Transcript Literature Informatics 7th September, 2013

Ansuman Chattopadhyay, Ph.D.
•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/molbio
[email protected]
Genomic achievements since the Human Genome Project
http://www.hsls.pitt.edu/molbio
Progress in Genomics
Source: Eric Green; HGP10 Symposium
http://www.hsls.pitt.edu/molbio
DNA Sequencing Cost
http://www.hsls.pitt.edu/molbio
Big DATA Biology
Multi-Gene
System-wide
High-throughput
Multi-Institution
Single Gene
Single Protein
Single lab
http://www.hsls.pitt.edu/molbio
Growth of PubMed Citations
266
K
67K
• Breast
Cancer
104K
• Schizophrenia
9.9K
• BRCA1
. p53
Lu et al. Database (Oxford). 2011: baq036
Aug 20th 2013
http://www.hsls.pitt.edu/molbio
What are Browser Enhancers ?
Bookmarklets :
bookmarks stored in a web browser that
contains JavaScript commands to extend the
browser's functionality.
a bookmarklet might allow the user to select text on a page,
click the bookmarklet, and be presented with a search engine
results page for the search term selected.
Wikipedia
Example : Library Proxy Server Bookmarklets
Example: Mendeley’s Web Importer
Example: Mendeley’s Web Importer
Molecular Biology Information Service
Workshops
License Commercial
Software
Bioinformatics
http://www.hsls.pitt.edu/molbio
One-on-one
consultations
Challenges for Biomedical Scientists
5669 Journals
23 million Citations
GWAS
NGS Tech
Molecular Databases
Microarray
Cancer Genome
High Throughput Technologies
Challenges for Biomedical Scientists
Challenges for Biomedical Scientists
what is its
function ?
how is it
calculated ?
workflow: copy, paste, and Google
what is its
structure?
InfoBoosters
www.hsls.pitt.edu/infoboosters
InfoBoosters
InfoBoosters
Infoboosters
Infoboosters
InfoBoosters
What is its
function ?
How is it
calculated ?
What is its
structure?
Data Integration
InfoBoosters
InfoBoosters
Create Your Own InfoBooster
WWW.hsls.pitt.edu/infoboosters
InfoBooster Generator
Clinical Trials.gov
1
InfoBooster Generator
Go to the Clinical Trials.gov Website and do a search with a one-word search term, such as asthma
2
InfoBooster Generator
COPY the URL from the search result page
InfoBooster Generator
WWW.hsls.pitt.edu/molbio/infoboosters
3
4
5
InfoBooster Generator
InfoBooster Generator
InfoBooster Generator
WWW.hsls.pitt.edu/infoboosters
InfoBooster Generator
InfoBoosters
Pros
1. SIMPLE—
Easy to use, create, & install
2. UNIVERSAL—
Compatible w/most OS & browsers
3. SEAMLESS—
Integrates published lit & other databases
Thank you!
Any questions?
Ansuman Chattopadhyay
[email protected]
http://www.hsls.pitt.edu/guides/genetics