PDFDataExtractor: A Tool for Reading Scientific Text and Interpreting Metadata from the Typeset Literature in the Portable Document Format

The layout of portable document format (PDF) files is constant to any screen, and the metadata therein are latent, compared to mark-up languages such as HTML and XML. No semantic tags are usually provided, and a PDF file is not designed to be edited or its data interpreted by software. However, data held in PDF files need to be extracted in order to comply with open- source data requirements that are now government-regulated. In the chemical domain, related chemical and property data also need to be found, and their correlations need to be exploited to enable data science in areas such as data-driven materials discovery. Such relationships may be realized using text-mining software such as the chemistry-aware natural-language-processing tool, ChemDataExtractor; however, this tool has limited data-extraction capabilities from PDF files. This study presents the PDFDataExtractor tool, which can act as a plug-in to ChemDataExtractor. It outperforms other PDF-extraction tools for the chemical literature by coupling its functionalities to the chemical-named entity-recognition capabilities of ChemDataExtractor. The intrinsic PDF-reading abilities of ChemDataExtractor are much improved. The system features a template-based architecture. This enables semantic information to be extracted from the PDF files of scientific articles in order to reconstruct the logical structure of articles. While other existing PDF-extracting tools focus on quantity mining, this template-based system is more focused on quality mining on different layouts. PDFDataExtractor outputs information in JSON and plain text, including the metadata of a PDF file, such as paper title, authors, affiliation, email, abstract, keywords, journal, year, document object identifier (DOI), reference, and issue number. With a self-created evaluation article set, PDFDataExtractor achieved promising precision for all key assessed metadata areas of the document text.

Automated summary

This article introduces the PDFDataExtractor tool, which can be used as a plugin for ChemDataExtractor to extract information from PDF files. Compared to other PDF extraction tools, PDFDataExtractor performs better in the field of chemical literature. It is capable of extracting semantic information from the PDF files of scientific articles and reconstructing the logical structure of the articles.