The blog of the OpenCitations Infrastructure

Silvio Peroni

Today, we have published the bi-monthly release of COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations.

More than 733M citations now available in COCI

We’re happy to announce POCI, the OpenCitations Index of PubMed open PMID-to-PMID citations, an RDF dataset containing details of all the citations from publications bearing PubMed Identifiers (PMIDs) to other PMID-identified publications, harvested from the National Institutes of Health Open Citations Collection (NIH-OCC). The citations available in POCI are treated as first-class data entities, with … Continue reading Discover POCI, the index

Chiara Di Giambattista

We’re happy to announce

 POCI


 , the OpenCitations Index of PubMed open PMID-to-PMID citations

, an RDF dataset containing details of all the citations from publications bearing PubMed Identifiers (PMIDs) to other PMID-identified publications, harvested from the National Institutes of Health Open Citations Collection (NIH-OCC). The citations available in POCI are treated as first-class data entities, with

Discover POCI, the index of open citations from PubMed

In March, The Global Sustainability Coalition for Open Science Services (SCOSS) celebrated, together with the generous funders and the projects involved (including OpenCitations), the achievement of an amazing milestone: a total of 4 million Euros raised so far for supporting the growth and development of Open Science Infrastructures.

Posted on August 10th 2022 by Chiara Di Giambattista  ← Previous post: The OpenCitations Roadmap is now publicly available on Trello  → Next post: New documents that present OpenCitations’ mission, unique benefits, present status and future plans  In March, The Global Sustainability Coalition for Open Science Services (SCOSS) celebrated, together with the generous funders and the projects involved (including OpenCitations), the achievement of an

Two years of achievements within the ‘SCOSS family’ (and it’s not over yet!)

The incentives for new OpenCitations innovative solutions Two years ago, in their canonical 2020 QSS paper on OpenCitations, Silvio Peroni and David Shotton anticipated the creation of the new database, OpenCitations Meta, able to “offer a faster and richer service” by storing bibliographic metadata “in house”. Meta would “

 avoid duplication of data by efficiently permitting us to keep […] a single copy of the metadata for each of the

OpenCitations and EC funding: OpenAIRE Nexus and RISIS2

On September 27, OpenCitations’ director Silvio Peroni, together with Niels Stern (DOAB/OAPEN) and James MacGregor (PKP), held the online workshop “How Open Infrastructure Benefits Libraries” during the Open Access Tage 2021. Open-Access-Tage (Open Access Days) are the annual central platform for the steadily growing

 Open Access and Open Science community from Germany, Austria and Switzerland

,

Open Access&nbsp;Tage&nbsp;2021: valuable insights from the libraries in the German-speaking region

University of Oxford

David M. Shotton

Yesterday I gave a lightning talk at the 2021 OASPA Conference, with the title

 OpenCitations – what does the future hold?

The poster accompanying my talk, published on Zenodo at https://doi.org/10.5281/zenodo.5526713, is reproduced below. Here is what I said: = = = Most of the talks at this conference have focussed on open access to textual content.

OpenCitations in Five Hundred Words

OpenCitations is excited to announce that the California Digital Library (CDL) has joined our growing list of contributors. CDL’s commitment to sustainable open scholarship has great value for the global scholarly community.

California Digital Library invests in OpenCitations

In his call for open citations, Dario Taraborelli hailed the scholarly citation graph (in which the nodes (vertices) are individual academic publications and the links (edges) represent bibliographic citations from one publication to another) as one of humankind’s most important intellectual achievements.

Reflections on the global citation graph

We now seek applicants for a new three-year research fellowship to be held from March 2021, for which the application closing deadline is 7 February 2021. Plan: to strengthen the current technical and computational infrastructure.

A year ago, at the end of 2019, OpenCitations was selected by the Global Sustainability Coalition for Open Science Services (SCOSS, https://scoss.org) for its second round of crowdfunding support, since SCOSS believes that OpenCitations aligns well with Open Science goals and is an innovative service.

Seeking applicants for three-year research fellowship position

We congratulate and thank Elsevier, the world’s largest academic publisher, for endorsing the DORA Declaration on Research Assessment (https://sfdora.org/), thereby joining the hundreds of other publishers and scientific organizations which have endorsed DORA over the previous eight years, and also for making a commitment to open the references from all its journal articles submitted to Crossref.

Elsevier endorses DORA and opens its journal article reference lists

This is a summer of great news for OpenCitations. Thanks to the generous support received from the scholarly community during the first year of SCOSS adoption, we’re happy to announce the appointment of three new colleagues to work for OpenCitations at the Research Centre for Open Scholarly Metadata (University of Bologna).

