University of Oxford

David M. Shotton

**Executive summary  
**

*Introduction  
*

To general readers of this blog, this post will appear different from
normal posts. Rather than being about a particular topic, it pulls
together a summary of the work undertaken over the past year within the
Open Citations Project supported by the JISC, and is primarily intended
to assist JISC evaluation of the project and its outputs. Details of the
work undertaken and the outputs from this project have mostly been
described in previous blog posts, to which this post will frequently
refer.

*Project scope and purpose  
*

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 information in RDF
and to make citation links as easy to traverse as Web links.

*Project aims  
*

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.

- <div>

  To **convert the reference lists within all the PMC Open Access subset
  articles to RDF**, and their publication as open linked data that
  third parties can use in novel ways.

  </div>

*Principle deliverables and outputs  
*

- The [SPAR](http://purl.org/spar/) (Semantic Publishing and
  Referencing) Ontologies.

- [Graffoo](http://www.essepuntato.it/graffoo) and
  [LODE](http://lode.sourceforge.net/), 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 Blog](http://opencitations.wordpress.com/) in
  which activities and outputs are described.

- The **Open Citations Corpus** of bibliographic citation data encoded
  in RDF and published as Open Linked Data.

- <div>

  The
  [[OpenCitations.net]{style="color: blue;text-decoration: underline"}](http://opencitations.net)
  web site, to provide user access to the [Open Citations
  Corpus](http://opencitations.net/source-data/).

  </div>

-     The [Open Citations Project
  software](https://github.com/opencitations/)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.

*Primary beneficiaries  
*

- Scholars worldwide, particularly in the biomedical sciences, by
  providing better access to bibliographic and citation data.
- Academic publishers and repository managers, by providing a semantic
  infrastructure and tools to enable their outputs and holdings to join
  the semantic web of open linked data.

**Background  
**

In 2008, Katie Portwin and I had an enjoyable summer 'souping up' a
*PLoS Neglected Tropical Diseases* article by Reis *et al*. (2008) \[1\]
that I had downloaded as an XML file from the journal web site in late
April, one week after it had been published. The resulting enhanced
publication, available
[here](http://imageweb.zoo.ox.ac.uk/pub/2008/plospaper/latest/), became
an exemplar of what is possible in the realm of semantic publishing,
while undertaking that work was very influential in shaping the course
of my more recent activities.

One of the things we undertook was to mark up the reference list with
annotations that clarified the nature of the cited entity (e.g. book,
journal article, medical report) and the reason the authors had cited
those entities (used data from, obtained background from, extended,
etc.) -- annotation that we took care to verify with the authors
themselves before publishing them!

While we undertook that work manually, it quickly became apparent that
what we needed was an ontology from which a controlled vocabulary of
such terms could be used to create both human- and machine-readable
metadata describing the citations and the cited entities. We therefore
developed a draft ontology that we subsequently split to form the basis
of the first two ontologies of the suite of
[SPAR](http://purl.org/spar/) (Semantic Publishing and Referencing)
Ontologies described
[elsewhere](http://opencitations.wordpress.com/2010/10/14/introducing-the-semantic-publishing-and-referencing-spar-ontologies/)
on this blog, namely [CiTO](http://purl.org/spar/cito/), the Citation
Typing Ontology to describe the relationships between the citing and
cited entities, and [FaBiO](http://purl.org/spar/fabio/), the
FRBR-aligned Bibliographic Ontology, to describe the cited entities
themselves.

Using these tools, we were able to mark up the reference list from Reis
*et al*., and publish it as RDF.

From there it was but a small step to dream of the day when the
references from all biomedical research articles would be published as
open linked data, and to think what we could do to make that dream a
reality.

And it was obvious where to start -- with the Open Access subset of
journal articles available in PubMed Central (PMC), all nicely marked up
in XML using the National Library of Medicine DTD.

**Table of contents  
**

The various aspects of the Open Citations Project and its outputs are
described in the following blog posts, complete with diagrams, data
tables, and screen shots where appropriate. These are organized into the
following set of distinct topics:

- Standards

- The SPAR ontologies for bibliographic and data entities and their
  citations

- Graffoo and LODE -- tools for ontology visualization and documentation

- Third-party applications of our ontologies

- Mappings to the SPAR ontologies, and exemplar RDF encodings

- Development of data citation methods and protocols

- <div>

  The creation of the Open Citation Corpus of linked bibliographic
  citation data

  </div>

**1 Standards**

[[Advantages of Ontological Standards in
Scholarly Publishing]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/87)

[[Nomenclature for citations
and references]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/144)

**2 The SPAR ontologies for categorizing bibliographic and data entities
and their citations  
**

The SPAR ontologies described in the following blog posts were developed
jointly with Silvio Peroni, a brilliant graduate student from the
University of Bologna, who spent the last six months of 2010 working
with me as an intern in Oxford, where he became an honorary member of
the Open Citations Project, contributing very significantly to our
achievements. His supervisor Fabio Vitali and the Department of
Information Science at the University of Bologna are to be congratulated
and thanked for their enlightened requirement that all their graduate
students spend an internship overseas, since without his collaboration
and great skill, much of this development would not have been possible
within the available time, if at all.

[[Introducing the Semantic Publishing and Referencing
(SPAR) Ontologies]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/16)

[[New web site for the
SPAR ontologies]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/55)

[[Functional clustering of
CiTO properties]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/91)

[[Extending FRBR
within FaBiO]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/95)

[[Categorising bibliographic resources with FaBiO
and SKOS]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/101)

[[CiTO4Data -- a new data-centric citation
typing ontology]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/128)

[[Using FaBiO to describe
data entities]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/131)

**3 Graffoo and LODE -- tools for ontology visualization and
documentation  
**

These tools have been developed by Silvio Peroni, an honorary member of
the Open Citations Project, as explained above.

