Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles

Journal of Biomedical Semantics
Şenay KafkasJohanna R McEntyre

Abstract

In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating the literature with biomolecular databases. Using text-mining methods to identify and extract a variety of core biological database accession numbers, we found that the supplemental data files contain many more database citations than the body of the article, and that those citations often take the form of a relatively small number of articles citing large collections of accession numbers in text-based files. Moreover, citation of value-added databases derived from submission databases (such as Pfam, UniProt or Ensembl) is common, demonstrating the reuse of these resources as datasets in themselves. All the database accession numbers extracted from the supplementary data are publicly accessible from http://dx.doi.org/10.5281/zenodo.11771. Our study suggests that supplementary data should be considered when linking articles with data, in curation pipelines, and in information retrieval ta...Continue Reading

References

Jun 5, 2013·PloS One·Şenay KafkasJohanna R McEntyre

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Citations

Jan 4, 2018·Journal of Biomedical Semantics·Xu DongliangWang Bailing
Jun 8, 2017·Journal of Biomedical Semantics·Şenay KafkasJohanna McEntyre

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Software Mentioned

Ensembl
Apache Tika
Accession Number Annotation (
Whatizit
InterPro IPR
Ensembl EN
UniProt PDBe
ANA
omim
ArrayExpress

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