions exist today (e.g. Open Journal Systems/Drupal, Rhaptos/Zope) but limited features in 2006

publishing platforms are proprietary or hosted by a third party (PLoS)

most publishers treat online journals as digital repositories for research articles

“ end of the road” for research articles

online backseat to print journals ($$)

the internet changes everything

cheap and fast

global

quick search and retrieval

open source solutions exist today (e.g. Open Journal Systems/Drupal, Rhaptos/Zope) but limited features in 2006

big ideas for transforming journal publishing open source publishing platform semantic repository to mine the unknown (semantic) relationships in research articles a “Web 2.0” user interface provide features for post-publication annotation and discussion allowing for a “living” document notes inline with the content comments and discussions ratings © by wales.nhs.uk

open source publishing platform

semantic repository to mine the unknown

(semantic) relationships in research articles

a “Web 2.0” user interface

provide features for post-publication annotation

and discussion allowing for a “living” document

notes inline with the content

comments and discussions

ratings

… embarked down the path Topaz non-profit development team funded by the Moore Foundation intended as a journal publishing system for many types of publishing scholarly communications / Open Access eScience / eScholarship education libraries / museums semantic publishing platform based on Fedora institutional repository and Mulgara triple-store Topaz (back-end glue) Object to Triple Mapping (OTM) Object Query Language (OQL) © by Michael James Ambra journal publishing system (front-end user interface)

Topaz non-profit development team funded by the Moore Foundation

intended as a journal publishing system for many types of publishing

scholarly communications / Open Access

eScience / eScholarship

education

libraries / museums

semantic publishing platform based on Fedora

institutional repository and Mulgara triple-store

Topaz (back-end glue)

Object to Triple Mapping (OTM)

Object Query Language (OQL)

© by Michael James

Ambra journal publishing system (front-end user interface)

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) an Object-Triples-Mapping (OTM) library modeled after Hibernate Object-Relational Mapping (ORM) except the database is made of RDF triples instead of a relational database. provides a query language based on objects (OQL) an "object" based query syntax makes life a bit easier for developers OQL example select all articles with a given title: select a.id, a.author from Article a where a.title = 'Hello Dolly';

an Object-Triples-Mapping (OTM) library

modeled after Hibernate Object-Relational Mapping (ORM)

except the database is made of RDF triples instead of a relational database.

provides a query language based on objects (OQL)

an "object" based query syntax

makes life a bit easier for developers

OQL example

select all articles with a given title:

select a.id, a.author from Article a where a.title = 'Hello Dolly';

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) defines Java classes maps the classes into RDF Ambra defines models which are mapped into sets of triples in various graphs such as “article”, “annotation”, etc. models defined in Ambra provides support for storing files to a separate blob store (Fedora and/or Akubra) provides storage and retrieval of files and triples in a single transaction necessary to render an article with associated metadata (e.g. notes, ratings, etc.)

defines Java classes maps the classes into RDF

Ambra defines models which are mapped into sets of triples in various graphs

such as “article”, “annotation”, etc. models defined in Ambra

provides support for storing files to a separate blob store (Fedora and/or Akubra)

provides storage and retrieval of files and triples in a single transaction

necessary to render an article with associated metadata (e.g. notes, ratings, etc.)

Ambra first application built on Topaz journal publishing platform with “Web 2.0” features uses the FreeMarker templating engine to display the content received from Topaz service. uses the DOJO JavaScript toolkit to handle complex user interactions like annotations, ratings, etc. provides social networking features (in-line notes, comments, trackbacks) turns a reader of scientific articles into a knowledge contributor, knowledge that can be used by other users living document!

first application built on Topaz

journal publishing platform with “Web 2.0” features

uses the FreeMarker templating engine to display the content received from Topaz service.

uses the DOJO JavaScript toolkit to handle complex user interactions like annotations, ratings, etc.

provides social networking features (in-line notes, comments, trackbacks)

turns a reader of scientific articles into a knowledge contributor, knowledge that can be used by other users

living document!

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 Ambra inserts data into Mulgara in the following cases article Ingest post-publication annotations (comment, note, rating, trackback) admin actions (volume and issue collections, annotation moderation, etc.) user actions (create or edit a user profile) Mulgara uses OTM to pull data from Fedora and Mulgara Ambra transforms XML to HTML displays notes, comments, ratings, etc.

Ambra inserts data into Mulgara in the following cases

article Ingest

post-publication annotations (comment, note, rating, trackback)

admin actions (volume and issue collections, annotation moderation, etc.)

user actions (create or edit a user profile)

Mulgara uses OTM to pull data from Fedora and Mulgara

Ambra transforms XML to HTML

displays notes, comments, ratings, etc.

article ingest (1) Ambra expects an article package that contains an XML file in NLM-DTD format ( http://dtd.nlm.nih.gov/publishing/ ) <?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>...

Ambra expects an article package that contains an XML file in NLM-DTD format ( http://dtd.nlm.nih.gov/publishing/ )

article ingest (2) Ambra transforms the XML into an OTM object that Topaz pushes into Mulgara. <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 transforms the XML into an OTM object that Topaz pushes into Mulgara.

Ambra – future development article level metrics impact of the article above and beyond citations RDFa automatic article relationships semantic enhancement REST-based API ingest and publish many types of content / data structured and unstructured tags enhance search and browse direct access to Mulgara’s triple store sparql endpoint, RDFa

article level metrics

impact of the article above and beyond citations

RDFa

automatic article relationships

semantic enhancement

REST-based API

ingest and publish many types of content / data

structured and unstructured

tags

enhance search and browse

direct access to Mulgara’s triple store

sparql endpoint, RDFa

semantic enhancement of content add value to the content of a research article highlight text for selected terms protein names genus / species disease location / habitat etc. provide links to external sources to create new user interactions

add value to the content of a research article

highlight text for selected terms

protein names

genus / species

disease

location / habitat

etc.

provide links to external sources to create new user interactions

© by David Shotton

system requirements minimum - single server (Linux) with 8 Gb RAM … better (based on PLoS journals): 1 server for Fedora and Mulgara with 8Gb RAM 1 server for Ambra and Topaz with 8Gb RAM 1 server for Apache and CAS with 4Gb RAM PLoS journals on Ambra / Topaz 800k visits / month ~2 million pageviews / month Amazon AMI to test Ambra / Topaz available

minimum - single server (Linux) with 8 Gb RAM

… better (based on PLoS journals):

1 server for Fedora and Mulgara with 8Gb RAM

1 server for Ambra and Topaz with 8Gb RAM

1 server for Apache and CAS with 4Gb RAM

PLoS journals on Ambra / Topaz

800k visits / month

~2 million pageviews / month

Amazon AMI to test Ambra / Topaz available

resources Ambra website http:// www.ambraproject.org / Ambra mailing lists: http:// lists.topazproject.org/mailman/listinfo/ambra -users http://lists.topazproject.org/mailman/listinfo/ambra-dev Topaz website http:// www.topazproject.org / Fedora Commons website http://fedoracommons.org/ Richard Cave – rcave at plos.org

Ambra website

http:// www.ambraproject.org /

Ambra mailing lists:

http:// lists.topazproject.org/mailman/listinfo/ambra -users

http://lists.topazproject.org/mailman/listinfo/ambra-dev

Topaz website

http:// www.topazproject.org /

Fedora Commons website

http://fedoracommons.org/

Richard Cave – rcave at plos.org