Archives and Information Retrieval Reading Introduction to Bioinformatics

Archives and Information Retrieval Reading: Introduction to Bioinformatics. Arthur M. Lesk. Fourth Edition Chapter 4

Introduction • Learning objectives: • What is the general arrangement of biological data in the public databases? • To know the information retrieval skills that will allow you to make effective use of the databases. • To become familiar with basic operations. • How does one retrieve information on a particular subject in the literature?

Primary public domain bioinformatics servers Public Domain Bioinformatics Facilities National Center For Biotechnology Information (NCBI) United States Databases Analysis Tools European Bioinformatics Institute (EBI) United Kingdom Databases Analysis Tools Genome Net (KEGG & DDBJ) Japan Databases Analysis Tools

The Archives • Massive biological experimental data • These biological information databases can be classified into two types • The first level databases • Come from the raw data which were obtained via the experiments. “simple” • The second level databases • Further reorganized based on. . in order to achieve some specific goals

The Archives • Some examples: • The first level databases • Nucleic acid sequence databases: Gen. Bank, EMBL Data Library, DNA Database of Japan (DDBJ) • Protein sequence database: SWISS-PROT, PIR • Protein structure database: PDB • The second level databases • GDB • TRANSFAC • SCOP

Nucleic acid sequence databases • International DNA Sequence Database Collaboration • NCBI (Gen. Bank) – USA (1982) • EMBL (Data Library)– Europe (1982) • DDBJ (DNA Data Bank)– Japan (1988)

NCBI • Established in USA in 1988 as a national resource for molecular biology information • creates public databases • conducts research in computational biology • develops software tools for analyzing genome data • disseminates biomedical information

Nucleic acid sequence databases • Gen. Bank • • • nucleic acid sequence and the protein sequence literature work biological annotation A new release is made every two months Gen. Bank information retrieval system

NCBI ENTREZ • A platform that provides access to and links to databases with biological information ENTREZ Pub. Med. Line Gen. Bank Protein Genomes databases Pop. Set Taxonomy OMIM

NCBI ENTREZ Med. Line OMIM Literature Database of human genes and genetic disorders Gen. Bank Database of all publicly available DNA sequences Protein databases Database of amino acid sequences from Swiss. Prot, PIR, PRF, PDB, and translations from annotated coding regions in Gen. Bank and Ref. Seq. Genomes Database of genomes from organisms and viruses Pop. Set Taxonomy Database of DNA sequences that have been collected to analyze the evolutionary relatedness of a population. Database of names of organisms with sequences in Gen. Bank or Prot

Pub. Med Center • the U. S. National Library of Medicine's digital archive of life sciences journal literature • Access to the full text of articles in PMC is free, except where a journal requires a subscription for access to recent articles

OMIM-Online Mendelian Inheritance in Man • A catalog of human genes linked to diseases • Began by Victor A. Mc. Kusick at Johns Hopkins University • A good place to start when you want to research a certain disease or biological molecule • This database is cross-referenced to Pub. Med and other NCBIbased databases

Complete ENTREZ database divisions

How to submit sequence data to Gen. Bank • Bankit based web interface • http: //www. ncbi. nlm. nih. gov/Bank. It • Sequin program • http: //www. ncbi. nlm. nih. gov/Sequin

Protein databases • The Protein Information Resource (PIR) was established in 1984 by the National Biomedical Research Foundation (NBRF). • The PIR Protein Sequence Database evolved from the original NBRF Protein Sequence Database, developed over 20 years • PIR-International is a collaboration between NBRF, the Munich Information Center for Protein Sequences (MIPS), and the Japan International Protein Information Database (JIPID) • collect and publish what is now the oldest and largest database of biomolecular sequence, source, literature, and feature information.

PIR • PIR-International Protein Sequence Database: an annotated, nonredundant and cross-referenced database of protein sequences. • PIR Alignment Database, PIR-ALN: contains sequence alignments of superfamilies, families and homology domains produced from information in the Protein Sequence Database. • FAMBASE Family Database: a searchable database containing a single representative sequence from each protein family. • RESID Database of Amino Acid Modifications: based on feature information in the Protein Sequence Database.

PIR • http: //www-nbrf. georgetown. edu/pir/

SWISS-PROT • http: //www. ebi. ac. uk/swissprot/ • an well-annotated protein sequence database established in 1986. • It is maintained collaboratively by the Swiss Institute for Bioinformatics (SIB) and the European Bioinformatics Institute (EBI). • a curated protein sequence database that provides a high level of annotation, a minimal level of redundancy and a high level of integration with other databases. Note: Uni. Prot. KB/Tr. EMBL and Uni. Prot. KB/Swiss-Prot have been incorporated into the Uni. Prot (Universal Protein Resource). a one-stop shop allowing easy access to all publicly available information about protein sequences.

PROSITE • http: //ca. expasy. org/prosite/ • a method of determining what is the function of uncharacterized proteins translated from genomic or c. DNA sequences. • a database of biologically significant sites • patterns formulated in such a way that with appropriate computational tools it can rapidly and reliably identify to which known family of protein (if any) the new sequence belongs.

PDB • http: //www. rcsb. org/pdb/ • The single international repository for public data on the 3 dimensional structures of biological macromolecules • Is established by the Brookhaven National Lab of United States • The contents are primarily experimental data derived from X-ray crystallography and NMR experiments • Rasmol may demonstrate 3 D structure of the biological macromolecule according to the PDB document