GoPubMed versus PubReminer comparison

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  • 1. GoPubMed versus PubReMiner for analyzing PubMed search results: A head to head comparison of two free web ‘data mining’ tools Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 2. Introduction Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
    • Searching PubMed/MEDLINE requires MeSH term mapping & natural language analysis
    • Search strategies can be improved by examining textwords, MeSH terms etc., in relevant papers already found
    • GoPubMed & PubReMiner
      • two free data-mining tools used to statistically analyze PubMed search results
      • statistical analyses of search fields (e.g. publication years, MeSH terms, author names)
    • Some different fields covered (e.g. PubReMiner provides chemical substance name search, GoPubMed does not)
    • Head to head comparisons using PubMed citations & PMIDs on fields covered by both
  • 3.
    • PubReMiner is a data mining tool, mining PubMed - MEDLINE abstracts
    • Query entered as text, using PubMed format, or as PMIDs
    • Provides bibliometric statistical analysis of search results
    • Displayed in hyperlinked ‘frequency tables’ by year, journal, authors, textwords, MeSH terms, chemical substance names and country
    Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 4.
    • GoPubMed - a knowledge-based semantic browsing tool for life sciences
    • One of the first web 2.0 / semantic search engines
    • Uses two ontologies: GoGene & MeSH (& lists proteins)
    • Statistics feature is a “semanto-bibliometric analysis” of search results
    Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 5. Methods Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
    • A series of PubMed searches were conducted
    • Main search topic: “borderline personality disorder”[mh] AND “therapy”[mh]
    • Search developed to yield small number of records (n=129)
      • Period covered: 2006-2010
    • PubMed IDs (PMIDs) entered into GoPubMed & PubReMiner
    • Statistical results were compared to those obtained by hand
    • Discrepancies in performance of tools was examined
  • 6. Results
    • Publication year
    • PubReMiner (PRM) displays chronologically
    • GoPubMed (GPM) displays by frequency
    PRM: GPM: No discrepancies found using either tool vs Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 7. Author Names
    • Giustini D*[au] entered in PubMed: 8 records found – PMIDs entered
    • PubReMiner found all
    • GoPubMed only found 7 – split into three entries
    PRM: GPM: vs Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011 ∑ =8 ∑ =7
  • 8. Country
    • PRM:
    PRM: vs GPM: Minor discrepancies found with both tools: a ‘tie’ Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 9. Journal names
    • GoPubMed enters different journal abbreviations for same journal
    • eISSN/ISSN given different short forms
    • Not all are correct NLM title abbreviations
    PRM: GPM:
  • 10. MeSH terms
    • Presented very differently in PubReminer & GoPubMed
    • PRM includes MeSH subheadings:
  • 11.
    • GoPubMed presents a neater table; no subheadings
    • But you may need to click through many, many pages
    MeSH terms Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 12. PubReminer vs Actual PubMed Results MeSH terms: Accuracy Two indexed records were not included : PMIDs: 20579633 / 20107104 Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 13.
    • MeSH terms & chemical substance names NOT read for two PMIDs: 20579633 20107104
    Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 14. GoPubMed vs Actual PubMed Results MeSH terms: Accuracy GoPubMed does NOT report MeSH terms as assigned by NLM!!! Major discrepancies observed
  • 15. Example GoPubMed Record: Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 16. Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 17. Curating GoPubMed Record: Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 18. Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • 19. ‘ Won’ by default Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
    • Variances found in results for every field covered by both tools (except publication year)
    • Problems found in results for both tools
    • PubReMiner found to produce better results for fields covered by both
    N/A = not available with this tool Summary of GoPubMed and PubReMiner comparisons
  • 20. Conclusions Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
    • GoPubMed & PubReMiner are useful supplements for devising searches
    • Use to determine common terms, keywords & MeSH, top authors, journals
    • Use GoPubMed & PubReMiner with caution in developing search strategies
      • Examine bibliographic records, indexing, ‘related articles’ features in PubMed
    • Watch developments in PubReMiner & GoPubMed
  • 21. Questions? Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
    • Sue Bradley, Health Librarian, Consultant, Vancouver BC
    • Dean Giustini, UBC Biomedical Branch Library
    Creative Commons Attribution 2.5 Canada Licence