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Updates from Europe PMC, a global database of life sciences literature

Maria Levchenko

 | 28 May 2024


Connecting publications and software

Europe PMC joins the SoFAIR project

Modern science increasingly relies on software, from data collection and analysis to modeling complex systems. As part of our mission, Europe PMC integrates open access literature with research outputs, such as data and software, to support innovation. To further this effort we have joined forces with the SoFAIR project, a collaborative initiative to empower reuse of open research software.

Making software visible

Today, software is an integral part of research, helping us advance scientific discovery at an unprecedented rate. To ensure transparency and reproducibility research software needs to be appropriately shared and cited. Software citation practices are increasingly adopted by the scientific community, but there are still hurdles to overcome. Code associated with research articles is often absent from the reference list and is not cited as a first-class bibliographic record. This makes it difficult to discover and reuse existing research software and results in lack of credit for research software developers.

The SoFAIR project addresses this critical issue by connecting publications with the software that was used, developed or shared in the course of a research project. This helps ensure that research software adheres to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles, initially designed for research data.

The project relies on existing open infrastructure to:

1. Identify research software within scholarly manuscripts;

2. Assign persistent identifiers for software;

3. Permanently archive the code.

Mentions of research code in open access articles will be detected using machine learning models and validated by publication authors. Software citations identified in this project will be shared through the Europe PMC Annotations platform. Similar to data citations, software citations will be available through the Europe PMC Annotations API.

We believe that the work that goes into developing and maintaining research software needs to be recognised. Registering persistent identifiers for software makes it easily citable and helps give credit where it’s due. We hope that SoFAIR will deliver the necessary step-change in the way research software is identified, validated, registered and archived for the long term.

Participating institutions

SoFAIR is a €499,000 international collaboration awarded through the CHISTERA Open Research Data & Software Call. It is coordinated by The Open University, in conjunction with Inria; Brno University of Technology; the Institute for Literary Research of the Polish Academy of Sciences (IBL-PAN); and the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI), which operates Europe PMC.

For more information, please visit the SoFAIR project website and official social media accounts.

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Partnerships & funding

Europe PMC is a service of the Europe PMC Funders' Group, in partnership with EMBL’s European Bioinformatics Institute (EMBL-EBI); and in cooperation with the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NCBI/NLM) . It includes content provided to the PubMed Central (NLM/PMC) archive by participating publishers.