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Background. There is huge bulk of full-text biomedical literatures accessible in accessible repositories like PubMed Central (PMC). However, a abundant cardinal of the affidavit are in Portable Document Architecture (PDF) and do not accommodate apparent argument architecture accessible for argument mining and accustomed accent processing (NLP). Although there abide abounding PDF-to-text converters, they still ache from several challenges while processing biomedical PDFs, such as the actual archetype of titles/abstracts, segmenting references/acknowledgements, appropriate characters, jumbling errors (the amiss adjustment of the text), and chat boundaries.
Methods. In this paper, we present bioPDFX, a atypical apparatus which complements weaknesses with strengths of assorted advanced methods and again applies apparatus acquirements methods to abode all issues above
Results. The agreement after-effects on publications of Genome Wide Association Studies (GWAS) approved that bioPDFX decidedly bigger the affection of XML comparing to advanced PDF-to-XML converter, arch to a biomedical database added acceptable for argument mining.
Discussion. Overall, the accomplished activity developed in this cardboard makes the appear abstract in anatomy of PDF files abundant bigger ill-fitted for argument mining tasks, while hardly convalescent the all-embracing argument affection as well. The account is accessible to admission advisedly at URL: http://textmining.ucsd.edu:9000 . A account of PubMed Central IDs of the 941 accessories (see Supplemental File 1) acclimated in this abstraction is accessible for download at the aforementioned URL. The instructions of how to run the account with a PubMed ID are declared in Supplemental File 2.
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