Open Science

The term open access refers to the unrestricted access and reuse of peer-reviewed scientific journal articles. Reading is free - without paywalls or subscription fees; reuse is legitimized and usually governed by a Creative Commons Attribution license. Under such a license, authors retain the copyright and give users perpetual rights to read, copy, distribute and further use an article, as long as the work is properly cited. The publisher has a non-exclusive license to publish the article. There can be some restrictions on further use such as prohibiting commercial use. In addition, authors are allowed to deposit their articles in any repository (e.g. university), and reuse their own figures and text without needing explicit permission from a publisher. Shortly after publishing, the articles are usually archived and indexed in public repositories, such as PubMed Central. Open access articles are fully accessible by search engines and often available for text mining, which further enhances the use of the results and their visibility.

The different types of open access publishing are often referred to as diamond, gold and green:

Diamond open access means permanent and free access to published scientific works for readers with no publication fees (i.e. no APCs - article processing charges) for the authors. This model is applied for all articles of the Beilstein Journals (i.e. the Beilstein Journal of Organic Chemistry, the Beilstein Journal of Nanotechnology and the Beilstein Magazine) as well as the conference proceedings.

With the gold open access model, the author pays a fee (APCs usually range from 500–5,000 EUR) to the publisher to cover production costs, and the copyright holder (usually the author) grants readers permanent and royalty-free access to the article. Unfortunately, some publishers place limits on the reuse of the articles, restrict text and data mining, hold the copyright (or only transfer it upon additional payment), and even adopt the practice of allowing only “temporary open access”.

Another open access model is the green or self-archiving model. Here, the author deposits a version (usually a pre-production version) of the article in a freely accessible repository (e.g. preprint server). Which version of the article is allowed to be deposited and whether there is an embargo period depends on the policies of the publisher.

The maintenance of a publication infrastructure, careful processing of submitted manuscripts, peer-review process and other quality assessments, and publication and dissemination of articles does cost money – this must be covered by the author, reader or the public. This is true for any scientific paper, including open access publications. With the gold and green open access models, authors usually pay APCs to cover these costs in order to make their articles publicly available. In contrast, the Beilstein Journals are completely funded by the Beilstein-Institut, driven by the belief that scientific knowledge is a social good and should be available without barriers.

Thus, the Beilstein diamond open access model maximizes the potential for exchanging ideas and provides a valuable contribution to those with limited financial means by leveling the playing field and giving everyone an equal chance to publish and read scientific publications of high quality. In 2015, the Beilstein Journals were awarded the DOAJ Seal which recognizes the exceptionally high level of publishing standards and best practices adhering to these journals.

In 2002, a small group gathered in Budapest, under the auspices of the Open Society Foundation, to promote the free distribution of research articles over the internet. The result was the Budapest Open Access Initiative, whose declaration was the first major international statement and recognized the major event of the open access movement. The Bethesda Statement on Open Access Publishing followed in 2003. This statement defined the concept of open access and underlined its support. In the same year, under the auspices of the Max Planck Society and the European Cultural Heritage Online, the Berlin Declaration on Open Access and Knowledge in the Science and Humanities was published, and signed by many participants in the conference on Open Access to the Data and Results of the Sciences and Humanities. This statement includes the acknowledgment of the increasing impact of online research resources and encourages researchers and institutions to advocate and publish in open access platforms and to support an open access infrastructure.

Further important developments include: the launch of the PubMed Central repository by the NIH in 2000 and BioMed Central publishing their first article. In 2001, the Public Library of Science (PLoS) was launched and in 2003 the Directory of Open Access Journals was established. In 2005, the Beilstein-Institut launched the Beilstein Journal of Organic Chemistry. In 2005, the NIH mandated depositing of articles in PubMed Central, and the Wellcome Trust started implementing its open access mandate, followed the RCUK and ERC in 2006, and HHMI in 2007. In 2010, the Beilstein-Institut launched the Beilstein Journal of Nanotechnology. A timeline of the beginning of the open access movement can be found here.

In 2011, the European Commission outlined measures to improve access to scientific data in Europe. This was centered on the Horizon 2020 program (2014–2020) which mandates open access and includes an open research data pilot. This pilot was extended in 2016 to include recommendations for realizing the European Science Cloud (EOSC) by 2020.

