1. PubMed +
Alternate Interfaces
RETRIEVAL ANALYSIS, EASY PDFS AND DATA
VISUALIZATION FOR THE MEDICAL RESEARCHER
Ryan McComas, MLIS

2. Introduction
2
 PubMed: Public data source of biomedical citation
information. Has its own search interface, pubmed.gov
 PubMed’s information retrieval model has certain
shortcomings
 Advances in data storage capabilities, text mining, search
and data linking technology, and human-computer
interaction has enabled researchers to create applications
for PubMed’s database

3. Introduction
3
 Problems with PubMed:
 Difficulty with link resolver
 Unranked results
 NO statistics and analysis!

4. Introduction
4
 There are many tools, but today we are going to
outline three that make searching, retrieving and
understanding relevant literature easier and faster:
 GoPubMed
 MEDSUM
 Quertle
http://library.mskcc.org

5. GoPubMed: stats and visualization
5

6. GoPubMed: stats and visualization
6
 Accepts PubMed query syntax [mesh], [au], etc. (called
“tags”)
 Two major fields for concept searching:
(MeSH)
(Gene Ontology)
◦ Ontology=detailed relational and conceptual hierarchy.

7. GoPubMed: stats and visualization
7
 Sorting and refining results
 Left-hand column – Sort, refine, and analyze results using
filters.
 View statistics in tabs above results.
 Export PubMed citations without saving to a text file.

8. MEDSUM: Results Analysis
8

9. 9
MEDSUM: Results Analysis

10. 10
1) how PubMed translates Shows authors,
the query journals, research
2) the number of associated biases, and MeSH
articles categories and years
Gives the top Major MeSH
Returns the number of papers Headings for papers with
broken down by year (going MeSH entries
back to 1945 max)
MEDSUM: Results Analysis

11. Quertle: Semantic Search
11

12. Quertle: Semantic Search
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 Quertle searches whole concepts rather than simply keywords
or terms matching.
 Left-hand sidebar: filter and refine results.
 Power terms ($) allow you to search for classes of objects.
 Export citations to EndNote and RefWorks.
 Many libraries have partnered with Quertle to make links
to full text available for subscription databases.

13. Quertle: Semantic Search
13
 Quertle Search Tips
 SUBJECT-VERB-OBJECT model of searching
 Find definitions
 Use Power Terms to specify classes of topics
 Search broadly with search terms in the then filter
results.

14. More Resources
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 David Rothman’s blog:
http://davidrothman.net/category/technology/3rd-party
/
 Lu, Z. (2011). PubMed and beyond: A survey of web
tools for searching biomedical literature. Database.
doi:10.1093/database/baq036
 Email: ryanraymccomas@gmail.com