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Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?

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  • Devabhaktuni Srikrishna
  • Marc A Coram

Abstract

Author-supplied citations are a fraction of the related literature for a paper. The “related citations” on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related. Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations. The algorithm to generate these search terms involved automatically extracting noun phrases from the paper using natural language processing tools, and ranking them by the number of occurrences in the paper compared to the number of occurrences on the web. We define search queries having at least one instance of overlap between the author-supplied citations of the paper and the top 20 search results as citation validated (CV). When the overlapping citations were written by same authors as the paper itself, we define it as CV-S and different authors is defined as CV-D. For a systematic sample of 883 papers on PubMed Central, at least one of the search terms for 86% of the papers is CV-D versus 65% for the top 20 PubMed “related citations.” We hypothesize these quantities computed for the 20 million papers on PubMed to differ within 5% of these percentages. Averaged across all 883 papers, 5 search terms are CV-D, and 10 search terms are CV-S, and 6 unique citations validate these searches. Potentially related literature uncovered by citation-validated searches (either CV-S or CV-D) are on the order of ten per paper – many more if the remaining searches that are not citation-validated are taken into account. The significance and relationship of each search result to the paper can only be vetted and explained by a researcher with knowledge of or interest in that paper.

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  • Devabhaktuni Srikrishna & Marc A Coram, 2011. "Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?," PLOS ONE, Public Library of Science, vol. 6(9), pages 1-11, September.
    • Handle: RePEc:plo:pone00:0024920
    DOI: 10.1371/journal.pone.0024920
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    References listed on IDEAS

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    1. M.H. MacRoberts & B.R. MacRoberts, 2010. "Problems of citation analysis: A study of uncited and seldom-cited influences," Journal of the Association for Information Science & Technology, Association for Information Science & Technology, vol. 61(1), pages 1-12, January.
    2. Zhaohui Sun & Mounir Errami & Tara Long & Chris Renard & Nishant Choradia & Harold Garner, 2010. "Systematic Characterizations of Text Similarity in Full Text Biomedical Publications," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-6, September.
    3. M.H. MacRoberts & B.R. MacRoberts, 2010. "Problems of citation analysis: A study of uncited and seldom‐cited influences," Journal of the American Society for Information Science and Technology, Association for Information Science & Technology, vol. 61(1), pages 1-12, January.
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