Biological databases
Aims
The purpose of this course is to provide the concepts used in organizing biological informational data into databases, the structure of the databases and retrieval of data. Multipurpose informational (general) databases, as well as specialized databases focusing onto particular aspects of bioinformatics or onto particular (e.g. individualized) targets of analysis, will be described and discussed. Attention is also giving to incorporation of new data types, integration of data and tools, and relational database management.
Contents 1. Introduction
- Defining the data labyrinth ; surviving the data flood
- Routes to acquisition and collection of nucleotide sequence data - Routes to acquisition and collection of amino-acid sequence data - Routes to global analysis of gene expressions
- Routes to target discovery/validation in toxicogenomics and pharmacogenomics - Early “packages” of data collection and analysis tools (Staden package, PC/gene, etc.) 2. Development of biological databases
- Datatypes
- File formats (GenBank, EMBL, FASTA, PDB, ASN-1, ...) - Annotation
- Curation - Indexing
- The Biostandards Project 3. Biological databases
a. Factual databases (data repositories)
- The International Nucleotide Sequence Database Effort (DDJB-EMBL-GenBank) - Protein sequence databases (SWISS-PROT, PIR)
- Structure databases (PDB)
- Specialized data repositories (EST, SNP, genome, protein interaction, 2D-PAGE, MS-fragment-ion, and microarray databases)
b. Knowledge bases
- Protein families and motifs databases (PROSITE, BLOCKS, PFAM, ...) - Classification databases for sequences (COG) and structures (CATH, SCOP) - Pathway databases (KEGG, EcoCyc ...)
- Genome and genome diversity databases (...OMIM...) c. Computational databases
- Automated genome annotation (Pedant) - Calculated structures databases (3D Crunch) 4. Data retrieval / User interface
- Browsing
- Text-based query (Entrez, SRS, ...)
- Sequence-based query (BLAST, FASTA, ...) - Data mining
