Digital resources in the Social Sciences and Humanities OpenEdition Our platforms OpenEdition Books OpenEdition Journals Hypotheses Calenda Libraries OpenEdition Freemium Follow us

Open Citations Extension Project

I am pleased to announce that the JISC have funded an extension to the Open Citations Project to run from 1st August 2012 until 31st January 2013, during which we will review and revise the technology used to create the Open Citations Corpus, will update the content provided by PubMed Central, and will improve its presentation.  We will also prototype value-added services over the open citations data, to demonstrate their usefulness and to justify further funding that will permit a major expansion of the corpus in 2013 to include reference lists from subscription-access journals, including those from Nature Publishing Group, Science and other AAAS publications, and Oxford University Press.  In preparation for this, we will collaborate with CrossRef to determine how best to ingest reference data into the Open Citations Corpus in an on-going manner.

Full details are given in the Case for Support.  Watch this space!

Oxford University Press to support Open Citations

I am delighted to announce that Cathy Kennedy, OUP’s Senior Publisher for Journals, has just written to me as follows:

“Oxford University Press is delighted to support the Open Citation Corpus initiative in the interest of furthering and disseminating scholarship.  We are making the reference lists of articles in a number of journals we own available for inclusion in the Open Citations Corpus, and will be consulting further with our partner societies on extending the initiative to include their journals in due course”.

OUP thus becomes the third publisher of subscription-access journals, and the first university press, to declare its willingness to make the reference lists in journal articles publicly available.  Congratulations, OUP!

Are we starting to see the beginning of a sea change in attitudes?  Watch this space.

Open Citations and Semantic Publishing

Given the renewed interest among publishers in the Open Citations Corpus, following the decisions by Nature Publishing Group, publisher of Nature, and by the American Association for the Advancement of Science, publisher of Science, to open their citation data for inclusion in the corpus, I thought it would be helpful to provide links to videos of two conference presentations I gave that describe the Open Citations Corpus in the context of our other work in the area of semantic publishing.

The first of these was an invited contribution with the title Enriching Scientific Citations to Facilitate Knowledge Discovery, given to publishers at the Scientific, Technical and Medical Publishers Innovations Seminar 2010 entitled “Flows in Flux: how publishing technologies change the researcher’s life”, held in London, UK, on 3rd December 2010:

lecture: http://river-valley.tv/media/conferences/stm-innovation-2010/0202-David-Shotton/

slides: http://imageweb.zoo.ox.ac.uk/pub/2010/Presentations/SHOTTON_Citations_STM-Innovations-Seminar-03Dec2010.pdf

abstract: http://imageweb.zoo.ox.ac.uk/pub/2010/Presentations/STM_Innovations_Seminar_2010_ABSTRACTS.pdf

The second presentation, given almost a year later, was an invited contribution with the title The SPAR (Semantic Publishing and Referencing) Ontologies and the Open Citation Corpus, given to librarians at SWIB11 (Semantic Web in Bibliotheken; Semantic Web in Libraries Conference 2011) “Scholarly Communication in the Web of Data”, held in Hambrug, Germany on 30th November 2011:

lecture: http://www.scivee.tv/node/39208

slides: http://imageweb.zoo.ox.ac.uk/pub/2011/presentations/Shotton_SWIB11_SPARandOpenCitationCorpus_30Nov2011.pptx.pdf

abstract: http://imageweb.zoo.ox.ac.uk/pub/2011/presentations/Shotton_Abstract_for_Presentation_at_SWIB11.pdf

Further details of the Open Citations Corpus and the SPAR ontologies, and their applications are, of course, given in this Open Citations and Semantic Publishing blog, for which the following two posts provide the best introduction for those coming here for the first time:

JISC Open Citations Project – Final Project Blog Post

Introducing the Semantic Publishing and Referencing (SPAR) Ontologies

Science joins Nature in opening reference citations

Hot on the heels of my announcement on Monday that Nature Publishing Group has agreed to open its articles’ reference lists, I am delighted to announce that Science Magazine, the American Association for the Advancement of Science’s premier global science weekly, together with the other AAAS journals Science Signalling and Science Translational Medicine, will also open their articles’ reference lists, and contribute the bibliographic citations contained within these lists as open linked data to an expanded Open Citations Corpus, where they will be freely available for everyone to use in whatever manner they choose.

