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Title: 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 generatemore » 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.« less

Authors:
 [1];  [2];  [1];  [2];  [3];  [4];  [5];  [1];  [6];  [7];  [8];  [9];  [2]
  1. Univ. of California, Lo Jolla, CA (United States). Center for Research in Biological Systems
  2. Oregon Health and Science Univ., Portland, OR (United States). Dept. of Medical Informatics and Clinical Epidemiology
  3. Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA (United States)
  4. Karolinska Institutet, Stockholm (Sweden)
  5. Leon and Norma Hess Center for Science and Medicine, Icahn School of Medicine at Mount Sinai, New York, NY (United States)
  6. Scientific Outreach, Faculty of 1000 Ltd, London (United Kingdom)
  7. John Wiley and Sons, Hoboken, NJ (United States)
  8. Lawrence Berkeley Lab., CA (United States)
  9. Elsevier, Amsterdam (Netherlands)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
Contributing Org.:
Resource Identification Initiative Members are listed here: https://www.force11.org/node/4463/members
OSTI Identifier:
1209491
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
F1000Research
Additional Journal Information:
Journal Volume: 4; Journal Issue: 134; Journal ID: ISSN 2046-1402
Publisher:
F1000Research
Country of Publication:
United States
Language:
English
Subject:
96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Bandrowski, Anita, Brush, Matthew, Grethe, Jeffery S., Haendel, Melissa A., Kennedy, David N., Hill, Sean, Hof, Patrick R., Martone, Maryann E., Pols, Maaike, Tan, Serena, Washington, Nicole, Zudilova-Seinstra, Elena, and Vasilevsky, Nicole. The Resource Identification Initiative: A cultural shift in publishing. United States: N. p., 2015. Web. doi:10.12688/f1000research.6555.1.
Bandrowski, Anita, Brush, Matthew, Grethe, Jeffery S., Haendel, Melissa A., Kennedy, David N., Hill, Sean, Hof, Patrick R., Martone, Maryann E., Pols, Maaike, Tan, Serena, Washington, Nicole, Zudilova-Seinstra, Elena, & Vasilevsky, Nicole. The Resource Identification Initiative: A cultural shift in publishing. United States. https://doi.org/10.12688/f1000research.6555.1
Bandrowski, Anita, Brush, Matthew, Grethe, Jeffery S., Haendel, Melissa A., Kennedy, David N., Hill, Sean, Hof, Patrick R., Martone, Maryann E., Pols, Maaike, Tan, Serena, Washington, Nicole, Zudilova-Seinstra, Elena, and Vasilevsky, Nicole. 2015. "The Resource Identification Initiative: A cultural shift in publishing". United States. https://doi.org/10.12688/f1000research.6555.1. https://www.osti.gov/servlets/purl/1209491.
@article{osti_1209491,
title = {The Resource Identification Initiative: A cultural shift in publishing},
author = {Bandrowski, Anita and Brush, Matthew and Grethe, Jeffery S. and Haendel, Melissa A. and Kennedy, David N. and Hill, Sean and Hof, Patrick R. and Martone, Maryann E. and Pols, Maaike and Tan, Serena and Washington, Nicole and Zudilova-Seinstra, Elena and Vasilevsky, Nicole},
abstractNote = {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.},
doi = {10.12688/f1000research.6555.1},
url = {https://www.osti.gov/biblio/1209491}, journal = {F1000Research},
issn = {2046-1402},
number = 134,
volume = 4,
place = {United States},
year = {Fri May 29 00:00:00 EDT 2015},
month = {Fri May 29 00:00:00 EDT 2015}
}

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Enhanced consumption of salient solutions following pedunculopontine tegmental lesions
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Power failure: why small sample size undermines the reliability of neuroscience
journal, April 2013


Cautionary notes on the use of NF-κB p65 and p50 antibodies for CNS studies
journal, January 2011


An Investigation of the Specificity of Research Antibodies against NF-κB-subunit p65
journal, November 2013


A Comparative Antibody Analysis of Pannexin1 Expression in Four Rat Brain Regions Reveals Varying Subcellular Localizations
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Works referencing / citing this record:

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Engineered Ovarian Cancer Cell Lines for Validation of CAR T Cell Function
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Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines
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Improving transparency and scientific rigor in academic publishing
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Role of epithelial–mesenchymal transition involved molecules in the progression of cutaneous melanoma
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Continuous cuprizone intoxication allows active experimental autoimmune encephalomyelitis induction in C57BL/6 mice
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Revisiting the scientific method to improve rigor and reproducibility of immunohistochemistry in reproductive science†
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Improving transparency and scientific rigor in academic publishing
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Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis
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A snapshot of 3649 Web-based services published between 1994 and 2017 shows a decrease in availability after 2 years
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Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines
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