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
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.
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
12. Quertle: Semantic Search
12
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
14
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