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Tag: references

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>.

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>.

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.

Five stars of online journal articles Diagram

 

★  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.

Reis et al. original

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.

Reis et al. enhanced

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.

JISC Open Citations Project web site

The JISC Open Citations Project website at http://opencitations.net exists for several purposes:

and, most importantly,

The JISC Open Citations Project Home Page

For the purposes of this demonstration, we are running an instance of Fuseki, that provides access to the Open Citation Corpus in an underlying TDB quad store, with a local patch to enable query timeouts, as was done for the SPARQL endpoint of CLAROS, a related project in which we have been intimately involved.

The web site and the underlying RDF citation data follow key linked data principles:

  • We don’t use blank nodes
  • All URIs are dereferenceable and content-negotiable.
  • Where possible we use standard identifiers based on DOIs, ISSNs and ISBNs.

For users wishing to jump into the data, we provide tabs to access data about journals and articles, each giving greater detail about the contents as one clicks in.

The Journals page

Each Journal page displays metadata about the journal, and links to useful information and the ability to download the journal metadata in a variety of formats.


Details of one journal

The articles tab displays a subset of about 10% of the entire corpus, for speed of loading the demonstration.

The Articles Page

Each ‘article’ page displays details about the selected article and its citation network, using graphviz, along with a user input form to customise the display of the network, namely for input or output citations, and for different forms of display. The article metadata and the citation diagrams can be downloaded in various formats.

Input citations for Codon, C. (2007). Maturation and degradation of RNA in bacteria. Current Opinion in Microbiology 10(3): 271-278. doi:10.1016/j.mib.2007.05.008.

We also display the RDF properties of each entity, allowing a ‘follow your nose’ style of data discovery. Each page lists the SPARQL queries that were run to generate it, enabling the user to see how the site works and to tweak the queries for their own ends.

Further work is planned to display citations along a time axis, and to develop other tools to permit users to exploit the data.

Nomenclature for citations and references

Reis et al. (2008) [1] cites an earlier paper from Albert Ko’s research group, Ko et al. (1999) [2].

In conventional parlance, as the following diagram shows, the word “reference” can mean either what is found in the text, what is found in the reference list, the act of citation, or the object of the citation itself, as in the sentence “All the references you will need to prepare for the journal club are on Kevin’s desk”.

This situation does not make for unambiguous machine-readable encoding, so to improve the situation we have, in the SPAR (Semantic Publishing and Referencing) Ontologies, introduced a more principled way of referring to these items and actions, as the second diagram illustrates:

This permits us to create RDF describing all aspect of the citation process. Within the body of the text we have an in-text citation containing an in-text reference pointer, while the actual bibliographic reference that the in-text reference pointer denotes is to be found within the article’s reference list. That bibliographic reference references the cited article, while the whole performative act of including the reference in the article constitutes the act of citation.

Are we all clear now?

[1] Reis RB, Ribeiro GS, Felzemburgh RDM, Santana FS, Mohr S, Melendez AXTO, Queiroz A, Santos AC, Ravines RR, Tassinari WS, Carvalho MS, Reis MG, Ko AI (2008) Impact of Environment and Social Gradient on Leptospira Infection in Urban Slums. PLoS Negl Trop Dis 2(4): e228. doi:10.1371/journal.pntd.0000228

[2]    Ko AI, Reis MG, Ribeiro Dourado CM, Johnson WD Jr, Riley LW and the Salvador Leptospirosis Study Group. (1999) Urban epidemic of severe leptospirosis in Brazil. Lancet 354: 820–825. doi:10.1016/S0140-6736%2899%2980012-9.

Input data for Open Citations – the PMC Open Access Subset

PubMed, created by the US National Library of Medicine in DATE, holds bibliographic records and abstracts for essentially all journal articles published in the biomedical sciences. It currently records almost a million new entries each year!

PubMed Central (PMC), created as an extension of PubMed, is designed to hold full text articles from among the PubMed entries. At present, PMC holds entries for ~9.3% of the papers indexed in PubMed published between 1980 and 2010, 1,428,675 out of a total of 15,319,102. Many of these PMC articles (192,452 for the years 1980 to 2010, ~13.5% of the PMC holdings) are truly Open Access articles, that users can download and repurpose as they will. However, the majority are articles from subscription access journals deposited in PMC under licence agreements with funding agencies that, while providing read access to the full text, prevent readers from downloading the articles and from making derivative works.