[[Graffoo, a Graphical Framework for
OWL Ontologies]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/71)

[[Using LODE for
ontology visualization]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/62)

**4  Third-party applications of our ontologies  
**

Our work to develop a standard semantic infrastructure for bibliographic
and data entities and their citation is new. Nevertheless, we have
received encouraging responses when we have presented our work at
international publishing venues such as the 2010 ALPSP Conference and
the 2010 STM Innovation Conference.

Apart from local applications at the University of Oxford, the
University of Bologna, and the University of Manchester (for the Utopia
Project), and adoption of the SPAR ontologies by the University of
Harvard both to complement SWAN (Semantic Web Applications in
Neuromedicine) and to mark up astrophysics data (Accomazzi and Dave
(2011) Semantic Interlinking of Resources in the Virtual Observatory
Era. [arXiv:1103.5958](http://arxiv.org/abs/1103.5958)), we have
expressions of interest from PLoS, Nature and Il Mulino, a major
academic publisher in Italy, who are looking to improve their metadata
encoding as RDF. We are also interacting with the British Library in
mapping the DataCite Metadata Kernel to RDF (see below), and with the
Dryad Data Repository in creating RDF mappings of Dryad metadata to RDF
and, as part of the JISC Dryad-UK Project, in developing
[MIIDI](http://www.miidi.org/) and MIIDI-structured RDF metadata for
infectious disease papers and datasets, using SPAR ontologies where
appropriate, with the aim of permitting authors to submit rich metadata
to Dryad.

The following blog posts describe uptake and use of CiTO in CiteULike
and WordPress.

[[Use of CiTO
in CiteULike]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/31)

[[How to employ CiTO
in CiteULike]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/43)

[[Using CiTO
in WordPress]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/1044)

**5 Mappings to the SPAR ontologies, and exemplar RDF encodings  
**

[[Comparison of BIBO
and FaBiO]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/109)

[[BIBO2SPAR, an RDF Mapping of BIBO to the
SPAR Ontologies]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/113)

[[DataCite2RDF -- Mapping DataCite Metadata Scheme Terms
to ontologies]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/139)

**6 Development of data citation methods and protocols  
**

[[Nomenclature for data publications
and citations]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/144)

[[Questions of granularity -- Dryad's use of DataCite DOIs for data
citation]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/148)

[[How to
cite data]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/153)

[[Pensoft Journals policy and author guidelines on data publication
and citation]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/156)

**7 The creation of the Open Citation Corpus of linked bibliographic
citation data  
**

This achievement is almost entirely as the result of the excellent work
of our chief data wrangler Alex Dutton, whose skill and natural feel for
linked data has done wonders for this project.

The following set of blog posts describe the starting corpus from PubMed
central, our transformation of it to RDF, the problems we encountered
along the way, the resulting Open Citations Corpus, and the potential
uses to which the resulting open citation data can now be put. [  
]{style="background-color: yellow"}

[[Input data for Open Citations -- the PMC Open
Access Subset]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/168)

[[Garbage in, garbage out -- problems with
bibliographic references]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/174)

[[Who wrote this paper? Author list problems in PubMed
Central references]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/178)

[[Citation
correction methods]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/182)

[[The citation processing pipeline and the Open
Citations Corpus]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/185)

[[JISC Open Citations Project
web site]{style="color: blue;text-decoration: underline"}](https://opencitations.hypotheses.org/200)

[Like a kid with a new train set! Exploring citation
networks](http://opencitations.wordpress.com/2011/07/03/like-a-kid-with-a-new-train-set-exploring-citation-networks/)

**  
JISC Administrative Data for Open Citations Project**

This information, extracted from the [JISC Expo DOAP (Description of a
Project)
spreadsheet](https://spreadsheets.google.com/ccc?key=0ArsNASxXZiL6dC1mWWFMMjRWSmVha0E1WmdlQ05KcEE&hl=en#gid=7), 
is to be found in a [separate blog post,
here](http://opencitations.wordpress.com/2011/07/03/jisc-administrative-data-for-open-citations-project/).

**The Future  
**

While this is the formal Final Blog Post for the JISC-funded Open
Citations Project, that was funded for a year from 1^st^ July 2010, our
work is not yet finished. We cherish grand ideas for the liberation of
the reference lists from all scholarly journal articles, using the Open
Citations Corpus as an exemplar, in collaboration with publishers and
organizations such as CrossRef who handle such citation data on behalf
of publishers on a daily basis.

This work will only be finished when it is longer up to an individual
academic research group to take on the task of citation liberation, but
when each publisher publishes the citation data from each of their
journal articles as open linked data on their own web sites, marked up
using agreed ontological standards that we have proposed, freely
available for scholar around the world, from Bangladesh to Zimbabwe, and
from Holland to New Zealand, to use and explore, independent of their
ability to afford subscription access to the journal articles from which
the citations are made.


**Executive summary **  *Introduction *  To general readers of this blog, this post will appear different from normal posts. Rather than being about a particular topic, it pulls together a summary of the work undertaken over the past year within the Open Citations Project supported by the JISC, and is primarily intended to assist JISC evaluation of the project and its outputs.

Messaggi di Rogue Scholar

JISC Open Citations Project – Final Project Blog Post