The OpenCitations team is growing – announcing three new appointments!

“*What role does ‘open’ play in making this project special?”*  This apparently easy, but not banal, question was asked in the Open Publishing Awards nomination form, and at OpenCitations we prefaced our answer to it by stating “For OpenCitations, ‘open’ is the crucial value and the final purpose.” We consider the free availability of bibliographic citation data to be a necessary condition for the establishment of an open knowledge graph, and

OpenCitations receives the Open Publishing Award in Open Data

2021 is just behind us. Since January is “the Monday of the months”, as F. Scott Fitzgerald once wrote[1], it’s a good time to take stock of what happened at OpenCitations during the past year.

Five reasons why 2021 has been a great year for OpenCitations

Guest blog post by Alberto Martín-Martín, Facultad de Comunicación y Documentación, Universidad de Granada, Spain &lt;albertomartin@ugr.es&gt;

 In this post, as a contribution to Open Access Week, Alberto Martín-Martín shares his comparative analysis of COCI and other sources of open citation data with those from subscription services, and comments on their relative coverage.

Comprehensive bibliographic metadata is essential for the

Coverage of open citation data approaches parity with Web of Science and Scopus

Authors: Ludo Waltman, Bianca Kramer, David Shotton

 In this blog post, Ludo Waltman, Bianca Kramer, and David Shotton, co-founders with colleagues of the Initiative for Open Abstracts, celebrate the first anniversary of the initiative.

On September 24 last year, the Initiative for Open Abstracts (I4OA) was launched.

The Initiative for Open Abstracts: Celebrating our first anniversary

Community, governance, and shared goals

: these are the key concepts that you would have heard discussed, had you listened in on September 21 at the Open Science Fair 2021 to the sessions entitled “ScholeXplorer and OpenCitations as the new frontier of open citation indexing” and “The perils of being invisible.

About engagement and evanescence: OpenCitations at the Open Science Fair 2021

The interconnection between Wikipedia and Wikidata is now larger than ever.   The Wikipedia Citations dataset currently includes around 30M citations from Wikipedia pages to a variety of sources – of which 4M are to scientific publication.

Wikipedia Citations in Wikidata

We are now proud to announce the third release of COCI, which contains more than 624 million DOI-to-DOI citation links coming from both ‘the ‘Open’ and the ‘Limited’ sets of Crossref reference data.

COCI is the OpenCitations Index of Crossref open DOI-to-DOI citations, all released as CC0 material, and is described in the article Heibi I, Peroni S, Shotton D (2019). Software review: COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations.

 Scientometrics

121(2): 1213-1228.

More than 624 million citations now available on COCI

The OpenCitations Enhancement Project Final report for the Alfred P. Sloan Foundation


 Report period: 1st May 2017 – 30 November 2018.

The OpenCitations Enhancement Project &#8211; final report

Since 1st January 2018, Crossref has had a new reference distribution policy, described at https://www.crossref.org/reference-distribution/.  There are three possible options for setting the reference distribution preference from which a publisher can choose, these being ‘Closed’, ‘Limited’ and ’Open“.  If the ‘Closed’ option is chosen, the references will only be used for the Crossref Cited-by service, and are not distributed via any of the

The new Crossref reference distribution policy

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.

Access to Citation Data

Among the external services used, the

 ORCID Public API

is of crucial importance for the task of author disambiguation. During the OCC ingestion workflow, the main metadata of an article are usually retrieved from the Crossref API.

Using the ORCID Public API for author disambiguation in the OpenCitations Corpus

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.

Five Stars Ontology

Executive summary Introduction To general readers of this blog, this post will appear different from normal posts.

Executive summary


 Introduction

To general readers of this blog, this post will appear different from normal posts. Rather than being about a particular topic, it pulls together a summary of the work undertaken over the past year within the Open Citations Project supported by the JISC, and is primarily intended to assist JISC evaluation of the project and its outputs.

JISC Open Citations Project &#8211; Final Project Blog Post

DataCite is an international organisation, founded in 2009, which promotes the use of DOIs (Digital Object Identifiers) for published datasets, in order to establish easier access to research data, to increase acceptance of research data as legitimate contributions in the scholarly record, and to support data archiving to permit results to be verified and re-purposed for future study. Its founding members were the British Library;

Questions of granularity &#8211; Dryad&#8217;s use of DataCite DOIs for data citation, and the Annotation Ontology

The JISC Open Citations Project website at http://opencitations.net exists for several purposes: To hold introductory information about the JISC Open Citations Project. To hold contact information for the project team.

