Transcript Title

Professional Development Course 1 –
Molecular Medicine
June 07, 2011
Ansuman Chattopadhyay, PhD
Head, Molecular Biology Information Services
Health Sciences Library System
University of Pittsburgh
[email protected]
http://www.hsls.pitt.edu/guides/genetics
Genomic achievements since the Human Genome Project.
ED Green et al. Nature 470, 204-213 (2011) doi:10.1038/nature09764
HSLS Molecular Biology Information Service
http://www.hsls.pitt.edu/guides/genetics
Ansuman Chattopadhyay, Ph.D.
[email protected]
•1990-1996
University of Nebraska-Lincoln
PhD. in Biochemistry
Protein synthesis initiation in eukaryotic system
•1997-2001
Vanderbilt University School of Medicine, Nashville
Research Fellow
Epidermal Growth Factor (EGF) mediated signal transduction
•2001-2002
Cellomics Inc., Pittsburgh
Knowledge Engineer
•2002- 2006
Information Specialist in Molecular Biology and Genetics
HSLS, University of Pittsburgh
•2006- Present
Head, Molecular Biology Information Service
HSLS, University of Pittsburgh
http://www.hsls.pitt.edu/guides/genetics
June 07:
Literature Informatics
June 08:
Genome Browsers
Growth of PubMed Citations
225
K
91K
• Schizophrenia
7.9K
• BRCA1
56 K
Lu et al. Database (Oxford). 2011; 2011: baq036
• Breast
Cancer
. p53
Feb 24, 2011
http://www.hsls.pitt.edu/guides/genetics
Topics
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PubMed query construction using Medical
Subject Headings (MESH) terms
NextGen literature mining tools
Text similarity search engine for finding
related articles, suitable journals for
manuscript submission ..etc
Search engine for finding disease causing
genes and disease causing SNPs
On line reference management tools
Post publication metrics
http://www.hsls.pitt.edu/guides/genetics
Literature Informatics

What genes are reported to be associated
with the disease SCHIZOPHRENIA?

Find published literature on DENGUE
OUTBREAKS in India with statistical and
numerical data on this outbreaks.
http://www.hsls.pitt.edu/guides/genetics
Literature Informatics
Schizophrenia: 91,997
Schizophrenia gene: 6664
Citations: 20 million
Journals: 5200
Dengue outbreaks in India: 302
Dengue outbreaks statistics India: 18
http://www.hsls.pitt.edu/guides/genetics
Challenges
 Am
I getting everything /
the right things?
 How
to digest this?
http://www.hsls.pitt.edu/guides/genetics
PubMed Search
 Am

I getting the right things?
Construct PubMed queries with
MeSH terms using MeSH browser
http://www.hsls.pitt.edu/guides/genetics
Medical Subject Headings (MeSH)
The U.S. National Library of
Medicine's controlled
vocabulary (thesaurus)
Arranged in a hierarchical
manner called the MeSH Tree
Structures
Updated annually
http://www.hsls.pitt.edu/guides/genetics
MeSH Vocabulary
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Headings
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Subheadings
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attached to headings to describe a specific aspect of a
concept (adverse effects , metabolism, diagnosis, therapy)
Supplementary Concept Records
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over 24,000 representing concepts found in the biomedical
literature (Body Weight, Kidney, Radioactive Waste)
over 172,000 terms in a separate chemical thesaurus updated weekly (cordycepin , valspodar , tacrolimus binding protein 4)
Publication Types
(Letter, Review, Randomized Controlled Trial)
http://www.hsls.pitt.edu/guides/genetics
MeSH Tree Structure
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A. Anatomy
B. Organisms
C. Diseases
D. Chemical and Drugs
E. Analytical, Diagnostic and
Therapeutic Techniques and Equipment
F. Psychiatry and Psychology
G. Biological Sciences
H. Physical Sciences
I. Anthropology, Education,
Sociology and Social Phenomena
J. Technology and Food and Beverages
K. Humanities
L. Information Science
M. Persons
N. Health Care
V. Publication Characteristics
Z. Geographic Locations
http://www.hsls.pitt.edu/guides/genetics
MeSH Indexing
Source: NLM
http://www.hsls.pitt.edu/guides/genetics
MeSH Indexing
PMD: 18045777
http://www.hsls.pitt.edu/guides/genetics
MeSH Indexing
http://www.hsls.pitt.edu/guides/genetics
PubMed Search

