Early adopters of the OpenCitations Data Model

OpenCitations is very pleased to announce its collaboration with four new scholarly Research and Development projects that are early adopters of the recently updated OpenCitations Data Model, described in this blog post.

The four projects are similar, in that they each are independently using text mining and optical character recognition or PDF extraction techniques to extract citation information from the reference lists of published works, and are making these citations available as Linked Open Data. Three of the four will also use the OpenCitations Corpus as publication platform for their citation data.  The academic disciplines from which these citation data are being extracted are social science, humanities and economics. Continue reading “Early adopters of the OpenCitations Data Model”

Citations as First-Class Data Entities: The OpenCitations Data Model

Requirements for citations to be treated as First-Class Data Entities

In my introductory blog post, I listed five requirements for the treatment of citations as first-class data entities.  The second of these requirements is that they must have metadata structured using a generic yet appropriately detailed data model.

To fulfil that requirement, OpenCitations is pleased to announce the publication on 13 February 2018 of the OpenCitations Data Model, v1.6 [1].  This replaces the previous version, v1.5.3, published on 13 July 2016. Continue reading “Citations as First-Class Data Entities: The OpenCitations Data Model”

Citations as First-Class Data Entities: Introduction

Citations are now centre stage

As a result of the Initiative for Open Citations (I4OC), launched on April 6 last year, almost all the major scholarly publishers now open the reference lists they submit to Crossref, resulting in more than half a billion references being openly available via the Crossref API.

It is therefore time to think carefully about how citations are treated, and how they might be better handled as part of the Linked Open Data Web. Continue reading “Citations as First-Class Data Entities: Introduction”

OpenCitations and the Initiative for Open Citations: A Clarification

Some folk are confused, but OpenCitations and the Initiative for Open Citations, despite the similarity of their names, are two distinct organizations.

OpenCitations (http://opencitations.net) is an open scholarly infrastructure organization directed by Silvio Peroni and myself, and its primary purpose is to host and build the OpenCitations Corpus (OCC), an RDF database of scholarly citation data that now contains almost 13 million citation links. Continue reading “OpenCitations and the Initiative for Open Citations: A Clarification”

The Sloan Foundation funds OpenCitations

The OpenCitations Enhancement Project funded by Sloan

The Alfred P. Sloan Foundation, which funds research and education in science, technology, engineering, mathematics and economics, including a number of key technology projects relating to scholarly communication, has agreed to fund The OpenCitations Enhancement Project, a new project to develop and enhance the OpenCitations Corpus.

As readers of this blog will know, the OpenCitations Corpus is an open scholarly citation database that freely and legally makes available accurate citation data (academic references) to assist scholars with their academic studies, and to serve knowledge to the wider public.

Objectives

The OpenCitations Enhancement Project, funded by the Sloan Foundation for 18 months from May 2017, will make the OpenCitations Corpus (OCC) more useful to the academic community both by significantly expanding the volume of citation data held within the Corpus, and by developing novel data visualizations and query services over the stored data.

At OpenCitations, we will achieve these objectives in the following ways:

(a) By establishing a new powerful physical server to handle the Corpus data and offer adequate performance for query services.

(b) By increasing the rate of data ingest into the Corpus, by integrating with server 30 small data-ingest computers, Raspberry Pi 3Bs, working in parallel to harvest references, thus increasing the current rate of corpus data ingest some thirty-fold to about half a million citation links per day.

(c) By employing a post-doctoral computer science research engineer specifically to develop information visualisation interfaces and sense-making tools that will both provide smart ways of envisaging and comprehending the citation data stored within the OpenCitations Corpus, and will also ease the task of manual curation of the OCC.

Personnel

This post-doctoral appointment will start in the autumn of 2017, once the new hardware has been commissioned and programmed. We seek a highly intelligent, skilled and motivated individual who is an expert in Web Interface Design and Information Visualization, and who can demonstrate a commitment to increasing the openness of scholarly information. A formal advertisement for this post, which will be held at the University of Bologna in Italy under the supervision of Dr Silvio Peroni, will be published in the near future. In the mean time, individuals with the relevant skills and background who would like to express early interest in joining the OpenCitations team in this role should contact him by e-mail to <silvio.peroni@opencitations.net>.

