gopubmed versus pubreminer comparison
TRANSCRIPT
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GoPubMed versus PubReMinerfor analyzing PubMed search results:
A head to head comparison of two free web ‘data mining’ tools
Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, Alberta May 2011
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Introduction
Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, 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
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• 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 ConferenceCalgary, Alberta May 2011
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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
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Methods
Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, 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
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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 ConferenceCalgary, Alberta May 2011
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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 ConferenceCalgary, Alberta May 2011
∑=8 ∑=7
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Country
PRM:
PRM:
vs
GPM:
Minor discrepancies found with both tools: a ‘tie’
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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:
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MeSH terms
• Presented very differently in PubReminer & GoPubMed• PRM includes MeSH subheadings:
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• GoPubMed presents a neater table; no subheadings
• But you may need to click through many, many pages
MeSH terms
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PubReminer vs Actual PubMed Results
MeSH terms: Accuracy
Two indexed records were not included: PMIDs: 20579633 / 20107104
Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, Alberta May 2011
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MeSH terms & chemical substance names NOT read for two PMIDs: 20579633 20107104
Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, Alberta May 2011
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GoPubMed vs Actual PubMed Results
MeSH terms: Accuracy
GoPubMed does NOT report MeSH terms as assigned by NLM!!!
Major discrepancies observed
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Example GoPubMed Record:
Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, Alberta May 2011
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Curating GoPubMed Record:
Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, Alberta May 2011
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Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, Alberta May 2011
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‘Won’ by default
Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, 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 bothN/A = not available with this tool.
N/A = not available with this tool
Summary of GoPubMed and PubReMiner comparisons
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Conclusions
Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, 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
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Questions?
Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, Alberta May 2011
Sue Bradley, Health Librarian, Consultant, Vancouver BC
Dean Giustini, UBC Biomedical Branch Library
Creative Commons Attribution 2.5 Canada Licence