Retrieve published articles
on
 Dengue outbreaks in India
including
 Statistical and numerical data on dengue
outbreaks
http://www.hsls.pitt.edu/guides/genetics
PubMed Query Using MeSH
http://www.ncbi.nlm.nih.gov/mesh
http://www.hsls.pitt.edu/guides/genetics
Find articles on “Dengue outbreaks
in India” by searching PubMed
using MeSH terms
Resources
•Mesh Browser : http://www.ncbi.nlm.nih.gov/mesh
•PubMed: http://www.ncbi.nlm.nih.gov/pubmed
Link to the video tutorial:
http://media.hsls.pitt.edu/media/molbiovideos/pubmedsearch1.swf
http://www.hsls.pitt.edu/molbio
PubMed Query Using MeSH
http://www.hsls.pitt.edu/guides/genetics
PubMed Query Using MeSH
http://www.hsls.pitt.edu/guides/genetics
Building a PubMed Query
http://www.hsls.pitt.edu/guides/genetics
Building a PubMed Query
http://www.hsls.pitt.edu/guides/genetics
Building a PubMed Query
http://www.hsls.pitt.edu/guides/genetics
Building a PubMed Query
http://www.hsls.pitt.edu/guides/genetics
Building a PubMed Query
http://www.hsls.pitt.edu/guides/genetics
Building PubMed Queries
Term
Boolean
Term
Boolean
Dengue
AND
Outbreaks
823
Dengue *
AND
Outbreaks
746
Dengue
AND
Outbreaks
AND
India
123
Dengue*
AND
Outbreaks
AND
India
116
Dengue
AND
Outbreaks/
AND
statistics and
numerical
data
India
7
Dengue*
AND
Outbreaks/
statistics
and
numerical
data
India
7
AND
http://www.hsls.pitt.edu/guides/genetics
Term
# papers
Useful Links for MeSH
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MESH Browser: http://www.ncbi.nlm.nih.gov/mesh
18 ways to improve your Pubmed searches by Carrie Iwema
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Searching by using the MeSH Database. NCBI Handbook :
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http://bitesizebio.com/2008/03/05/18-ways-to-improve-your-pubmedsearches/
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part
=pubmedhelp#pubmedhelp.Searching_by_using_t
Link to Wikipedia, Youtube videos, blogs etc on “medical
subject heading”:

http://www.kosmix.com/topic/Medical_Subject_Headings?
http://www.hsls.pitt.edu/guides/genetics
PubMed Query

What genes are reported to be associated
with the disease SCHIZOPHRENIA ?
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Topic-Specific PubMed Queries
http://www.hsls.pitt.edu/guides/genetics
Topic-Specific PubMed Queries
http://www.nlm.nih.gov/bsd/special_queries.html
http://www.hsls.pitt.edu/guides/genetics
Find genes that are reported to be
associated with the disease
SCHIZOPHRENIA by searching PubMed
Resources
•PubMed Clinical Queries: http://www.ncbi.nlm.nih.gov/pubmed/clinical
Link to the video tutorial:
http://media.hsls.pitt.edu/media/molbiovideos/pubmedsearch2.swf
http://www.hsls.pitt.edu/molbio
Research on Optimal Search Strategies
http://www.hsls.pitt.edu/guides/genetics
PubMed Search Result Display
How to digest
this?
http://www.hsls.pitt.edu/guides/genetics
Latest Innovations in Literature Searching

GoPubMed
Display search results
sorted into meaningful
topics and subtopics
http://www.hsls.pitt.edu/guides/genetics
GoPubMed
www.gopubmed.com
http://www.hsls.pitt.edu/guides/genetics
Find genes that are reported to be
associated with the disease
SCHIZOPHRENIA by using GoPubMed
Resources
• GoPubMed: http://www.gopubmed.org/web/gopubmed/2?WEB10O00h00100090000
Link to the video tutorial:
http://media.hsls.pitt.edu/media/molbiovideos/gopubmed.swf
http://www.hsls.pitt.edu/molbio
GoPubMed Search Result
http://www.hsls.pitt.edu/guides/genetics
GoPubMed Search Result Analysis
http://www.hsls.pitt.edu/guides/genetics
GoPubMed Search Result Analysis
http://www.hsls.pitt.edu/guides/genetics
Latest Innovations in Literature Searching
http://www.hsls.pitt.edu/guides/genetics
GoPubMed