Expected Outcomes

By the end of the OpenCitations Enhancement Project, we will have harvested approximately 190 million citation links obtained from the reference lists of about 4.4 million scholarly articles (~15% of Web of Science’s coverage). In this way, in a significant initial step towards the comprehensive literature coverage we seek for the OCC, we will establish the OpenCitations Corpus as a valuable and persistent free-to-use global scholarly on-line Linked Open Data service.

In so doing, we aim at empower the global community by liberating scholarly citation data from their current commercial shackles, publishing such data with a Creative Commons CC0 Public Domain Dedication that will enable novel third-party services to be built over them.

The Initiative for Open Citations

OpenCitations are pleased to announce the launch of the Initiative for Open Citations (I4OC) , a fresh momentum in the scholarly publishing world to open up data on the citations that link research publications.  OpenCitations are proud to be a founder of I4OC, and we encourage those remaining publishers whose journal article reference lists are still closed to embrace this sea change in attitude towards open citation data. The other I4OC founding organizations are Wikimedia Foundation, PLOS, eLife, DataCite, and the Centre for Culture and Technology at Curtin University,

Until recently, the vast majority of citation data were not openly available, even though all major publishers freely share their article metadata through Crossref. Before I4OC started, only about 1% of the reference data deposited in Crossref were freely available. Today that figure has jumped to 40% [1].

Publishers

In recent months, following earlier indications of willingness reported in this blog, several publishers have made the decision to release these metadata publicly, including the American Geophysical Union, Association for Computing Machinery, BMJ, Cambridge University Press, Cold Spring Harbor Laboratory Press, EMBO Press, Royal Society of Chemistry, SAGE Publishing, Springer Nature, Taylor & Francis, and Wiley. These publishers join other publishers who have been opening their references through Crossref for some time. The full list of scholarly publishers now opening their reference data via Crossef is given in [2].

These decisions stem from discussions that have been taking place since a call-to-action to open up citations was made by Dario Taraborelli of the Wikimedia Foundation at the 2016 OASPA Conference on Open-Access Publishing. The creation of I4OC was spearheaded by Jonathan Dugan, Martin Fenner, Jan Gerlach, Catriona MacCallum, Daniel Mietchen, Cameron Neylon, Mark Patterson, Michelle Paulson, Silvio Peroni, myself and Dario Taraborelli. The purpose of I4OC is to coordinate these efforts and to promote the creation of a comprehensive, freely-available corpus of scholarly citation data.

Benefits

Such a corpus will be valuable for new as well as existing services, and will allow many more interested parties to explore, mine, and reuse the data for new knowledge. The key benefits that arise from a fully open citation dataset include:

  1. The establishment of a global public web of linked scholarly citation data to enhance the discoverability of published content, both subscription access and open access. This will particularly benefit individuals who are not members of academic institutions with subscriptions to commercial citation databases.
  2. The ability to build new services over the open citation data, for the benefit of publishers, researchers, funding agencies, academic institutions and the general public, as well as to enhancing existing services.
  3. The creation of a public citation graph to explore connections between knowledge fields, and to follow the evolution of ideas and scholarly disciplines.

Stakeholders

The Internet Archive, Mozilla, the Wellcome Trust, and twenty eight other projects and organizations have formally put their names behind I4OC as stakeholders in support of openly accessible citations. The full list of stakeholders is given in [3].

Endorsements

Dario Taraborelli, Head of Research at the Wikimedia Foundation, said:

“Citations are the foundation for how we know what we know. Today, tens of millions of scholarly citations become available to the public with no copyright restriction. We look forward to more organizations joining this initiative to release, and build on these data.”

