Introduction of bioinformatics and Biological Database

高雄醫學大學生物醫學暨環境生物學系

助理教授 張學偉2006/08/08

Outline

Fields of Bioinformatics Genome Projects Today Database issue in “Nucleic Acids

Research” Server issue in “Nucleic Acids Research”

Post-Genomic Era: Lots of Data!

“The study of genetic and other biological information using computer and statistical techniques.”

A Genome Glossary, Science, Feb 16, 2001

Bioinformatics

Bioinformatics is the discipline of biology that has evolved to gather, store and manage in specialized databanks the vast amounts of biological data, which it then mines for knowledge

生物資訊的領域

資料庫的建立與整合

序列分析結構 /功能分析

實驗資料分析 知識管理

ref. 中央研究院計算中心通訊 Vol.19 No.20

生物資訊學

Biotech and Computer Science

1953 1958 1974 1981 1990 1992 2003

Watson and CrickDNA double helix discovery

Computerrevolution begin

Stan Cohen and Herb Boverrecombinant DNA molecule

First portablecomputer begin

Human genomeproject begin

World web site

Human genomefully mapped

Breaking pointof Biotechnology

The breaking point of Biotechnology is Human Genome Project

GenBankGCG Package

Bioinformatics- hot issues

Genome Analysis Pipeline Analysis Genome Annotation SNP

Data warehouse/ Databases integration New Algorithm Literature Mining System Biology/ Microarray Analysis

The growth of Genbank (updates)

Prediction: data size doubles every 14 months

44,575,745,176 bases, from 40,604,319 reported sequences (up to Dec.,15, 2004)

Biological databases

Like any other database Data organization for optimal analysis

Data is of different types Raw data (DNA, RNA, protein sequences) Curated data (DNA, RNA and protein

annotated sequences and structures, expression data)

The growth of public domain bio-databases

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(The Molecular Biology Database Collection from Nucleic Acids Research)

“The Gene Ontology (GO) project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism.”

A few key points:GO is a “structured” vocabulary, which is really a specialized type of a “controlled” vocabulary.

Gene Ontology database

The ontologies in GO are intended to describe three biological areas, “molecular function”, “biological processes” and “cellular components”.

GO was originally developed through the collaboration of the members of three model organism projects: SGD, the Saccharomyces Genome database; FlyBase, the Drosophila genome database; and MGD/GXD, the Mouse Genome Informatics databases.

What GO is Not

1. GO is not a way to unify biological databases. Sharingnomenclature is a step toward unification, but is not, in itself,sufficient.

2. GO is not a dictated standard, mandating nomenclatureacross databases. Groups participate because of self-interestand cooperate to arrive at a consensus.

3. GO does not define homologies between gene products fromdifferent organisms. The use of the GO results in sharedannotations for gene products from different organisms, andthis may reflect an evolutionary relationship, but the sharedannotation is in itself not sufficient for such a determination.

Swimming in Data Sources

Database Integration

http://nar.oxfordjournals.org/content/vol34/suppl_1/index.dtl