BIOL368/F16:Week 14

This journal entry is due on Tuesday, December 6 at midnight PDT (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Individual Journal Assignment

• Store this journal entry as "username Week 14" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Link to this assignment from your journal entry.
  • Don't forget to add the "BIOL368/F16" category to the end of your wiki page.

Part 1: Biological Databases (In class activity for November 22)

Each year, the journal Nucleic Acids Research (NAR) devotes the first issue in January to biological databases. The goal of this assignment is to dive into the deep end of the pool and experience the breadth and depth of biological databases available on the Web. This "Part 1" assignment is worth a total of 20 points (as part of the information literacy points for the course).

Read

• 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
• Slides from DataONE.org
  • DataONE: Why Data Management
• DataONE: Data Sharing

Assignment: Database Profile

• For this exercise, you will work individually. Choose a database from this issue; each person should choose a different database to profile.
  • Zach - HPSC
  • Isai - SIDER
  • Anu - eggNOG
  • Avery - Withdrawn
  • Will - International Nucleic Acid Sequence Database ^-^
  • Courtney - BindingDB
  • Mia - GeneWeaver
  • Shivum - Panther
  • Matt O. - hPSCreg
• Nucleic Acids Research Database Issue Table of Contents 2016
• Answer the questions below on your Week 14 individual journal page.
• In class on Tuesday, November 29, each person will give a 5-minute lightning talk (worth 3 points) to tell the rest of the class about his or her database. You will use your wiki page and the database web page itself for the presentation (no PowerPoint slides).
• Read the article about the database from the Nucleic Acids Research journal and then go online to the database itself. When you answer the questions below, provide a hyperlink to the page that you got the information from (there must be at least one link per answer).
  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?
  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?
  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.
      • Is the Web site well-organized?
      • Does it have a help section or tutorial?
      • 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.

Academic Honesty

As discussed in class, each weekly individual journal assignment needs to conclude with an Acknowledgments and References section.

Acknowledgments

In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge (see below).

1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. An appropriate statement could be (but is not limited to) the following:
   • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
     • Sign this statement with your wiki signature.
2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
3. If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style. If you need to reference content, use your References section (see below).
4. You must also include this statement unless otherwise noted: "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source."

References

• In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
  • data
  • facts
  • images
  • documents, including the scientific literature
• The references in this section should be accompanied by in text citations on your page that refer to these references.
• The references should be formatted according to the APA guidelines.
• For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.

Shared Journal Assignment

• Store your journal entry in the shared BIOL368/F16:Class Journal Week 14 page. If this page does not exist yet, go ahead and create it.
• Link to the shared journal entry from your user page; this should be part of your template.
• Link the shared journal page to this assignment page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL368/F16" category to the end of the wiki page (if someone hasn't done it first).

Note: the shared journal assignment will be posted next week as part of Part 2 of this assignment, due at midnight on Tuesday, December 6.