Software review: The JATSdecoder package\u2014extract metadata, abstract and sectioned text from NISO-JATS coded XML documents; Insights to PubMed central\u2019s open access database

Ingmar Böschen

doi:10.1007/s11192-021-04162-z

Abstract

JATSdecoder is a general toolbox which facilitates text extraction and analytical tasks on NISO-JATS coded XML documents. Its function JATSdecoder() outputs metadata, the abstract, the sectioned text and reference list as easy selectable elements. One of the biggest repositories for open access full texts covering biology and the medical and health sciences is PubMed Central (PMC), with more than 3.2 million files. This report provides an overview of the PMC document collection processed with JATSdecoder(). The development of extracted tags is displayed for the full corpus over time and in greater detail for some meta tags. Possibilities and limitations for text miners working with scientific literature are outlined. The NISO-JATS-tags are used quite consistently nowadays and allow a reliable extraction of metadata and text elements. International collaborations are more present than ever. There are obvious errors in the date stamps of some documents. Only about half of all articles from 2020 contain at least one author listed with an author identification code. Since many authors share the same name, the identification of person-related content is problematic, especially for authors with Asian names. JATSdecoder() reliably extracts key metadata and text elements from NISO-JATS coded XML files. When combined with the rich, publicly available content within PMCs database, new monitoring and text mining approaches can be carried out easily. Any selection of article subsets should be carefully performed with in- and exclusion criteria on several NISO-JATS tags, as both the subject and keyword tags are used quite inconsistently.

Highlights

Scientists from all over the world cumulate knowledge to describe and better understand the causes and effects in a very wide range of research areas
The unified structure and letter representations may be useful for any text mining project on NISO-JATS coded content
The R package JATSdecoder (Böschen 2021) is an infrastructure software that contains a set of functions to extract and unify content from scientific literature coded in NISO-JATS format

Summary

Introduction

Scientists from all over the world cumulate knowledge to describe and better understand the causes and effects in a very wide range of research areas. The unified structure and letter representations may be useful for any text mining project on NISO-JATS coded content. PMC’s NXML files follow a well documented structure called NISO-JATS (National Center for Biotechnology Information 2014) It makes most article content and meta information accessible if used adequately by the editorial and/or technical implementation team. The Content ExtRactor and MINEr CERMINE (Tkaczyk et al 2015) is a sophisticated PDF to text conversion tool that extracts metadata, full text and parsed references from scientific articles and outputs a NISO-JATS coded XML file that is processable with JATSdecoder. The R package JATSdecoder (Böschen 2021) is an infrastructure software that contains a set of functions to extract and unify content from scientific literature coded in NISO-JATS format.

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Discussion