The Resource Identification Initiative: A cultural shift in publishing

Abstract

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as “What other studies used resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( www.scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources.

Assessing the uptake of persistent identifiers by research infrastructure users

“…As data citation initiatives have gained more prominence, interest has grown for similar initiatives for other scholarly resources, including for software, geological physical samples, biological laboratory resources, and research facilities [17,18,19]. We use the term “research infrastructures” as an overarching grouping of multiple kinds of resources, building on terminology established in international contexts [20,21].…”

Developing high-quality mouse monoclonal antibodies for neuroscience research – approaches, perspectives and opportunities

“…, “AB_1234567”), to ensure the unambiguous description of any particular Ab. This unique identifier is then built into the larger Research Resource Identification Initiative (www.scicrunch.org/resources) or RRID (Table 2) [51] such that each Antibody Registry unique identifier becomes a corresponding RRID identifier ( e.g. , “AB_1234567” becomes “RRID:AB_1234567”).…”

“…, “AB_1234567” becomes “RRID:AB_1234567”). Certain neuroscience journals, including JCN , have embraced this effort, requiring an Antibody Registry/RRID number for all Abs used, while other journals have been making slower progress in this regard [51]. The full implementation of the RRID:AB system should go a long way towards clearly defining which Ab was used for which experiment, as it is fairly common that references to Abs are incomplete, insufficiently clear, or in some cases completely absent, a problem exacerbated by journals with strict space limitations that have decided to dispense with experimental details [52].…”

Key components of data publishing: using current best practices to develop a reference model for data publishing

“…Eighteen months later, the project was able to report both a cultural shift in researcher behaviour and a significant increase in the potential reproducibility of relevant research. As discussed in Bandrowski et al [28], the critical factor in this initiative's success in gaining acceptance and uptake was the integrated way in which it was rolled out. A group of stakeholders including researchers, journal editors, subject community leaders, and publishers-within a specific discipline, neuroscience-worked together to ensure a consistent message.…”

“…An exam- 27 Among the analyzed workflows, it was generally understood that data citation which properly attributes datasets to originating researchers can be an incentive for deposit of data in a form that makes the data accessible and reusable, a key to changing the culture around scholarly credit for research data. 28 http://wokinfo.com/products_tools/multidisciplinary/dci/. 29 http://grants.nih.gov/grants/guide/rfa-files/RFA-HL-14-031.html.…”