Third-Party PubMed Tools

Third-Party

Tools

Now that’s a horse of a different color…

Photo credit: dianecordell on flickr

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Introductions

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PubMed

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PubMed

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APIs

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PubMed

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PubMed

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Group Projects

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PubMed

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Group Projects

Discussion

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Evaluation

By you will be able to…

• Describe the history of end-user access to MEDLINE

• Name and develop search strategies for at least three* third-party PubMed tools

• Identify situations in which searching with a third-party tool would be beneficial

• Stay current with new developments related to third-party PubMed tools

HOW WE GOT HEREA brief history of end-user access to MEDLINE

1897:First volume of Index Medicus published.

1964:MEDLARS became operational

Computer room at the National Library of Medicine, 1960s

1971:MEDLINE (“MEDLARS online”) provides online access to a subset of references

Texas Instruments Silent 700 with Acoustic Coupler

1986:Health professionals started running their own searches with PC-based Grateful Med

1997:PubMed is born!

Free Web-based access to MEDLINE

1997:PubMed is born!

Free Web-based access to MEDLINE

Today

• 20 million article citations and counting

• More than 5,000journals indexed

• Goes back in time to the 1940’s

• Searched 1.6 billiontimes in 2010

2002:NLM says “take our data, too!”

Entrez Programming Utilities (Eutils) introduced

Drive traffic to your data, not your website!

-David Hale, NIHyour website!

PubMed API (eUtils)

• API = Application Programming Interface

• Makes data available for use in other programs or interfaces

Alternatives

SLIM v.2

Agenda

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Introductions

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PubMed

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APIs

4Case Studies

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CASE STUDIES

Themes

• Relevance

• Visualization

• Mobile access

• Simplification

Research Question

• What is the role of vitamin D in preventing or alleviating the symptoms of multiple sclerosis?

http://pubmed.gov

eTBlast

Developed by:

Virginia Biometrics Institute

Claim to fame:

Analyzes large chunks of text

http://etest.vbi.vt.edu/etblast3/

Developed by: Biomedical informaticist Jeff Saffer & molecular

toxicologist Vicki Burnett

Claim to fame:Search results based on relationships;

Power Terms™

http://www.quertle.info/v2/

Themes

• Relevance

• Visualization

• Mobile Access

• Simplification

LigerCat

Developed by:Biology of Aging project at Marine Biological

Laboratory – Woods Hole Oceanographic Institution Library

Claim to fame:Produces tag clouds based on MeSH headings

http://ligercat.ubio.org/

Runs MeSHsearch directly in PubMed

PubAnatomy

Developed by:National Center for Integrative Bioinformatics,

University of Michigan

Claim to fame:Maps the journal literature to brain anatomy and

gene expression correlations

http://www.ncibi.org/gateway/pubanatomy.html

PubAnatomy

Ali Baba

Developed by:Institut für Informatik, Humboldt-Universität,

Berlin

Claim to fame:Graphically summarizes search results to reveal

relationships and associations

http://alibaba.informatik.hu-berlin.de/

Ali Baba

What are the risk factors of treating G6PD-

deficient malaria patienswith primaquine?

Themes

• Semantic searching

• Visualization

• Mobile Access

• Simplification

PubMed Mobile Beta

Developed by:

National Center for Biotechnology Information, National Library of Medicine

Claim to fame:

Simplified access to basic PubMed features

http://www.ncbi.nlm.nih.gov/m/pubmed/

PubMed Mobile Beta

PubMed for Handhelds

Developed by:

Lister Hill Center, National Library of Medicine

Claim to fame:

Unique search options - PICO, askMEDLINE, disease associations

http://pubmedhh.nlm.nih.gov/

PubMed for Handhelds

PubMed Mobile (Android)

Developed by:

CRinUS

Claim to fame:

The best PubMed app for Android so far

http://www.cyrket.com/p/android/com.bim.pubmed/

PubMed CLIP (iPhone)

Developed by:

Groupnet Corporation

Claim to fame:

Lots of options for saving and sharing references.

http://www.groupnet.co.jp/products/pubmedclip/en/

Themes

• Semantic searching

• Visualization

• Mobile Access

• Simplification

Developed by:A Boston clinical pathologist who founded

PubGet, Inc.

Claim to fame:Better than your library’s link resolver at

retrieving PDFs

http://pubget.com/

iPubMed

Developed by:

Researchers at the University of California, Irvine and Tsinghua University, China

Claim to fame:

Fast, fuzzy searches.

http://ipubmed.ics.uci.edu/

GROUP EXERCISES

Pick a card…

In groups of 2 or 3, explore a third-party PubMed tool and prepare to report:

• Developer(s)

• Key features

• When you’d use it

• Negative aspects

DISCUSSION QUESTIONS

What ideas from third-party developers should NCBI adopt for PubMed?

Which third-party tool(s) are you likely to use again? In what circumstances?

Thank you!

Alison Aldrich

NN/LM PNR

http://nnlm.gov/pnr

(800) 338-7657

[email protected]