PubMed Alternative Interfaces

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Contents

Last Update

  • Updated.jpg 30 May 2014

Introduction

See also Expert searching | GoPubMed | Open search | PubMed - MEDLINE | PubReMiner | Semantic search | Web 2.0

Alternative PubMed interfaces can be used to search PubMed - MEDLINE in such a way that new information patterns or insights may be revealed. Through a combination of data mining, linguistic analysis, statistical methodologies and semantic algorithms, alternative PubMed interfaces provide ways to examine the biomedical literature from unique perspectives. The National Library of Medicine (U.S.) encourages software developers to create innovative tools to search Medline. Commercial services such as Dialog and EBSCO - as well as academic libraries, bioinformatics organizations, pharmaceutical companies and software startups - lease copies of the PubMed database (see leasing data) and build alternate interfaces to search it. For a different view of searching the biomedical literature, try some of the tools below.

Criteria for inclusion

An alternative PubMed interface is one that:

  • searches a current (live or recent) version of the PubMed - MEDLINE database
  • is in active development or maintenance
  • has an interface or features that distinguish it from PubMed - MEDLINE

For a comprehensive evaluation of alternative PubMed interfaces, see 28 systems surveyed in Lu, Database 2011.

Alternative PubMed search tools

  • BabelMeSH - http://babelmesh.nlm.nih.gov/
    • "Search MEDLINE/PubMed using medical terms or phrases in Arabic, Chinese, English, French, German, Italian, Japanese, Korean, Portuguese, Russian, and Spanish. Citations and abstracts retrieved will be in English only."
  • EBIMed
    • somewhat slow in retrieving results; allows a very low number (20) of query terms
  • FABLE - http://fable.chop.edu/
    • Article Finder: find articles mentioning a gene of interest.
    • Gene Lister: find genes associated with one or more keywords.
  • an information extraction tool, FACTA+ was a winner in the National Library of Medicine’s software development challenge. The algorithms extract relationships from your query, searching in PubMed, PubMedCentral, TOXLINE, Biomed Central, NIH, FDA, and other agency grant proposals, as well as biomedical news sources
  • GoPubMed - http://www.gopubmed.com
    • The search bar auto-completes queries similar to the functionality provided by Google's Autocomplete feature.
    • Faceted browsing by term frequency, MeSH headings, author, location and date of publication.
    • Statistics for query results, including top years, countries, cities, journals, terms, and authors.
    • Visualization of publications over time, location, and network of authors.
    • Good graphics as well as usability improvements.
  • MeSH On Demand
    • identifies MeSH Terms in your text using NLM's Medical Text Indexer (MTI) tool; a list of MeSH Terms relevant to your text will be shown
  • PubFocus - http://www.pubfocus.com/ Note: does not seem to be updated as of 2013
    • Provides statistics based on publication trends, publishing journals (Journal Rank and H-index) and first and last author.
  • PubGet - http://pubget.com/
    Home pubget logo.gif
    • Focus is on quick access to full-text versions of articles.
    • Works with many institutional link-resolvers in order to provide access to subscription articles.
  • Quertle - http://www.quertle.info/v2/
    • Semantic-based relationship driven search.
    • Autocomplete and Google-suggest style searching.
    • Faceted browsing of results (called filters) for date and type of publication and key concepts.
    • Term highlighting, Full-text links.

'Best of breed' alternative PubMed interfaces?

Biblimed.png
  • Biblimed - http://www.biblimed.fr/
    • smart, Gallic, streamlined
    • http://twitter.com/#!/BibliMed
    • new(ish) alternative interface to PubMed; made improvements to its search interface
    • easy to navigate & intuitive, system suggests keywords from MeSH and awaits validation before running search
  • GoPubMed - http://www.gopubmed.com
    Gopubmed2.gif
    • social, semantic, multifaceted classifier
    • auto-completes queries similar to Google's Autocomplete
    • faceted browsing by term frequency, MeSH headings, author, location and date of publication
    • statistics for query results, top years, countries, cities, journals, terms and authors
    • visualization of publications over time, location, and network of authors
      Quertle 15.jpg
    • good graphics as well as usability improvements; use with caution some numbers are inaccurate
      #GoPubmed - http://twitter.com/#!/search?q=%23GoPubmed
  • Quertle - http://www.quertle.info/v2/
    • semantic, search, language master
    • auto-complete and Google-suggest style searching
    • faceted browsing of results (filters) for date, type of publication and key concepts
    • term highlighting, full-text links
    • finds facts within documents; creates its own database of 200 million relationships
    • reports on what is relevant to your query; based on thorough understanding of biology and chemistry
    • built from the ground up to address the unique needs of this technical literature
  • PubFocus - http://www.pubfocus.com/ Note: does not seem to be updated as of 2013
    Pubfocus.gif
    • bibliometric, rank-enabled, analytical
    • statistics provided based on publication trends, journal rank & H-index, first and last authors
    • discerns research activity in any given biomedical area; search outputs generated by MEDLINE/PubMed are not well classified requiring lengthy analysis
    • automates analysis of search by enriching it with two bibliometric indicators of publication quality: journal impact factor and volume of forward references
    • provides basic volumetric statistics; prioritizes citations and evaluates author impact on field; analyses occurrences of key terms within citations by utilizing controlled vocabularies
  • Pubget - http://pubget.com/
    • speedy, indispensable, fulltext
    • Pubget allows you to browse PDFs quickly; display PDFs directly when available
      Home pubget logo.gif
    • depends on whether viewer has subscription access through local university, hospital, or special library
    • viewers with no access can view open access publications and limit display to those publications

References

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