JISC Open Citations Project web site

CiTO v2.0 contains just two main object properties,

 cito:cites

and its inverse

 cito:isCitedBy

, each of which as thirty-two sub-properties. Intentionally, these properties are not constrained as to domain or range, thereby maximising their applicability in a wide range of citation contexts.

Functional clustering of CiTO properties

Jodi Schneider of DERI has posted on her blog at http://jodischneider.com/blog/2010/10/18/cito-in-the-wild/ a most helpful description of how to employ CiTO properties characterizing bibliographic citations as tags for references in CiteULike.  Thanks, Jodi!

How to employ CiTO in CiteULike

This blog post is to introduce the first four ontologies of SPAR, the Semantic Publishing and Referencing Ontologies, an integrated ecosystem of generic ontologies shown diagrammatically in the ‘flower’ diagram below (Figure 1). The ontologies can be used either individually or in conjunction, as need dictates.

Introducing the Semantic Publishing and Referencing (SPAR) Ontologies

Discover DOCI, the OpenCitations Index of Datacite open DOI-to-DOI citations

We’re excited to introduce

 DOCI, the OpenCitations Index of Datacite open DOI-to-DOI citations

, a new tool containing citations derived from publications bearing DataCite DOIs to other DOI-identified publications, harvested from DataCite.

Discover DOCI, the index of open citations from DataCite

OpenCitations is managed by the newly formed Research Centre for Open Scholarly Metadata at the University of Bologna. The new International Advisory Board for OpenCitations is formally part of the Research Centre for Open Scholarly Metadata. The Board has been created to assist the Directors of OpenCitations by providing stakeholder community input that will guide the future activities and direction of OpenCitations.

As mentioned in an earlier blog post, OpenCitations has been selected by SCOSS for its second round of crowd-funding support from stakeholders within the open scholarship community.

Announcing the Research Centre for Open Scholarly Metadata and the International Advisory Board for OpenCitations

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.

Citations as First-Class Data Entities: Introduction

What is Related Work? Related Work is a user-friendly Web application developed to provide a means of browsing citation links, as the basis for a planned recommendation service for the best articles to read.

What is Related Work?
 


 Related Work

is a user-friendly Web application developed to provide a means of browsing citation links, as the basis for a planned recommendation service for the best articles to read.

Open Citations and Related Work projects merge

David writes: Dr Heinrich Hartman is a new colleague of mine, who, having been working in the Mathematical Institute of Oxford University, has just returned to Germany to start a new job in a leading semantic web research group, that of Steffan Staab at the Institute for Web Science and Technologies, University of Koblenz-Landau.

Why openness benefits research

JATS, the Journal Article Tag Suite, defines a vocabulary of XML elements and attributes used to describe the content and metadata of journal articles.  In this post, I describe the mapping of JATS to RDF, so that publishers’ XML article metadata encoded using JATS might become part of the web of linked data.

Mapping JATS to RDF

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”.

Nomenclature for citations and references

We want to express our gratitude to the 18 institutional members and customers of the Consortium of Swiss Academic Libraries which have now pledged 89,250 euros to support OpenCitations over the next three years. This generous donation is part of a total funding of

Swiss Institutions pledge 89,250 Euros to OpenCitations

We are most grateful to the Dutch Research Council (NWO) for its commitment to sustaining the activities and developments of three SCOSS-selected infrastructures (PKP, OpenCitations and ROR) together with the Netherlands Reproducibility Network.

The Dutch Research Council sustains OpenCitations

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

Science joins Nature in opening reference citations

Graffoo

 ,

a Graphical Framework for OWL Ontologies [1], is a wonderful new open source tool developed by Silvio Peroni that can be used to present the classes, properties and restrictions within OWL ontologies, or sub-sections of them, as clear and easy-to-understand diagrams.

Graffoo, a Graphical Framework for OWL Ontologies

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.

Input data for Open Citations &#8211; the PMC Open Access Subset

Silvio Peroni has recently created LODE (Live OWL Documentation Environment;

Using LODE for ontology visualization

Research Information

can be defined as an information (sometimes referred to as metadata) relating to the conduct and communication of research.

OpenCitations supports the Barcelona Declaration on Open Research Information for a fundamental transformation in the research information landscape

The first month of the new year has almost come to an end, and we at OpenCitations have dedicated these weeks after the holiday season to retrace the progress we reached as an open infrastructure throughout 2023, an activity that has become a tradition in the past few years.