Liz Ferguson, VP Publishing Development, Wiley, said:

“Wiley is delighted to support I4OC by opening our citation metadata via Crossref. Collaborating with other publishers further contributes to sustainable and standardized infrastructure that will benefit the research community. We are particularly excited by the potential to expose networks of research that would otherwise lie hidden or take years to discover.”

Robert Kiley, Head of Open Research at the Wellcome Trust, said:

“The open availability of citation data will help all funders better evaluate the research they fund. The progress that I4OC has made is an essential first step and we encourage all publishers to publicly share this data.”

Mark Patterson, Executive Director of eLife, said:

“It’s fantastic to see the interest that’s being shown by so many publishers in making their reference list metadata publicly available. We hope that this new momentum will encourage all publishers to follow suit, and that new services and tools can be built around these open data.”

Catriona MacCallum Advocacy Director, PLOS, said:

“Creating an open database of citations will allow researchers to perform independent analyses of how scientific ideas are communicated through article citations, and a transparent way of tracking the influence of particular articles. By opening up these metadata via Crossref, publishers are providing a vital contribution to Open Science.”

Future growth

Many other publishers have expressed interest in opening up their reference data. They can do this very easily via Crossref, with a simple email to support@crossref.org requesting they turn on reference distribution for all their DOI prefixes. This is required even for publishers of open access articles, since by default references submitted to the Crossref Cited-By Linking service are closed, as previously explained here.  I4OC will provide regular updates on the growth of the public citation corpus, how the data are being used, additional stakeholders and participating publishers as they join, and as new services are developed.

I4OC and OpenCitations

Through the efforts of I4OC, scholarly citation data will be increasingly available to any interested party through all of Crossref’s Metadata Delivery Services, including the REST API and bulk metadata dumps. From this open source, OpenCitations will progressively import the citation data into the OpenCitations Corpus, describe them using the SPAR Ontologies according to the OCC metadata model, and make them available in RDF under a Creative Commons public domain dedication as Linked Open Data.  Potential users should be aware that is will take some considerable time before all the new citation data now available via the Crossref API are ingested into the OpenCitations Corpus.

I4OC links

Footnotes

[1] 40% is the percentage of publications with open references out of the total number of publications with reference metadata deposited with Crossref. As of March 2017, nearly 35 million articles with references are deposited with Crossref.

[2] Full list of publishers now making their citation data open via Crossref.

[3] Full list of I4OA supporting stakeholder organizations.

Open Citations is dead. Long live OpenCitations.

OpenCitations logo 50% with words greyBG

In October 2015, I asked Silvio Peroni, my long-term colleague in the development of the SPAR Ontologies, to become Co-Director of the Open Citations Project, and to work with me in taking forward the prototype Open Citations Corpus (OCC), originally developed at the University of Oxford with the support of Jisc, with the aim of developing it into a production service of real use to scholars.

The result is OpenCitations, a new instantiation of the OCC hosted by the Department of Computer Science and Engineering of the University of Bologna, based on a new metadata schema and employing several new technologies to automate the ingestion of fresh citation metadata from authoritative sources.

Since the beginning of July 2016, OpenCitations has been ingesting and processing accurate bibliographic references harvested from the reference lists of scholarly papers available in Europe PubMed Central, enriched by metadata from Crossref. These scholarly citation data are described using the SPAR Ontologies according to the new OpenCitations metadata document [1], and are published under a Creative Commons public domain dedication (CC0), so that others may freely build upon, enhance and reuse them for any purpose, without restriction under copyright or database law. We have described the new OpenCitations Corpus, and the new software developed by Silvio to create it, in [2].

OpenCitations is being continuously populated from the scholarly literature, and, as of 30th March 2017, has ingested the references from 123,989 citing bibliographic resources, and contains information about 5,307,857 citation links to 3,469,648 cited resources.

The whole OCC is now available for querying (via SPARQL), and for browsing by means of a very simple Web interface that shows only the data about bibliographic entities (e.g. https://w3id.org/oc/corpus/br/1). Additional more user-friendly interfaces will be available in the coming months. The entire contents of the OpenCitations Corpus (OCC) are also archived every month as data dumps that are made available online through Figshare. Each dump comprises several zip archives, each containing either data or provenance information of a particular sub-dataset of the OCC.