Preparations to expand the corpus in this manner, by integration with the reference processing pipeline of the CrossRef Cited-By Linking service, will be undertaken over the last six months of this year, and incorporation of the references from the AAAS journals into the expanded Open Citations Corpus is planned to commence in the first half of 2013.

Now that the world’s two most presigeous scientific journals have declared their hands, it is time for other subscription-access publishers to step up and join them, for the reasons given in my earlier post.  I am presently in discussion with a small number of other major STM publishers, and hope to be able to make further announcements in the near future.  However, there are many other publishers with whom I have not yet been able to make personal contact.  Those who would also like to become ‘early adopters’ of the Open Citations publishing model should contact me at <david.shotton@zoo.ox.ac.uk>.

Access to Citation Data

The JISC, in response to its invitation to tender, has recently funded Curtis+Cartwright Consulting Ltd, a research and strategy consultancy, to undertake an independent study entitled Access to Citation Data: A Cost-Benefit and Risk Review and Forward Look.  Evidence gathering for the study has just started, and the consultants are due to produce a report on this subject by next February.  This report will be one of a series of high profile reports that the JISC is commissioning to inform the UK FE/HE sector on key issues relating to digital infrastructure.

The JISC has invited me to serve on the steering group for this study, which will in particular be reviewing the Open Citations Corpus, both to provide intelligence and to act as a case study and as a potential recommended corpus of citation data.

I look forward to working with the review team, starting later this month, and anticipate that we will benefit from this investigation as well as contribute to it, since we anticipate that Curtis+Cartwright will be able to advise on sustainable business models for such open access citation data corpora.

Nature to open its reference list data

Bibliographic references are the links that knit together independent scholarly endeavours.  I am thus delighted to announce that Nature Publishing Group, publisher of Nature, Nature Genetics and many other leading journals, has agreed to open its articles’ reference lists, initially for a selected number of NPG journals, and contribute the bibliographic citations contained in these lists as open linked data to an expanded Open Citations Corpus, where they will be freely available for everyone to use in whatever manner they choose.  Preparations to expand the corpus in this manner, by integration with the reference processing pipeline of the CrossRef Cited-By Linking service, will be undertaken over the next six months of this year, and incorporation of the references from the selected NPG journals into the expanded Open Citations Corpus is planned to commence in the first half of 2013.

As the first subscription-access publisher to opening its reference lists in this way, Nature Publishing Group is further demonstrating its commitment to ‘lead from the front’ in its embrace of new semantic publishing technologies.  Only two months ago, this publisher announced its decision to open up the bibliographic records of its journal articles as open linked data.  On 4th April, NPG’s Linked Data Platform press release read:

“Nature Publishing Group (NPG) today is pleased to join the linked data community by opening up access to its publication data via a linked data platform. NPG’s Linked Data Platform is available at http://data.nature.com.      The platform includes more than 20 million Resource Description Framework (RDF) statements, including primary metadata for more than 450,000 articles published by NPG since 1869. In this first release, the datasets include basic bibliographic information (title, author, publication date, etc) as well as NPG-specific ontology terms. These datasets are being released under an open metadata license, Creative Commons Zero (CC0), which permits maximal use/re-use of this data.      NPG’s platform allows for easy querying, exploration and extraction of data and relationships about articles, contributors, publications, and subjects. Users can run web-standard SPARQL Protocol and RDF Query Language (SPARQL) queries to obtain and manipulate data stored as RDF. The platform uses standard vocabularies such as Dublin Core, FOAF, PRISM, BIBO and OWL, and the data is integrated with existing public datasets including CrossRef and PubMed.      More information about NPG’s Linked Data Platform is available at http://developers.nature.com/docs. Sample queries can be found at http://data.nature.com/query. ”