Looking back to look ahead: OpenCitations’ achievements in 2023

The Workshop on Open Citations and Open Scholarly Metadata will come back to Bologna, on 26-27 October 2023.

We are pleased to announce that, after two online editions, the 2023 edition of the

 Workshop on Open Citations and Open Scholarly Metadata

will come back to

 Bologna

, on

 26-27 October 2023

. – https://workshop-oc.github.io.

Workshop on Open Citations and Open Scholarly Metadata 2023: apply now to participate!

In OpenCitations, we like to define our infrastructure organization as “community-based” and “community-driven”, and we really mean it. The support coming from the number of academic libraries and consortia coming after OpenCitations’ involvement in the 2nd SCOSS funding cycle has made it possible, starting from 2020, to make OpenCitations develop from a small university project based on time-limited grant incomes to being an

OpenCitations needs you: support the change in research practices

OpenCitations recalls what has achieved over the past year, in terms of technical developments, community building, and internal organization.

2023 has arrived, and it’s the time to put aside the old agendas and to fill the freshly printed organizers with new tasks. However, it is also worth looking back over the achievements of the past year.  So, before consigning 2022 to the archives, we want to take a moment to recall and celebrate all that OpenCitations has achieved over the past year, in terms of technical developments, community building, and our own internal organization.

OpenCitations’ 2022: one year, numerous outcomes

No-one is quite sure of the total number of scholarly publications within the global corpus. Indeed that number will be strongly influenced by the degree to which, in addition to books and journal articles, one includes within the definition of scholarly publications ‘grey literature’ such as reports published by official bodies, patents, etc.

Academia’s missing references

We are happy to announce OpenCitations’ participation in a number of

 online conferences and events

during the next few weeks. Our directors Silvio Peroni and David Shotton will be speaking at the Open Science Fair 2021, the OASPA Conference 2021 and Open Access Tage.

Save the&nbsp;dates:&nbsp;OpenCitations’&nbsp;September&nbsp;events

The initial vision

Now that OpenCitations is hosting over one billion freely available scholarly bibliographic citations, this is perhaps an opportune moment to look back to the start of this initiative.

From little acorns . . . A retrospective on OpenCitations

OpenAIRE-Nexus is an H2020 project funded by the European Commission which aims at bringing together, within the European Open Science Cloud (EOSC), fourteen new services focused on the development and promotion of Open Science.

 OpenCitations is directly involved

in this project through the Department of Classical Philology and Italian Studies at the University of Bologna.

New research fellowship position to work on the EOSC

For the second year, OpenCitations has taken part in the LIBER annual conference.  **LIBER **(Ligue des Bibliothèques Européennes de Recherche – Association of European Research Libraries) is a network that gathers 440 research libraries, based in more than 40 countries all over the world, with the mission of supporting Europe’s research libraries

OpenCitations at LIBER Annual Conference 2021: ‘How Can Open Infrastructures Support the Role of Research Libraries?’

The memorable date 20/02/2020 saw the publication by MIT Press of the first issue of Volume One of a new journal,

 Quantitative Science Studies

(QSS), the official open access journal of the International Society for Scientometrics and Informetrics (ISSI). QSS’s Editor in Chief is Ludo Waltman (CWTS, University of Leiden, Netherlands), Vincent Larivière (Université de Montréal, Montreal, Quebec, Canada) and Staša Milojević

The first issue of Quantitative Science Studies

Open Citation: Definition

The OpenCitations Data Model

In a previous series of blog posts we proposed the treatment of bibliographic citations as first-class data entities, permitting citations to be endowed with descriptive properties.

COCI, the OpenCitations Index of Crossref open DOI-to-DOI references

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 fifth and final of these requirements is that there must be a Web-based

 identifier resolution service

that takes the citation identifier as input and returns a description of the citation.

Citations as First-Class Data Entities: The Open Citation Identifier Resolution Service

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 first of these requirements is that they must be definable in a machine-readable manner as a member of the class “Citation”, and describable using appropriate ontology terms.

Citations as First-Class Data Entities: Citation Descriptions

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

OpenCitations and the Initiative for Open Citations: A Clarification

Good news!  Today, on January 16th 2018, Oxford University Press (OUP) announced its participation in the Initiative for Open Citations, and requested Crossref to turn on reference sharing for all OUP deposited references from more than half a million publications.  Oxford University Press is the largest university press in the world, publishing in 70 languages and 190 countries.

