1. Biological Databases By : Lim Yun Ping E mail : yunping@chitre.net
National University of Singapore

2. Overview Introduction What is a database
What type of databases can we access
What roles do they play
What type of information can we get from them
How do we access these information

3. What is a database ? Convenient method of vast amount of information
Allows for proper storing, searching & retrieving of data.
Before analyzing them we need to assemble them into central, shareable resources

4. Why databases ?
Means to handle and share large volumes of biological data
Support large-scale analysis efforts
Make data access easy and updated
Link knowledge obtained from various fields of biology and medicine

5. Different Database Types
depends on the nature of information stored
(sequences, 2D gel or 3D structure images)
manner of storage (flat files, tables in a relational database, etc)
In this course we are concerned more about the different types of databases rather than the particular storage

6. Features Most of the databases have a web-interface to search for data
Common mode to search is by Keywords
User can choose to view the data or save to your computer
Cross-references help to navigate from one database to another easily

7. Biological Databases

8. Types Of Biological Databases Accessible
There are many different types of database but for routine sequence analysis, the following are initially the most important
Primary databases
Secondary databases
Composite databases

9. Nucleic Acid Databases
Primary databases
Contain sequence data such as nucleic acid or protein
Example of primary databases include :
Nucleic Acid Databases
EMBL
Genbank
DDBJ
Protein Databases
SWISS-PROT
TREMBL
PIR

10. Secondary databases Or sometimes known as pattern databases
Contain results from the analysis of the sequences in the primary databases
Example of secondary databases include :
PROSITE
Pfam
BLOCKS
PRINTS

11. Composite databases Combine different sources of primary databases.
Make querying and searching efficient and without the need to go to each of the primary databases.
Example of composite databases include :
NRDB – Non-Redundant DataBase
OWL

12. Nucleic acid Databases
NCBI :
NCBI, at the NIH campus, USA
EMBL : European Molecular Biology Laboratory, UK
DDBJ
DDBJ : DNA Databank of Japan
Nucleic acid Databases

13. The International Sequence Database Collaboration
GenBank
EMBL
DDBJ

14. The International Sequence Database Collaboration
These three databases have collaborated since Each database collects and processes new sequence data and relevant biological information from scientists in their region e.g. EMBL collects from Europe, GenBank from the USA.
These databases automatically update each other with the new sequences collected from each region, every 24 hours. The result is that they contain exactly the same information, except for any sequences that have been added in the last 24 hours.
This is an important consideration in your choice of database. If you need accurate and up to date information, you must search an up to date database.

15. Amount Of Data Grows Rapidly
As of June 2003, there were bases
in sequence

16. How to access them NCBI : http://www.ncbi.nlm.nih.gov/
Main Sites
NCBI :
EMBL :
DDBJ :
full release every two months
incremental and cumulative updates daily
available only through internet ftp://ftp.ncbi.nih.gov/genbank/
66.3 Gigabytes of data

17. The Internet and WWW

18. NCBI : http://www.ncbi.nlm.nih.gov/
NCBI, a division of NLM at the NIH campus, USA
EXPASY : Swiss Institute of Bioinformatics
Kyoto Encyclopedia of Genes and Genomes

19. National Centre for Biotechnology Information
Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information all for the better understanding of molecular processes affecting human health and disease.

21. Entrez
Entrez is a search and retrieval system that integrates information from databases at NCBI.

23. BNIP

25. Accession Number : Unique identifier Source : Organism’s common name
Brief description of the sequence.
Accession Number : Unique identifier
Source : Organism’s common name
Formal scientific name
Contains information on the publications such as the authors, and topic titles of the journals that discuss the data reported in the record.
Contains the contact information of the submitter
Contains the information about the genes, gene products and regions of biological significance reported in the sequence &
length of sequence
scientific name of the source organism
Taxon ID number, Map location

26. Coding sequence (region of the nucleotides that correspond to the sequence of amino acid). This is also the location that contains the start and stop codon.
Region of biological interest
The amino acid translation corresponding to the nucleotide coding sequence

27. How to understand the output
Unique Identifiers :
Each entry in a database must have a unique identifier
EMBL Identifier (ID)
GENBANK Accession Number (AC)
Other information is stored along with the sequence.
Each piece of information is written on it's own line, with a code defining the line. For example,
DE, description;
OS, organism species;
AC, accession number. Relevant biological information is usually described in the feature table (FT).

28. Genbank Flat File Format
Refer to Summary Description of the Genbank Flat File Format Or

29. ExPASy
Expert Protein Analysis System proteomics server of the Swiss Institute of Bioinformatics (SIB)
dedicated to the analysis of protein sequences and structures

30. Databases on the Expasy server
SWISS-PROT and TrEMBL - Protein knowledgebase
PROSITE - Protein families and domains
SWISS-2DPAGE - Two-dimensional polyacrylamide gel electrophoresis
ENZYME - Enzyme nomenclature
SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules
SWISS-MODEL Repository - Automatically generated protein models

31. SWISS-PROT
A curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases

32. TrEMBL
Computer-annotated supplement to SWISS-PROT

33. Enzyme nomenclature database http://tw.expasy.org/enzyme/

34. ENZYME Database
A repository of information relative to the nomenclature of enzymes
Describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided

35. Access to ENZYME by EC number by enzyme class
by description (official name) or alternative name(s)
by chemical compound
by cofactor

38. Kyoto Encyclopedia of Genes and Genomes
K E G G
Kyoto Encyclopedia of Genes and Genomes

39. A structured database containing information about metabolic pathways in many organisms.

40. KEGG Part of the GenomeNet database system
Linked to all accessible databases by search engines; LIGAND & BRITE

43. Link to other pathways
Enzyme
Compound

45. Summary
Biological databases represent an invaluable resource in support of biological research.
We can learn much about a particular molecule by searching databases and using available analysis tools.
A large number of databases are available for that task. Some databases are very general while some are very specialised. For best results we often need to access multiple databases.

46. Common database search methods include keyword matching, sequence similarity, motif searching, and class searching
The problems with using biological databases include incomplete information, data spread over multiple databases, redundant information, various errors, sometimes incorrect links, and constant change.

47. Database standards, nomenclature, and naming conventions are not clearly defined for many aspects of biological information. This makes information extraction more difficult
Retrieval systems help extract rich information from multiple databases. Examples include Entrez and SRS.
Formulating queries is a serious issue in biological databases. Often the quality of results depends on the quality of the queries.
Access to biological databases is so important that today virtually every molecular biological project starts and ends with querying biological databases.

48. The End