JISC Administrative Data for Open Citations Project

Data copied from JISC Expo DOAP (Description of a Project) spreadsheet at https://spreadsheets.google.com/ccc?key=0ArsNASxXZiL6dC1mWWFMMjRWSmVha0E1WmdlQ05KcEE&hl=en#gid=7.

Project title: The Open Citations Project

Project tag: jiscopencite

Short project description

We will publish reference lists from Open Access biomedical journal articles as Linked Open Citation Data at http://opencitations.net.

Long project description

The Open Citations Project is global in scope, designed to change the face of scientific publishing and scholarly communication. Specifically, it aims to make it possible to publish bibliographic and citation information in RDF and to make citation links as easy to traverse as Web links.

To achieve this goal, we have had four primary aims:

  • To create a semantic infrastructure that makes possible the description of citations, references and bibliographic entities in RDF, since we found existing ontologies inadequate for our purpose.
  • To extend that semantic infrastructure to handle data citations and data entities, as well as bibliographic citations and bibliographic entities, mindful of Philip Bourne’s prediction that soon there will be no meaningful difference between a journal article and a database entry.
  • To provide exemplars of how these ontologies can be applied to real-world data, by creating mappings from existing encodings to RDF, and by creating RDF metadata relating to bibliographic and data entities and their citations.
  • To convert the reference lists within all the PMC Open Access subset articles to RDF, and to publish them as open linked data that third parties can use in novel ways.

Principle deliverables and outputs

  • The SPAR (Semantic Publishing and Referencing) Ontologies.
  • Graffoo and LODE, two novel tools for ontology visualization and documentation.
  • Mappings of various existing metadata schemes to RDF using SPAR.
  • Development of data citation methods and protocols
  • The Open Citations Corpus of bibliographic citation data encoded in RDF and published as Open Linked Data.
  • The OpenCitations.net web site, to provide user access to the Open Citations Corpus.
  • The Open Citations Project software used for processing the Pubmed Central Open Access corpus into Open Linked Data.

The net result is open citation data from life science journal articles available on the web, for utilization by academics, for citation network analysis applications, and for tracking the impact of research grant funding.

Secondary deliverables and outputs

Blog posts describing the experience and process by which the primary products from the project was produced: http://opencitations.wordpress.com/.

JISC Website Keywords

Data & Text Mining

Data Services & Collections

Open Technologies

Resource Discovery

Standards, Tools & Techniques

Web 2.0

Name of lead institution: University of Oxford

Department where project is primarily locate: Department of Zoology

Postcode where the project team is primarily based:  OX1 3PS

Name of person(s) responsible for JISC project documentation and reporting: Dr David Shotton

Email of person responsible for project documentation and reporting: david.shotton@zoo.ox.ac.uk

Phone / Skype for Person responsible for project documentation: 01865-271193 / skype: davidshotton

Names and roles of all people working on the project team

Dr David Shotton, Principal Investigator and Project Manager

Mr Benjamin O’Steen, Technical Developer – employed 50% FT from 01-07-2010 to 30-06-2011

Mr John Mansfield, Citation Data Manager – employed 100% FT from 14-07-2010 to 13-08-2010

Mr Alex Dutton, Citation Data Manager – employed 50% FT from 04-10-2010 to 30-06-2011

Names and roles of any and all project partners: None

Emails of all the team members, consultants, partners and any other person who will be working on or with the project

David Shotton <david.shotton@zoo.ox.ac.uk>

Benjamin O’Steen <bosteen@gmail.com>

John Mansfield <jbmansfield@gmail.com>

Silvio Peroni <speroni@cs.unibo.it>

Peter Murray-Rust <pm286@cam.ac.uk> (PI of Open Bibliography sister project – liaison)

Named end users who will be testing or using your software outputs

Anusha Ranganathan <anusha.ranganathan@bodleian.ox.ac.uk>

Steve Pettifer <steve.pettifer@manchester.ac.uk>

Tim Clark <twclark@nmr.mgh.harvard.edu>

Paolo Ciccarese <paolo.ciccarese@gmail.com>

Rahul Dave <rahuldave@gmail.com>

Alberto Accomazzi <aaccomazzi@cfa.harvard.edu>

Martin Fenner <fenner.martin@mh-hannover.de>

Egon Willighagen <egon.willighagen@gmail.com>

See also Final Blog Post http://opencitations.wordpress.com/2011/07/01/jisc-open-citations-project-%E2%80%93-final-project-blog-post/.

