Mining MEDLINE for problems associated with vitamin D

AMIA Annu Symp Proc. 2013 Nov 16;2013:300-8. eCollection 2013.


This paper presents a two-step approach to generating comprehensive abstractive overviews for biomedical topics. It starts with a sensitivity-maximizing search of MEDLINE/PubMed and MeSH-based filtering of the results that are then processed using NLP methods to extract relations between entities of interest. We evaluate this approach in a case study based on the IOM report on the role of vitamin D in human health. The report defines disorders that serve as health indicators for the role of vitamin D. We evaluate the abstractive overviews generated using MeSH indexing and the extracted relations using the disorders listed in the IOM report as reference standard. We conclude that MeSH-based aggregation and filtering of the results is a useful and easy step in the generation of abstractive overviews. Although our relation extraction achieved 83.6% recall and 92.8% precision, only half of the disorders of interest participated in these relations.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Intramural

MeSH terms

  • Abstracting and Indexing*
  • Calcium / administration & dosage
  • Data Mining*
  • Dietary Supplements / adverse effects
  • Humans
  • Medical Subject Headings*
  • Natural Language Processing*
  • Vitamin D Deficiency
  • Vitamin D* / administration & dosage
  • Vitamin D* / adverse effects
  • Vitamin D* / blood


  • Vitamin D
  • Calcium