Establishing Institutional Scores With the Rigor and Transparency Index: Large-scale Analysis of Scientific Reporting Quality

Menke, Joe; Eckmann, Peter; Özyurt, İbrahim Burak; Roelandse, Martijn; Anderson, Nathan; Grethe, Jeffrey S.; Gamst, Anthony; Bandrowski, Anita

doi:10.2196/37324

Cited by 17 publications

(15 citation statements)

References 54 publications

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“…While it is still easy to find papers citing antibodies with insufficient information to uniquely identify the reagent, such as authors just citing the protein and vendor, a truly terrible practice, it is getting less common. A recent study of all accessible antibody sentences (in ∼2M documents) in the open access literature found that antibody catalog numbers or RRIDs (making them uniquely identifiable) in papers is becoming much more common, going from 12% of antibody references in 1997 to 31% in 2020 ( 16 ). It is unknown to what extent this welcome change is due to efforts of the Antibody Registry, but with over 300K antibody RRIDs in the scientific literature, the contribution is not insignificant.…”

Section: Discussionmentioning

confidence: 99%

The Antibody Registry: ten years of registering antibodies

Bandrowski

Pairish²,

Eckmann

et al. 2022

Nucleic Acids Research

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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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Section: Discussionmentioning

confidence: 99%

The Antibody Registry: ten years of registering antibodies

Bandrowski

Pairish²,

Eckmann

et al. 2022

Nucleic Acids Research

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“…Like Menke et al (2022), here we used SciScore (Ver 2, RRID:SCR_016251) to check each paper that contained a reference to an animal or antibody from our exemplar stock centers. Figure 4 shows the comparison of the overall RTI vs the papers gathered that refer to one of the stock centers.…”

Section: Analysis Of the Rigor And Transparency Indexmentioning

confidence: 99%

Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact

Piekniewska,

Anderson,

Roelandse

et al. 2024

Preprint

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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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“…Together, these approaches bring us a few steps closer to making use of new evidence at a much quicker pace. Further, measuring research quality indicators in an automated way may allow for the benchmarking of research improvement activities over time (Wang, Hair, et al, 2021;Menke et al, 2022).…”

Section: Keeping Up To Date With the Literaturementioning

confidence: 99%

Systematic Online Living Evidence Summaries: emerging tools to accelerate evidence synthesis

Hair¹,

Wilson²,

Wong³

et al. 2022

Preprint

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Systematic reviews and meta-analysis are the cornerstones of evidence-based decision making and priority setting. However, traditional systematic reviews are time and labour intensive, limiting their feasibility to comprehensively evaluate the latest evidence in research-intensive areas. Recent developments in automation, machine learning and systematic review technologies have enabled efficiency gains. Building upon these advances, we developed Systematic Online Living Evidence Summaries (SOLES) to accelerate evidence synthesis. In this approach, we integrate automated processes to continuously gather, synthesise and summarise all existing evidence from a research domain, and report the resulting current curated content as interrogatable databases via interactive web applications. SOLES can benefit various stakeholders by (i) providing a systematic overview of current evidence to identify knowledge gaps, (ii) providing an accelerated starting point for a more detailed systematic review, and (iii) facilitating collaboration and coordination in evidence synthesis.

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Establishing Institutional Scores With the Rigor and Transparency Index: Large-scale Analysis of Scientific Reporting Quality

Cited by 17 publications

References 54 publications

The Antibody Registry: ten years of registering antibodies

The Antibody Registry: ten years of registering antibodies

Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact

Systematic Online Living Evidence Summaries: emerging tools to accelerate evidence synthesis

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