Oxford e-Research Centre

University of Oxford, UK

OpenCon 2017 OxfordWeston 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

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

How to find open content – use Google Scholar

Use Google Scholar

Links on the right take you to Open Access copies – works well

On the publisher’s web site

Use Google Scholar

Links on the right take you to Open Access copies

Open Access copy at Academia.edu

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

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

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/

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/, http://80.82.77.83/ and http://80.82.77.84/ 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.”

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

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

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

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

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

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

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/

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/

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

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

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

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

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

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

Thank you!

david.shotton@opencitations.net

David Shotton

Website: http://opencitations.netEmail: contact@opencitations.netTwitter: @opencitationsBlog: https://opencitations.wordpress.com