bioPDFX: preparing PDF scientific articles for biomedical text mining

Abstract

Background. There is huge amount of full-text biomedical literatures available in public repositories like PubMed Central (PMC). However, a substantial number of the papers are in Portable Document Format (PDF) and do not provide plain text format ready for text mining and natural language processing (NLP). Although there exist many PDF-to-text converters, they still suffer from several challenges while processing biomedical PDFs, such as the correct transcription of titles/abstracts, segmenting references/acknowledgements, special characters, jumbling errors (the wrong order of the text), and word boundaries. Methods. In this paper, we present bioPDFX, a novel tool which complements weaknesses with strengths of multiple state-of-the-art methods and then applies machine learning methods to address all issues above Results. The experiment results on publications of Genome Wide Association Studies (GWAS) demonstrated that bioPDFX significantly improved the quality of XML comparing to state-of-the-art PDF-to-XML converter, leading to a biomedical database more suitable for text mining. Discussion. Overall, the whole pipeline developed in this paper makes the published literature in form of PDF files much better suited for text mining tasks, while slightly improving the overall text quality as well. The service is open to access freely at URL: http://textmining.ucsd.edu:9000 . A list of PubMed Central IDs of the 941 articles (see Supplemental File 1) used in this study is available for download at the same URL. The instructions of how to run the service with a PubMed ID are described in Supplemental File 2.

Weakly supervised learning of biomedical information extraction from curated data

“…For other papers, we collected 965 full texts in PDF. These PDF files were all transcribed into XML using bioPDFX [ 46 ], a tool that we built on top of PDFX [ 47 ], to prepare PDF papers for biomedical text mining.…”