OpenCitations blog – Page 14 – The blog of the OpenCitations Infrastructure

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.” .

Five Stars article published in D-Lib Magazine

I recently posted a brief description of an article entitled The Five Stars of Journal Articles, pointing to a preprint of this article in Nature Preceedings. This is to announce that a revised and extended version of that article has now been published in D-Lib Magazine [1].

While D-Lib Magazine does not undertake formal peer review of its articles, and has a policy of not publishing articles that have previously appeared elsewhere in the same form, this Five Stars article has benefited from substantial comments made by colleagues on the Nature Preceedings preprint (see the D-Lib article’s Acknowledgements for details). Those comments constituted an effective post-publication responsive peer review of the preprint, and stimulated me to make a major revision and expansion of the text, resulting in significant enhancements to both the content and the quality of the resulting D-Lib article. I am grateful both to my colleagues who contributed to that post-publication community review of the preprint, and to the staff of D-Lib Magazine for their understanding of its value.

[1] David Shotton (2012). The Five Stars of Online Journal Articles — a Framework for Article Evaluation. D-Lib Magazine (January/February 2012), Volume 18, Number 1/2. doi:10.1045/january2012-shotton.

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.

2011 retrospective: meetings on the future of research communications

What a year it has been! Four key meetings were held during 2011, bringing together academics, computer scientists and scholarly publishers to discuss the future of scholarly communication. The first of these, a workshop entitled Beyond the PDF, organized and hosted in January 2011 by Philip Bourne at the University of California, San Diego, itself built on an earlier HyPER workshop organized in May 2010 in Amsterdam by Anita de Waard of Elsevier Labs (de Waard et al. 2009, [1]). It was followed by a meeting entitled Beyond Impact, organized by Cameron Neylon of STFC at the Wellcome Trust headquarters in London in May 2011, that considered alternative metrics to the journal impact factor for the evaluation of research – and particularly researcher – merit. In August 2011, a further meeting on The Future of Research Communication, organized by Phil Bourne of UCSD, Tim Clark of Harvard University, Robert Dale of Macquarie University, Anita de Waard of Elsevier Labs, Ivan Herman of the W3C, Eduard Hovy of the University of Southern California and myself, was held in Germany as a Schloss Dagstuhl Perspectives Workshop. This led to the formation of the Force11 Community dedicated to the improvement of research communication and e-scholarship, and to the publication in October 2011 of the Force11 White Paper (Bourne et al., 2011), that was submitted as evidence both to the Royal Society’s Science as a Public Enterprise project and to the UK Cabinet Office’s public consultation Making Open Data Real. Finally, in October 2011, Microsoft Research and Harvard University jointly hosted a meeting in Cambridge, Massachusetts, entitled Transforming Scholarly Communication, that took these ideas forward.

Additionally, the benefits of Semantic Web technologies for libraries were recently discussed at the 2011 annual Semantic Web in Libraries meeting entitled Scholarly Communication in the Web of Data, held in Hamburg, Germany, in November 2011.

The thinking undertaken at these meetings contributed significantly to the formulation of my paper entitled The Five Stars of Online Journal Articles described in a previous post, and significantly advanced the community’s thinking as a whole both on semantic publishing of journal articles and on the issues surrounding research data publication.

I’m looking forward to what 2012 brings!

[1] de Waard A, Buckingham Shum S, Carusi A, Park J, Samwald M, and Sándor Á (2009). Hypotheses, Evidence and Relationships: The HypER Approach for Representing Scientific Knowledge Claims. In: Proceedings 8th International Semantic Web Conference, Workshop on Semantic Web Applications in Scientific Discourse (26 Oct 2009, Washington DC.). Lecture Notes in Computer Science, Springer Verlag: Berlin. http://oro.open.ac.uk/18563/.

Comments on IS DATA PUBLICATION THE RIGHT METAPHOR?

Is Data Publication the Right Metaphor? is an essay by Mark Parsons and Peter Fox to be published in the Data Science Journal, for which a preprint has been provided for open pre-publication community peer review at http://mp-datamatters.blogspot.com/2011/12/seeking-open-review-of-provocative-data.html.

To supplement the discussion this excellent essay has already prompted, I would like to add some belated comments relating to DOIs for dataset versions, peer review of datasets, metadata as first class scientific objects, and linking the data publication and linked data metaphors.

