Bioinformatics Databases Overview

1
Bioinformatics Databases Overview

• Microarray Database Systems

2
Biological Database

• NCBI a large, organized body of persistent
  data, usually associated with computerized
  software designed to update, query, and retrieve
  components of the data stored within the system.
• http//www.ncbi.nlm.nih.gov/About/primer/bioinform
  atics.html

3
Background

• Complete genome sequence (structural)
• Human Genome Project
• Functional genomics
• bioinformatics data mining, data integration
• Application
• new discoveries
• gene function, disease gene
• drugs
• new diagnosis methods
• new treatments

4
Background (2)

• Major Databases
• NCBI GenBank (US)
• EBI EMBL (UK)
• CIB DDBJ (Japan)
• Purposes
• public research data submission and sharing
• data retrieval and analysis resources

5
Types of Databases

• Nucleotide
• GenBank, EMBL NSD
• Protein
• SWISS-PROT
• Molecular Structure
• Protein NCBI, EBI MSD
• Gene Expression
• EBI ArrayExpress, NCBI GEO
• Regulation Network
• KEGG
• Species-specific
• mouse, fly, etc.

6
Human Genome Project

• identify all the approximately 30,000 genes in
  human DNA
• determine the sequences of the 3 billion chemical
  base pairs that make up human DNA
• store this information in databases
• improve tools for data analysis
• transfer related technologies to the private
  sector
• address the ethical, legal, and social issues
  (ELSI) that may arise from the project

7
Human Genome Project (2)

• History
• BERAC Recommendation, 1987
• 1990, US DOE and NIH
• working draft 2001, with Celera Genomics
• original timeline 2005
• new timeline 2003, complete sequence
• Phases
• draft, 90, 1 error
• complete, gt 99, 0.01 error

8
Celera Genomics

• Craig Venter
• Shotgun method
• Celera/Science agreement
• not to reproduce, redistribute, re-package, adapt
  or prepare derivative works of Celera data for
  third party, in any form whatsoever, for any
  purpose
• prevent large scale downloads and incorporation
  of this data into GenBank/EMBL/DDBJ

9
NCBI

• National Center for Biotechnology Information
• 1988, US Congress
• DOE, NIH
• System for data storage and analysis
• Advancing methods for data retrieval and analysis
• Facilitation of use

10
NCBI (2)

• Database
• GenBank
• Database Retrieval
• Entrez, PubMed, Locus Link, Texonomy Browser
• Data Analysis
• BLAST, Electronic PCR, ORF Finder, UniGene, Human
  MapViewer

11
GenBank
12
GenBank (2)

• History
• NIGMS/NIH, since 1982
• Los Alamos National Lab
• Annotation and organization
• BBN Lab Inc.
• Maintenance, distribution
• IntelliGenetics, 1987
• Operation
• NCBI, 1988
• Main Purpose
• data submission, data repository

13
GenBank (2)

• Flat file format
• Data Divisions
• 17 divisions
• Organismal Divisions
• 1. PRI - primate sequences  2. ROD - rodent
  sequences  3. MAM - other mammalian seq  4. VRT
  - other vertebrate seq  5. INV - invertebrate
  sequences  6. PLN - plant, fungal, and algal 
  7. BCT - bacterial sequences  8. VRL - viral
  sequences  9. PHG - bacteriophage seq10. SYN -
  synthetic sequences11. UNA - unannotated
  sequences

• Functional Divisions
• 12.EST - EST sequences (expressed sequence tags)
• 13. PAT - patent sequences
• 14. STS - STS sequences (sequence tagged sites)
• 15. GSS - GSS sequences (genome survey sequences)
• 16. HTG - HTGS sequences (high throughput genomic
  sequences)
• 17. HTC - unfinished high-throughput cDNA
  sequencing

14
EST (Expressed Sequence Tag)

• Partial cDNA sequences of genes expressed in
  different tissues
• 5 and 3 partial sequencing

15
EMBL
16
EMBL (2)

• EBI (European Bioinformatics Institute)
• building, maintaining and providing biological
  databases and information services to support
  data deposition and exploitation.
• Format

17
ArrayExpress
18
ArrayExpress (2)

• a public repository of microarray based gene
  expression data
• MIAME recommendations
• Minimum Information About a Microarray Experiment
• Data submission in MAGE-ML
• XML format

19
PDB
20
PDB (2)

• Protein Data Bank
• http//www.rcsb.org/pdb/
• processing and distribution of 3-D biological
  macromolecular structure data