The Wellcome Trust funds OpenCitations

The Open Biomedical Citations in Context Corpus funded by the Wellcome Trust

The Wellcome Trust, which funds research in big health challenges and campaigns for better science, has agreed to fund The Open Biomedical Citations in Context Corpus, a new project to enhance the OpenCitations Corpus, as part of the Open Research Fund programme.

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.


The Open Biomedical Citations in Context Corpus, funded by the Wellcome Trust for 12 months from March 2019, will make the OpenCitations Corpus (OCC) more useful to the academic community by significantly expanding the kinds of citation data held within the Corpus, so as to provide data for each individual in-text reference and its semantic context, making it possible to distinguish references that are cited only once from those that are cited multiple times, to see which references are cited together (e.g. in the same sentence), to determine in which section of the article references are cited (e.g. Introduction, Methods), and, potentially, to retrieve the function of the citation.

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

  • by extending the OpenCitations Data Model so as to describe how the in-text reference data should be modeled in RDF for inclusion in the OpenCitations Corpus;
  • by develping scripts for extracting in-text references from articles within the Open Access Subset of biomedical literature hosted by Europe PubMed Central;
  • by extending the existing ingestion workflow so as to add the new in-text reference data into the Corpus;
  • by developing appropriate user interfaces for querying and browsing these new data.


We are looking for a post-doctoral computer scientist / research engineer specifically to achieves the aforementioned objectives. This post-doctoral appointment will start the 1st of March 2019. We seek a highly intelligent, skilled and motivated individual who is expert in Python, Semantic Web technologies, Linked Data and Web technologies. Additional expertise in Web Interface Design and Information Visualization would be highly beneficial, plus a strong and demonstrable commitment to open science and team-working abilities.

The minimal formal requirement for this position is a Masters degree in computer science, computer science and engineering, telecommunications engineering, or equivalent title, but it is expected that the successful applicant will have had research experience leading to a doctoral degree. The position has a net salary (exempt from income tax, after deduction of social security contributions) in excess of 23K euros per year.

The formal advertisement for this post – which will be held at the Digital Humanities Advanced Research Centre (DHARC), Department of Computer Classical Philology and Italian Studies, University of Bologna, Italy, under the supervision of Dr Silvio Peroni – is published online, and it is accompanied by the activity plan (in Italian and English). The application must be presented exclusively online by logging in the website (default in Italian, but there is a link to switch the language in English). People who do not have a email account must register to the platform. The deadline for application is the 25th January 2019 at 15:00 Central Europe Time. Please feel free to contact Silvio Peroni (silvio dot peroni at unibo dot it) for further information.

People involved

The people formally involved in the projects are:

  • Vincent Larivière – École de Bibliothéconomie et des Sciences de l’Information, Université de Montréal, Canada;
  • Silvio Peroni (Principal Investigator) – Digital Humanities Advanced Research Centre (DHARC), Department of Computer Classical Philology and Italian Studies, University of Bologna, Italy, and Director of OpenCitations;
  • David Shotton – Oxford e-Research Centre, University of Oxford, Oxford, UK, and Director of OpenCitations;
  • Ludo Waltman – Centre for Science and Technology Studies (CWTS), Leiden University, Netherlands.

In addition, the project is supported by Europe PubMed Central (EMBL-EBI, Hinxton, UK).

Cite this blog post
Silvio Peroni (2018, December 23). The Wellcome Trust funds OpenCitations. OpenCitations blog. Retrieved April 22, 2024, from

4 thoughts on “The Wellcome Trust funds OpenCitations”

  1. Everything we will develop will be released as open source software. It would be possible indeed to use existing software, like GROBID, but, honestly, the first stage will concern the parsing of XML files in the OA subset of Europe PubMed Central, which should avoid us to use ML techniques for the extraction.

  2. Thanks and congratulations. When you say “scripts for extracting in-text references from articles”, do you plan to use and develop shared free software tools such as GROBID?

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