JATSdecoder
CRANJATSdecoderMaRDI QIDQ73527FDOQ73527
A Metadata and Text Extraction and Manipulation Tool Set
Last update: 12 October 2023
Copyright license: GNU General Public License, version 3.0
Software version identifier: 1.1.2, 1.1.1, 1.1, 1.2.0
Provides a function collection to extract metadata, sectioned text and study characteristics from scientific articles in 'NISO-JATS' format. Articles in PDF format can be converted to 'NISO-JATS' with the 'Content ExtRactor and MINEr' ('CERMINE', <https://github.com/CeON/CERMINE>). For convenience, two functions bundle the extraction heuristics: JATSdecoder() converts 'NISO-JATS'-tagged XML files to a structured list with elements title, author, journal, history, 'DOI', abstract, sectioned text and reference list. study.character() extracts multiple study characteristics like number of included studies, statistical methods used, alpha error, power, statistical results, correction method for multiple testing, software used. An estimation of the involved sample size is performed based on reports within the abstract and the reported degrees of freedom within statistical results. In addition, the package contains some useful functions to process text (text2sentences(), text2num(), ngram(), strsplit2(), grep2()). See Böschen, I. (2021) <doi:10.1007/s11192-021-04162-z> Böschen, I. (2021) <doi:10.1038/s41598-021-98782-3> and Böschen, I (2023) <doi:10.1038/s41598-022-27085-y>.
- Software review: The JATSdecoder package—extract metadata, abstract and sectioned text from NISO-JATS coded XML documents; Insights to PubMed central’s open access database
- Evaluation of JATSdecoder as an automated text extraction tool for statistical results in scientific reports
- Evaluation of the extraction of methodological study characteristics with JATSdecoder
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