Matthew R Allegretti Week 14

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Week 14 Assignment

Part 1

Purpose

To familiarize myself with the various aspects of biological databases.

Methods and Results

  1. What database did you access? (link to the home page of the database)
  2. What is the purpose of the database?
  3. What biological information does it contain?
    • "MitoAge contains calculated mtDNA compositional features of the entire mitochondrial genome, mtDNA coding (tRNA, rRNA, protein-coding genes) and non-coding (D-loop, insertions) regions, codon usage for each protein-coding gene, and longevity records for over 900 species from all taxa of the Kingdom Animalia."
    • http://www.mitoage.info/
  4. What species are covered in the database?
    • 922 species of animals, sorted by order, are covered including:
      • 206 species of Actinopterygii
      • 1 specie of Bivalvia
      • 1 specie of Chromadorea
      • 1 specie of Malacostraca
      • 4 species of Sarcopterygii
      • 29 species of Amphibia
      • 6 species of Cephalaspidomorphi
      • 1 species of Echinoidea
      • 390 species of Mammalia
      • 152 species of Aves
      • 35 species of Chondrichthyes
      • 2 species of Insecta
      • 94 species of Reptilia
    • http://www.mitoage.info/browse/taxonomy/
  5. What biological questions can it be used to answer?
    • How mitochondrial DNA plays a role in animal longevity, and other influences mtDNA has on the lifecycle of an animal.
    • http://www.mitoage.info/
  6. What type (or types) of database is it (sequence, structure model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])?
  7. What individual or organization maintains the database?
  8. What is their funding source(s)?
  9. Is there a license agreement or any restrictions on access to the database?
    • "The MitoAge database is free for all purposes, including commercial, educational, and research purposes, provided however that you cite the usage of MitoAge in subsequent presentations, publications, etc. Although referring to the URL might be enough in some cases (e.g., teaching and websites), for scientific publications we ask that you cite the paper describing MitoAge."
    • http://www.mitoage.info/terms/
  10. How often is the database updated? When was the last update?
  11. Are there links to other databases?
  12. Can the information be downloaded? And in what file formats?
  13. Evaluate the “user-friendliness” of the database.
    1. Is the Web site well-organized?
      • Yes. It is well organized with a number of easy to locate links.
    2. Does it have a help section or tutorial?
    3. Run a sample query. Do the results make sense?
  • Some Definitions
    • Electronic curation occurs when someone writes a program to add information to a database record from another database.
    • Manual curation occurs when a human reviews the information being added to a record to validate it as true.
    • In-house is when the human works for the database organization.
    • Community is when the database allows members of the scientific community that don't work for the database organization to add information to the record.

Part 2

Our group project is located on Matt's Week 14 Page.

References

Acknowledgements

This individual journal entry was completed by me and not copied from another source.

Useful links

Course Home Page