Open Access in Biology

A large and steadily growing number of open access journals now shape the publishing landscape in biology. Initiatives such as Plan S and Plan U (Sever et al., 2019), as well as the nationwide licensing agreements concluded within the framework of Projekt DEAL, are also bringing about structural change towards open access as the standard publishing model in biology. Preprint servers such as bioRxiv are increasingly gaining in importance because they enable authors to rapidly disseminate their research results before the completion of peer re­view processes. Besides scholarly articles and the research data that underpin them, software developments are important research outcomes. Open access to these outcomes is ensured by a large number of repositories and databases.

Open Access Journals

As of November 2021, the Directory of Open Access Journals (DOAJ) listed 880 open access journals under the keyword Biology. The most important of these journals include:

One of the locomotives of the open access movement in biology is the publisher Public Library of Science (PLOS). With the foundation of the journal PLOS Biolo­gy in 2003, it laid a foundation stone for the dissemination of the open access idea in the life sciences. Besides PLOS Biology, PLOS now runs further journals, including PLOS ONE. The latter is considered to be the archetypal megajournal – this model has since been adopted by many other publishers (e.g. Nature Portfolio’s Scientific Reports). An important characteristic of these megajournals is the fact that submitted manuscripts are evaluated exclusively on the basis of their scientific validity. Refusals on the grounds of lack of relevance do not hap­pen. Against this backdrop, PLOS ONE is one of the largest scholarly journals in the world based on the number of articles published per annum. Another publisher that plays a pioneering role in open access is BioMed Central, which runs a large number of journals and is co-founder of the Open Access Scholarly Publishers Association (OASPA). The open access journal Open Biology was founded by the Royal Society in 2011. In 2012, the Howard Hughes Medical Institute, the Max Planck Society, and the Wellcome Trust founded the journal eLife with the declared aim of providing a high quality alternative to Nature, Science, and Cell.

Video about the Funding of Open Access Articles

Open Access Books

As of November 2021, the Directory of Open Access Books (DOAB) listed over 250 titles in the category Biology, life sciences. OAPEN listed over 80 titles under the rubric Biology, life science (as of November 2021).

Although open access books have not played a prominent role in biology to date, there are numerous open access (text)books that stand out for their high quality. They include, for example, Microbiology, a book published collabora­tively by OpenStax and the American Society for Microbiology Press.

Disciplinary Repositories

The most important repositories in biology include:

  • arXiv: Operated by Cornell University Library, this e-print server has for several years now had a Quantitative Biology section with 11 categories.
  • bioRxiv: This preprint server specifically for the life sciences has been provided by Cold Spring Harbor Laboratory since 2013. Although use of the server had increased even before the onset of the COVID-19 pandemic, this growth has intensified further since then.
  • Preprints: This multidisciplinary platform also has a biology section.
  • PaleorXiv: This sub-discipline-specific preprint server offers preprints from palaeontology.
  • PUBLISSO-Fachrepositorium Lebenswissenschaften (FRL): Hosted by ZB MED, this repository offers authors the possibility of self-archiving their texts and research data
  • PubMed Central and Europe PubMed Central: These platforms are the largest venues in the world for post-print versions of publications. The US National Institutes of Health (NIH) require that the post-print version of manuscripts arising from NIH-funded projects be made publicly available on PubMed Central no later than 12 months after the date of publication in a journal. These manuscripts do not necessarily have to be made available under an open licence, nor must they be part of the BMC Open Access Subset, which can be separately downloaded and searched.

Although the use of preprints is not yet as widespread in the biosciences as it is, for example, in physics, it has increased significantly in recent years. Initiatives such as Plan U (Sever et al., 2019) and ASAPbio (Accelerating Science and Publication in biology) advocate making the preprint versions of all scholarly articles freely accessible.  

An overview of relevant repositories is provided by the Open Directory of Open Access Repositories (OpenDOAR).

Video about Self-Archiving Rights

Open Science in Biology

In the biosciences, there are many projects – also in collaboration with other disciplines – that develop as grassroots movements and address various aspects of the scientific process in the spirit of the open science idea. They aim, for example, to increase the public online availability of research data (open data), software source code (open source), lab journals (open notebook science), manuscript peer reviews (open peer review), teaching materials (open educational resources), the quantification of the impact of publications (open metrics), and applications for research funding, including their reviews (Miet­chen, 2014). However, open science also means opening up science to society (citizen science; e.g. Finde den Wiesenknopf). Some journals also see a need to increase the transparency of research. For example, since 2014, PLOS ONE has required that all data underpinning research must be made available together with the publication. PLOS Biology and PLOS Genetics support the Research Resource Identification Initiative, which helps researchers to assign unique identifiers to their research materials and methods. In biology, too, numerous communities have adopted the FAIR Principles in order to ensure more efficient and sustainable use of data and software.

For many years now, there have been repositories and databases for some data in biology. For example, via websites and application programming interfaces (APIs), the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI), in particular, offer structured access to various data collections, such as sequences and structures of biomolecules like DNA, RNA, and proteins. As of November 2021, re3data listed some 900 peer-reviewed data repositories in the area of biology

Despite all these initiatives and offerings, it is clear that by no means all re­search communities in biology are being reached, and by no means all technical potential is being adequately used to ensure the effective sharing of knowledge. This discrepancy between theoretical possibilities and actual implementation can be explained, among other things, by the fact that the ways in which resear­chers and the outputs of their research are evaluated when jobs and funding are being allocated remain unchanged. The evaluation criteria are generally limited to formal publications in scholarly journals and the Journal Impact Factor. This practice impacts the motivation of scholars and scientists to make their results, data, and methods publicly available at an early stage, and thus prevents the broad and rapid reuse of these resources. A rethinking of the evaluation of research outputs is desirable. This is precisely the change to which the signatories of the Declaration on Research Assessment (DORA) aspire. Specifically, they advocate that, besides making the necessary infrastructure available, incentives should be created for making the results of scholarly research available to the public as early as possible and free of technical, financial, and legal barriers.

The National Research Data Infrastructure (NFDI), which is currently under construction in Germany, is another important project in the area of open science in biology. Within the framework of this project, new technical and structural foundations will be created for research data management in the whole of Germany. In the first two selection rounds of the National Research Data Infrastructure Programme, several consortia from the life sciences and biomedical research (DataPlant, GHGA, NFDI4BioDiversity, NFDI4Health, NFDI4Microbiota) received funding. By making infrastructure, know-how, and training available, and also by developing and establishing (metadata) standards, these consortia aim to promote open and efficient science as well as the implementation of the FAIR Principles and cultural change in that direction.


Further Reading

Content editor of this page: Prof. Dr. Konrad Förstner, ZB MED – Information Centre for Life Sciences (Last updated: November 2021)