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Biology in silico : Online tools for “ omics ” 7 th August 2013. Ansuman Chattopadhyay , PhD Carrie L Iwema , PhD, MLS, AHIP Molecular Biology Information Services Health Sciences Library System University of Pittsburgh [email protected] [email protected]

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biology in silico online tools for omics 7 th august 2013

Biology in silico: Online tools for “omics”7th August 2013

AnsumanChattopadhyay, PhD

Carrie L Iwema, PhD, MLS, AHIP

Molecular Biology Information Services

Health Sciences Library System

University of Pittsburgh

[email protected]@pitt.edu

hsls molecular biology information service
HSLS Molecular Biology Information Service

http://www.hsls.pitt.edu/molbio

slide3

AnsumanChattopadhyay, 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/molbio

slide4

Carrie L Iwema, PhD, MLS, AHIP

[email protected]

  • 1993-2001
  • SUNY Upstate Medical University, Syracuse
  • PhD in Neuroscience
  • Specificity of connectivity in the mammalian olfactory system
  • 2001-2005
  • Yale University School of Medicine, New Haven
  • Postdoctoral Fellow
  • Development & regeneration in the mammalian olfactory system
  • 2004-2006
  • Southern Connecticut State University, New Haven
  • Masters in Library Science
  • 2006- 2007
  • Johns Hopkins Medical Institutions, Welch Medical Library, Baltimore
  • Basic Science Librarian
  • 2007- Present
  • University of Pittsburgh, Health Sciences Library System, Pittsburgh
  • Information Specialist in Molecular Biology

http://www.hsls.pitt.edu/molbio

slide5

Topics

Literature Informatics

Bioinformatics Databases & Software

HSLS MolBio Services

http://www.hsls.pitt.edu/molbio

in silico support
In silico Support

http://www.hsls.pitt.edu/molbio

topics
Topics
  • Literature Informatics
    • Comprehensive search:
      • MESH term based PubMed Search
      • PubMed special topics query
    • Next-generation literature search tools:
      • GoPubMed, eTBlast
      • GLAD4U, Quertle
      • HuGE Navigator

http://www.hsls.pitt.edu/molbio

growth of pubmed citations
Growth of PubMed Citations

. p53

Lu et al. Database (Oxford). 2011: baq036

Aug 5th 2013

http://www.hsls.pitt.edu/molbio

literature informatics
Literature Informatics
  • What genes are reported to be associated with the disease SCHIZOPHRENIA?
    • Find published literature with statistical and numerical data on DENGUE OUTBREAKS in India.

http://www.hsls.pitt.edu/molbio

literature informatics1
Literature Informatics

Schizophrenia: 104,388

Schizophrenia gene: 8,459

Citations: 22 million

Journals: >5600

Dengue outbreaks in India: 394

Dengue outbreaks statistics India: 29

http://www.hsls.pitt.edu/molbio

challenges
Challenges
  • Am I getting everything / the right things?
  • How to digest this?

http://www.hsls.pitt.edu/molbio

pubmed search
PubMed Search
  • Am I getting the right things?
    • Construct PubMed queries with MeSH terms using MeSH browser

http://www.hsls.pitt.edu/molbio

medical subject headings mesh
Medical Subject Headings (MeSH)

http://www.hsls.pitt.edu/molbio

mesh vocabulary
MeSH Vocabulary
  • Headings
    • 26,853 concepts found in the biomedical literature (Body Weight, Kidney, Radioactive Waste)
  • Subheadings
    • attached to headings to describe a specific aspect of a concept (adverse effects, metabolism, diagnosis, therapy)
  • Supplementary Concept Records
    • over 214,000 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/molbio

mesh tree structure
MeSH Tree Structure
  • A. AnatomyB. OrganismsC. DiseasesD. Chemicals and DrugsE. Analytical, Diagnostic and Therapeutic Techniques and EquipmentF. Psychiatry and PsychologyG. Phenomena and ProcessesH. Disciplines and OccupationsI. Anthropology, Education, Sociology and Social PhenomenaJ. Technology, Industry, AgricultureK. Humanities L. Information Science M. Named Groups N. Health CareV. Publication Characteristics Z. Geographicals

