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Piekniewska A, Anderson N, Roelandse M, Lloyd KCK, Korf I, Voss SR, de Castro G, Magnani DM, Varga Z, James-Zorn C, Horb M, Grethe JS, Bandrowski A. Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact. bioRxiv 2024:2024.01.15.575636. [PMID: 38293091 PMCID: PMC10827057 DOI: 10.1101/2024.01.15.575636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Research resources like transgenic animals and antibodies are the workhorses of biomedicine, enabling investigators to relatively easily study specific disease conditions. As key biological resources, transgenic animals and antibodies are often validated, maintained, and distributed from university based stock centers. As these centers heavily rely largely on grant funding, it is critical that they are cited by investigators so that usage can be tracked. However, unlike systems for tracking the impact of papers, the conventions and systems for tracking key resource usage and impact lag behind. Previous studies have shown that about 50% of the resources are not findable, making the studies they are supporting irreproducible, but also makes tracking resources difficult. The RRID project is filling this gap by working with journals and resource providers to improve citation practices and to track the usage of these key resources. Here, we reviewed 10 years of citation practices for five university based stock centers, characterizing each reference into two broad categories: findable (authors could use the RRID, stock number, or full name) and not findable (authors could use a nickname or a common name that is not unique to the resource). The data revealed that when stock centers asked their communities to cite resources by RRID, in addition to helping stock centers more easily track resource usage by increasing the number of RRID papers, authors shifted from citing resources predominantly by nickname (~50% of the time) to citing them by one of the findable categories (~85%) in a matter of several years. In the case of one stock center, the MMRRC, the improvement in findability is also associated with improvements in the adherence to NIH rigor criteria, as determined by a significant increase in the Rigor and Transparency Index for studies using MMRRC mice. From this data, it was not possible to determine whether outreach to authors or changes to stock center websites drove better citation practices, but findability of research resources and rigor adherence was improved.
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Affiliation(s)
| | | | | | - K C Kent Lloyd
- Mouse Biology Program, Comprehensive Cancer Center, and Department of Surgery, School of Medicine, University of California, Davis
| | - Ian Korf
- University of California Davis, Department of Molecular and Cellular Biology; UC Davis Genome Center
| | - S Randal Voss
- Ambystoma Genetic Stock Center, Spinal Cord and Brain Injury Research Center, University of Kentucky
| | | | | | - Zoltan Varga
- Zebrafish International Resource Center, Institute of Neuroscience, University of Oregon
| | - Christina James-Zorn
- Cincinnati Children's Research Foundation, Division of Developmental Biology, www.Xenbase.org
| | - Marko Horb
- National Xenopus Resource, Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory
| | - Jeffery S Grethe
- University of California at San Diego, School of Medicine, Department of Neuroscience
| | - Anita Bandrowski
- University of California at San Diego, Department of Neuroscience; SciCrunch Inc
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Thibault RT, Amaral OB, Argolo F, Bandrowski AE, Davidson AR, Drude NI. Open Science 2.0: Towards a truly collaborative research ecosystem. PLoS Biol 2023; 21:e3002362. [PMID: 37856538 PMCID: PMC10617723 DOI: 10.1371/journal.pbio.3002362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/31/2023] [Indexed: 10/21/2023] Open
Abstract
Conversations about open science have reached the mainstream, yet many open science practices such as data sharing remain uncommon. Our efforts towards openness therefore need to increase in scale and aim for a more ambitious target. We need an ecosystem not only where research outputs are openly shared but also in which transparency permeates the research process from the start and lends itself to more rigorous and collaborative research. To support this vision, this Essay provides an overview of a selection of open science initiatives from the past 2 decades, focusing on methods transparency, scholarly communication, team science, and research culture, and speculates about what the future of open science could look like. It then draws on these examples to provide recommendations for how funders, institutions, journals, regulators, and other stakeholders can create an environment that is ripe for improvement.