Oxford University Press opens its references!

Yesterday (November 23rd 2017) I was working with Daniel Ecer of eLife (&lt;d.ecer@elifesciences.org)&gt; to dig some hard facts out of the analyses he undertook on data he downloaded from Crossref in September 2017 (Ecer, 2017).  In this, the first of two related posts, I report the results for

 all publishers

. **The analyses show that, of the 33,672,763 journal articles documented in Crossref that have accompanying

Milestone for I4OC – open references at Crossref exceed 50%

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 Initiative for Open Citations

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.

Open Citations is dead.  Long live OpenCitations.

Following the decision to merge the planned development of the Open Citations Corpus with the

 Related Work

Project, described in the previous blog post, we proposed to develop one underlying data store, one data model and one RDF representation.

Open Citations developments

Two significant barriers prevent comprehensive reference availability through Crossref. The first barrier   First, two-thirds of Crossref’s publisher-members, in particular the smaller ones, do not submit references along with the other details of their publications. Many of these published works are of types (e.g. abstracts, editorials and news items) that lack any references.

Barriers to comprehensive reference availability

As introduced in a previous blog post, COCI is the OpenCitations Index of Crossref open DOI-to-DOI references, all released as CC0 material.

New release of COCI: 445M DOI-to-DOI citation links now available

Previously, my blog posts relating to semantic publishing have appeared in this

 Open Citations Blog

. However, because of the merger of the Open Citations Project with the Related Work Project, described here, this Open Citations Blog has been renamed

 Open Citations and Related Work

and has been opened to contributions from others involved in developing Open Citations and Related Work.

The start of something new

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.

The Five Stars of Online Journal Articles

Want to keep yourself updated about the ongoing activities of OpenCitations? We have now publicly released the OpenCitations Roadmap, available on Trello.com:  https://trello.com/b/RprHYoKL/opencitations  The OpenCitations Roadmap consists of a board fulfilled with colour-labelled cards which present the goals so far reached, the present projects and activities, and the future plans.

The OpenCitations Roadmap is now publicly available on Trello

If you are a leader of a Library or a Research Institution and would like to learn more about the existing open infrastructures that could help your institution to evolve in the research environment, but you don’t know where to look for, you can now use Infra Finder, a brand-new tool aimed at foster discovery, adoption, and investment for open infrastructure services.

Find OpenCitations on Infra Finder, a new tool to discover and support Open Infrastructures

“The competitive benefits of closing access to citation data diminish with each new citation released to the public domain, but the benefits of open data remain. Going forward, citation data is almost completely public domain”

. With these words, from the article “A tipping point for open citations data“ (July 15, 2021), Ian Hutchins celebrated the threshold crossing of one billion citations on public-domain databases in February 2021.

Crossing a significant threshold: more than one billion citations now available in COCI!

At the end of 2019, OpenCitations was selected by

 The Global Sustainability Coalition for Open Science Service (SCOSS)

for presentation to the international scholarly community for crowd-sourced sustainability funding, along with the Public Knowledge Project (PKP) and the Directory of Open Access Books (DOAB). Since 2017, SCOSS has been helping identify non-commercial services essential to Open Science, and making

OpenCitations and SCOSS: one year of support

COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations, has just been extended with more than 31 million additional citations.

We are proud to announce that COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations, has just been extended with more than

 31 million additional citations

. As introduced in an earlier blog post and an open-access article recently published on

 Scientometrics

, COCI is our first OpenCitations Index of open citations.

Additional 31 million citations in COCI

Open Citation Identifier: Definition

In-Text Reference Pointer Identifier: Definition

Rationale   Readers of this blog will be familiar with Open Citation Identifiers (OCIs), described in an earlier post and formally defined in [1]. OCIs enable bibliographic citations, treated as first class information entities, to be uniquely identified and referenced, and are used to identify the &gt;624 million individual citations indexed in the latest release of COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations, as

Introducing InTRePIDs – In-Text Reference Pointer Identifiers

Shotton CitationIDs PIDapalooza 24-01-18 REVISED.pptx

Setting our bibliographic references free: towards open citation data

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 fourth of these requirements is that they must be identifiable using a global persistent identifier scheme.

Citations as First-Class Data Entities: Open Citation Identifiers

This post introduce two exemplar queries for interrogating the OpenCitations Corpus.