http://www.hsls.pitt.edu/molbio

mesh indexing
MeSH Indexing

Source: NLM

http://www.hsls.pitt.edu/molbio

mesh indexing1
MeSH Indexing

PMD: 18045777

http://www.hsls.pitt.edu/molbio

medical subject heading mesh
Medical Subject Heading (MeSH)

http://www.hsls.pitt.edu/molbio

mesh indexing2
MeSH Indexing

http://www.hsls.pitt.edu/molbio

pubmed search1
PubMed Search
  • Retrieve published articles on
    • Dengue outbreaks in India

Including

    • Statistical and numerical data

http://www.hsls.pitt.edu/molbio

pubmed query using mesh
PubMed Query Using MeSH

http://www.ncbi.nlm.nih.gov/mesh

http://www.hsls.pitt.edu/molbio

slide23

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/clres2705/mesh.swf

http://www.hsls.pitt.edu/molbio

pubmed query using mesh1
PubMed Query Using MeSH

http://www.hsls.pitt.edu/molbio

pubmed query using mesh2
PubMed Query Using MeSH

http://www.hsls.pitt.edu/molbio

building a pubmed query
Building a PubMed Query

http://www.hsls.pitt.edu/molbio

building a pubmed query1
Building a PubMed Query

http://www.hsls.pitt.edu/molbio

building a pubmed query2
Building a PubMed Query

145

http://www.hsls.pitt.edu/molbio

building a pubmed query3
Building a PubMed Query

http://www.hsls.pitt.edu/molbio

building a pubmed query4
Building a PubMed Query

9

http://www.hsls.pitt.edu/molbio

building pubmed queries
Building PubMed Queries

http://www.hsls.pitt.edu/molbio

useful links for mesh
Useful Links for MeSH
  • MeSH Browser: http://www.ncbi.nlm.nih.gov/mesh
  • 18 ways to improve your Pubmed searches by Carrie Iwema
    • http://goo.gl/B8rFf
  • Searching by using the MeSH Database. NCBI Handbook :
    • http://goo.gl/X4UAe

http://www.hsls.pitt.edu/molbio

pubmed query
PubMed Query
  • What genes are reported to be associated with the disease SCHIZOPHRENIA ?
    • Topic-Specific PubMed Queries

http://www.hsls.pitt.edu/molbio

topic specific pubmed queries
Topic-Specific PubMed Queries

http://www.nlm.nih.gov/bsd/special_queries.html

http://www.hsls.pitt.edu/molbio

slide35

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/clres2705/scz.swf

http://www.hsls.pitt.edu/molbio

pubmed special topic queries
PubMed Special Topic Queries

http://www.hsls.pitt.edu/molbio

search filters
Search Filters

http://www.hsls.pitt.edu/molbio

pubmed search filter medical genetics
PubMed Search Filter: Medical Genetics
  • ("schizophrenia"[MeSH Terms] OR "schizophrenia"[All Fields]) AND (("genetics, medical"[MeSH Terms] OR ("genetics"[All Fields] AND "medical"[All Fields]) OR "medical genetics"[All Fields] OR ("medical"[All Fields] AND "genetics"[All Fields])) OR ("genotype"[MeSH Terms] OR "genotype"[All Fields]) OR "genetics"[Subheading] AND ("genetics"[Subheading] OR "genetics"[All Fields] OR "genetics"[MeSH Terms]))

http://www.hsls.pitt.edu/molbio

pubmed search result display
PubMed Search Result Display

How to digest

this?

http://www.hsls.pitt.edu/molbio

latest innovations in literature searching
Latest Innovations in Literature Searching
  • GoPubMed

