1. The Integrated Microbial Genome (IMG) systems
Nikos Kyrpides 1

2. Data analysis
Data Integration
Comparative Analysis

3. Data management system for comparative analysis of biological data
What is the Matrix?
Data management system for comparative analysis of biological data
IMG
Genes
Genomes
Functions
Metadata
Clusters
SNPs
Proteomics
Regulons
Transcriptomes I M G

4. Integrated Microbial Genomes (IMG) [It’s easier to analyze 1000 genomes than a single one]
What is IMG:
IMG is a data management system for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context.
Mission:
To become the Home of Microbial Genome and Metagenome Analysis
Background:
 Launched on March 2005
 3 Releases/Year
 >5,000 unique visitors per month
 >300 citations
Current Status:
10,671 Genomes
24 Million Genes
Bacteria: 5709
Archaea:
Eukarya: 183
Plasmids: 1190
Viruses:
USERS CAN
Search data
Browse data
Compare data
Export data
Gfragments:579

5. http://img.jgi.doe.gov/ USERS CAN Search data Browse data Compare data
Export data
USERS CAN
Submit data
Annotate data

6. Data Model Abstraction Example: IMG Operations
Genes present in G1
and absent from G2, G3, G4 and G5
G1 G2 G3 G4 G5 g3 g2 g1
Gene occurrence profile across genomes
Genes
Gene occurrence profiles across pathways
Genomes
Pathways shared by genomes
Perhaps you can mention that the dimensional modeling approach has a positive impact in data exploration. 1 and 2 are examples of slice and dice and the result is data reduction and focus on relevant to the question data set.
Functions/ Pathways

7. IMG Data Integration Genes Genomes Functions 24.2M 10671
COG GO
Pfam
TIGRfam
InterPro
KEGG
BioCyc
SEED
Protein product
MyIMG
IMG Terms
IMG Pathways
IMG Networks
Groupings
Phylogenetic
Phenotypic
Ecotypic
Disease
Geographical
Isolation
RNAs, Proteins
Sequence Clusters
Positional clusters
Regulatory clusters
Fusions
Operons
Expression
Genes
24.2M
Genomes
Functions
10671

8. IMG Toolkit Chromosome Map Function Profile Gene Synteny Abundance
Profiles
Functional
Categories
Projects
IMG Pathway
Metadata
Search
Phylogenetic
Genome
Clustering
Compare
Annotations
KEGG
Maps
Distribution
Chromosomal
Artemis
VISTA
Recruitment
Plot
Fragment

9. Challenges and Opportunities
Annotations
Annotations
Quality
Metadata
Genes
Functions
Data
Analysis
New data types and tools
Integration
# genes and genomes
Scaling

10. Metadata Curation Metadata Types Organism Information
K. Liolios
Metadata Types
Organism Information
Genome Project Information
Sequencing Information
Environmental Metadata
Host Metadata
Organism Metadata

11. Metagenome Classification
Genomes vs Metagenomes

12. Challenges and Opportunities
Annotations
Annotations
Quality
Metadata
Genes
Functions
Data
Analysis
New data types and tools
Integration
# genes and genomes
Scaling

13. Finding unique genes Obligate parasite of horses
Causes human disease in tropical areas (melioidosis)

14. Phylogenetic profiler finds 548 unique genes in B. mallei
However, 497 of them in fact exist in B. pseudomallei, but they have not been called as real genes.
The difference in gene models reveals 89.2% error rate in unique genes

15. Program Informatics Production Challenges
Annotations
Quality
Data Management
IMG
Single cells
OMICS data
Scale
# genes and genomes
Scaling

16. MGM Workshop Attendees http://www.jgi.doe.gov/meetings/mgm/index.html
Europe:
Belgium
Czech Rep
Denmark
Estonia
Finland
France
Germany
Greece
Ireland
Italy
Hungary
Netherlands 4
Norway
Russia
Portugal
Poland
Spain
Sweden
Switzerland 1
UK 10
Asia:
China
Hong Kong
India
Israel
Japan
Korea
Malaysia
Philipines
Saudi Arabia 4
Singapore
Taiwan
Thailand
Turkey
North America: 356
Canada
Mexico
USA
South America: 21
Argentina
Brazil
Chile
Colombia
Ecuador
Peru
Uruguay
Africa:
Algeria
Egypt
Ethiopia
Oceania:
Australia
New Zeeland 2
545 /48 Countries
April 20, 2012