Week 4

This journal entry (including presentation slides) is due on Thursday, February 8, at 12:01am Pacific time.

Objectives

The purpose of this assignment is:

• to deeply explore and perform a critical review of an existing biological database.
• to communicate your findings in an effective oral presentation.
• to gain and perform a self-assessment of your scientific data literacy skills.

Individual Journal Assignment

For this week, both partners will contribute to the same journal entry in lieu of individual journal entries.

• Store this journal entry as "database name Week 4" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.) Each partner would invoke their template on the database page you collaboratively create.
  • 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 "Journal Entry" category to the end of your wiki page.
• For your assignment this week, both partners will contribute to answering the questions on your collaborative database page (see below) and to preparing and delivering your database presentation. There will not be a separate individual page this week.
• Your collaborative database page must have an Acknowledgments and References section.

Homework Partners

You must give the details of the interaction with your partner in the Acknowledgments section of your journal assignment. Homework partners for this week are:

• Hailey & Dean NeMO
• Charlotte & Natalija AgeAnnoMO
• Katie & Andrew Monarch Initiative wiki page, Monarch Initiative website

A note on grading for this week...

• The database page created by both partners is worth 12 points.
• The shared reflection is worth 3 points.
• The PowerPoint presentation given in class is worth 35 points.

NAR Database Evaluation and Presentation

Each year, the journal Nucleic Acids Research (NAR) devotes the first issue in January to biological databases. The Week 3 Assignment introduced you to four "gold standard" biological databases. In this assignment you will use what you learned to evaluate a different biological database. Collectively, through presentations, you will gain experience with the breadth and depth of biological databases available on the Web:

• Read (if you haven't already done so):
  • Introduction to the 2024 NAR Database Issue: Rigden, D. J. & Fernández, X. M. (2019). The 2024 Nucleic Acids Research database issue and the online molecular biology database collection. Nucleic acids research, 52(D1): D1–D9. https://doi.org/10.1093/nar/gkad1173
  • Slides from DataONE.org
    • DataONE: Why Data Management
    • DataONE: Data Sharing
• Together with your partner, choose your database:
  • Nucleic Acids Research Database Issue Table of Contents 2024
  • Nucleic Acids Research Database Issue Database List
    • Make sure that the database you choose has a corresponding paper in the 2024 issue.
    • You may not choose a database from NCBI, EBI, or the DNA Databank of Japan. You may not choose Ensembl, UniProt, SGD, or other major model organism database. The intent for this exercise is to pick something that is not one of the "major" databases.
    • Sign up for your database by editing this page next to you and your partner's names. Dr. Dahlquist must approve all database choices.

Database Evaluation

For your assignment, create a new wiki page to profile your database. For this week, there will be one page per set of partners; both partners will contribute content and notes for their electronic lab notebook to the same page; you do not need to have separate individual journal entries for this week.

• The name of your page should be "Database name Week 4".

Read the article about the database from the Nucleic Acids Research journal and then go online to the database itself. In keeping with Academic Honesty and citation practices, when you answer the questions below, provide a hyperlink to the page that you got the information from. There should be at least one hyperlink per answer.

• General information about the database
  1. What is the name of the database? (link to the home page)
  2. What type (or types) of database is it?
     1. What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
     2. What type of data source does it have?
        • primary versus secondary ("meta")?
        • curated versus non-curated?
          • if curated, is it electronic versus human curation?
            • if human curation, is it in-house staff versus community curation?
  3. What individual or organization maintains the database?
     • public versus private
     • large national or multinational entity or small lab group
  4. What is their funding source(s)?
• Scientific quality of the database
  1. Does the content appear to completely cover its content domain?
     • How many records does the database contain?
     • What claims do the database owners make about coverage in the corresponding paper?
  2. What species are covered in the database? (If it is a very long list, summarize.)
  3. Is the database content useful? I.e., what biological questions can it be used to answer?
  4. Is the database content timely?
     • Is there a need in the scientific community for such a database at this time?
     • Is the content covered by other databases already?
  5. How current is the database?
     • When did the database first go online?
     • How often is the database updated?
     • When was the last update?
• General utility of the database to the scientific community
  1. Are there links to other databases? Which ones?
  2. Is it convenient to browse the data?
  3. Is it convenient to download the data?
     • In what file formats are the data provided?
       • What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
       • Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
  4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
     • Is the website well-organized?
     • Does it have a help section or tutorial?
     • Are the search options sensible?
     • Run a sample query. Do the results make sense?
  5. Access: Is there a license agreement or any restrictions on access to the database?
• Summary judgment
  1. Would you direct a colleague unfamiliar with the field to use it?
  2. Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, or seems amateur.

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.

PowerPoint Presentation

Each pair will prepare and give a 12-15 minute PowerPoint presentation based on their assigned database in class on Thursday, February 8.

• You will need to prepare ~12-15 slides (assume 1 slide per minute of presentation).
  • Please follow the Presentation Guidelines PowerPoint on Brightspace for how to format your slides.
  • You may give a live demo of the database if you wish, but practice carefully so that you can do the presentation in 15 minutes.
    • Alternately, you may choose to show screen shots instead of the live demo.
• You need to present the information you gathered about your database that you listed in your review above, but organized as a presentation.
• Your presentation (both the slides and the oral presentation) will be evaluated by the instructors using the rubric shown here in the four areas:
  • Content and message
  • Organization
  • Visuals/slides
  • Individual contribution, including speaking style and delivery
• Your PowerPoint slides must be uploaded and linked to on your database wiki page by the journal deadline of 12:01 AM on Thursday, February 8.
  • You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
• Finally, your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
  1. What is the speakers’ take-home message? (One short sentence)
  2. What is the best thing about this presentation?
  3. What needs improvement (please be constructive)?
  4. Please comment on the speaking style (language and delivery) of each presenter.

Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 4 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first 👏🏼)
• Link to your journal entry from your user page.
• Link back from the journal entry to your user page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).

Reflect

A set of core competencies for scientific data literacy is listed in the section below. Answer the following questions on the shared Class Journal Week 4 page:

1. Name two of these core competencies are you most skilled with (or which is most familiar to you)? Where and how did you gain the skills/become familiar?
2. Name two of these core competencies that you want to know more about? Why?

Scientific Data Literacy Core Competencies

1. Databases and Data Formats
   • Understand how to query relational databases, and be familiar with data types and formats for the discipline.
2. Discovery and Acquisition of Data
   • Locate and utilize disciplinary data repositories, and identify appropriate data sources
3. Data Management and Organization
   • Understand the lifecycle of data, and use data management plans to track subsets of processed data.
4. Data Conversion and Interoperability
   • Migrate data from one format to another, and understand the benefits of standard data formats.
5. Quality Assurance
   • Use metadata and screening procedures to recognize artifacts, incompletion, or corruption of data sets.
6. Metadata
   • Interpret metadata from external sources, and annotate data so it can be used by external users.
7. Data Curation and Re-use
   • Recognize the role of curation throughout the data lifecycle in its value in effective reuse of data.
8. Cultures of Practice
   • Know the practices, values, and norms of discipline as they relate to managing, sharing, and curating data.
9. Data Preservation
   • Understand the technology, resource, and organizational components of preserving data.
10. Data Analysis
    • Understand the basic analysis tools of their discipline including workflow management tools.
11. Data Visualization
    • Use visualization tools of discipline, and understand the advantages of the different types of visualization.
12. Ethics, including citation of data
    • Understand intellectual property, privacy, and the ethos of the discipline around sharing and citing data.