What is a Biological Database

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A collection of experimental and theoretical data, organized in a way that its contents can be easily accessed, managed, updated, retrieved
The activity of preparing a database can be divided in to:
Collection of data
Making it available to a multi-user system


Why to learn biological databases?

To know where to submit your data, e.g., sequence
To know where to discover the biological meaning of your experimental data, e.g., microarray data
To learn how to use bioinformatics tools to access database efficiently

Biological database structure (I)

Flat-file database
A flat file is a file containing records that have no structured interrelationship.
E.g., MS Word documents saved as “text only”, comma-separated values (CSV) file
Ups and downs
It takes up less space than a structured file.
Easy to set up and learn
However, it requires the application to have knowledge of how the data is organized within the file, i.e., mark-up and tags

Biological database structure (II)

Relational database
Is a collection of data items organized as a set of formally-described tables
E.g., your school record
Need DBMS, need to learn e.g., SQL
Object oriented database
Object and class, inheritance; need to learn object-oriented language, e.g., C++

Databases of biological databases

List key databases of value to the biological community
The Molecular Biology Database Collection: 2004 update -- Galperin 32 (Supplement 1): D3 -- Nucleic Acids Research


Sequence databases

Nucleic acid sequence databases
Contain primary nucleotide sequence data
Repositories, i.e. the content of these databases are not curated
Protein sequence databases
Contain secondary and primary protein sequence data
Some are curated, others are just extracts from other databases

Nucleotide sequence repositories

Three primary centres exchange information on a daily basis
GenBank
EMBL
DDBJ
All three use the same Feature Table Definition

GenBank

US primary nucleotide sequence resource
Established in 1988
Maintained by National Center for Biotechnology Information, Bethesda, MD
Contains a release section and a new section as EMBL
NCBI HomePage
Entries has a format that is different from EMBL

EMBL

Europe’s primary nucleotide sequence resource
Established 1980 in Heidelberg by EMBL, now maintained by EBI
Main sources are direct submissions from individual researchers, genome project and patent applications
The EMBL Nucleotide Sequence Database: Access
Entries has a format that differs from GenBank and DDBJ

DNA Data Bank of Japan

Mainly collects data from Japanese activities (but accepts submissions from any researcher in any country)
Began DNA repository activities in 1986 endorsed by the Ministry of Education, Science, Sports, and Culture
DDBJNA Data Bank of Japan
Entries has the same format as GenBank

Protein databases

SWISS-PROT and TREMBL
Developed by Swiss Institute of Bioinformatics (SIB) and European Bioinformatics Institute (EBI)
PIR
A collaboration between National Biomedical Research Foundation (NBRF), Munich Center for Protein Studies (MIPS) and Japan International Protein Information Database (JIPID)
IntoPro
Developed by EBI, University of Manchester, Sanger Institute, …


Swiss-Prot / TREMBL

Swiss-Prot
UniProtKB/Swiss-Prot
Curated database
Aims to provide a high level of annotations (e.g., function, domain structure, post-translational modifications)
Divided into Swissprot_rel and Swissprot_new
Not divided into sections based on species
Note the data format


TREMBL
Contains translated sequences from the EMBL database
Divided into
SP-TREMBL with sequences that are candidates for incorporation into SWISS-PROT
REM-TREMBL that will not be incorporated into SWISS-PROT

PIR(PROTIEN INFORMATION RESOURSE)

Welcome to PIR [Protein Information Resource]
The aims are similar to SWISS-PROT
Grows at a higher rate than the SWISS-PROT, but has a lower level of annotation per entry
The PIR consists of four sections:
PIR1. Fully Classified Entries
PIR2. Verified and Classified Entries
PIR3. Unverified Entries
PIR4. Un-encoded or Un-translated Entries

InterPro

InterPro: Home
An integrated database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.

Protein structures

Primary structure: the order of amino acids

Secondary structure: conformations, mainly alpha helices and beta sheets

Tertiary structure: the complete three dimensional folding of the polypeptide

Quaternary structure: exists if the protein is composed of two or more polypeptide chains



Structural databases

Contain information on the three-dimensional structure of molecules, chiefly proteins
Data is primarily based on x-ray crystallography (>80%), NMR, or theoretical models (<2%)
Examples of such databases
Protein databank (PDB) - RCSB Protein Data Bank
Molecular Modeling Database (MMDB) - Structure Home

Genome databases

Differ from sequence databases by being more heterogeneous and diverse
A genome database organizes all information on an organisms genome
Genetic mapping: locate genes relative to each other and with a distance measured as percentage recombination
Physical mapping: ranges from cytogenetic maps (banding patterns of chromosomes) to the positions of clone contigs
Sequence data

NCBI’s genome section
Genome Home
Ensembl
A system to produce and maintain automatic annotations of selected genomes
http://www.ensembl.org
TIGR Microbial Genomes
Comprehensive Microbial Resource
J. Craig Venter Institute

Metabolic databases

Describe enzymes, reactions, substrates, products, and biochemical reactions
Data are specific for different organisms (“type organisms”) as well as general overviews and links to sequence and structure databases

Pathways - KEGG

Pathways, sequences, genomic maps
Search for objects in pathways
Generate possible reaction pathways
Compare two genome maps
Infer presence of pathway in organism 2 by comparison with organism 1


Molecular interaction databases

BIND
BIND is an expanding database of biomolecular interaction, pathway and complex information.
BOND Web Portal
DIP
catalogs experimentally determined interactions between proteins.
DIP:Home


Expression databases

Functional genomics
DNA arrays (cDNA probes on a chip) are used to assess the RNA levels of different genes (several hundreds at a time)
Measurements are taken at intervals after some treatment is initialized
Genes are grouped in clusters according to expression profile
Reverse engineering of expression levels of these groups are used to propose regulatory genetic networks
No unified format for DNA-chip data yet, although work is in progress
Example of gene expression databases are
EBI ArrayExpress database – ArrayExpress Home
NCBI Gene Expression Omnibus (GEO)

Phylogenetic databases

Primary (repositories) and secondary (data analysis and interpretation) database
Primary databases contain information on the result of phylogenetic analyses (trees, taxonomic names), data, and assumptions on which the analyses are base
Secondary databases contain interpretations and assembled phylogenetic hypotheses for all kinds of taxa
Examples
TreeBase – http://www.herbaria.harvard.edu/treebase/index.html (Primary)
Tree of Life – Tree of Life Web Project (Secondary)


Database search systems – Entrez

Entrez is a search and retrieval system that integrates information from databases at NCBI
Entrez cross-database search
Includes PubMed, GenBank, OMIM, MMDB, etc.

Database search system – SRS

SRS - Sequence Retrieval System
SRS@EMBL-EBI
Several dozen servers provide access to over 300 different databanks


Gene Ontology

the Gene Ontology
The goal of the Gene Ontology Consortium is to produce a dynamic controlled vocabulary that can be applied to all organisms
Enable consistency in cross-species annotation
Three ontologies under development
Molecular function, biological process, and cellular component

Literature databases

http://bioinfolab.unl.edu/emlab/Cour...BIOS897_L2.pdf


Bio-databases: A short word on problems

Even today we face some key limitations
There is no standard format
Every database or program has its own format
There is no standard nomenclature
Every database has its own names
Data is not fully optimized
Some datasets have missing information without indications of it
Data errors
Data is sometimes of poor quality, erroneous, misspelled

What to take home

Databases are a collection of data
Need to access and maintain easily and flexibly
Biological information is vast and sometimes very redundant
Distributed databases bring it all together with quality controls, cross-referencing and standardization
Computers can only create data, they do not give answers

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