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Affiliation(s)
- Robert T. Thibault
- 1 Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, Unites States of America
| | - Olavo B. Amaral
- Institute of Medical Biochemistry Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Anita E. Bandrowski
- FAIR Data Informatics Lab, Department of Neuroscience, UCSD, San Diego, California, United States of America
- SciCrunch Inc., San Diego, California, United States of America
| | - Alexandra R, Davidson
- Institute for Evidence-Based Health Care, Bond University, Robina, Australia
- Faculty of Health Science and Medicine, Bond University, Robina, Australia
| | - Natascha I. Drude
- Berlin Institute of Health (BIH) at Charité, BIH QUEST Center for Responsible Research, Berlin, Germany
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Crawford DC, Hoye ML, Silberberg SD. From Methods to Monographs: Fostering a Culture of Research Quality. eNeuro 2023; 10:ENEURO.0247-23.2023. [PMID: 37553250 PMCID: PMC10411680 DOI: 10.1523/eneuro.0247-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Affiliation(s)
- Devon C Crawford
- Office of Research Quality, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Mariah L Hoye
- Office of Research Quality, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Shai D Silberberg
- Office of Research Quality, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
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Gallo C. Artificial Intelligence for Personalized Genetics and New Drug Development: Benefits and Cautions. Bioengineering (Basel) 2023; 10:bioengineering10050613. [PMID: 37237683 DOI: 10.3390/bioengineering10050613] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
As the global health care system grapples with steadily rising costs, increasing numbers of admissions, and the chronic defection of doctors and nurses from the profession, appropriate measures need to be put in place to reverse this course before it is too late [...].
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Affiliation(s)
- Crescenzio Gallo
- Department of Clinical and Experimental Medicine, University of Foggia, 71121 Foggia, Italy
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Bandrowski A, Pairish M, Eckmann P, Grethe J, Martone M. The Antibody Registry: ten years of registering antibodies. Nucleic Acids Res 2023; 51:D358-D367. [PMID: 36370112 PMCID: PMC9825422 DOI: 10.1093/nar/gkac927] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/28/2022] [Accepted: 11/07/2022] [Indexed: 11/14/2022] Open
Abstract
Antibodies are ubiquitous key biological research resources yet are tricky to use as they are prone to performance issues and represent a major source of variability across studies. Understanding what antibody was used in a published study is therefore necessary to repeat and/or interpret a given study. However, antibody reagents are still frequently not cited with sufficient detail to determine which antibody was used in experiments. The Antibody Registry is a public, open database that enables citation of antibodies by providing a persistent record for any antibody-based reagent used in a publication. The registry is the authority for antibody Research Resource Identifiers, or RRIDs, which are requested or required by hundreds of journals seeking to improve the citation of these key resources. The registry is the most comprehensive listing of persistently identified antibody reagents used in the scientific literature. Data contributors span individual authors who use antibodies to antibody companies, which provide their entire catalogs including discontinued items. Unlike many commercial antibody listing sites which tend to remove reagents no longer sold, registry records persist, providing an interface between a fast-moving commercial marketplace and the static scientific literature. The Antibody Registry (RRID:SCR_006397) https://antibodyregistry.org.
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Affiliation(s)
- Anita Bandrowski
- Department of Neuroscience, UCSD, San Diego, CA 92093, USA
- SciCrunch Inc, San Diego, CA 92093, USA
| | | | - Peter Eckmann
- Department of Neuroscience, UCSD, San Diego, CA 92093, USA
- SciCrunch Inc, San Diego, CA 92093, USA
| | - Jeffrey Grethe
- Department of Neuroscience, UCSD, San Diego, CA 92093, USA
- SciCrunch Inc, San Diego, CA 92093, USA
| | - Maryann E Martone
- Department of Neuroscience, UCSD, San Diego, CA 92093, USA
- SciCrunch Inc, San Diego, CA 92093, USA
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Elston DM. Meeting the need for trusted information in a changing world. J Am Acad Dermatol 2023; 88:23. [PMID: 35931218 DOI: 10.1016/j.jaad.2022.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 10/16/2022]
Affiliation(s)
- Dirk M Elston
- Department of Dermatology and Dermatologic Surgery, Medical University of South Carolina, Charleston, South Carolina.
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Fritsche E, Barenys M, Hogberg HT. Editorial: Methods and protocols in neurotoxicology. Front Toxicol 2022; 4:1031667. [PMID: 36337915 PMCID: PMC9634543 DOI: 10.3389/ftox.2022.1031667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/14/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Ellen Fritsche
- IUF–Leibniz Research Institute for Environmental Medicine, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
- *Correspondence: Ellen Fritsche,
| | - Marta Barenys
- GRET, INSA-UB, and Toxicology Unit, Pharmacology, Toxicology, and Therapeutical Chemistry Department, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Helena T. Hogberg
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Durham, NC, United States
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