Display search results

sorted into meaningful

topics and subtopics

http://www.hsls.pitt.edu/molbio

gopubmed
GoPubMed

www.gopubmed.com

http://www.hsls.pitt.edu/molbio

slide43

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/clres2705/gopubmed.swf

http://www.hsls.pitt.edu/molbio

gopubmed search result
GoPubMed Search Result

http://www.hsls.pitt.edu/molbio

gopubmed search result analysis
GoPubMed Search Result Analysis

http://www.hsls.pitt.edu/molbio

gopubmed search result analysis1
GoPubMed Search Result Analysis

http://www.hsls.pitt.edu/molbio

latest innovations in literature searching1
Latest Innovations in Literature Searching

http://www.hsls.pitt.edu/molbio

gopubmed1
GoPubMed
  • Noteworthy links

GoPubMed: exploring PubMed with the Gene Ontology. DomsA,Schroeder M., Nucleic Acids Res. 2005 Jul 1; 33 (Web Server issue):W783-6. http://www.ncbi.nlm.nih.gov/pubmed/15980585

http://www.hsls.pitt.edu/molbio

pubmed driven web tools
PubMed driven Web Tools

http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/

http://www.hsls.pitt.edu/molbio

pubmed based tools
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/molbio

extract gene list from literature
Extract gene list from Literature

http://www.quertle.info/

http://www.hsls.pitt.edu/molbio

questions for quertle
Questions for Quertle
  • What genes cause Asthma?
  • What cell lines are used in diabetes research?
  • Which cell types are known to express EGFR?
  • What animals are used in studies for diabetes?
  • Which protein kinases activate TP53?

http://www.hsls.pitt.edu/molbio

slide53

A short video on Quertle

  • Resources
  • Quertle: www.quertle.info

Link to the video tutorial:

http://media.hsls.pitt.edu/media/molbiovideos/quertle-ac0212.swf

http://www.hsls.pitt.edu/molbio

literature to gene list
Literature to gene list
  • GLAD4U
    • http://bioinfo.vanderbilt.edu/glad4u/

http://www.hsls.pitt.edu/molbio

search engine just for human genetics
Search Engine Just for Human Genetics

CDC HuGENavigator : http://hugenavigator.net/

http://www.hsls.pitt.edu/molbio

slide57

Find human genesreported to be associated with Asthma

  • Find human SNPsreported to be associated with Asthma
  • Resources
  • HugeNavigator: http://hugenavigator.net/HuGENavigator/home.do

Link to the video tutorial:

http://media.hsls.pitt.edu/media/clres2705/asthma.swf

http://www.hsls.pitt.edu/molbio

search engine just for human genetics1
Search Engine Just for Human Genetics

http://www.hsls.pitt.edu/molbio

search engine just for human genetics2
Search Engine Just for Human Genetics

CDC HuGENavigator : http://hugenavigator.net/

http://www.hsls.pitt.edu/molbio

search engine just for human genetics3
Search Engine Just for Human Genetics

http://hugenavigator.net/HuGENavigator/huGEPedia.do

http://www.hsls.pitt.edu/molbio

search engine just for human genetics4
Search Engine Just for Human Genetics

CDC HuGENavigator : http://hugenavigator.net/

http://www.hsls.pitt.edu/molbio

gwas catalog
GWAS Catalog
  • http://www.genome.gov/multimedia/illustrations/GWAS_2010_2nd.pdf

http://www.hsls.pitt.edu/molbio

gwa studies catalog
GWA Studies Catalog

http://www.genome.gov/gwastudies/

http://www.hsls.pitt.edu/molbio

find disease causing snps
Find Disease Causing SNPs

http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do

What SNPs are associated

  • with “Schizophrenia”?

http://www.hsls.pitt.edu/molbio

text based similarity search tools
Text-based Similarity Search Tools

Search Box:

http://www.hsls.pitt.edu/molbio

text similarity search tools
Text Similarity Search Tools
  • eTBLAST

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

http://www.hsls.pitt.edu/molbio

text similarity search tools1
Text Similarity Search Tools
  • eTBLAST

http://www.hsls.pitt.edu/molbio

text similarity search tools2
Text Similarity Search Tools

http://www.hsls.pitt.edu/molbio

d j vu a database of highly similar citations
Déjà Vu: a Database of Highly Similar Citations

