1. Biological databases: Collection, storage and maintenance
Biological Database as a collection of data that is structured, searchable, updated periodically, and cross-referenced

2. Biological databases: Collection, storage and maintenance
Heterogeneous content
~ Complex data type (Text base sequence, Blobs, images of cells and tissue , 3-D molecular structure, biochemical pathway, model data , scalar and vector fields
Hierarchical data organization
Dynamic nature
Accessibility
Quality

3. The first database was of proteins
Atlas of Protein Sequence and Structure (1965)
edited by Margaret Dayhoff .
It contains protein sequence that published at that time (Foundation of PIR)
Yeast t-RNA with 77 bases was first nucleotide sequence data base
Protein structural data base with 10 entries was first constructed in 1972.
First genome data base was published on 1995 with that Haemophilus influenzae

5. ~100 GB

6. 162886727 loci, 150,141,354,858 bases, from 162,886,727 sequences as of
15th Feb 2013

7. Categories of Databases
Data Type (Data heterogeneity)
Maintainer Status
Technical Design
Data Source
Data Access
And/or other parameter

8. 1. Categories of Databases: Data Type
Taxonomy Database
Genome Database
Sequence database
Structure Database
Proteomic Database
Micro-array Database
Enzyme Database
Disease Database
Pathway Database
Literature Database… Many More

9. Nucleotide Databases Nucleotide Databases dbEST PopSet dbGSS Probe
dbSNP RefSeq
dbSTS TPA
Nucleotide Trace Archive
GenBank UniGene
HomoloGene UniSTS
MGC

10. Protein Databases
3D Domains PROW Proteins
RefSeq Protein Clusters
Structure Databases
Conserved Domains Structure (MMDB)
3D Domains
Taxonomy Databases
Taxonomy
Genome Databases
Cancer Chromosomes Genome Project
COGs Genomes Gene

11. Expression Databases
GEO Profiles SAGE
GEO Datasets
Chemical Databases
PubChem BioAssay
PubChem Compound
PubChem Substance

12. 2. Categories of Databases: Maintainer Status
NCBI (Federal Govt. agency of USA) (
EBI/EMBL(Non-profit academic organization) (
SIB (Quasi-academic non-profit foundation) (

14. 3. Categories of Databases: Technical Design
Flat file (Information store in text files)
XML (Extensible markup language)
(Hierarchical semi-structured model)
Relational model (Highly structured model)
(It has tables with rows (tuples or record) and columns (field) supports by RDBMS like SQL, Oracle, DB2)
Object-oriented database management system
ASN.1 (abstract syntax notation)

17. This information is organised into a tabular form, as it usually done in relational DB. The number of columns (fields) in such DB is much larger than in the table below.
An index of these fields can be made, which allows very fast search of a DB using one or few field simultaneously.
The information in one DB can be cross-referenced to that in another DB. For instance DNA, protein and reference DB have all been cross-references so that moving between them is readily accomplished.
Accession Organism Reference Name Keywords Sequence No
E. coli Medline1, LexA SOS regulon, ATGCCGG…
protein repressor,…
H. sapiens Medline2, glucorticoid transcriptional CCGATAAC
receptor regulator

18. Example of object-oriented DB

19. Comparison Structure Advantages Disadvantages Flat File
Fast data retrieval, Simple structure, easy programming
Difficult to process multiple value, adding new data require reprogramming, slow without the key
Hierarchical
Addition and deletion easy, fast retrieval through higher level records, multiple association with like records
Pointer require large computer storage, pointer path restricts access, each association requires repetitive data
Relational
Easy access, minimal training for users, flexible for unforeseen enquiry, easy modification, physical storage of data can be changed without affecting the relationship
Sequential access is slow, prone to logical mistakes, method of storage impact processing time, new relation require considerable processing
Comparison

20. Database
Data
Data format
Data type
GenBank
OMIM
DNA/RNA seq, phynotype, genotype
Text file/ASN.1
Text, Numeric
Text file
GDB
AceDB
Genetic map
Relational/MySQL
Object oriented
Medline
NCBI
Literature
Seq, str, literature
ASN.1
Text
PDB
BLAST
ClustalW
KEGG
Microarray
Structure
Seq, Analysis
Metabolic path
Microarray data
Oracle
Fasta
HTML text, binary
RDBMS, Excel
3D Image
Images, text

21. 4. Categories of Databases: Data Source
Type -1
Primary (From experimental sources)
Nucleic acid sequence, protein sequence, protein structure
Secondary (From already existing primary database)
Genomic (TiGR human gene index), Proteomic (Prosite, CATH)
Type -2
Nucleic acids
Literature (pubmed)
Biomacromolecules
Pathways

22. DNA Sequence Database
National Center for Biotechnology Information (NCBI)
DNA Databank of Japan (DDBJ)
European Molecular Biology Laboratory (EMBL)

23. Protein sequence Database

24. European Bioinformatics Institute Swiss Institute of Bioinformatics
Georgetown University

25. Exchange data on a hourly basis
International Nucleotide Sequence Database Collaboration (INSD).
Exchange data on a hourly basis
Mirroring
Data backup

26. Protein structure Database http://www.rcsb.org/pdb/index.html

27. PDB

28. PDB

29. Secondary database

33. 5. Categories of Databases: Data Access
Publicly available
Available with copyright
Browsing but not downloadable
Academic but not free
Commercial access with payment

34. 6. Categories of Databases: Others
Completeness
Curation (annotation)
…..

35. ENTREZ
DB of different kind merged together and become global hubs of knowledge.

36. 1. Nucleotide Sequence Databases
2. RNA sequence databases
3. Protein sequence databases
4. Structure Databases
5. Genomics Databases (non-human)
6. Metabolic Enzymes and Pathways; Signaling Pathways
7. Human and other Vertebrate Genomes
8. Human Genes and Diseases
9. Microarray Data and other Gene Expression Databases
10. Proteomics Resources
11. Other Molecular Biology Databases

37. For a detailed list and full coverage see

40. NCBI resources
Databases
Online analysis tools

52. Sequence Retrieval System (http://srs.ebi.ac.uk)