SlideShare a Scribd company logo
Improving the quality of pre-prints with
automated checks
Leslie
McIntosh, PhD
Ripeta, founder and CEO
@ripetaReview
What’s Happening in Preprints?
What’s happening in preprints?
No standard way of reporting or
removing preprints
32 Retracted + 3 ‘Letters of
Concern’ from Covid preprints
Still exploring checks
Automating checks
Automation in Preprints
Will authors
improve
manuscripts?
Ripeta, LLC. All rights reserved. This is not to be shared without official permission.
ripetaReview
Ripeta, LLC. All rights reserved. This is not to be shared without official permission.
ripetaReview Quality
review of
one paper
ripetaReview
Ripeta, LLC. All rights reserved. This is not to be shared without official permission.
ripetaReview
Sample ripetaReview
Research Quality
Study Objective: Yes
Professionalism
ID: Confirmed with ORCID
Funding Statement: Yes
Reproducibility
DAS: Yes
Data Location: In paper
Code Availability: No
Data Location
Result: Text found
The data used to support the findings of this study are included
within the article.
Recommendations: Please consider depositing data and
materials into an accessible repository. Having data easily
accessible has shown to increase the number of citations to
your article. This also assists in making your work
reproducible.
Relationship between the ABO Blood Group and the COVID-19
Susceptibility
DOI: 10.1101/2020.03.11.20031096
Results
Feedback
Will authors
improve
manuscripts?
(ResearchSquare)
33% of authors
corrected and re-
uploaded their
preprint
Can quality
papers be
quickly
identified?
Ripeta, LLC. All rights reserved. This is not to be shared without official permission.
ripetaReport
Ripeta, LLC. All rights reserved. This is not to be shared without official permission.
ripetaReport Report of
Portfolio of
Publications
Sample ripetaReport (Wellcome Trust)
ripetaReporting
Can quality
papers be
quickly
identified?
(Covid preprints)
Automation in Preprints
Quality
Indicators
Research
Professionalism
Reproducibility
info@ripeta.com
Research
Relationship between the ABO Blood Group and the COVID-19 Susceptibility
DOI: 10.1101/2020.03.11.20031096
Here, we investigated the relationship between the ABO blood type
and the susceptibility to COVID-19 in patients from three hospitals in
Wuhan and Shenzhen, China to test if the former may be a biomarker
for the latter.
Study Objective
Scientific
Headings
Abstracts, Background/Introduction, Methods
Professionalism
Reproducibility
Relationship between the ABO Blood Group and the COVID-19 Susceptibility
DOI: 10.1101/2020.03.11.20031096
Data Availability
The data used to support the findings of this study are included within the article.
Data Availability
The data used to support the findings of this study are included within the article.
{Not Found}
Data Availability
Statement
Data Location
Code Availability
Can automation
save time?
Covid Preprint
Analyses
ripetaScore Outcome Citations
Similarity nCoV spike protein
10.1101/2020.01.30.927871 Low Withdrawn 50
Hydroxychloroquine
10.1101/2020.03.16.20037135 Medium Questioned 3000
ABO Blood Group
10.1101/2020.03.11.20031096
Medium Overhyped 150
Potential vaccine targets
10.1101/2020.02.03.933226 High Published 450
Article DOI Study
Purpose
Author-
ship
Funding
Statement
Data
location
DAS Code
availability
10.1101/2020.01.30.927871 Yes 2 No None No No
Uncanny similarity of unique inserts in the 2019-nCoV spike
protein to HIV-1 gp120 and Gag
Methodology
Retrieval and alignment of nucleic acid and protein sequences
We retrieved all the available coronavirus sequences (n=55) from NCBI viral
genome database (https://www.ncbi.nlm.nih.gov/) and we used the GISAID (Elbe
& Buckland-Merrett, 2017)[https://www.gisaid.org/] to retrieve all available full-
length sequences (n=28) of 2019-nCoV as on 27 Jan 2020. Multiple sequence
alignment of all coronavirus genomes was performed by using MUSCLE
software (Edgar, 2004) based on neighbour joining method. Out of 55
coronavirus genome 32 representative genomes of all category were used for
phylogenetic tree development using MEGAX software (Kumar et al., 2018). The
closest relative was found to be SARS CoV.
Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an
open-label non-randomized clinical trial
Article DOI Study
Purpose
Author-
ship
Funding
Statement
Data
location
DAS Code
availability
10.1016/j.ijantimicag.2020
.105949
Yes 1 Yes None No No
Elisabeth Bik took a close look at the IJAA article and
detailed a long list of serious problems with the study,
including questions about its ethical underpinnings, messy
confounding variables, missing patients, rushed and
conflicted peer review, and confusing data.
Relationship between the ABO Blood Group and the COVID-19 Susceptibility
Article DOI Study
Purpose
Author-
ship
Funding
Statement
Data
location
DAS Code
availability
10.1101/2020.03.11.200310
96
Yes 4 Yes In paper Yes No
Preliminary identification of potential vaccine targets for the COVID-19
coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies
Article DOI Study
Purpose
Author-
ship
Funding
Statement
Data
location
DAS Code
availability
10.1101/2020.02.03.933226 Yes 4 Yes External
repo
Yes Yes
Can automation
save time?
(SpringerNature &
bioRxiv/medRxiv Preprints)
4 minutes
instead of 40 hours
to check 400+
manuscripts
Does automation
solve all problems?
Automated checks
can make
better science easier
Follow us @RipetaReview for more memes
Follow us for weekly
academic highlights,
transparency tips, and more!
@RipetaReview
@Ripeta
info@ripeta.com
www.ripeta.com
Stay
Informed
Leslie McIntosh
CEO
Cynthia Hudson
Vitale
COO, co-founder
Chris Westling
Data Engineer
Ruth Whittam
Data Scientist,
Lead
Josh Sumner
Data Scientist,
Intern
Leah Haynes
Data Scientist,
Intern
ripetinis
Paola Ortega
Saborío
Data Engineer
August
DeVore
Editor
ripeta.com
info@ripeta.com
Appendix
ripetaData Research Professionalism Reproducibility
Open Access Ethical Approval Statement Data Availability Statements
Abstract Ethical Approval Organization Data Locations - Repository
Study Objective Author Contribution Statement Data Locations - PID
Funding Statement Competing Interests Data Locations - Identifiers
Funding Source Funding Source Data Locations - URL
Funding Grant ID Funding Grant ID Analysis Software
Count of Authors (single) Analysis Software Version
Self-Citations Statistical Methods
Author Identification Code Availability Statement

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McIntosh "Improving the quality of preprints with automated checks"

  • 1. Improving the quality of pre-prints with automated checks
  • 2. Leslie McIntosh, PhD Ripeta, founder and CEO @ripetaReview
  • 4. What’s happening in preprints? No standard way of reporting or removing preprints 32 Retracted + 3 ‘Letters of Concern’ from Covid preprints Still exploring checks Automating checks
  • 7. Ripeta, LLC. All rights reserved. This is not to be shared without official permission. ripetaReview
  • 8. Ripeta, LLC. All rights reserved. This is not to be shared without official permission. ripetaReview Quality review of one paper ripetaReview
  • 9. Ripeta, LLC. All rights reserved. This is not to be shared without official permission. ripetaReview Sample ripetaReview Research Quality Study Objective: Yes Professionalism ID: Confirmed with ORCID Funding Statement: Yes Reproducibility DAS: Yes Data Location: In paper Code Availability: No Data Location Result: Text found The data used to support the findings of this study are included within the article. Recommendations: Please consider depositing data and materials into an accessible repository. Having data easily accessible has shown to increase the number of citations to your article. This also assists in making your work reproducible. Relationship between the ABO Blood Group and the COVID-19 Susceptibility DOI: 10.1101/2020.03.11.20031096 Results Feedback
  • 10. Will authors improve manuscripts? (ResearchSquare) 33% of authors corrected and re- uploaded their preprint
  • 12. Ripeta, LLC. All rights reserved. This is not to be shared without official permission. ripetaReport
  • 13. Ripeta, LLC. All rights reserved. This is not to be shared without official permission. ripetaReport Report of Portfolio of Publications Sample ripetaReport (Wellcome Trust)