http://dejavu.vbi.vt.edu/dejavu/duplicate/

http://www.hsls.pitt.edu/molbio

journal author name estimator
Journal Author Name Estimator

http://www.biosemantics.org/jane/

http://www.hsls.pitt.edu/molbio

automated email notification tool
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/molbio

my ncbi
My NCBI

1

2

3

http://www.hsls.pitt.edu/molbio

my ncbi1
My NCBI

4

http://www.hsls.pitt.edu/molbio

my ncbi email notification
My NCBI email Notification

http://www.hsls.pitt.edu/molbio

reference management tools
Reference Management Tools

Connotea

CiteULike

Mendeley

Zotero

Web pages

online

Scientific Research

Papers

downloadable

EndNote

http://www.hsls.pitt.edu/molbio

post publications metrics
Post Publications Metrics
  • 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: CiteULikeand Connotea
  • Comments: left by readers of each article
  • Notes: left by readers of each article
  • Blog posts: aggregated from Postgenomic, Nature Blogs, Bloglines, andResearch Blogging
  • Ratings: left by readers of each article

http://www.hsls.pitt.edu/molbio

impact factor
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/BFrom Wikipedia

http://www.hsls.pitt.edu/molbio

scopus journal analyzer
Scopus Journal Analyzer

http://www.hsls.pitt.edu/molbio

isi journal impact factor
ISI Journal Impact Factor

http://www.hsls.pitt.edu/molbio

journal impact factor
Journal Impact Factor

http://admin-apps.isiknowledge.com/JCR/JCR?RQ=RECORD&rank=1&journal=ACTA+CRYSTALLOGR+A

http://www.hsls.pitt.edu/molbio

h index
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/molbio

article level metrics
Article Level Metrics

http://www.hsls.pitt.edu/molbio

slide86

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/clres2705/impact.swf

http://www.hsls.pitt.edu/molbio

molecular databases
Molecular Databases
  • Nucleic Acids Research : Annual databases Issue
  • NAR: Annual Web Server Issue
  • Oxford Journal : Bioinformatics
  • BioMedCentral: BMC Bioinformatics

http://www.hsls.pitt.edu/molbio

biomedical life sciences search engines
Biomedical & Life Sciences Search Engines
  • OBRC : University of Pittsburgh

http://www.hsls.pitt.edu/molbio/obrc

  • Vadlo

http://vadlo.com/

  • OReFil : University of Tokyo

http://orefil.dbcls.jp/

http://www.hsls.pitt.edu/molbio

slide90

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
Life Sciences Search Engine

http://www.hsls.pitt.edu/obrc/

http://www.hsls.pitt.edu/molbio

life sciences search engine1
Life Sciences Search Engine

http://www.hsls.pitt.edu/molbio

hsls obrc
HSLS OBRC

http://www.hsls.pitt.edu/molbio

molecular databases catalog
Molecular Databases Catalog

http://www.hsls.pitt.edu/molbio

search hsls molbio
Search.HSLS.MolBio

http://www.hsls.pitt.edu/molbio/

http://www.hsls.pitt.edu/molbio

search hsls molbio1
Search.HSLS.MolBio
  • Integrated search system
    • Databases & Software
    • Articles on Databases & Software
    • Genes/Proteins
    • Pathways
    • Protocols
    • Seminar/Talks Videos
    • Recommended Articles
  • Tabbed browsing
  • Clustered search results

http://www.hsls.pitt.edu/molbio

search term phosphorylation
Search term: “phosphorylation”

http://www.hsls.pitt.edu/molbio

molecular databases and software search term phosphorylation
Molecular Databases and Software:search term: “Phosphorylation”

http://www.hsls.pitt.edu/molbio

search result page
Search Result Page

http://www.hsls.pitt.edu/molbio

citation trackers
Citation Trackers

http://www.hsls.pitt.edu/molbio

search pubmed articles on databases and software phosphorylation
Search PubMed Articles on Databases and Software : “phosphorylation”

http://www.hsls.pitt.edu/molbio

articles on databases and software
Articles on Databases and Software

http://www.hsls.pitt.edu/molbio

protocols
Protocols:

http://www.hsls.pitt.edu/molbio

seminar talks video
Seminar Talks Video

http://www.hsls.pitt.edu/molbio

seminar talks video1
Seminar Talks Video

http://www.hsls.pitt.edu/molbio

recommended articles
Recommended Articles

Faculty of 1000 Biology: a literature awareness tool that

highlights and reviews the most interesting papers published

in the biological sciences, based on the recommendations of a

faculty of well over 2300 selected leading researchers.

