Selection of Resources for the Development of an Information Service Program in Molecular Biology an

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Selection of Resources for the Development of an
Information Service Program in Molecular Biology
and Genetics

• Ansuman Chattopadhyay, PhD
• Information Specialist in Molecular Biology and
  Genetics
• Health Sciences Library System
• University of Pittsburgh

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Topics

• Multi Step Life Sciences Research
• Literature Retrieval
• Sequence Analysis
• Laboratory Resources
• University of Pittsburgh HSLS Molecular Biology
  Information Service Program

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Life Sciences Research- A Multi Step Process
Hypothesis Generation
Knowledge Mining
Sequence Analysis
Laboratory Bench Work
Mol Biol Information Service
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Literature Retrieval Resources
Hypothesis Generation
Knowledge Mining
Laboratory Bench Work
Sequence Analysis
PubMed --CellSpace Knowledge
Miner --PubGene --Genomatix BiblioSphere
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Too much information
83,130
31,596
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Literature Retrieval Resources
http//www.pubgene.org
http//www.genomatix.de/
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What is CellSpace ?

• CellSpace is a bioinformatics tool-- a
  knowledge mining system that automatically
  detects, analyzes, and reports the logical
  relationships between four types of terms found
  in the research literature
• molecule proteins, genes, drugs
• function biological processes and disease states
• cell type
• organism

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What is CellSpace ?
CellSpace Knowledge Miner
Literature Association
Cells Systems
Molecules
Functions
Organisms

• Molecules
• Molecules
• Drugs
• Genes
• Proteins

Molecules
Functions
Cells Systems

• Functions
• Biological
• Functions
• Disease
• States

Organisms
Cells Systems Cells, Sub-cellular
Components,Tissues and Organs
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What you can do with CellSpace?

• Start with a single protein (or other molecule)
  and
• find its functions, the diseases in which it is
  implicated,
• and related molecules.
• Start with a disease or biological function and
  find
• related molecules, or related functions.
• Start with two or more functions, and find the
  related
• molecules that they have in common

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What you can do with CellSpace?

• Start with results from a high-throughput
  experiment
• (such as a cluster of co-regulated genes from
• microarray analysis), and easily find the
  functions
• that they share.
• Start with the results of proteomics
  experiments, and
• quickly screen the data to distinguish published
  
• interactions from novel ones.
• .View the literature that supports the
  connections
• found in CellSpace.

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Start with a disease or biological function and
find related molecules, or related functions
CellSpace Knowledge Miner

• Find molecules related to apoptosis

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5
1
2
Drag and drop
3
4
Click to select
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Find molecules associated with apoptosis
Get references
Results are presented with statistical likelihood
value
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CellSpace Knowledge Miner
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How CellSpace Works?
CellSpace computers analyze the National Library
of Medicine's MEDLINE database, performing
proprietary statistical correlation analyses
regarding the organisms, cell types, biological
processes, and molecules reported in 655
selected life science research journals. The
molecular relationships extracted from the
literature are then stored in the CellSpace
database, which can be queried via the CellSpace
user interface. The information is updated every
two weeks
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PubGene
The Network Browser tool displays literature
association networks for a gene. The Set Cover
Article Search tool will let you search the
literature using a set covering algorithm. The
set covering algorithm is particularly useful to
search for literature references for large sets
of terms.
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PubGene
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PubGene
The query gene is shown with bright red font in
the graph, its direct neighbors are shown with
darker red font, and neighbours of neighbours
are shown with black font
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BiblioSphere
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BiblioSphere
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BiblioSphere
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BiblioSphere
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BiblioSphere
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BiblioSphere
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Resources comparison
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Resources comparison
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Information Hubs
Hypothesis Generation
Knowledge Mining
Sequence Analysis
Laboratory Bench Work
The molecular biology and genetics resources
that can serve as information hubs, an access
point to retrieve a broad range of information
through a small number of selected web-based
public databases
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Information Hubs

• UCSC Genome Bioinformatics Resources
• Genes detail page Genome Browser
• Family Browser Proteome Browser
• SwissProt
• LocusLink / Entrez Gene
• Gene Cards
• Gene Lynx
• Incyte Proteome Bioknowledge Library
• Human Protein Reference Database
• Organism Genome Consortium sites

