Archives and Information Retrieval

1. Archives and Information Retrieval CSC 487/687 Computing for Bioinformatics

2. 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?

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

4. 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

5. The Archives • Some examples: • The first level databases • Nucleic acid sequence databases: GenBank, 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

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

7. 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

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

9. ENTREZ PubMed PopSet Genomes Protein databases OMIM Taxonomy GenBank MedLine NCBI ENTREZ • A platform that provides access to and links to databases with biological information

10. MedLine Literature Database OMIM Database of human genes and genetic disorders GenBank Database of all publicly available DNA sequences Database of amino acid sequences from SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq. Protein databases Database of genomes from organisms and viruses Genomes Database of DNA sequences that have been collected to analyze the evolutionary relatedness of a population. PopSet Taxonomy Database of names of organisms with sequences in GenBank or Prot NCBI ENTREZ

11. PubMed 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

12. OMIM-Online Mendelian Inheritance in Man • A catalog of human genes linked to diseases • Began by Victor A. McKusick 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 PubMed and other NCBI-based databases

13. How to submit sequence data to GenBank • Bankit based web interface • http://www.ncbi.nlm.nih.gov/BankIt • Sequin program • http://www.ncbi.nlm.nih.gov/Sequin

14. On-class exercise

15. 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.

16. PIR • PIR-International Protein Sequence Database: an annotated, non-redundant 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.

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

18. 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: UniProtKB/TrEMBL and UniProtKB/Swiss-Prot have been incorporated into the UniProt (Universal Protein Resource). a one-stop shop allowing easy access to all publicly available information about protein sequences.

19. PROSITE • http://ca.expasy.org/prosite/ • a method of determining what is the function of uncharacterized proteins translated from genomic or cDNA 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.

20. 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 3D structure of the biological macromolecule according to the PDB document