The Open Citations Project has to date worked exclusively with the Open Access subset (OASS) of PMC. As of 24 January 2011, there were 204,637 OASS articles, including a few published before 1980. In almost all of these OASS articles, the reference lists were nicely marked up in NLM-DTD XML, making the task of identifying individual references straightforward. In a few cases, the articles were present as scanned page images, lacking any internal markup – those we were unable to process.

From the XML reference lists of these papers, we were able to identify and extract 6,325,178 individual references, which, together with the bibliographic information we had on the OASS articles themselves gave us 6,529,815 independent bibliographic records of both citing and cited entities. As explained in the next blog post, these records showed varying degrees of completeness and accuracy.

Using the Entrez API, we were able to use PubMed IDs, where these were available in the references, to extract a further 2,304,143 bibliographic records from PubMed, which, in the ideal world, would each exactly duplicate the information we had previously obtained from the OASS bibliographic reference containing that PubMed ID. As we shall describe, these additional PubMed records proved exceptionally useful in correcting imperfect OASS references.

Since the OASS articles cite papers outside the OASS, as well as a few within it, the majority of the bibliographic information we thus acquired related to papers represented within PubMed but not within PubMed Central. And because many OASS papers independently contained references to the most highly cited biomedical papers, many of our records were to the same bibliographic entities.

An important part of our data processing was thus to coalesce independent references from different OASS articles to the same multiply cited papers into a set of unique bibliographic records, each for one paper. Once this had been achieved, we were left with 3,578,598 unique bibliographic records, 204,637 describing the OASS articles themselves, and 3,373,961 describing articles outside the OASS, mostly from subscription-access journals.

The following table and figure tabulates and illustrates the number of papers in each category between 1980 and 2010 inclusive. The most striking thing about these data are that they show how, between these years, the relatively small number of articles in the Open Access subset of PMC (approx. 200,000 articles) referenced >20% of all PubMed Central papers published between 1950 and 2010 (approx. 15.3 million papers), and in doing so reference all the most important highly cited papers in every field of biomedical endeavour. This inclusive coverage means that citation graphs created from the Open Citations dataset will capture all the important aspects of any field.

Table 1

Year

Number of papers
 

Pubmed

PMC

OASS

Cited by OASS
1950-1979

5,128,602

427,877

8352

146027
1980

278,069

23,218

631

15708
1981

278,069

23,685

543

16627
1982

292,219

25,215

740

18389
1983

305,725

25,688

738

21263
1984

314,737

26,316

543

23249
1985

331,706

25,916

637

25780
1986

345,501

26,721

590

28761
1987

363,754

27,834

555

32222
1988

381,976

28,802

442

36320
1989

398,620

29,855

616

42005
1990

398,620

30,143

704

48422
1991

407,465

31,337

733

53655
1992

412,457

32,325

719

61091
1993

420,935

33,203

1055

70272
1994

431,160

33,456

1279

80206
1995

441,967

34,276

1148

91814
1996

452,218

34,755

1155

101853
1997

451,533

34,800

1314

114967
1998

469,466

36,179

1341

131510
1999

469,466

37,534

1420

146623
2000

528,243

39,047

1608

170330
2001

542,854

40,235

2546

179203
2002

560,006

43,265

3199

195879
2003

590,317

46,442

4015

211423
2004

634,432

51,416

6005

229423
2005

694,687

60,411

10333

236678
2006

740,007

72,295

14264

238387
2007

777,311

87,744

20070

222085
2008

824,612

120,004

31416

190071
2009

862,372

146,413

41848

124894
2010

918,598

120,145

40245

27877
Total

15,319,102

1,428,675

192,452

3,186,987
% of PubMed  

9.33%

  

20.80%
% of PMC    

13.47%

  

Figure 1

Figure 2

The OASS source data give the types of cited entity, aggregated after coalescing, shown in the Figure 3.

Figure 3