  • 18. Research Relationship between the ABO Blood Group and the COVID-19 Susceptibility DOI: 10.1101/2020.03.11.20031096 Here, we investigated the relationship between the ABO blood type and the susceptibility to COVID-19 in patients from three hospitals in Wuhan and Shenzhen, China to test if the former may be a biomarker for the latter. Study Objective Scientific Headings Abstracts, Background/Introduction, Methods
  • 20. Reproducibility Relationship between the ABO Blood Group and the COVID-19 Susceptibility DOI: 10.1101/2020.03.11.20031096 Data Availability The data used to support the findings of this study are included within the article. Data Availability The data used to support the findings of this study are included within the article. {Not Found} Data Availability Statement Data Location Code Availability
  • 22. Covid Preprint Analyses ripetaScore Outcome Citations Similarity nCoV spike protein 10.1101/2020.01.30.927871 Low Withdrawn 50 Hydroxychloroquine 10.1101/2020.03.16.20037135 Medium Questioned 3000 ABO Blood Group 10.1101/2020.03.11.20031096 Medium Overhyped 150 Potential vaccine targets 10.1101/2020.02.03.933226 High Published 450
  • 23. Article DOI Study Purpose Author- ship Funding Statement Data location DAS Code availability 10.1101/2020.01.30.927871 Yes 2 No None No No Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag Methodology Retrieval and alignment of nucleic acid and protein sequences We retrieved all the available coronavirus sequences (n=55) from NCBI viral genome database (https://www.ncbi.nlm.nih.gov/) and we used the GISAID (Elbe & Buckland-Merrett, 2017)[https://www.gisaid.org/] to retrieve all available full- length sequences (n=28) of 2019-nCoV as on 27 Jan 2020. Multiple sequence alignment of all coronavirus genomes was performed by using MUSCLE software (Edgar, 2004) based on neighbour joining method. Out of 55 coronavirus genome 32 representative genomes of all category were used for phylogenetic tree development using MEGAX software (Kumar et al., 2018). The closest relative was found to be SARS CoV.
  • 24. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial Article DOI Study Purpose Author- ship Funding Statement Data location DAS Code availability 10.1016/j.ijantimicag.2020 .105949 Yes 1 Yes None No No Elisabeth Bik took a close look at the IJAA article and detailed a long list of serious problems with the study, including questions about its ethical underpinnings, messy confounding variables, missing patients, rushed and conflicted peer review, and confusing data.
  • 25. Relationship between the ABO Blood Group and the COVID-19 Susceptibility Article DOI Study Purpose Author- ship Funding Statement Data location DAS Code availability 10.1101/2020.03.11.200310 96 Yes 4 Yes In paper Yes No
  • 26. Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies Article DOI Study Purpose Author- ship Funding Statement Data location DAS Code availability 10.1101/2020.02.03.933226 Yes 4 Yes External repo Yes Yes
  • 27. Can automation save time? (SpringerNature & bioRxiv/medRxiv Preprints) 4 minutes instead of 40 hours to check 400+ manuscripts
  • 29. Automated checks can make better science easier Follow us @RipetaReview for more memes
  • 30. Follow us for weekly academic highlights, transparency tips, and more! @RipetaReview @Ripeta info@ripeta.com www.ripeta.com Stay Informed
  • 31. Leslie McIntosh CEO Cynthia Hudson Vitale COO, co-founder Chris Westling Data Engineer Ruth Whittam Data Scientist, Lead Josh Sumner Data Scientist, Intern Leah Haynes Data Scientist, Intern ripetinis Paola Ortega Saborío Data Engineer August DeVore Editor
  • 33. ripetaData Research Professionalism Reproducibility Open Access Ethical Approval Statement Data Availability Statements Abstract Ethical Approval Organization Data Locations - Repository Study Objective Author Contribution Statement Data Locations - PID Funding Statement Competing Interests Data Locations - Identifiers Funding Source Funding Source Data Locations - URL Funding Grant ID Funding Grant ID Analysis Software Count of Authors (single) Analysis Software Version Self-Citations Statistical Methods Author Identification Code Availability Statement