OpenCitations makes available a SPARQL endpoint for querying the data included in the OpenCitations Corpus. While several queries are possible according to the model described in the website (and, with more details, in the official metadata document of the Corpus), we have received some requests by users of the service for exemplar queries.

Querying the OpenCitations 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.

Three publications describing the Open Citations Corpus

OpenCitations Team

Ongoing work on the Open Citations extensions project is now reaching the point of visualising – at very much a prototype level at this stage – the outputs of our earlier efforts to import and index the PubMed Central Open Access subset and arXiv. Earlier in this project I asked David to specify a list of questions that he thought researchers might hope to answer by querying our Open Citations Corpus;

Open Citations – Doing some graph visualisations

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.

Why publishers should open their references

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.

Comments on IS DATA PUBLICATION THE RIGHT METAPHOR?

JATS, the Journal Article Tag Suite, defines a vocabulary of XML elements and attributes used to describe the content and metadata of journal articles.  As described in the previous post, we have mapped the metadata elements of the JATS Journal Publishing Tag Set to RDF, so that publishers’ XML article metadata encoded using JATS might become part of the web of linked data.

An entry form for JATS metadata

Bibliographic references are the links that knit together independent scholarly endeavours.

Nature to open its reference list data

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

.

Five Stars article published in D-Lib Magazine

Evidence submitted by David Shotton in response to the Royal Society’s Policy Study “Science as a Public Enterprise” Call for Evidence, addressing the following two topics raised by that call:

 Getting Researcher buy-in.

How do we get researchers to be more willing to share data? What is there to be learned from disciplines such as genomics which have norms which favour wide sharing of data?

Why researchers don’t publish data

Alistair Miles, of SKOS fame, who formerly worked in our research group, spent yesterday afternoon catching up with us, and has written a nice blog post on the MalariaGEN Informatics Blog describing our current activities, including our work on the Open Citations Corpus, and how they might intersect with the data management activities of the MalariaGEN, the Malaria Genome Epidemiology Network for which he now works.

Current Projects at the Image Bioinformatics Research Group in Oxford

Data copied from JISC Expo DOAP (Description of a Project) spreadsheet at https://spreadsheets.google.com/ccc?key=0ArsNASxXZiL6dC1mWWFMMjRWSmVha0E1WmdlQ05KcEE&amp;hl=en#gid=7.

 Project title

: The Open Citations Project

 Project tag

: jiscopencite

 Short project description

We will publish reference lists from Open Access biomedical journal articles as Linked Open Citation Data at

JISC Administrative Data for Open Citations Project

As previously described, the PubMed Central Open Access subset of journal articles yielded 6,529,815 independent bibliographic records of both citing and cited entities, while our use of the PubMed Entrez API provided a further 2,304,143 bibliographic records for the same cited entities. Before converting these references into RDF to create the Open Citations Corpust, we attempted to remove errors in the data.

Citation correction methods

To illustrate three kinds of problems in obtaining correct author lists for Open Citation data from articles in the PubMed Central Open Access subset (OASS), I take three examples, the first of which is the result of a publication policy, the second due to mis-handling of an authorship attribution at the time of publication, and the third exemplifing errors introduced when handling non-English personal names.

Who wrote this paper?  Author list problems in PubMed Central references

The Open Citations Project has aimed to liberate bibliographic references from biomedical research literature as Open Linked Data, using as its starting corpus the Open Access Subset (OASS) of articles within PubMed Central. The greatest problem faced during this project, naively unanticipated before we started, was the extend of incompleteness, noise and errors of various sorts within the reference information extracted from the OASS articles.

Garbage in, garbage out &#8211; problems with bibliographic references

In addition to using CiTO and CiTO4Data to describe relationships of relevance to data entities, as discussed in the previous blog post, FaBiO, the FRBR aligned Bibliographic Ontology described elsewhere, another member of the suite of SPAR (Semantic Publishing and Referencing) Ontologies, also has a number of classes and properties specifically designed for addressing data, software, metadata and other non-bibliographic entities.

Using FaBiO to describe data entities

BIBO v1.3, the Bibliographic Ontology developed by Bruce D’Arcus and Frédérick Giasson [1], was the first OWL ontology dedicated to describing bibliographic entities, and has attracted a wide group of users. It provided the much-needed ability to describe the nature of cited works in RDF to a high degree of granularity, in terms of Title, Abstract, Journal, Volume, Pages, ISSN, DOI, dataCopyrighted, editor, etc.

OpenCitations blog

The Open Biomedical Citations in Context Corpus: Progress Report

The Wellcome Trust funds OpenCitations