Noteworthy links
--- GoPubMed: exploring PubMed with the Gene Ontology. Doms A,
Schroeder M., Nucleic Acids Res. 2005 Jul 1; 33 (Web Server issue):
W783-6. http://www.ncbi.nlm.nih.gov/pubmed/15980585
--- Wiki, YouTube ,Blogs and Tweets:
http://www.kosmix.com/topic/GoPubmed?
http://www.hsls.pitt.edu/guides/genetics
Genomic achievements since the Human Genome Project.
ED Green et al. Nature 470, 204-213 (2011) doi:10.1038/nature09764
Search Engine Just for Human Genetics
CDC HuGENavigator : http://hugenavigator.net/
http://www.hsls.pitt.edu/guides/genetics
Find human genes that are reported to be
associated with the Asthma
Find human SNPs that are reported to be
associated with the Asthma
Resources
• HugeNavigator:
http://hugenavigator.net/HuGENavigator/home.do
Link to the video tutorial:
http://media.hsls.pitt.edu/media/molbiovideos/asthma.swf
http://www.hsls.pitt.edu/molbio
Search Engine Just for Human Genetics
http://www.hsls.pitt.edu/guides/genetics
Search Engine Just for Human Genetics
CDC HuGENavigator : http://hugenavigator.net/
http://www.hsls.pitt.edu/guides/genetics
GWAS Catalog
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http://www.genome.gov/multimedia/illustrations/GWAS_2010_2nd.pdf
http://www.hsls.pitt.edu/guides/genetics
Search Engine Just for Human Genetics
http://hugenavigator.net/HuGENavigator/huGEPedia.do
http://www.hsls.pitt.edu/guides/genetics
Search Engine Just for Human Genetics
CDC HuGENavigator : http://hugenavigator.net/
http://www.hsls.pitt.edu/guides/genetics
Find Disease Causing SNPs
http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do
What SNPs are associated
with “Schizophrenia”?
http://www.hsls.pitt.edu/guides/genetics
Search Engine for NIH funded research

http://projectreporter.nih.gov/reporter.cfm
http://www.hsls.pitt.edu/guides/genetics
Text-based Similarity Search Tools
Search Box:
http://www.hsls.pitt.edu/guides/genetics
Text Similarity Search Tools
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eTBLAST
http://etest.vbi.vt.edu/etblast3/
http://www.hsls.pitt.edu/guides/genetics
Text Similarity Search Tools
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eTBLAST
http://www.hsls.pitt.edu/guides/genetics
Text Similarity Search Tools
http://www.hsls.pitt.edu/guides/genetics
Déjà Vu: a Database of Highly Similar Citations
http://dejavu.vbi.vt.edu/dejavu/duplicate/
http://www.hsls.pitt.edu/guides/genetics
Journal Author Name Estimator
http://www.biosemantics.org/jane/
http://www.hsls.pitt.edu/guides/genetics
PubMed based Tools
http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/
Lu et al. Database (Oxford). 2011; 2011: baq036
http://www.hsls.pitt.edu/guides/genetics
Literature Search Tools
http://www.hsls.pitt.edu/guides/genetics
Literature Search Workflow
Authors
Topics
L
I
T
E
R
A
T
U
R
E
Global Map
Authors Networks
S
E
A
R
C
H
Journals
http://www.hsls.pitt.edu/guides/genetics
Genes
Online Reference Management Tools
http://www.hsls.pitt.edu/guides/genetics
Automated email Notification Tool
http://www.ncbi.nlm.nih.gov/sites/myncbi/
Save your searches at My NCBI and set up an email notification on
new publication based on your search query
http://www.hsls.pitt.edu/guides/genetics
My NCBI
1
2
3
http://www.hsls.pitt.edu/guides/genetics
My NCBI
4
http://www.hsls.pitt.edu/guides/genetics
My NCBI email Notification
http://www.hsls.pitt.edu/guides/genetics
Reference Management Tools
Connotea
Web pages
online
CiteULike
Mendaley
Scientific Research
Papers
Zotero
EndNote
Refworks
http://www.hsls.pitt.edu/guides/genetics
downloadable
Post Publication Metrics
http://www.hsls.pitt.edu/guides/genetics
Post Publications Metrics
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Journal level : Impact Factor
Author level: H-Index
Article level:
Article usage statistics: HTML pageviews, PDF
downloads and XML downloads
Citations from the scholarly literature: PubMed
Central, Scopus and CrossRef
Social bookmarks: CiteULike and Connotea
Comments: left by readers of each article
Notes: left by readers of each article
Blog posts: aggregated from Postgenomic, Nature
Blogs, Bloglines, and Research Blogging
Ratings: left by readers of each article
http://www.hsls.pitt.edu/guides/genetics
Impact Factor