We very much hope that NPG’s example will encourage other subscription-access publishers to open their own journal article reference lists, and become early adopters of Open Citations.  Reasons why subscription-access publishers should willingly join NPG and open their citation data are given in my previous blog post.  While at first coverage among subscription-access publishers will be incomplete, this expanded Open Citation Corpus will, I am sure, draw in increasing numbers of publishers, and in true Web 2.0 style will become more useful the more publishers participate, resulting in value-added bibliographic and bibliometic services being created over the open data. Other subscription-access publishers who would like to contribute their journal article references to the Open Citations Corpus should contact me at <david.shotton@zoo.ox.ac.uk>.

Why publishers should open their references

Why should the publishers of subscription-access journals, who presently generate income from the sale of access to peer-reviewed full text scholarly articles, be willingly open the reference lists of these articles, and contribute these to the Open Citations Corpus for publication as open linked data? I would like to suggest the following reasons:

1. There is a general move towards open data, which is widely regarded as a common good. This includes citation data, i.e. bibliographic references from one article to another (in RDF Turtle format: A cito:cites B . ).
2. The reference lists at the end of journal articles are works of scholarship by the authors, who have chosen to include certain references and exclude other potentially citable papers from the reference list. However, the references themselves are simply items of bibliographic data, formatted according to the journal style, and do not benefit from the author’s creative input.
3. The reference list, together with the front matter (including the bibliographic information about the article itself) and the abstract, has traditionally been included within the copyright protection enjoyed by the article as a whole. However, the bibliographic information about the article and the article’s abstract are commonly made freely available, for example through PubMed. This same openness should now be afforded to the reference list within each article.
4. There is a home for such reference citation data: the Open Citations Corpus has been specifically created to house and publish scholarly bibliographic citation data, and is now preparing to welcome article reference lists from subscription-access journals, to supplement those already contributed from open-access journals.
5. For those publishers who already contribute their reference information to CrossRef as part of its Cited-By Linking service, this can be accomplished without any change to the publisher’s own publishing workflows, just by giving permission for CrossRef to flag the articles of certain journals as having open references. Open Citations intends to collaborate with CrossRef by harvesting the reference lists from such flagged articles, parsing them into RDF, and adding them to the Open Citations Corpus. Provided that the references are already being submitted to CrossRef, no work will have to be done by the publisher, and no changes in publishing procedure will be involved.
6. Open Citations will publish each reference list as an independent RDF Named Graph, with a unique URI, thereby protecting the integrity of the article reference list as a unit of scholarship, the source of which will be explicitly acknowledged.
7. The open citations data will then be offered back to publishers to use as they wish, e.g. for visualization of citation networks, calculation of metrics, etc., providing easier and more usable access to their own citation data than is currently afforded by commercial providers, who do not provide such data in linked data format.
8. Publishers will also be free to host their own open citations data, should they wish to do so.
9. For the majority of publishers, who would still receive subscriptions on the full articles themselves, opening their article reference lists in this way will cost nothing in terms of lost revenue.
10. Indeed, participation in the Open Citation Corpus will bring the following benefits to subscription-access publishers:
– Access to services to be built over the aggregated open citations data, for example an automated reference correction service available to editors upon receipt of a manuscript, for the automated pre-publication correction of errors in reference lists prior to article publication.
– Increased exposure to users of the references to the publisher’s own journal articles – a form of advertising. While at first coverage among subscription-access publishers will be incomplete, this expanding Open Citation Corpus will, in true Web 2.0 style, become more useful the more publishers participate.
– Even while coverage is incomplete, the Open Citations Corpus by its very nature contains reference citations to all the key papers published in every field covered – currently to all the key papers published in every biomedical field, enabling readers more easily to identify and find the most highly cited papers of each contributing publisher.
– Opening citations data will result in white-listing and general good-will from funding agencies, government and other advocates of open data, who might otherwise mandate publication by grantees in alternative open-access journals.
– Opening citations data will lead to support from scholars and researchers themselves, who wil be more inclined to publish in that publisher’s journals, feeling that at last the publishers would be giving back to them some of their own data, rather than selling it back to them as at present.