Despite the fact that OpenCitations presently contains only a small proportion of global citation data, it is important to realize that, because of the very nature of scholarly citation, even this partial coverage includes citations of the most important papers in every biomedical field, these critical papers being characterized by the high number of their inward citation links.

[1] Silvio Peroni, David Shotton (2016). Metadata for the OpenCitations Corpus. figshare. https://dx.doi.org/10.6084/m9.figshare.3443876

[2] 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.
https://w3id.org/oc/paper/occ-lisc2016.html

Three publications describing the Open Citations Corpus

Last September, I attended the Fifth Annual Conference on Open Access Scholarly Publishing, held in Riga, at which I had been invited to give a paper entitled The Open Citations Corpus – freeing scholarly citation data.  A recording of my talk is available here, and my PowerPoint presentation is separately available here.  My own reflections on the major themes of the conference are given in a separate Semantic Publishing Blog post.

While in Riga preparing to give that talk about the importance of open citation data, I received an invitation from Sara Abdulla, Chief Commissioning Editor at Nature, to write a Comment piece for their forthcoming special issue on Impact.  My immediate reaction was that this should be on the same theme, an idea to which Sara readily agreed.  The deadline for delivery of the article was 10 days later!

As soon as the Riga conference was over, I first assembled all the material I had to hand that could be relevant to describing the Open Citations Corpus (OCC) in the context of conventional access to academic citation data from commercial sources.  That gave me a raw manuscript of some five thousand words, from which I had to distil an article of less than 1,300 words.  I then started editing, and asked my colleagues Silvio Peroni and Tanya Gray for their comments.

The end result, enriched by some imaginative art work by the Nature team, was published a couple of weeks later on 16th October [1], and presents both the intellectual argument for open citation data, and the practical obstacles to be overcome in achieving the goal of a substantial corpus of such data, as well as giving a general description of the Open Citations Corpus itself and of the development work we have planned for it.

Because of the drastic editing required to reduce the original draft to about a quarter of its size, all material not crucial to the central theme had to be cut.  I thus had the idea of developing the original draft subsequently into a full journal article that would include these additional themes, particularly Silvio’s work on the SPAR ontologies described in this Semantic Publishing Blog post [2], Tanya’s work on the CiTO Reference Annotation Tools described in this Semantic Publishing Blog post, and a wonderful analogy between the scholarly citation network and Venice devised by Silvio.  I also wanted to give authorship credit to Alex Dutton, who had undertaken almost all of the original software development work for the OCC.  For this reason, instead of assigning copyright to Nature for the Comment piece, I gave them a license to publish, retaining copyright to myself so I could re-use the text.  I am pleased to say that they accepted this without comment.

Silvio and I then set to work to develop the draft into a proper article.  The result was a ten-thousand word paper submitted to the Journal of Documentation a week before Christmas [3].  We await the referees’ comments!

 References

[1]     Shotton D. (2013).  Open citations.  Nature 502: 295–297. http://www.nature.com/news/publishing-open-citations-1.13937. doi:10.1038/502295a.

[2]     Peroni S and Shotton D (2012). FaBiO and CiTO: ontologies for describing bibliographic resources and citations. Web Semantics: Science, Services and Agents on the World Wide Web. 17: 33-34. doi:10.1016/j.websem.2012.08.001.

[3]    Silvio Peroni, Alexander Dutton, Tanya Gray, David Shotton (2015). Setting our bibliographic references free: towards open citation data. Journal of Documentation, 71 (2): 253-277. http://dx.doi.org/10.1108/JD-12-2013-0166; OA at http://speroni.web.cs.unibo.it/publications/peroni-2015-setting-bibliographic-references.pdf

This is the main article about OpenCitations, which includes several background information and the main ideas and works supporting the whole project, the Corpus, and some possible future developments in terms of new kinds of data to be included, e.g. citation functions.

 

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