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David Shotton - OpenCon Oxford, 1st Dec 2017

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David Shotton, Senior Researcher, Oxford eResearch Centre: http://oerc.ox.ac.uk/people/DavidShotton
Director, OpenCitations http://opencitations.net

Tony Epstein (Sir Michael Anthony Epstein, discoverer of the Epstein-Barr virus) once said to me something I’ve never forgotten:

“Research that is not published is wasted research.”

We live today in an era of open scholarship and open data, in which the Web is the primary means of communication. For many people, information that is not freely published on the Web might as well not exist. It is thus “wasted research”.

However, within academia, we also have to live in the legacy world of subscription-access journals and subscription-access citation indexes such as Web of Science and Scopus – freely available only to members of rich scholarly institutions like Oxford University that pays hundreds of thousands of dollars annually to obtain access for their members, not to the rest of the world including scholars in developing nations.

Today I will briefly discuss the five factors desirable for scholarly publications – the Five Stars of Online Journal Articles: peer review, open access, enriched content, available datasets and machine-readable metadata [1].

I will then discuss how bibliographic citations, which permit an author to give credit to another person's endeavours and integrate our independent acts of scholarship into a global knowledge network, are being freed from commercial restrictions by publication in the OpenCitations Corpus (http://opencitations.net), an open repository of scholarly citation data that others may build upon, enhance and reuse for any purpose [2, 3].

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

[2] David Shotton (2013). Open citations. Nature, 502 (7471): 295-297. http://dx.doi.org/10.1038/502295a

[3] Silvio Peroni, David Shotton, Fabio Vitali (2016). Freedom for bibliographic references: OpenCitations arise. Proceedings of 2016 International Workshop on Linked Data for Information Extraction (LD4IE 2016): 32-43.

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David Shotton - OpenCon Oxford, 1st Dec 2017

