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 identify the exact resources that are reported or to answer basic questions such as "How did other studies use 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 articles and thereby improve identifiability and scientific 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 articles prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example, a model organism database 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 (http://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 articles have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40, with RRIDs appearing in 62 different journals to date. Here we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources.

Reproducibility in Computational Neuroscience Models and Simulations

“…Another NIF-affiliated project, the Resource Identification Initiative (RII) provides similar standardized Research Resource Identifiers (RRIDs) for organisms, antibodies, software tools, and databases. Dozens of journal editors have partnered with RII to promote the use of RRIDs [151]. The Mathematical Modeling Ontology (bioportal.bioontology.org/ontologies/MAMO) provides standard terms for classifying categories of models ( e.g ., MAMO 0000045 : differential equation model is a child of MAMO 0000003 : mathematical model ).…”

Assessing and tracing the outcomes and impact of research infrastructures

“…The repeatability and reproducibility of some computational processes do have dependencies on these lowest levels of the technological chain (Easterbrook, 2014). Similar questions exist in the biomedical fields, where there is interest in increasing the identification and traceability of laboratory and experimental resources, such as antibodies, tissue samples, and chemical reagents (Bandrowski et al, 2015;Singh Chawla, 2015). The notion of scientific reproducibility with respect to research infrastructures and resources represents a related, but separate, avenue of investigation (see, e.g., Baker et al, 2014;James et al, 2014).…”

RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods

“…The editors of Neuron have taken this on as a cause and joined the Research Resource Identification Initiative (Bandrowski et al, 2016) as a practical and easy method of improving research reproducibility by not just removing outdated practices, but replacing them with the current best practices for identifying and tracking research resources used in studies.…”

“…After our successful pilot (Bandrowski et al, 2016), many additional journals have adopted use of RRIDs, and Neuron has joined this effort by changing their instructions to authors and requesting inclusion of RRIDs in their publications. Neuron authors are now asked to follow resource citation guidelines (see Neuron RRID guidelines, http://www.cell.com/neuron/rrid) such that a resource citation would be reported as follows: BioLegend, cat# 101230, RRID: AB_2129374 (vendor, vendor ID, machine-readable ID).…”