Openness and transparency in research are becoming increasingly important, driven partly by scientists who want to dig beneath a paper’s surface to uncover those golden nuggets of data, code, and even the original preprints associated with these articles for use in their own studies.
Scholarly publishers have been fulfilling these needs. The result: Research papers are becoming more than just static articles published in refereed journals, and the full depth and breadth of resources behind many research papers can be seen by anyone as independent research “objects” that are shareable, citable, reusable, and most importantly, make studies reproducible for others.
The protocol: A key research “object”
Arguably one of the most important elements of research is the protocol, which has the potential to provide other scientists with detailed instructions to reproduce and build on the work.
These protocols can enhance an article’s method section by covering detailed instructions about how to conduct experiments, computational models, equipment operation, and other processes reported in a manuscript’s methodology. They are valuable in their own right, published independently. They can serve as a detailed roadmap for researchers to consistently test and reproduce others’ research in the same way as the original authors had done it—irrespective of a paper’s findings.
The Protocol Exchange, an open-access repository of protocols developed by Nature Research and housed on Research Square, enhances and maximizes the value of protocols by supporting their distribution and shareability across various disciplines in the natural sciences.
Like Research Square, the Protocol Exchange functions as a preprint server. Authors can deposit their methodologies, whether they are submitted to Nature Research journals or not.
These protocols can be published as preprints. They can be published in journals as stand-alone articles, and they can be used as an 'object' for one or more research papers.
Advantages of using the Protocols Exchange
Researchers who upload protocols the Exchange bring a host of benefits to themselves and the scientific community:
- Reproducibility. In a 2016 study by Nature that helped uncover a crisis in reproducibility, more than 70% of researchers surveyed tried and failed to reproduce other scientists’ experiments; and more than half of respondents failed to reproduce their own experiments.The Protocol Exchange has been solving these issues by promoting a detailed and consistent format that scientists can use to reproduce others’ research.
- Clarity. The Protocol Exchange provides a format that sets a clear and consistent standard for protocols across the natural sciences, allowing a description of methods in detail so that it is easy for readers to see, build on, and reproduce another author’s work. To help accomplish this, formatting covers step-by-step descriptions of procedures, reagents and equipment used, troubleshooting, and anticipated results.
- Shareability. Protocols on the Exchange are published under a Creative Commons Attribution licence, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as the appropriate credit is given.
- Transparency and openness. Just like preprints posted by authors on Research Square, protocols posted directly on the Exchange are made freely available to the research community for comment. All comments and versions are visible, creating a detailed record of the protocol’s development and the influences driving its changes. There are a growing number of platforms that offer opportunities for the scientific community to come together through transparency and openness.
- Tracking and permanence. All protocols uploaded to the Protocols Exchange are assigned their own permanent digital object identifiers (DOIs). By assigning separate DOIs to protocols, authors can identify any research papers where their protocol was used. They also allow a seamless, permanent link between papers and the full details of the protocol.
- Versioning. Through versioning, protocols are not eliminated and replaced; they are updated and improved, with all past versions remaining associated with the original DOI. And while all versions of a protocol can be accessed, the most recent version is fully discoverable. In short, versioning helps ensure the methods sections of research papers never get outdated. Versioning also gives the scientific community a clear reference point for the exact protocol and version used in a paper.
- The potential for enhanced peer reviews. A dedicated resource like the Protocol Exchange supports a higher-quality peer-review process. Peer reviewers can refer to the protocol—along with code and data if it has been published—to enhance the vetting process for manuscripts.
Expanding protocols to new frontiers
While the Protocol Exchange is primarily used by individuals in the traditional life sciences, protocols can be used across literally any discipline.
Examples of protocol use can be nearly infinite.
Computational science experts develop protocols to help researchers get consistent and effective results through their mathematical models and computational techniques.
Food scientists use protocols to ensure consistent standards for performing analysis and experimentation. This ultimately supports consistent quality for the mass production of foods.
Researchers in the public health community develop protocols that can ensure consistency in anything from the collection of tissue samples to the collection of survey data.
While protocols might not look the same across all scientific fields, protocols can be useful to literally any discipline that uses methods for gathering, conducting, and reporting research. In other words, any scientific discipline can benefit from protocols and platforms like the Protocol Exchange.
How various disciplines might need specific format adaptations remains to be seen. Developing these adaptations requires more dialogue between scholarly publishers and scientists in various fields of study.
Browse and discover more about the Protocol Exchange on Research Square: https://protocolexchange.researchsquare.com, or contact [email protected] to discuss advancing protocols in disciplines outside the natural sciences.