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Information Hubs
Gene Expression Data
Sequence Genomic,mRNA Protein
LocusLink
UCSC Family browser
RNA Structure
SwissProt
Protein Structure
OMIM
GeneCards
CGAP
UCSC Genes Detail Page
GO Annotations Molecular function Bio
pathways Cellular component
Other Species
GeneLynx
PubMed
Mouse Genome Informatics
AceView
UCSC genome browser
UCSC Proteome browser
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Information Hubs
http//genome.ucsc.edu/cgi-bin/hgGene?hgsid314086
63dbhg16hgg_geneU14680hgg_chromchr17hgg_sta
rt41570859hgg_end41650551
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Information Hubs
http//www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l
672
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Information Hubs
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Information Hubs
http//bioinfo.weizmann.ac.il/cards-bin/carddisp?B
RCA1searchBRCA1sufftxt
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Information Hubs
http//www.hprd.org/protein/00218
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Information Hubs
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Information Hubs
Sequence
Disease
Expression in Organ/Tissue Cell Type Tumor Type
Gene Ontology terms
Proteome BioKnowledge Library
Protein Interactions
Gene Regulation
Protein Modifications
Literature Excerpts
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Resources Comparison
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Genome Browsers
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Molecular Database Catalog
http//nar.oupjournals.org/

• Nucleic Acids Research Database Issue

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Growth of Molecular databases
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Database Catalog
http//www.infobiogen.fr/services/dbcat/
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Sequence Analysis
Hypothesis Generation
Knowledge Mining
Sequence Analysis
Laboratory Bench Work
MolBiol Tools Restriction mapping, PCR primer
design
Sequence Search
Sequence Alignment
Sequence Manipulation
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Web Server Catalog
http//nar.oupjournals.org/

• Nucleic Acids Research Database Issue

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Sequence Analysis
http//www.bioinformatics.vg/
http//healthlinks.washington.edu/index.cfm?id210
BCCB7-511A-4C6B-8B40-DFC47AABEA7F
http//www.hsls.pitt.edu/guides/genetics
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Sequence Analysis
http//www.bioinformatics.vg/
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Sequence Analysis
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Sequence Analysis
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Sequence Analysis
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Sequence Analysis
DNAStar
LaserGene
PC/Mac
PC/Mac
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Sequence Analysis
Vector NTI
Software
Database
DNA/RNA Protein Oligo Enzyme Gel Marker Blast
Result Analysis Result
Vector NTI core AlignX ContigExpress GenomBench Bi
oAnnotator
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Sequence Analysis

• VectorNTI Advanced software suit consists of
  five independent
• yet interconnected components
•  
• Vector NTI core the cornerstone application for
  Vector NTI suite,
• provides tools for sequence analysis and
  molecule manipulation.
• AlignX a multiple sequence alignment tool
• ContigExpress a DNA sequence assembly and
  sequencing
• project management tool
• GenomBench a tool for genomic DNA sequence
  analysis
• and annotation
• BioAnnotator a tool for functional annotation of
  DNAs
• and proteins

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Sequence Analysis

• Using vector NTI molecular biologists can
•  
• Perform routine sequence analysis tasks such as
  restriction
• mapping, identifying protein coding regions or
  finding
• sequence motifs and carrying out sequence
  similarity searches
• Generate recombinant cloning strategies and
  protocols
• Design and analyze PCR primers
• Catalog a growing number of plasmids and PCR
  primers,
• in order to track the origin and lineage of
  recombinant molecules
• Run in silico gel electrophoresis
• Perform and edit multiple sequence alignments on
  proteins
• and nucleic acids
• Create publication quality graphics and more

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Laboratory Resources
Hypothesis generation
Knowledge Mining
Sequence Analysis
Laboratory Bench work
Protocols
Useful Laboratory Resources
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Laboratory Resources
http//www.interscience.wiley.com/c_p/index.htm
Basic Protocol Alternate Protocol Commentary Crit
ical Parameters Troubleshooting Time
Considerations Key References Internet Resources
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Laboratory Resources
http//researchlink.labvelocity.com/
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HSLS Mol Biol Information Service
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HSLS Mol Biol Information Service
http//www.hsls.pitt.edu/guides/genetics
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Website Usage Report
http//www.hsls.pitt.edu/guides/genetics
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Workshops
May 2003-April 2004
Workshop 1 Information Hubs 2 Sequence
Similarity Searching 3 DNA Protein
Analysis Tools 4 CellSpace
Knowledge Miner 5 VectorNTI
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One-on-one Consultation
Total 70
2003
2004
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..only half of biomedical researchers using
genome databases are familiar with the tools that
can be used to actually access the data. ..
all scientists on the planet must be empowered to
use these powerful databases to unravel
longstanding scientific mysteries. atabases to
unravel longstanding scientifi c
Andreas D. Baxevanis Francis S. Collins
Nature Genetics, September 2002,
Vol 32