GoPubMed versus PubReminer comparison
Upcoming SlideShare
Loading in...5
×
 

GoPubMed versus PubReminer comparison

on

  • 2,531 views

 

Statistics

Views

Total Views
2,531
Views on SlideShare
2,421
Embed Views
110

Actions

Likes
1
Downloads
20
Comments
0

2 Embeds 110

http://blogs.ubc.ca 109
http://translate.googleusercontent.com 1

Accessibility

Upload Details

Uploaded via as Adobe PDF

Usage Rights

CC Attribution-NonCommercial-ShareAlike LicenseCC Attribution-NonCommercial-ShareAlike LicenseCC Attribution-NonCommercial-ShareAlike License

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

GoPubMed versus PubReminer comparison GoPubMed versus PubReminer comparison Presentation Transcript

  • 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
  • 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
    • 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
    • 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
  • 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
  • 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
  • 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
  • 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
  • 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:
  • MeSH terms
    • Presented very differently in PubReminer & GoPubMed
    • PRM includes MeSH subheadings:
    • 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
  • 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
    • MeSH terms & chemical substance names NOT read for two PMIDs: 20579633 20107104
    Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • GoPubMed vs Actual PubMed Results MeSH terms: Accuracy GoPubMed does NOT report MeSH terms as assigned by NLM!!! Major discrepancies observed
  • Example GoPubMed Record: Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • Curating GoPubMed Record: Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • Sue Bradley, Dean Giustini – CHLA/ABSC Annual Conference Calgary, Alberta May 2011
  • ‘ 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
  • 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
  • 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