Depositing and reporting of reagents: Accelerating open and reproducible science.
The following blog was written by Angela Abitua (ORCiD ID: 0000-0002-8059-4050) and Joanne Kamens (ORCiD ID: 0000-0002-7000-1477) from Addgene. PLOS is excited to support reagent repositories such as Addgene as yet another step to improve scientific reproducibility. Open access to research findings and the underlying methods, materials and data, and issues surrounding reproducibility, replication, and research waste will be discussed this June 2-5 at the 6th World Conference on Research Integrity in Hong Kong, where PLOS ONE’s Senior Editor, Renee Hoch, will present a talk on data availability and image integrity.
Without materials and data, there is no research. Barriers to scientific progress can result from something as basic as not having access to reliable, validated information for research materials. That barrier is raised further when scientists cannot obtain samples or data in a timely fashion. Data and material repositories are breaking down these barriers. As a publisher, PLOS is supporting better, more open science by recommending repositories and encouraging use of standardized, unique identifiers for materials.
Centralized depositing of materials advances science in so many ways. It saves authors the time and burden of shipping requested materials. Researchers who request from repositories save time by not having to recreate reagents or wait months or years to receive samples. Many scientists have been on the receiving end of a request that was filled by an incorrect or degraded sample, which further delays research. Repositories like the ones recommended by PLOS handle the logistics of material requests, letting the scientists focus on what’s important: doing research.
For example, repositories make it possible for researchers to get access to different cell lines (American Type Culture Collection, Coriell Institute), plant materials (Arabidopsis Biological Resource Center), organisms (Bloomington Drosophila Stock Center, Caenorhabditis Genetics Center, European Xenopus Resource Centre, Jackson Laboratory), plasmids (Addgene, DNASU, PlasmID) and many other biological materials. Moreover, many of these repositories provide web-based databases that are easy to search and provide openly available information about each material.
For reagent reporting, many repositories also support unique and persistent identification of reagents. Identifiers like Research Resource Identifiers (RRIDs) make it easy for authors to cite materials and improves reporting through standardized identification and a permanent link to information about each reagent. For example, each Drosophila strain at the Bloomington Fly stock Center is assigned a fly stock RRID. For mice, the Mutant Mouse Resource and Research Centers (MMRRC) provides a mouse RRID for mutant mouse strains. For plasmids, Addgene will automatically register a plasmid RRID upon deposit.
Depositing increases materials transparency and reproducibility
Addgene currently contains over 70,000 unique plasmids and has distributed over 1,000,000 plasmids worldwide since 2004. At Addgene, depositing plasmids is free and straightforward, with the added bonus that it provides quality control measures that contribute to improved reproducibility. Addgene performs full plasmid sequencing and each plasmid is assigned a unique RRID identifier, along with a plasmid webpage that provides sequence data, cloning information, and associated protocols. This ensures researchers have detailed information about each plasmid reagent. Moreover, each Addgene plasmid page provides an Articles Citing this Plasmid section which allows researchers to learn how the plasmid was used and validated by different labs.
Recognition and credit for depositing authors
Depositing materials at the time of publication also provides benefits to both authors and publishers. Depositing authors gain recognition and are cited whenever requestors use the published materials in their own research articles. In fact, data from Addgene supports that depositing published plasmids in Addgene’s repository increases their use and results in increased article citations. Deposition at the point of publication also ensures timely distribution of materials. Finally, the information linked to each deposited reagent serves as reliable open data for the materials reported in the publication, simplifying the manuscript-writing process. Overall, PLOS’s support of reagent repositories, follows the publisher’s steps in improving data availability and protocol sharing and is a welcome addition for improving materials access and scientific reproducibility.
New sharing practices will change science for the better
By encouraging authors to deposit materials at the time of publication, journals will help accelerate research through timely distribution and accurate identification of reagents. Biological repositories exist to serve the scientific community. Take Addgene’s involvement in the explosive advancement of CRISPR research. Since 2012, over 8,400 CRISPR plasmids have been deposited and Addgene has distributed over 144,000 CRISPR plasmids worldwide, enabling researchers to share, modify, and improve this game-changing molecular tool. It is a prime example of the positive impact that biological repositories are making on research.
Thanks to PLOS’s updated recommendations, the importance of depositing and sharing reagents is finally getting some much-needed recognition. If the positive outcomes of PLOS’s data availability and protocol sharing policies is any indication of what’s in store for open material sharing, the future of science looks bright: speedier, more transparent, and more reproducible research.
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