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The Resource Identification Initiative: a cultural shift in publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N, RINL Resource Identification Initiati - Brain Behav (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Center for Research in Biological Systems UCSD 9500 Gillman Dr.#0446 la Jolla California 92093-0446.

ABSTRACT
A central tenet in support of research reproducibility is the ability to uniquely identify research resources, that is, 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 papers 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 manuscripts 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 papers 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.

No MeSH data available.


Pre‐ and postpilot identifiability. Resources (primary antibodies, organisms, and tools) were considered identifiable if they contained an accurate RRID or by using the same criteria as described in (Vasilevsky et al. 2013). For tools (software and databases, which were not previously analyzed), these resources were considered identifiable if they contained an RRID or reported the manufacturer and version number. The total number of resources for each type is: primary antibodies prepilot, n = 140; primary antibodies postpilot, n = 465; organisms prepilot, n = 58; organisms postpilot, n = 139; noncommercial tools prepilot, n = 59; noncommercial tools postpilot, n = 101. The y‐axis is the average percent identifiable for each resource type. Variation from this average is shown by the bars: error bars indicate upper and lower 95% confidence intervals. Asterisks indicate significant difference by a z‐score greater than 1.96.
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brb3417-fig-0004: Pre‐ and postpilot identifiability. Resources (primary antibodies, organisms, and tools) were considered identifiable if they contained an accurate RRID or by using the same criteria as described in (Vasilevsky et al. 2013). For tools (software and databases, which were not previously analyzed), these resources were considered identifiable if they contained an RRID or reported the manufacturer and version number. The total number of resources for each type is: primary antibodies prepilot, n = 140; primary antibodies postpilot, n = 465; organisms prepilot, n = 58; organisms postpilot, n = 139; noncommercial tools prepilot, n = 59; noncommercial tools postpilot, n = 101. The y‐axis is the average percent identifiable for each resource type. Variation from this average is shown by the bars: error bars indicate upper and lower 95% confidence intervals. Asterisks indicate significant difference by a z‐score greater than 1.96.

Mentions: An outcome of this study was to determine if the use of RRIDs in the literature increased the identifiability of research resources. As shown in Figure 4, when authors were asked by their editors to provide RRIDs, regardless of their compliance with the RII project, the identifiability of research resources significantly increased. We calculated the percentage of identifiable research resources in the same journals, just before the pilot project and after. The reporting of research resources prepilot was consistent with findings from the 2013 study (Vasilevsky et al. 2013), in that roughly 50–60% were found to be identifiable. But, when asked by their editors, researchers used identifying information in 80–90% of research resources, showing that they presumably had the data available, but did not put it into their papers unless prompted by communication from the editors.


The Resource Identification Initiative: a cultural shift in publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N, RINL Resource Identification Initiati - Brain Behav (2015)

Pre‐ and postpilot identifiability. Resources (primary antibodies, organisms, and tools) were considered identifiable if they contained an accurate RRID or by using the same criteria as described in (Vasilevsky et al. 2013). For tools (software and databases, which were not previously analyzed), these resources were considered identifiable if they contained an RRID or reported the manufacturer and version number. The total number of resources for each type is: primary antibodies prepilot, n = 140; primary antibodies postpilot, n = 465; organisms prepilot, n = 58; organisms postpilot, n = 139; noncommercial tools prepilot, n = 59; noncommercial tools postpilot, n = 101. The y‐axis is the average percent identifiable for each resource type. Variation from this average is shown by the bars: error bars indicate upper and lower 95% confidence intervals. Asterisks indicate significant difference by a z‐score greater than 1.96.
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Related In: Results  -  Collection

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brb3417-fig-0004: Pre‐ and postpilot identifiability. Resources (primary antibodies, organisms, and tools) were considered identifiable if they contained an accurate RRID or by using the same criteria as described in (Vasilevsky et al. 2013). For tools (software and databases, which were not previously analyzed), these resources were considered identifiable if they contained an RRID or reported the manufacturer and version number. The total number of resources for each type is: primary antibodies prepilot, n = 140; primary antibodies postpilot, n = 465; organisms prepilot, n = 58; organisms postpilot, n = 139; noncommercial tools prepilot, n = 59; noncommercial tools postpilot, n = 101. The y‐axis is the average percent identifiable for each resource type. Variation from this average is shown by the bars: error bars indicate upper and lower 95% confidence intervals. Asterisks indicate significant difference by a z‐score greater than 1.96.
Mentions: An outcome of this study was to determine if the use of RRIDs in the literature increased the identifiability of research resources. As shown in Figure 4, when authors were asked by their editors to provide RRIDs, regardless of their compliance with the RII project, the identifiability of research resources significantly increased. We calculated the percentage of identifiable research resources in the same journals, just before the pilot project and after. The reporting of research resources prepilot was consistent with findings from the 2013 study (Vasilevsky et al. 2013), in that roughly 50–60% were found to be identifiable. But, when asked by their editors, researchers used identifying information in 80–90% of research resources, showing that they presumably had the data available, but did not put it into their papers unless prompted by communication from the editors.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Center for Research in Biological Systems UCSD 9500 Gillman Dr.#0446 la Jolla California 92093-0446.

ABSTRACT
A central tenet in support of research reproducibility is the ability to uniquely identify research resources, that is, 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 papers 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 manuscripts 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 papers 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.

No MeSH data available.