First, DOIs can easily be used to provide unique identifiers to datasets that undergo updating and versioning, as exemplified in the Dryad Data Repository, a repository for the publication of small heterogeneous biological datasets linked to peer-reviewed journal articles. Dryad DOIs permit the version numbers of each data package and of each of the data package’s constituent data files to be specified explicitly (see http://wiki.datadryad.org/wiki/DOI_Usage).

Second, relating to the problems of applying traditional models of peer review to datasets, it is important to realize a fundamental difference between a journal article and a dataset, namely that the journal article is an exercise in rhetorial persuasion, with the authors presenting selected data to convince the reader of the correctness of particular hypotheses – see, for example, papers on this topic by Anita de Waard et al. [1-3] – while datasets lack this rhetorial structure, and thus cannot be judged by the same standards of logical persuasiveness, fit between data and hypothesis, etc. Rather, datasets contain ‘mere facts’, albeit organized according to some underlying data model, and thus their review and quality control have to be “more like an audit that assures that a data set adheres to best practices of documentation, format, error characterization, etc.”. For this reason, citation links between datasets and the journal articles upon which they are based, as routinely given in the Dryad Data Repository, are of particular value, since the latter provide the peer-reviewed contextual framework within which to undestand the data.

Third, as mentioned by John Milner in the discussion of the essay at https://www.jiscmail.ac.uk/cgi-bin/webadmin?A1=ind1112&L=RESEARCH-DATAMAN, there is increasing recognition that the metadata describing a dataset should themselves also be recognised as independent first class scientific objects, with the possibility of publishing such a metadata file with its own DOI, either as a supplementary file within a data package, or as a ‘metadata paper’ within a ‘metadata journal’.

Finally, one way of linking the ‘data publication’ metaphor with the ‘linked data’ metaphor is to ensure that such metadata describing datasets are made available not only in human-readable form but also in machine-readable form, by publishing them as RDF, either as a separate named graph with a unique URI or embedded as RDFa within the human-readable metadata document.

Hope these comments help.

[1] de Waard, A., Breure, L., Kircz, J.G., Oostendorp, H. van (2006). Modeling Rhetoric in Scientific Publications. Current Res. in Inf. Sci. and Techn. pp. 352-356.

[2] de Waard, A., (2007). A Pragmatic Structure for the Research Article, in: Proceedings ICPW’07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL. (Eds.) Buckingham Shum, S., Lind, M. and Weigand, H. Published in: ACM Digital Library & Open University ePrint 9275.

[3] de Waard, A. and Kircz, J.G. (2008). Modeling scientific discourse – shifting perspectives and persistent issues, ELPUB2008. Open Scholarship: Authority, Community, and Sustainability in the Age of Web 2.0 – Proc. of the 12th Int. Conference on Electronic Publishing, June 2008, Eds. L. Chan and S. Mornati, pp. 234-245.

The Five Stars of Online Journal Articles

Many people will be familiar with Tim Berners-Lee’s five stars of linked data, categorising the publication of data on the web in levels of increasing usefulness. To complement these, I wish to propose the Five Stars of Online Journal Articles, in particular to characterize the potential for improvement to the primary medium of scholarly communication made possible by web technologies, including the semantic publishing approaches I have recommended and exemplified in recent presentations, blog posts and papers [1-5].

While Tim’s five stars of linked data are hierarchical, all relating to the same thing and each building on the preceding one, the five stars of online journal articles shown in the diagram below are complementary, forming a constellation arranged along five independent axes within a multi-dimensional publishing universe.

★ Peer review Ensure your your article is peer reviewed, to provide assurance of its scholarly value, quality and integrity.

★ Open Access Ensure others have cost-free open access to your published article, to ensure its greatest possible usefulness and readership.

★ Enriched content Use the full potential of web technologies and web standards to provide interactivity and semantic enrichment to the content of your online article.

★ Available datasets Ensure that all the data supporting the results you report are fully published under an open license, with sufficient metadata to enable their re-interpretation and reuse.

★ Machine-readable metadata Publish machine-readable metadata describing both your article and your cited references, so that these can be discovered automatically.