Number of named end users: 8

Project gmail account: None. Use <david.shotton@zoo.ox.ac.uk>

Project blog URI: http://opencitations.wordpress.com

RSS2 or ATOM feed for project blog: http://opencitations.wordpress.com/?feed=atom

URL of the code repository for versioned source code produced by project: https://github.com/opencitations/

See also http://github.com/benosteen/pairtree http://github.com/benosteen/rdfobject http://bitbucket.org/okfn/ofs http://code.google.com/p/opencitations/source/browse

URL for instructional documentation: http://opencitations.net/

OSS license you will you be using for the code generated from project: MIT license

Analytics Engine on your project blog, code repository and any other project web presence: Google Analytics being installed.

Creative Commons Licence used for project presentations and documentation: Creative Commons Attribution 3.0 Unported License

Creative Commons Licence used for project content: CCZero waiver

Project Start Date: 2010-06-01

Project End Date: 2011-06-30, extended to 2011-08-01

Total amount of money awarded to the project in Grant Letter: £99,998

Name of Institutional Budget Manager: Miriam Wood <miriam.wood@zoo.ox.ac.uk>

Link to final project post: https://opencitations.wordpress.com/2011/07/01/jisc-open-citations-project-%E2%80%93-final-project-blog-post/

PIMS URL for Project: https://pims.jisc.ac.uk/projects/view/1866

Link to Final Approved Published Budget: Pending.

JISC Open Citations: Wider Benefits to Sector & Achievements for Host Institution

One of the biggest challenges faced by modern scientists is information overload. The life sciences are probably the area most affected by it, with almost a million new entries being added to PubMed each year. While on-line publishing and bibliographic search engines have made the problem of finding individual research articles considerably easier, the present scholarly citation system inadequately exposes the knowledge networks that exist within the scientific literature, linking papers, authors and research projects.  Much of the problem stems from the lack of freely available citation data in machine-readable form.

In this Open Access age, it is a scandal that reference lists from journal articles, the core elements of the academic data cycle, are not freely available for use by scholars.   Current citation services are largely restricted to a small number of commercial companies whose valuable products are still insufficiently developed to satisfy all the needs of the academic community.

Google Scholar offers navigation through the citation network, but only in one direction – backwards. Thomson Reuter guards citation data in ISI Citation Index and Web of Knowledge as commercial assets, as does Elsevier for citation data in Scopus, with limited subscription-access search and display capabilities, and no methods for extracting citation data in bulk. Furthermore, they do not characterise the nature of citations between publications.

The value of citation data to the research community has grown as research evaluation has increased in importance. Citation metrics are increasingly used by institutions to establish their research quality, and by funding agencies to determine the effectiveness of their grant spending.

Citation data now need to be recognized as a part of the Commons – those works that are freely and legally available for sharing and reuse – extending the Science Commons / Open Knowledge Foundation philosophy to the world of scientific citation.

If machine-readable citation data for all scholarly publications were to be published freely on the Web, the construction and interrogation of citation networks would become trivially simple, with enormous advantages to scholarship. Thanks to CiteSeerX, citation data in computer science have been freely available for several years,

Similar access is now coming for other fields of scholarship, particularly for the biological sciences through CiteXplore. However, in none of these cases are the citation data available as Linked Open Data, and there are no convenient free tools, accessible to working research biologists, that permit them to visualize and navigate the literature by means of its citation network, or that permit knowledge analysts to pose generic questions over the whole corpus, such as determining whether those who publish in Open Access journals are more prone to cite other Open Access articles, in comparison with those who do not.

This project will produce citation information as Open, Linked Data which will address the short-comings of the current situation, aiming to provide researchers with the tools to explore the citation network.

JISC Open Citations: Aims, Objectives and Final Outputs

The Open Citations Project is global in scope, designed to change the face of scientific publishing.

It aims to make bibliographic citation links as easy to use as Web links. Its goals are three-fold:

  • To establish OpenCitations.net, a public RDF triplestore for biomedical literature citations.

(Note: In this context, a bibliographic citation is a reference within a particular citing work to another publication termed the cited work. This use of the word ‘citation’ should be clearly distinguished from the common related use of this word to indicate the cited work itself. Within this application, ‘cite’ and ‘citation’ denote the performative act of citation itself, not the target document of that citation.)

  • To harvest the reference lists from many current and recent open access journal articles, and to convert these datasets into RDF, starting with those in UK Pubmed Central, those published by the Public Library of Science and Biomed Central, those from other publishers willing for CrossRef to release their data, and articles from other Open Access repositories like EPrints.
  • To publish these citation datasets as Open Linked Data on the Talis Connected Commons Platform under an open data license in both human- and computer-accessible formats.

As such, the Open Citation Project seeks to promote citation datasets as first class information objects. The reference list from each article processed will be published as an individual named graph, with its own individual Digital Object Identifier (DOI) assigned by the relevant publisher via CrossRef or by the British Library on behalf of the DataCite Project.

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