gopubmed versus pubreminer comparison

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

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

• 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

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

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

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

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

Country

PRM:

PRM:

vs

GPM:

Minor discrepancies found with both tools: a ‘tie’

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

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

MeSH terms & chemical substance names NOT read for two PMIDs: 20579633 20107104

Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, 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 ConferenceCalgary, Alberta May 2011

Curating GoPubMed Record:

Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, Alberta May 2011

Sue Bradley, Dean Giustini – CHLA/ABSC Annual ConferenceCalgary, Alberta May 2011

‘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

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

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

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