Week 14 Individual Journal William P Fuchs

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Database Assignment

  • This Journal provides a commentary on database resourcing.

Answered Questions

  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?
  4. What species are covered in the database?
  5. What biological questions can it be used to answer?
    • This type of database can serve to answer questions regarding missing information that study needs to fulfill correlations or to provide insight that nucleic acid sequences can provide. International Nucleotide Sequence Database
  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])?
    • A collection of multiple country's nucleotide sequencing databases i.e.: UK database
  7. What individual or organization maintains the database?
    • There are multiple entities that manage the data base primarily: INSDC this group unifies the multiple sequence databases (DDBJ, ENA, NCBI).
  8. What is their funding source(s)?
    • Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) (to DDBJ); the European Nucleotide Archive is funded by the European Molecular Biology Laboratory; Wellcome Trust; European Commission FP7 and Horizon 2020 Programmes; Biotechnology, Biological Sciences Research Council and Oxford Nanopore Technologies. International Nucleotide Sequence Database Funding Tab.
  9. Is there a license agreement or any restrictions on access to the database?
  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?
    • Primarily, information could be collected in the formats: TEXT FASTA XML but it depends on which database is resourced for example: ENA (of Candida albicans).
  13. Evaluate the “user-friendliness” of the database.
    • One of the positive points of this database is that it has high organization and facilitates the user towards pertinent databases as well as thoroughly describe the mission/initiative of the database. Additionally, this database has attempted to consolidate multiple country hosted databases and makes it free for public use. However only one of the databases is secure in the form of "https" and it would be comforting for researchers to access more secure sites when collecting critical information.

References

Acknowledgements

This individual journal entry was completed by me and not copied from another source. William P Fuchs 18:31, 22 November 2016 (EST)

Week 14 see AninditaVarshneya BIOL368 Week 14 for detailed on project. I worked with Anindita Varshneya, Isai Lopez and Shivum A Desai out of class on 12/4/2016 and 12/5/2016 to compile work and collaborate repairs of the power point.

William P Fuchs 22:49, 5 December 2016 (EST)

Collaborative Work

All the work for Week 14 was placed on the following page:

Externals

Individual Journals

Class Journals

Assignments

Useful Links

  1. Bio Class Page
  2. BIOL368/F16:People
  3. Will Fuchs
  4. Link to LMU: http://www.lmu.edu/
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