  1. 1. Oxford e-Research Centre University of Oxford, UK OpenCon 2017 Oxford Weston Library 1 December 2017 © David Shotton 2017 Published under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Licence david.shotton@opencitations.net David Shotton Open publication – current progress Bibliographic resources and bibliographic citations
  2. 2. What proportion of academic papers are open?  Heather Piwowar et al. recently estimated that at least 28% of the scholarly literature is now Open Access, and for 2015, the most recent year they analyzed, the proportion is 47% Open Access  Piwowar, H. et al. The State of OA: A large-scale analysis of the prevalence and impact of Open Access articles. PeerJ Prepr. (2017). https://doi.org/10.7287/peerj.preprints.3119v1  They determined the so-called open-access citation advantage:  Accounting for age and discipline, Open Access articles receive 18% more citations than average  Many funders, including the US National Institutes of Health, the US National Science, the European Commission, the Wellcome Trust, and the Bill and Melinda Gates Foundation, make Open Access mandatory for grantees  For biomedical papers, this is achieved by putting articles in PubMed Central  PMC (https://www.ncbi.nlm.nih.gov/pmc/) holds ~4.5 million full text articles  Of these, over 1.6 million comprise the PMC open access subset
  3. 3. How to find open content – use Google Scholar  Use Google Scholar  Links on the right take you to Open Access copies – works well
  4. 4. On the publisher’s web site  Use Google Scholar  Links on the right take you to Open Access copies
  5. 5. Open Access copy at Academia.edu
  6. 6. How to find open content – use Unpaywall.org  Unpaywall is a browser plugin that used oaDOI behind the scenes to search for OA versions of journal articles you may be viewing on publishers’ web sites
  7. 7. Unpaywall uses oaDOI  oaDOI is a service that finds Open Access copies of articles identified by a DOI (Digital Object Identifier)  If it finds one, it puts an Unpaywall Open Access logo on the right of the article page  Clicking on that takes you to the Open Access version of the paper  A cool idea  However, in my experience it fails to catch many OA copies  because it uses BASE – the Bielefeld Academic Search Engine (https://www.base-search.net/), which only searches official Green Open Access repositories
  8. 8. Sci-Hub provides illegal access to subscription content  The pirate website Sci-Hub provides access to scholarly literature via full text PDFs illegally downloaded from behind publishers' paywalls  Its stated goal is to make research papers free, to aid academia  But several science journals have taken it to court for breach of copyright   Daniel Himmelstein et al. determined that Sci-Hub contains 70% of all ~81.6 million scholarly articles  This rises to 85% for those published in subscription-access journals, and 97% for articles published by Elsevier, the largest and least open publisher  Himmelstein, D. S., Romero, A. R., McLaughlin, S. R., Tzovaras, B. G. & Greene, C. S. Sci- Hub provides access to nearly all scholarly literature. PeerJ Prepr. (2017). https://peerj.com/preprints/3100/
  9. 9. The fight for open access can get nasty  Sci-Hub’s founder, Alexandra Elbakyan, is a fugitive from justice  Elsevier won a $15 million court order against her in June  Sci-Hub’s domain names sci-hub.io, sci-hub.ac and sci-hub.cc have recently been blocked, following another court order earlier this month  https://www.theregister.co.uk/2017/11/23/scihubs_become_inactive_ following_court_order/  But http://sci-hub.bz/, and still work  Martin Eve, Professor of Literature, Technology and Publishing at Birkbeck College, University of London, said:  “I think domain blocking is going to prove an ineffective technique to shutdown Sci-Hub permanently.  “Academic publishers would do better to reroute their efforts into developing business models for scholarly communications that allow open dissemination of educational research content and that are, therefore, immune to initiatives such as SciHub.”
  10. 10. Research publishing has changed very little over 350 years  We still have a linear narrative, with references  While the article has moved online, and may indeed be Open Access, the norm is to publish a static PDF file, mimicking the printed page  This is totally antithetical to the spirit of the Web, and ignores its great potential  Rather, we need lively journal content  Semantic mark-up of text  Interactive figures  Links between papers and datasets  Actionable numerical data  . . . what I have called Semantic Publishing
  11. 11. Our experiment in semantic enhancement of articles  To provide a compelling existence proof of the possibilities of semantic publication, we took an ordinary research article from PLoS Neglected Tropical Diseases and enhanced it as an exemplar  The results can be seen at http://dx.doi.org/10.1371/journal.pntd.0000228.x001
  12. 12. The Five Stars of Online Journal Articles  Shotton D (2012). The Five Stars of Online Journal Articles — a Framework for Article Evaluation. D-Lib Magazine 18 (1/2) (January/February 2012 issue). http://dx.doi.org/10.1045/january2012-shotton
  13. 13. The Reis et al. PLoS article, before and after enhancement  Before After  The article already scored well for open access (O) and peer review (P)  Our semantic enhancements gave considerable improvement in enhanced content (E), available datasets (A) and machine-readable metadata (M) P M A E O P M A E O
  14. 14. Citations - Crossref provides the fundamental infrastructure https://www.crossref.org/  Crossref is the registration agency of Digital Object Identifiers (DOIs) for scholarly publications (journal articles, conference papers, books, etc.)  Its head office is here in Oxford, at the Oxford Centre for Innovation  Most scholarly publishers are members, paying annual fees  For all scholarly publications that have DOIs  Crossref hold metadata (record of authors, title, publication year, etc.)  and also reference lists, if these are submitted by the publishers  Crossref presently holds over one billion references!  But the records on CrossRef are raw data, not organized or structured so that non-experts can query them in useful ways, such as asking for the highest-cited paper published by a particular university in a particular year
