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sentences describing how their study was limited; Seek & Blastn checks for common oligonucleotide problems; Ripeta checks several rigour criteria such as whether blinding was used in the study;
SciScore.com checks the rigour and also checks reagents such as antibodies, cell lines, and organisms as well as plasmids, and software tools. These tools provide output, which
can alert authors to a particular problem with their manuscript. However, these tools can also alert the reviewer or editor whether there is a particular problem or problems with the manuscript at hand. Several of these tools have been deployed across different parts of the literature. For example, JetFighter pings authors of any preprint in which a colour-blind non-compliant figure is detected. We understand that some authors do not appreciate this, but it is difficult to know if there is a better way to raise awareness. Several of the other tools (SciScore, Limitations-finder, OddPub, Barzooka) have recently been deployed together and provide a single report for COVID literature (see example report). It is still too early to tell whether there will be any improvement in the literature based on this work, but given the pace of publishing, especially in the preprints, a set of tools seems like an important step towards better science. Indeed, the editors of AACR, have
taken a long look at reproducibility issues in cancer biology as described last year in
Glossary
Rigour is defined as ‘the strict application of the scientific method to ensure robust and unbiased experimental design’ (National Institutes of Health, 2018).
RRIDs (research resource identifiers) are ID numbers assigned to help researchers cite key resources (antibodies, model organisms and software projects) in the biomedical literature to improve the transparency of research methods. RRIDs are also provided for other resources such as organisms, plasmids, and software tools. When RRIDs are not present in the RRID portal, authors are encouraged to register a new one.
MDAR (materials design analysis reporting) framework is a checklist for authors to use, and an elaboration document with background and instructions. The project components contain data from author and editor surveys and coder data from the evaluated checklists.
SciScore is an advanced text mining based tool that checks the methods section for the use of RRIDs and for compliance with the NIH rigour and transparency criteria. The latter include proper authentication of cell lines, an important step for many cancer researchers.
Automated Screening Working Group is a group of software engineers and biologists passionate about improving scientific manuscripts at scale. Our goal is to process every manuscript in the biomedical sciences as it is being submitted for publication to improve that manuscript. Each tool checks for a different set of transparency criteria, but together we can shed light on what your manuscript. We will build pathways for the tools to work together.
www.researchinformation.info | @researchinfo
Interesting for your journal? Check
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“These tools provide output, which can alert authors to a particular problem with their manuscript”
an editorial (Dang, 2018), however, theory must be put into practice. Although RRIDs have been encouraged in the instructions to authors of AACR journals over the last year, these recommendations have not been followed widely by all authors, most likely because it is a tedious task to do. Moving forwards, this recommendation will become a little more stringent as we have deployed SciScore (the Rigour criteria and RRID checker) in eJournalPress for all AACR journals as part of the submission workflow. All authors submitting a manuscript to AACR will receive a rigour adherence and key resource report that will help them to improve their manuscript and, if followed, should make the AACR’s research more reproducible. Ri
Martijn Roelandse is founder/consultant at
martijnroelandse.dev
Anita Bandrowski runs the RRID initiative and is the creator of SciScore..
A fully-referenced version of this article is available at
www.researchinformation.info
Product Spotlight
The right time to do the right thing about scientific reproducibility.
One thing that this pandemic has taught us is that not everything we do must be done in the same way as it “always was”. Science is now happening at a furious pace. Journals have been inundated by “that other paper” that has just been sitting around in a file drawer, until that is, the fast pace of life suddenly stops. So here we are, publishing so fast that it exasperates any previous problems with quality checks. Worse still, scientists working on COVID-19 argue that their studies must be released at the earliest.
So what is a publisher (traditional or preprint) to do? How can we possibly maintain quality in this type of environment?
Clearly we need a reviewer that can read at a thousand words per second, never gets tired, and does not refuse to review the paper.
That reviewer actually exists - meet SciScore. com. It can read a methods section of a manuscript in about a minute, and provides a report to editors, reviewers or authors about common rigor criteria that have or have not been addressed. SciScore has already read and reviewed all of the COVID manuscripts, and posted the results to twitter and
Hypothes.is. SciScore is also ‘reading’ all AACR papers giving the hard-working editors a hand, and will soon be working for any journal that works with the Editorial Manager platform.
August/September 2020 Research Information
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