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

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