Identifying biomedical research papers with incorrect nucleotide sequence reagents using targeted and screening approaches

Rachael A. West (1) , Guillaume Cabanac (2, 3) , Amanda Capes-Davis (1) , Jennifer A. Byrne (1) , Cyril Labbé (4)

1 Westmead Hospital [Sydney]
2 IRIT-IRIS - Recherche d’Information et Synthèse d’Information
3 UT3 - Université Toulouse III - Paul Sabatier
4 SIGMA - Systèmes d’Information - inGénierie et Modélisation Adaptables

Biomedical literature describing erroneous nucleotide sequence reagents could reduce research reproducibility. We therefore developed the semi-automatic fact-checking tool Seek & Blastn (SB) to verify the targeting/non-targeting status of published nucleotide sequences. We identified two corpora for SB analysis using targeted (key words to identify single gene knockdown (SGK) papers), and screening approaches (Gene journal papers from 2007-2018). SB analysis, supported by manual verification, detected 104/174 (60%) SGK papers and 262/933 (28.1%) Gene papers containing nucleotide sequence errors. Incorrect reagents may therefore represent a hidden problem within biomedical literature.

Mots clés: fact-checking; errors; scientific paper; biomedical

Domaines: Informatique [cs]

Rachael A. West, Guillaume Cabanac, Amanda Capes-Davis, Jennifer A. Byrne, Cyril Labbé. Identifying biomedical research papers with incorrect nucleotide sequence reagents using targeted and screening approaches. Australasian Interdisciplinary Meta-research & Open Science Conference (AIMOS 2019), Nov 2019, Melbourne, Australia. . ⟨hal-02976636⟩