a measure reflecting the average number of citations to
articles published in science and social science journals.
a proxy for the relative importance of a journal within its
field
developed by Eugene Garfield, the founder of
the Institute for Scientific Information (ISI)
•
A = the number of times articles published in 2006 and 2007 were cited
by indexed journals during 2008
B = the total number of "citable items" published in 2006 and 2007.
("Citable items" are usually articles, reviews, proceedings, or notes; not
editorials or Letters-to-the-Editor.)
•
2008 impact factor = A/B
•
http://www.hsls.pitt.edu/guides/genetics
From Wikipedia
Scopus Journal Analyzer
http://www.hsls.pitt.edu/molbio
ISI Journal Impact Factor
http://www.hsls.pitt.edu/molbio
FOLLOW-UP ANALYSIS OF REJECTED MANUSCRIPTS
SUBMITTED TO THE EMBO JOURNAL IN 2007:
http://www.nature.com/emboj/about/emboj_rejects_2007.html
http://www.hsls.pitt.edu/guides/genetics
Journal Impact Factor
http://admin-apps.isiknowledge.com/JCR/JCR?RQ=RECORD&rank=1&journal=ACTA+CRYSTALLOGR+A
http://www.hsls.pitt.edu/guides/genetics
Retrieve Journal Impact Factor
by searching Scopus and
ISI Web of Science
Resources
• Scopus: http://www.scopus.com/source/eval.url
•ISI Web of Science: http://admin-apps.isiknowledge.com/JCR/JCR?RQ=HOME
Link to the video tutorial:
http://media.hsls.pitt.edu/media/molbiovideos/impactfactors.swf
http://www.hsls.pitt.edu/molbio
H Index
•proposed by J.E. Hirsch of UCSD
•an index to quantify an individual's scientific research output
•provides a single-number metric of an academic's impact
combining quality with quantity
http://www.hsls.pitt.edu/guides/genetics
H-Index

Downloadable software: Publish or Perish
http://www.harzing.com/pop.htm
http://www.hsls.pitt.edu/guides/genetics
Article Level Metrics
http://www.hsls.pitt.edu/guides/genetics
Search Engine for
Bioinformatics Resources
http://www.hsls.pitt.edu/guides/genetics
Molecular Databases
http://www.hsls.pitt.edu/guides/genetics
Molecular Databases
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Nucleic Acids Research : Annual databases Issue
NAR: Annual Web Server Issue
Oxford Journal : Bioinformatics
BioMedCentral: BMC Bioinformatics
Growth of bioinformatics tools
http://www.hsls.pitt.edu/guides/genetics
Biomedical and Life Sciences Search Engines
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OBRC : University of Pittsburgh
http://www.hsls.pitt.edu/guides/genetics/obrc

Vadlo
http://vadlo.com/

OReFil : University of Tokyo
http://orefil.dbcls.jp/
http://www.hsls.pitt.edu/guides/genetics
Search for bioinformatics Resources
Locate online tools that predict phosphorylation sites
in a protein sequence.
Resources
• Search.HSLS.MolBio :
Link to the video tutorial:
http://media.hsls.pitt.edu/media/Search%20Bioinfo%20Resoursec.swf
http://www.hsls.pitt.edu/molbio
Life Sciences Search Engine
http://www.hsls.pitt.edu/obrc/
http://www.hsls.pitt.edu/guides/genetics
Life Sciences Search Engine
http://www.hsls.pitt.edu/guides/genetics
Summary




Construct a comprehensive PubMed query:
 MESH Browser
Retrieve gene/protein/disease information straight from a
PubMed search :
 GoPubmed
Find suitable journals for manuscript submission, etc…
 eTBLAST, JANE
Find disease causing genes and disease causing SNPs:
 HUGENavigator_ Geneprospector, Phenopedia,
GWASIntegrator
http://www.hsls.pitt.edu/guides/genetics
Summary

Setup email alert for new publications


Analyze popularity of a published article


My NCBI
Post Publication Metrics
Search for databases and software

OBRC
http://www.hsls.pitt.edu/guides/genetics
Links
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MESH Database: http://www.ncbi.nlm.nih.gov/mesh
PubMed Special Topic Queries:
http://www.nlm.nih.gov/bsd/special_queries.html
GoPubMed: http://www.gopubmed.com
CDC HuGENavigator : http://hugenavigator.net/
Novoseek: http://www.novoseek.com
etBLAST: http://etest.vbi.vt.edu/etblast3/
déjà vu: http://dejavu.vbi.vt.edu/dejavu/duplicate/
MyNCBI: http://www.ncbi.nlm.nih.gov/sites/myncbi/
OBRC: http://www.hsls.pitt.edu/guides/genetics/obrc
http://www.hsls.pitt.edu/guides/genetics
Recommended Readings


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Sequence - Evolution - Function Computational Approaches in Comparative Genomics. Koonin,
Eugene V; Galperin, Michael Y. Norwell (MA): Kluwer Academic Publishers; c2003, Chapter 3.7
PubMed.

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=sef&part=A55#A149
Searching by using the MeSH Database. NCBI Handbook Link

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part=pubmedhelp#pubmed
help.Searching_by_using_t
GoPubMed: exploring PubMed with the Gene Ontology. Doms A, Schroeder M., Nucleic Acids
Res. 2005 Jul 1; 33 (Web Server issue): W783-6.

http://www.ncbi.nlm.nih.gov/pubmed/15980585
PubMed and beyond: a survey of web tools for searching biomedical literature.
Lu Z.
Database (Oxford). 2011 Jan 18;2011:baq036. Print 2011.
PMID: 21245076 http://www.ncbi.nlm.nih.gov/pubmed/21245076
http://www.hsls.pitt.edu/guides/genetics