As my next blog post shows, one leading subscription-access publisher is now willing to open its journal article references in the way I have suggested.  Others who would like to so the same should contact me at <david.shotton@zoo.ox.ac.uk>.

Five Stars Ontology

To accompany today’s publication in D-Lib Magazine of the article The Five Stars of Online Journal Articles – a framework for article evaluation highlighted in the previous post, I have today also published The Five Stars Ontology, a simple ontology written in OWL 2 DL that forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies. It is intended for use by publishers and others wishing to encode Five Stars ratings, such as those exemplified in the D-Lib article, in machine-readable form, so they can accompany other machine-readable metadata for the article.  To exemplify this, the following RDF graph, shown in turtle notation, gives the Five Stars ratings for the D-Lib article itself:

<http://dx.doi.org/10.1045/january2012-shotton>
     fivestars:hasPeerReviewRating “3”^^xsd:nonNegativeInteger ;
     fivestars:peerReviewRatingComment “Post-publication responsive
          peer review of the preprint.” ;
     fivestars:hasOpenAccessRating “4”^^xsd:nonNegativeInteger ;
     fivestars:openAccessRatingComment “Gold/libre open access
          without author fee!” ;
     fivestars:hasEnhancedContentRating “1”^^xsd:nonNegativeInteger ;
     fivestars:enhancedContentRatingComment “Plentiful Web links in
          text and to all references. No additional semantic
          enhancement of text.” ;
     fivestars:hasAvailableDatasetsRating “0”^^xsd:nonNegativeInteger ;
     fivestars:availableDatasetsRatingComment “Not applicable.” ;
     fivestars:hasMachine-readableMetadataRating “1”^^xsd:nonNegativeInteger ;
     fivestars:machine-readableMetadataRatingComment “Structural
          markup in HTML only.” ;
     fivestars:hasOverallFiveStarsRating “9”^^xsd:nonNegativeInteger ;
     fivestars:overallFiveStarsRatingComment “The nature of this
          article, being a position paper rather than a research
          paper with primary research data, has influenced the
          overall rating obtained.” .

Comments on the paper Ceci n’est pas un hamburger

Very VERY occasionally I read a paper that is so well written, and which addressed the points so accurately and so eloquently, that I rejoice.  The paper by Pettifer et al. entitled Ceci n’est pas un hamburger: modelling and representing the scholarly article that appeared in Learned Publishing last October [1], is one of this special handful. 

It is beautifully written, and the scope of its coverage is highly pertinent to the recent discussions on the future of research communication detailed in the previous post.  It also has the benefit of being published as an Open Access paper in what is otherwise a subscription access journal. 

I particularly liked the authors’ evaluation of FRBR‘s classification into works, expressions and manifestations to describe the relative benefits and drawbacks of PDF, XML, and RDF as representations of a journal article, since that is exactly what Silvio Peroni and I modelled in FaBiO, the FRBR-aligned Bibliographic Ontology.

The paper is also an excellent introduction to Utopia Documents, the ‘smart’ PDF reader that the authors have developed, which is used to create the Semantic Biochemical Journal, and which is to be highly recommended for personal use to enrich the experience of reading articles in PDF format on-line.  The Utopia Documents software is freely available, and can be downloaded from http://www.utopiadocs.com.

[1] Pettifer S, McDermott P, Marsh J, Thorne D, Villeger A and Attwood TK (2011).  Ceci n’est pas un hamburger: modelling and representing the scholarly article.  Learned Publishing, 24 (3): 207-220.  http://dx.doi.org/10.1087/20110309.