In the USA, similar discussions were held, culminating in the directive from the White House Office of Science and Technology Policy, Washington, D.C., 2013 on Increasing Access to the Results of Federally Funded Scientific Research. This directive requires that agencies with over $100 million expenditure develop a plan to increase public access to the results of research funded by the Federal Government.

Today, many funding agencies, e.g. Wellcome Trust and the National Institutes of Health, require grantees to publish in open access journals or to deposit the accepted manuscript in a publically accessible repository such as PubMed Central after an embargo period. The Registry of Open Access Repository Mandates and Policies (ROARMAP) is a searchable international registry of open access mandates and policies adopted by universities, research institutions and research funders.

Open Access 2020 is an international initiative coordinated by the Max-Planck-Society that aims to induce the transformation of scholarly journals from subscription-based platforms to open access publishing. The Beilstein-Institut was one of the early signatories of this initiative. The principles of this initiative were discussed and agreed upon at the Berlin 12 Conference in 2015 and are embodied in an Expression of Interest, which has been endorsed by numerous international scholarly organizations.

The consequent extension of the principles of open access publishing is open science – an endeavor that aims at making it easier to publish and communicate scientific knowledge by providing free access to research results, encouraging researchers to share their data, and ensuring that data are complete, comprehensive and transparent. This will have impact on the whole research cycle, changing how science is disseminated and assessed, allowing results to be better interpreted, analyzed, reproduced and used to generate new knowledge. One of the pioneers of Open Science is the Royal Society in London, by beginning the publishing era with the Philosophical Transactions in 1665 and in modern times with its thought provoking publication in 2012 “Science as an Open Enterprise”.

The European Open Science Cloud (EOSC) aims to give Europe a global lead in scientific data infrastructure to ensure that European scientists reap the full benefits of data-driven science. The plan is to make all scientific data produced by the Horizon 2020 Programme open access by default. This will extend the current data pilot, whereby projects implement data management plans to make research data findable, accessible, interoperable and reusable (FAIR principles). The European Open Science Cloud will start by federating existing scientific data infrastructures, currently scattered across disciplines and member states in the GO-FAIR initiative.

An essential prerequisite for open science data is reporting guidelines and technical standards that provide the framework for the exchange of data from one laboratory to another without technical and textual barriers. However, scientific research has reached a stage in which improved technologies and methodologies contribute to the accumulation of a vast amount of data. Currently, this data is often poorly reported, often resulting in incomplete and even unusable data sets that are not suitable for replication or subsequent research and knowledge generation.
The problems became very obvious in the -omics disciplines such as genomics, proteomics and glycomics that applied new exciting technologies to primarily collect and rapidly publish a significant amount of data on gene, protein and oligosaccharide sequences but failed to provide essential metadata on sample preparation, data recording, sample identification and analysis, etc. A number of initiatives have been established in recent years to correct the situation in proteomics, genomics and biomedicine by creating specific reporting guidelines, which are catalogued at biosharing.org.

For more than ten years, the Beilstein-Institut has supported two data standardization projects: STRENDA which is concerned with the standardization of reporting enzymology data and MIRAGE with the reporting of glycomics experimental results. Both projects are widely accepted and acknowledged by the scientific community. To improve their practical use by both authors and journals, the STRENDA Guidelines have been recently implemented as a web-based front-end for STRENDA-DB. This supports authors by providing a data submission form that automatically checks the manuscript data prior to or during the publication process for compliance with the STRENDA Guidelines. The successful formal assessment is documented in a fact sheet that can be submitted with the manuscript to the journal. In addition, each dataset is assigned a DOI to allow easy tracking and referencing of data. The data become publicly available in the open access database only after the corresponding article has been peer-reviewed and published in a journal.

Free access to research data and information, in particular to raw experimental data, is a fundamental mandate of open science. Raw data includes not only experimental results but also additional data, often called metadata, that describe the experimental design, sample preparation, experimental conditions and machine settings and also provides further information about the methodologies for the analysis and interpretation of this data. The access to this data allows re-analysis and interpretation of processed data which is usually published in diagrams and tables.

Researchers can corroborate the soundness of the conclusions drawn from published data – this has strong potential to increase the quality of the peer-review process. In addition, raw data can provide the community with a goldmine of new insights and knowledge by interconnecting data from various sources, and it can inspire the generation of new hypotheses and experimental approaches. Despite the obvious advantages, there are still many reservations to share research data and a broad consensus must be achieved on the use, distribution, control and assignment of this data.