%0 Journal Article
%T Prospects for the automated extraction of mutation data from the scientific literature
%A Peter D Stenson
%A David N Cooper
%J Human Genomics
%D 2010
%I BioMed Central
%R 10.1186/1479-7364-5-1-1
%X Using Mutator, Kuipers et al.[1] identified 367 'unique GLA gene mutations' (listed in their Supplementary Table), 108 of which they claimed to be absent from the Human Gene Mutation Database (HGMD7). Despite the fact that the authors failed to evaluate Mutator with respect to 'standard' performance measures (eg precision and recall), their tool appears to be a significant improvement over previously published methods, particularly those that simply screened PubMed abstracts rather than full text [6,8-12]. In their comparison with HGMD data, however, Kuipers et al.[1] appear to have used the somewhat outdated (but nevertheless freely available) online version of the database (http://www.hgmd.org webcite) rather than the up-to-date subscription version, HGMD Professional (http://www.biobase-international.com/pages/index.php?id=hgmddatabase webcite). We examined the 108 GLA mutations claimed to be absent from HGMD, and found that 48 were actually present in HGMD Professional. Of the remainder, seven were listed in HGMD under an alternative mutation type (eg small indels), four still remained unresolved (in that the precise nature of the nucleotide change was unclear or ambiguous in the original report), while 24 were non-Fabry disease false positives (see below). The remaining 25 mutations (~7 per cent of the total number of bona fide GLA mutations), reported in 12 different papers, appear to have been inadvertently omitted by HGMD. This is most likely because (i) they were mentioned only briefly within the text of the article concerned and (ii) no hint of the articles' mutation content could have been gleaned from inspection of article titles, abstracts or keywords. False negatives appear to be less of a problem than false positives, with Mutator failing to recognise only nine of the GLA mutations logged by HGMD Professional.The success of Mutator in identifying these hitherto latent lesions certainly testifies to the future potential utility of automatic tools desig
%U http://www.humgenomics.com/content/5/1/1