Genome Data Management

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Genome Data Management

• Patrick Davis

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Genetics

• Genetics is an ideal field for the application of
  information technology
• Molecular genetics focuses on the chemical
  structure and function of genes at a very basic
  level
• Genes serve three primary purposes
• Replicating genetic information for successive
  generations
• Directing the construction of polypeptides
• Accumulating changes and mutations
• The use of mathematical or informational
  techniques to study biological systems is called
  bioinformatics

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Bioinformatics

• Several characteristics of biological data define
  the kinds of applications needed to represent it
• Biological data involves very complex
  relationships and hierarchical systems of data
• Data values in biological studies vary widely and
  unpredictably and can take many forms
• Biological database schemas change often they
  require flexible information systems
• Different biologists often represent the same set
  of data in different ways
• Biological databases are accessed most often to
  obtain data, not to change any value

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Bioinformatics (contd)

• Biologists typically have no experience with
  database applications useable interfaces are
  necessary
• Isolated values are useless without a specific
  biological context
• Biological problems require extremely complex
  data queries
• Outdated data is often needed to compare with new
  values archives are necessary

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The Human Genome Project

• The HGP is a popular application of
  bioinformatics methods
• Goals to map and find the purpose of the
  complete sequence of human genetics (between
  25,000 and 30,000 genes)
• Sequencing of nucleotides completed in 2003 the
  HGP continues to determine the function of
  individual genes and study ethical consequences
  of genetic research
• This Project has spawned various database systems
  centered on storing accurate DNA data

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Genome-Related Databases

• GenBank
• Over 100,000 species (30 billion nucleotides)
• Doubles approximately every year
• Genome Database (GDB)
• Human genes data mapping
• Associate biological information with individual
  genes
• Online Mendelian Inheritance in Man (OMIM)
• Holds genetic information about diseases
• Originally stored on a system of index cards

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For Further Reading

• Elmasri Chapter 29.4
• http//gdbwww.gdb.org/
• http//www.ornl.gov/sci/techresources/Human_Genome
  /home.shtml
• http//www.genome.gov/