Jordan T. Detamore Week 14

From OpenWetWare

Part 1: Biological Databases

Purpose

The purpose of the assignment was to learn about many different types of databases and explore a specific database in order to teach the class about it.

Methods/Results

  1. What database did you access? (link to the home page of the database)
  2. What is the purpose of the database?
    • The purpose of the database is to provide information about the genomics of rice by curating a collection of information from many different community sources IC4R Overview
  3. What biological information does it contain?
    • There is summary information, genome context, gene browser, transcripts information, expression level, homolog group, SNP variation information, post-translational modification, gene related literature, additional links to other functional annotation and sequences of genes of interest in rice IC4R Tutorial
  4. What species are covered in the database?
  5. What biological questions can it be used to answer?
  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?
    • A committee of people from the Beijing Institute of Genomics, China Agricultural University, Peking University, Huazhong University of Science and Technology, and Huazhong Agricultural University Commitee and Advisory Board
  8. What is their funding source(s)?
    • Strategic Priority Research Program of the Chinese Academy of Sciences
    • National Programs for High Technology Research and Development

Publications

  1. Is there a license agreement or any restrictions on access to the database?
    • There is no restriction to access to the database. Anybody can go to the website and access the information IC4R Terms
  2. How often is the database updated? When was the last update?
    • The website does not say how often it is updated but it was last updated on May 5, 2016

Information Commons for Rice

  1. Are there links to other databases?

Information Commons for Rice

  1. Can the information be downloaded? And in what file formats?
    • Information can be downloaded in .fasta and .pdf formats [1]
  2. Evaluate the “user-friendliness” of the database.
    1. Is the Web site well-organized?
    2. Does it have a help section or tutorial?
    3. Run a sample query. Do the results make sense?
      • Yes it provides examples of things to search and you can search by organism, ontology, or sequence Search Tap

Conclusion

I learned a lot about IC4R which is a database that tells you everything you need to know about the genome of rice. It was a very direct and accessible database that could be used by scientists of all experiences. I learned a lot about databases in general and am interested to hear my classmates present on their databases.

Acknowledgements

  • I received instruction from Dr. Dahlquist's in class
  • While I worked with the person noted above, this individual journal entry was completed by me and not copied from another source.
  • Jordan T. Detamore 16:41, 22 November 2016 (EST):

Part II

Joint Page: Courtney L. Merriam Week 14

Edited ppt: Schade Journal Club Part I

References

Rigden, D. J., Fernández-Suárez, X. M., & Galperin, M. Y. (2016). The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic acids research, 44(D1), D1-D6. doi: 10.1093/nar/gkv1356

The IC4R Project Consortium; Information Commons for Rice (IC4R). Nucl Acids Res 2015; 44 (D1): D1172-D1180. doi: 10.1093/nar/gkv1141


Useful links

Introductory tutorial

OpenWetWare help pages

Bioinformatics Lab Home Page

Kam D. Dahlquist

Jordan T. Detamore

LMU Seaver College of Science and Engineering

Template:Jordan T. Detamore

Assignments

Jordan T. Detamore Week 2

Jordan T. Detamore Week 3

Jordan T. Detamore Week 4

Jordan T. Detamore Week 5

Jordan T. Detamore Week 6

Jordan T. Detamore Week 8

Jordan T. Detamore Week 9

Jordan T. Detamore Week 10

Jordan T. Detamore Week 11

Jordan T. Detamore Week 12

Jordan T. Detamore Week 13

Jordan T. Detamore Week 14

Jordan T. Detamore Week 15

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