Third-Party PubMed Tools

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Nov 15, 2013 (3 years and 10 months ago)

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Third
-
Party

PubMed

Tools

Now that’s a horse of a different color…

Wisconsin Health Science Libraries Association

September 21, 2012



Holly Ann Burt, MLIS, AHIP

NN/LM GMR

Photo credit:
dianecordell

on
flickr

Objectives

Participants will be able to:


Use and teach others about the latest
updates to PubMed.gov


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

Agenda


Introductions


What’s new with
PubMed


The
PubMed

API


Case Studies


Group Exercises


Discussion Questions


Disaster resources:


CHEMM, REMM and DIMRC


DIS Specialization


GeneEd

-

http://geneed.nlm.nih.gov
/


LiverTox

-

http://livertox.nih.gov/


Searched
1.8 billion

times in 2011


MeSH turned
50
in 2010


What’s New at NLM?

What’s New with PubMed?

by the Numbers


More than
22 million
article citations


More than
5,600

journals indexed


Goes back in time to the
1800’s


Earliest MEDLINE citation: 1902


Earliest PubMed citation: 1809


Searched
1.8 billion

times in 2011


MeSH turned
50
in 2010


Updates

Recent changes:


Filters navigation bar


Results by year


Images from PubMed Central


History and Search Builder in
Advanced



My Bibliography accepts non
-
PubMed
items


Why Redesign?


“While retaining the robust functionality,
the interface was simplified to make it
easier to use while promoting scientific
discovery.”


-
NLM Technical Bulletin

Keeping Current


PubMed

New and Noteworthy


NLM Technical Bulletin


PUBMED
-
ALERTS@list.nih.gov


MEDLIB
-
L


NN/LM GMR Cornflower


PubMed

API

PubMed

API (
eUtils
)


API =
A
pplication
P
rogramming
I
nterface


Makes data available for use in other
programs or interfaces



Drive traffic to your data,
not your website!

-
David Hale, NIH


your website!


API Resources


How Stuff Works: How APIs Work:
http://tinyurl.com/27rw2kn


Explanation
of APIs, using conferencing software
as an example.


Entrex

AJAX:
http
://entrezajax.appspot.com
/



A third
-
party derivative of NCBI’s
EUtils

designed for launching searches directly from
the browser (improves speed
)


Alternatives

SLIM v.2

Case Studies

Themes


Semantic searching


Visualization


Simplification

Research Question


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

eTBlast

Developed by:

Virginia Biometrics Institute


Claim to fame:

Analyzes large chunks of text


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

eTBlast

Search

eTBlast

Graphic

Results

Quertle

Developed by:

Biomedical
informaticist

Jeff
Saffer

& molecular
toxicologist Vicki Burnett


Claim to fame
:

Search results based on relationships;

Power Terms™


http://www.quertle.info/

Quertle

Search

page

Quertle

Results

page

Themes
II


Semantic searching


Visualization


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/

LigerCat

search page

Runs
MeSH

search directly
in
PubMed

LigerCat

results page

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

Results

Themes
III


Semantic searching


Visualization


Simplification


PubGet

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/


PubGet

Search results

PMInstant

Developed by:

Jonathan
Bourman

with
Pubmed

AJAX API


Claim to fame
:

Fast. Very fast. Displays search results while you
are still typing.


http://pminstant.com/




PMInstant

Search Results

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

Discussion
Question I


What ideas from third
-
party developers

should NCBI adopt for PubMed?

Discussion
Question II


Which third
-
party tool(s) are you likely to

use again? In what circumstances?

Discussion
Question III


If you could offer NLM one piece

of advice, what would it be?

Thank you!