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nucleotide sequence reagents are characteristic of highly similar human gene knockdown studies, some of which have been retracted from the literature on account of possible research fraud.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.
Highlights
As biomedical science increases in both volume and complexity, the problem of irreproducible and incorrect published results is growing [1, 2]
The Seek & Blastn (S&B) tool involves 3 steps: identification and extraction of nucleotide sequences from text together with the associated claimed status of targeting or non-targeting (T/NT), blastn analyses [49], and fact-checking to confirm or deny the usage claim associated with each extracted nucleotide sequence (Fig 1)
In the case of nucleotide sequences, these analyses considered those sequences that manual analyses confirmed to have been correctly extracted by S&B, and associated with a predicted T/NT status (Figs 3 and 4)
Summary
As biomedical science increases in both volume and complexity, the problem of irreproducible and incorrect published results is growing [1, 2]. Semi-automated fact-checking of published nucleotide sequence reagents: The Seek & Blastn tool design, data collection and analysis, decision to publish, or preparation of the manuscript
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