Semi-automated fact-checking of nucleotide sequence reagents in biomedical research publications: The Seek & Blastn tool

PLoS One. 2019 Mar 1;14(3):e0213266. doi: 10.1371/journal.pone.0213266. eCollection 2019.

Abstract

Nucleotide sequence reagents are verifiable experimental reagents in biomedical publications, because their sequence identities can be independently verified and compared with associated text descriptors. We have previously reported that incorrectly identified nucleotide sequence reagents are characteristic of highly similar human gene knockdown studies, some of which have been retracted from the literature on account of possible research fraud. Because of the throughput limitations of manual verification of nucleotide sequences, we developed a semi-automated fact checking tool, Seek & Blastn, to verify the targeting or non-targeting status of published nucleotide sequence reagents. From previously described and unknown corpora of 48 and 155 publications, respectively, Seek & Blastn correctly extracted 304/342 (88.9%) and 1066/1522 (70.0%) nucleotide sequences and a predicted targeting/ non-targeting status. Seek & Blastn correctly predicted the targeting/ non-targeting status of 293/304 (96.4%) and 988/1066 (92.7%) of the correctly extracted nucleotide sequences. A total of 38/39 (97.4%) or 31/79 (39.2%) Seek & Blastn predictions of incorrect nucleotide sequence reagent use were correct in the two literature corpora. Combined Seek & Blastn and manual analyses identified a list of 91 misidentified nucleotide sequence reagents, which could be built upon through future studies. In summary, incorrect nucleotide sequence reagents represent an under-recognized source of error within the biomedical literature, and fact checking tools such as Seek & Blastn may help to identify papers and manuscripts affected by these errors.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Biomedical Research*
  • Humans
  • Indicators and Reagents / analysis*
  • Publications
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*

Substances

  • Indicators and Reagents

Grant support

We gratefully acknowledge funding from the Post-Truth Initiative, a Sydney University Research Excellence Initiative (SREI 2020) (to JAB), and from the US Office of Research Integrity grant ORIIR180038-01-00 (to JAB and CL). This work was supported by donations to the Children’s Cancer Research Unit of the Children’s Hospital at Westmead. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.