http://www.hsls.pitt.edu/molbio

recommended articles1
Recommended Articles

http://www.hsls.pitt.edu/molbio

microarray data analysis
Microarray Data Analysis

GeneSpring/Partek

Statistical packages

  • Ingenuity IPA
  • GeneGOMetacore
  • Explain

Literature findings

Biology

http://www.hsls.pitt.edu/molbio

discovery step pathway analysis
Discovery Step: Pathway Analysis

Gene List

http://www.hsls.pitt.edu/molbio

discovery step
Discovery Step
  • Gene List
        • Biological functions
        • Canonical Pathways
        • Interaction Networks

http://www.hsls.pitt.edu/molbio

common functions and pathways ipa analysis
Common Functions and Pathways: IPA Analysis

http://www.hsls.pitt.edu/molbio

common functions and pathways ipa analysis1
Common Functions and Pathways: IPA Analysis

http://www.hsls.pitt.edu/molbio

common pathways ipa
Common Pathways: IPA

http://www.hsls.pitt.edu/molbio

pathway map p53
Pathway Map: p53

Red:

Green:

http://www.hsls.pitt.edu/molbio

pathway map nfkb and tgf beta
Pathway Map: NFkB and TGF beta

http://www.hsls.pitt.edu/molbio

interaction network maps ipa
Interaction Network Maps: IPA

http://www.hsls.pitt.edu/molbio

interaction map with data overlay ipa
Interaction Map with Data Overlay: IPA

http://www.hsls.pitt.edu/molbio

pathway analysis genego metacore
Pathway Analysis: GeneGo Metacore

http://www.hsls.pitt.edu/molbio

metacore transcription regulation
Metacore: Transcription Regulation

http://www.hsls.pitt.edu/molbio

slide123

BioBase Explain: Key Molecules Prediction

Key Molecules

Over representation of

TF Binding site

Promoter

Microarray

http://www.hsls.pitt.edu/molbio

slide124

Biobase Explain: Key Mols Prediction

Common:

KM:108

TF:4

Key Molecules :677

TF: 12

2072

32 >2 fold up

583: NC

Over representation of

TF Binding site

Promoter

Microarray

http://www.hsls.pitt.edu/molbio

use of ingenuity genego and biobase
Use of Ingenuity, GeneGO and BioBase
  • DNA microarrays
  • Protein arrays
  • CHIP-chip
  • Search for
    • Gene/protein info (human, mouse, rat, yeast)
    • Drug/small molecule
    • Disease info
    • Promoter sequences
    • Transcription factors binding sites

http://www.hsls.pitt.edu/molbio

finding disease causing genes
Finding Disease Causing Genes

http://www.hsls.pitt.edu/molbio

metacore atherosclerosis core network
Metacore: Atherosclerosis (core network)

http://www.hsls.pitt.edu/molbio

atherosclerosis and alzheimers
Atherosclerosis And Alzheimers

From Wikipedia, the free encyclopedia

http://www.hsls.pitt.edu/molbio

pubmed search on atherosclerosis majr and alzheimer disease majr
PubMed Search on"Atherosclerosis"[Majr] AND "Alzheimer Disease"[Majr]

http://www.hsls.pitt.edu/molbio

atherosclerosis and alzheimers1
Atherosclerosis And Alzheimers

http://www.hsls.pitt.edu/molbio

hsls molecular biology information service1
HSLS Molecular Biology Information Service

http://www.hsls.pitt.edu/molbio

thank you any questions

Thank you!Any questions?

Carrie IwemaAnsumanChattopadhyay

[email protected]@pitt.edu

412-383-6887 412-648-1297

http://www.hsls.pitt.edu/molbio

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