  15. 15. The importance of citations  A citation permits an author to give credit to another person's endeavours  Direct citation is a key indicator of a cited publication’s significance  Citations also integrate our independent acts of scholarship into a global knowledge network  Bibliometric analysis of the citation network can reveal patterns of communication between scholars and the development and demise of academic disciplines  But aggregated citation data have been hidden behind subscription firewalls  In this Open Access age, it is a scandal that all citation data are not freely available for use by the scholars who created them  Citations now need to be recognized as a part of the Commons – basic facts that should be freely and legally available for sharing and reuse by all  The Initiative for Open Citations (I4OC) is working to achieve this
  16. 16. The Initiative for Open Citations  The Initiative for Open Citations is a collaboration between scholarly publishers, researchers and others to promote unrestricted availability of scholarly citations  Launched on April 6, 2017 Web site https://i4oc.org  Within a short space of time, I4OC has persuaded most of the major scholarly publishers to make their reference lists submitted to Crossref open  Before I4OC, only 1% of these were open  By the I4OC launch last April, that proportion was 40%  By September 2017, more that 50% of the almost one billion journal article references stored in Crossref were open  However, there is much more that publishers could do  52% of the journal articles documented at Crossref lack references  And of these that are submitted, almost 50% are yet not open  See https://opencitations.wordpress.com/2017/11/24/ milestone-for-i4oc-open-references-at-crossref-exceed-50/
  17. 17. The problem with Elsevier  The largest scholarly publisher is Elsevier  It has about 15 million journal article records in Crossref  References from journal articles published by Elsevier constitute 32% of all journal articles references stored at Crossref  While 75% of such references from other publishers are open NONE of the ~300 million references from Elsevier articles are open  As a consequence, of all journal article references deposited at Crossref that are not yet open, 65% are from journals published by Elsevier  I have just submitted an article to Nature that discusses this problem, entitled Open Citations – The Elephant in the Room to be published in the New Year  See https://opencitations.wordpress.com/2017/11/24/ elsevier-references-dominate-those-that-are-not-open-at-crossref/
  18. 18. Enhancing citation data - the OpenCitations Corpus  OpenCitations (http://opencitations.net) is an infrastructure organization directed by myself and by Silvio Peroni of the University of Bologna  Its primary purpose is to host and develop the OpenCitations Corpus (OCC), a Linked Open Data repository of bibliographic citation data covering all disciplines  The first OCC prototype was created here in Oxford in 2011  A new instance of the OCC, based on our revised OpenCitations Metadata Model, was then set up with my colleague Silvio Peroni at the University of Bologna  It has been ingesting scholarly references continuously since early July 2016  OCC provides the largest Linked Open Data collection of citations on the Web  Currently holds references from ~285,000 citing bibliographic resources  Provides >12 million citation links to over 6 million cited resources  These data are freely available under a CC0 public domain waiver
  19. 19. The SPAR (Semantic Publishing and Referencing) Ontologies FaBiO, the FRBR-aligned Bibliographic Ontology - an ontology for describing bibliographic entities (books, articles, etc.) CiTO, the Citation Typing Ontology - an ontology that enables the characterization of citations, both factually and rhetorically BiRO, the Bibliographic Reference Ontology - an ontology to define bibliographic records and references, and their compilation into bibliographic collections and reference lists, respectively http://www.sparontologies.net/  OCC data are described in RDF (JSON-LD) using, with other standard vocabularies, the SPAR (Semantic Publishing and Referencing) ontologies  These SPAR ontologies include
  20. 20. The OpenCitations ingestion rate  The OpenCitations Corpus is current ingesting ~8 million new citations per year  With new hardware funded by the Sloan Foundation OpenCitations Enhancement Project, this rate will increase thirty-fold early in 2018 to ~240 million new citations per year  By the end of 2018, the OpenCitations Corpus should hold ~250 million citations, compared to Web of Knowledge’s ~1.25 billion  Even this partial coverage will include citations of all important papers  A further five-fold increase in ingest rate - significant but achievable with additional resources (and funding!) - would enable us to reach parity by 2020
  21. 21. Where will the references come from?  We will quickly consume all 1.6 million OA articles in PubMed Central  We will then start harvesting the half-billion references from the ~18 million articles already made open at Crossref in response to The Initiative for Open Citations, of which OpenCitations is a founding member  Other possible sources of open citation data include  ArXiv (1.3 million preprints, mainly in physics and the hard sciences)  CiteSeerX (>120 million references from >6 million documents)  CitEc (11 million references from a million Economics papers)  References from pre-digital publications extracted by text mining, e.g.  From Bodleian catalogues of its holdings of illuminated manuscripts  In the Social Sciences, from the LOC-DB at the University of Mannheim  In Biological Taxonomy, mined into BioStor from the Biodiversity Heritage Library, e.g. http://biostor.org/reference/105357
  22. 22. Adopting the OpenCitations Data Model  The OpenCitations data model provides the possibility of interoperability between independent citation collections  Several other organizations and projects have adopted, or are considering adoption of the OpenCitations data model  This will provide immediate interoperability of RDF citation data  and will enable seamless import into the OpenCitations Corpus  In this way, we hope that OpenCitations can become a global hub for open citation data structured in RDF
  23. 23. 2017 The year of success - citation data are freed!  Two fantastic success stories  The Initiative for Open Citations https://i4oc.org/  The OpenCitations Corpus http://opencitations.net  Two Italian heros: Dario Taraborelli and Silvio Peroni
  24. 24. Thank you! david.shotton@opencitations.net David Shotton Website: http://opencitations.net Email: contact@opencitations.net Twitter: @opencitations Blog: https://opencitations.wordpress.com