Biological Database Systems

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Biological Database Systems

• Denis Shestakov,
• University of Turku/Tampere

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Course Information

• Contact info
• Email
• Office B6019, ICT
• Course URL http//users.utu.fi/denshe/biodb/index
  .html
• Course Blog (will be updated occasionally)
  http//biodb.wordpress.com/

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Course Information

• Course structure
• Lectures(topics) approx. 12 (plus todays intro
  and review lecture in the end of the course)
• Project work details will be given next time
• Exam easy to pass if all assignments are
  completed

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Course Information

• Project work
• Build database that combines data from several
  sources
• Please send to me your suggestions (if you have
  any) for project, otherwise project will be
  suggested by me
• Design part
• E-R schema, relational schema, XML schema
• Deploying part
• Data converters
• Building relational db ( XML-based db) based on
  corresponding schemas
• Performance comparison relational database vs.
  XML-based db vs. file storage system
• Invoking web services

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Course Information Literature

• Slides
• References in the end of slides
• Books
• Database Systems Concepts, 5th edition by
  Silbershatz, Korth Sudarshan, McGraw-Hill, 2005
  ISBN-10 0072958863
• Bioinformatics Managing Scientific Data by
  Lacroix Critchlow, Morgan Kaufmann, 2003
  ISBN-10 155860829X
• Articles
• Biological database design and implementation by
  Birney Clamp (the Ensembl project), Briefings
  in Bioinformatics, 5(1)31-38, 2004

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Biological Database Systems

• 1.1. Course Content
• 1.2. Course Objectives
• 1.3. Database and DBMS
• 1.4. Biological Databases

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Course content main topics

• Database concepts, overview of database design
  process
• Entity-relationship (ER) data model
• Relational data model
• Introduction to SQL
• XML and XML Schema
• Design of biological database systems

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Course content main topics

• Entity-attribute-value (EAV) modeling
• Model organism databases
• Web services
• Integration of biological data
• Analysis workflows

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Course focus

• Database issues
• Biology-specific
• Representation of biological data
• Design of biological databases
• NOT about
• Usage of existing databases
• Accessing/retrieving data from bio-databases

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Course goal

• Give basic knowledge of biological database
  design

- for molecular biology
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Do you need to know this?

• Work in wet laboratory
• One bioinformatician and many biologists
• Likely to be IT guru for others
• Expect to answer IT-related questions
  (database-related too)
• Work in bioinformatics lab
• Many bioinformaticians
• Group may maintain several dbs
• Basics are helpful
• Interested in creating/maintaining biological
  databases
• Start learning!
• Ask for more information

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Database?
From Merriam-Webster dictionary (http//www.merri
am-webster.com/dictionary/database)
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Database?

• A collection of data
• structured
• searchable (i.e., indexable)
• updated
• cross-referenced
• Objective
• Transform meaningless raw data into useful
  information which can be accessed and analyzed in
  the best way
• Database Management System (DBMS)
• software designed for the purpose of managing
  databases (access, insert, delete, update, etc.)

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DBMS database management system

• A set of tools that
• Store
• Extract
• Modify

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Biological Databases?

• Explosive growth in biological data
• E.g., tremendous increase in nucleotide sequences
  (first increase in data due to the polymerase
  chain reaction (PCR) technique development in
  1983)
• 1980 80 genes fully sequenced

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Biological Databases?

• EMBL Database Growth

Total nucleotides (Nov 07 188,490,792,445)
Number of entries(Nov 07 106,144,026)
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Biological Databases?

• Database systems are crucial for managing large
  and very large collections of data
• Data (genomic sequences, 3D structures, 2D gel
  analysis, microarrays.) directly submitted to
  databases
• Essential tools for biological research, like
  reading relevant literature

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Biological Databases History

• 1965
• Margaret Dayhoff et al. publish Atlas of Protein
  Sequences and Structures
• 1982
• EMBL initiates DNA sequence databases, followed
  within a year by GenBank and in 1984 by the DNA
  Database of Japan
• 1988
• EMBL/GenBank/DDBJ agree on common format for data
  elements

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Biological Databases some statistics

• More than 1000 different databases
• 968 databases reported in The Molecular Biology
  Database Collection 2007 update by Galperin,
  Nucleic Acids Research, 2007, Vol. 35, Database
  issue D3-D4
• Metabase database of biological databases,
  http//biodatabase.org/index.php/Main_Page
• Database sizes lt100kB to gt100GB (EMBL gt500GB)
• DNA gt100GB
• Protein 1GB
• 3D structure 5GB
• Update (adding new data) frequency daily to
  annually
• Freely accessible (as a rule)

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Some databases in the field of molecular biology

• AATDB, AceDb, ACUTS, ADB, AFDB, AGIS, AMSdb,
• ARR, AsDb, BBDB, BCGD, Beanref,
  Biolmage,
• BioMagResBank, BIOMDB, BLOCKS,
  BovGBASE,
• BOVMAP, BSORF, BTKbase, CANSITE, CarbBank,
• CARBHYD, CATH, CAZY, CCDC, CD4OLbase, CGAP,
• ChickGBASE, Colibri, COPE, CottonDB, CSNDB, CUTG,
• CyanoBase, dbCFC, dbEST, dbSTS, DDBJ, DGP,
  DictyDb,
• Picty_cDB, DIP, DOGS, DOMO, DPD, DPlnteract,
  ECDC,
• ECGC, EC02DBASE, EcoCyc, EcoGene, EMBL, EMD db,
• ENZYME, EPD, EpoDB, ESTHER, FlyBase, FlyView,
• GCRDB, GDB, GENATLAS, Genbank, GeneCards,
• Genline, GenLink, GENOTK, GenProtEC,
  GIFTS,
• GPCRDB, GRAP, GRBase, gRNAsdb, GRR, GSDB,
• HAEMB, HAMSTERS, HEART-2DPAGE, HEXAdb, HGMD,
• HIDB, HIDC, HlVdb, HotMolecBase, HOVERGEN, HPDB,
• HSC-2DPAGE, ICN, ICTVDB, IL2RGbase, IMGT, Kabat,
• KDNA, KEGG, Klotho, LGIC, MAD, MaizeDb, MDB,
• Medline, Mendel, MEROPS, MGDB, MGI, MHCPEP5
• Micado, MitoDat, MITOMAP, MJDB, MmtDB, Mol-R-Us,

Find more at http//biodatabase.org
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Categories of Biological Databases

• Nucleotide sequences
• Genomics (information on gene chromosomal
  location and nomenclature, provide links to
  sequence databases)
• Mutation/polymorphism (sequence variations linked
  or not to genetic diseases)
• Protein sequences
• Protein domain/family
• Proteomics (2D gel, MS)

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Categories of Biological Databases

• Microarray (high-dimensional data profiles of
  thousands of genes depending on
  hundreds/thousands of various conditions)
• Organism-specific
• 3D structure
• Metabolism (e.g., metabolic pathways graph
  data)
• Bibliography
• Others

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Biological Databases specific features

• Sub-class of scientific databases
• Autonomous many independent maintainers
• Heterogeneous data formats e.g., various data
  formats for the same data entities various types
  of biological data genomic, microarray,
  proteomic, ...
• Dynamic frequent and continuous changes in data
  content (and, more importantly, in data schema)
• Broad domain knowledge
• Workflow-oriented databases rich set of
  analysis tools
• Information integration is essential data
  aggregation from several databases

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Biological Databases integration
Figure is taken from Bioinformatics Managing
Scientific Data by Lacroix Critchlow, p.20