At present, many publishers primarily use the web simply as a cheap and convenient distribution medium for PDF documents that are essentially electronic facimiles of the printed page, ignoring the Web’s greater potential. The Five Stars of Online Journal Articles proposed here encapsulate a richer vision. Each star is highly desirable in its own right, but it is only by achieving them all in combination that we will really advance scholarly communication. Of course, the degree of achievement along each of these publishing axes can vary, analogous to the different stars within the constellation shining with varying luminosities.

So I want you to ask yourself:

“How do my online journal articles rate against these five stars?”

As an exercise in ‘drinking my own champagne’, I have evaluated references [1] to [4] against the five stars, and present those results, together with a full explanation of the five-point evaluation scale for each star, in an article [6] for which this blog post is summary. Here, to give you a flavour of that, I show the evaluations for Reis et al. (2008) (Reference [3]) before and after our semantic enhancements to that article that are separately described in Reference [2].

Original version of Reis et al. (2008) (http://dx.doi.org/10.1371/journal.pntd.0000228). Publisher: Public Library of Science.

Rating

Peer review (P) 3 Conventional peer review with author feedback.

Open Access (O) 4 Published in an open access journal with a Creative Commons attribution license.

Enriched content (E) 0 Article lacks useful web links in the text and lacks direct links to referenced papers.

Available datasets (A) 1 Figures and table within the article have their own DOIs, but are only downloadable as images, so that the data in the graphs and table are not available as actionable spreadsheets.

Machine-readable metadata (M) 1 Structural markup available in the XHTML version of the article.

Overall rating 9

Semantically enhanced version of Reis et al. (2008) (http://dx.doi.org/10.1371/journal.pntd.0000228.x001). Publisher: David Shotton, Oxford University.

Rating

Peer review (P) 3 Conventional peer review of the original article, with author feedback.

Open Access (O) 4 Enhanced version republished with a Creative Commons attribution license.

Enriched content (E) 4 Of many types, as fully described in Reference [2].

Available datasets (A) 2 Data for table and some figures kindly provided by the authors, and made available as downloadable actionable spreadsheets with their own DOIs.

Machine-readable metadata (M) 3 Structural and semantic markup within the text available as XHTML; embedded RDFa provides basic bibliographic information; two downloadable RDF files with their own DOIs accompany the enhanced article, one giving full bibliographic metadata about the article and the second providing bibliographic details, citation typing information and citation frequencies for all the cited references. Article summary available as a separate document, but not in machine-readable format.

Overall rating 16

Acknowledgements

I am most grateful to Bob DuCharme who, inspired by Berners-Lee’s five stars of linked data, challenged me to come up with five stars of online journal articles, following a talk I gave on semantic publishing. I also thank Tanya Gray and Katherine Fletcher for wise comments after reading preliminary drafts of the full paper [6], and wish particularly to acknowledge the specific input made by Silvio Peroni , who insisted that I specify evaluation scales for all five stars, and whose wise proposals concerning peer review and open access I have incorporated into the full paper.

References

[1] Shotton D (2009) Semantic Publishing: The coming revolution in scientific journal publishing. Learned Publishing 22: 85-94. doi:10.1087/2009202.

[2] Shotton D, Portwin K, Klyne G, Miles A (2009) Adventures in semantic publishing: exemplar semantic enhancement of a research article. PLoS Computational Biology 5: e1000361. doi: 10.1371/journal.pcbi.1000361.

[3] Reis RB, Ribeiro GS, Felzemburgh RDM, Santana FS, Mohr S, et al. (2008) Impact of environment and social gradient on Leptospira infection in urban slums PLoS Neglected Tropical Diseases 2: e228.

[4] Shotton D (2010) CiTO, the Citation Typing Ontology. J. Biomedical Semantics 1 (Suppl. 1): S6. doi:10.1186/2041-1480-1-S1-S6.

[5] Silvio Peroni S and Shotton D (2011). FaBiO and CiTO: ontologies for describing bibliographic resources and citations. (Submitted for publication). Preprint available at http://imageweb.zoo.ox.ac.uk/pub/2011/publications/fabiocito_ontology_paper_PREPRINT.pdf.

[6] Shotton D (2011). The Five Stars of Online Journal Articles – an article evaluation framework. (Submitted for publication). Preprint available at http://precedings.nature.com/documents/6542/version/1/files/npre20116542-1.pdf and at http://imageweb.zoo.ox.ac.uk/pub/2011/publications/Shotton_TheFiveStarsOfOnlineJournalArticles.pdf.