Difference between revisions of "Week 5"
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=== Review of a Database Article from ''NAR'' === | === Review of a Database Article from ''NAR'' === | ||
| − | + | Your group will submit a joint review paper as a PDF or Word document. Your review will be submitted to the ''NAR'' Database Issue editor and will be sent to the article authors. A manuscript review consists of three parts: | |
| − | + | # A brief summary of the article (typically 1-2 paragraphs) | |
| − | + | # Major revisions requested | |
| − | + | # Minor revisions requested | |
| − | + | # A determination whether the article should be accepted, revised or, rejected. | |
| − | + | The summary that your group will write, has to explicitly address the following points. These points are for the purpose of demonstrating your understanding of the article and database and are also criteria for acceptance of the article. For each of the points, please provide either a hyperlink to the web page that you got the information from or a page number from the manuscript. | |
| − | + | ||
# What is the purpose of the database? | # What is the purpose of the database? | ||
# What biological information does it contain? | # What biological information does it contain? | ||
# What species are covered in the database? | # What species are covered in the database? | ||
# What biological questions can it be used to answer? | # What biological questions can it be used to answer? | ||
| − | # What type (or types) of database is it | + | # 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), or not curated | ||
# What individual or organization maintains the database? | # What individual or organization maintains the database? | ||
# What is their funding source(s)? | # What is their funding source(s)? | ||
# Is there a license agreement or any restrictions on access to the database? | # Is there a license agreement or any restrictions on access to the database? | ||
# How often is the database updated? When was the last update? | # How often is the database updated? When was the last update? | ||
| − | # Are there links to other databases? | + | # Are there links to other databases? Which ones? |
| − | # Can the | + | # Can the data be downloaded? |
#* In what file formats? | #* In what file formats? | ||
# Evaluate the “user-friendliness” of the database. | # Evaluate the “user-friendliness” of the database. | ||
| − | #* Is the | + | #* Is the web site well-organized? |
#* Does it have a help section or tutorial? | #* Does it have a help section or tutorial? | ||
#* Run a sample query. Do the results make sense? | #* Run a sample query. Do the results make sense? | ||
Revision as of 22:35, 24 September 2015
This week's assignment is divided into three parts:
- Review of an article for the 2016 Nucleic Acids Research annual database issue: due on Tuesday, October 6, at midnight PDT. (Monday night/Tuesday morning), 22 points.
- Group oral presentation about the database you reviewed: due on Thursday, October 8, at midnight PDT. (Wednesday night/Thursday morning), 25 points.
- Your shared journal entry on the Class Journal Week 5 page: due on Thursday, October 8, at midnight PDT. (Wednesday night/Thursday morning), 3 points.
Contents
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 perform a self-assessment of your scientific data literacy skills.
Individual Journal Assignment
- Store this journal entry as "username Week 5" (i.e., this is the text to place between the square brackets when you link to this page).
- Link from your user page to this Assignment page.
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Don't forget to add the "Journal Entry" category to the end of your wiki page.
- Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
- For your assignment for this week only, there are special restrictions on your electronic laboratory notebook that you keep on your individual journal entry page. See the details of the assignment below for details.
Homework Partners
For this week, instead of having a single homework partner, you will work in groups of four. Furthermore, each group will submit a single joint assignment for the NAR review and oral presentation. The four groups are as follows:
- Mary Alverson, Brandon Litvak, Emily Simso, Kevin Wyllie
- Nicole Anguiano, Josh Kuroda, Erich Yanoschik, Kristen Zebrowski
- Brandon Klein, Ron Legaspi, Trixie Roque, Mahrad Saeedi
- Elena Olufson, Veronica Pacheco, Anu Varshneya, Jake Woodlee
Readings and General Guidelines
Each year, the journal Nucleic Acids Research (NAR) devotes the first issue in January to biological databases. In previous iterations of this course, students have reviewed a previously published article and database. However, this year, for the first time, you will be reviewing a manuscript and database that has been submitted to the journal for publication in the 2016 issue. Your reviews will be submitted to the journal editors to become part of the decision as to whether the manuscript will be published.
- Read (if you haven't already done so):
- Your group's assigned manuscript
Because you will be performing an anonymous peer review of your group's assigned article, the articles cannot be posted on this wiki, nor can we actually post the name or authors of the article. Similarly, your reviews cannot be posted to this public wiki, nor can your presentation slides. So, for this week only, your electronic laboratory notebook will consist of the required links (listed above, which are the same for every week), a log of when you worked on this assignment and when your group got together, and links to a secure sharing site for your review and presentation slides (which should only be shared with your group members, Dr. Dahlquist, and Dr. Dionisio).
Review of a Database Article from NAR
Your group will submit a joint review paper as a PDF or Word document. Your review will be submitted to the NAR Database Issue editor and will be sent to the article authors. A manuscript review consists of three parts:
- A brief summary of the article (typically 1-2 paragraphs)
- Major revisions requested
- Minor revisions requested
- A determination whether the article should be accepted, revised or, rejected.
The summary that your group will write, has to explicitly address the following points. These points are for the purpose of demonstrating your understanding of the article and database and are also criteria for acceptance of the article. For each of the points, please provide either a hyperlink to the web page that you got the information from or a page number from the manuscript.
- What is the purpose of the database?
- What biological information does it contain?
- What species are covered in the database?
- What biological questions can it be used to answer?
- 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), or not curated
- What individual or organization maintains the database?
- What is their funding source(s)?
- Is there a license agreement or any restrictions on access to the database?
- How often is the database updated? When was the last update?
- Are there links to other databases? Which ones?
- Can the data be downloaded?
- In what file formats?
- 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.
PowerPoint Presentation
Each group will prepare and give a 10-15 minute PowerPoint presentation based on their assigned database.
- All four groups will present in class on Thursday, October 8.
- Please follow the Presentation Guidelines for how to format your slides.
- You will need to prepare ~10-15 slides (assume 1 slide per minute of presentation).
- You need to present the information you gathered about your database that you listed in your wiki above, but organized as a presentation.
- 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.
- Your PowerPoint slides must be uploaded to the wiki page you created for your database, by midnight Monday/Tuesday, even if your group is scheduled to present on Thursday.
- You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
- Your presentation (both the slides and the oral presentation) will be evalutated by the instructors using the guidelines shown here.
- Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
- What is the speaker's take-home message (one short sentence)?
- What are the best points about the presentation's content, organization, clarity of visuals, and presentation style? Please give at least 2 specific examples.
- What points need improvement? How would you improve them? Please give at least 2 specific examples.
- Store your journal entry in the shared Class Journal Week 5 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.
- NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on 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
The following is a list of core competencies for scientific data literacy. After completing the all of the exercises in this assignment, answer the following questions on the shared Class Journal Week 5 page:
- Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
- Which of these core competencies (if any) did you gain a deeper understanding of by doing this exercise? What about the exercise taught you about them?
- Which of these core competencies (if any) do you want to know more about? Why?
Scientific Data Literacy Core Competencies
- Databases and Data Formats
- Understand how to query relational databases, and be familiar with data types and formats for the discipline.
- Discovery and Acquisition of Data
- Locate and utilize disciplinary data repositories, and identify appropriate data sources
- Data Management and Organization
- Understand the lifecycle of data, and use data management plans to track subsets of processed data.
- Data Conversion and Interoperability
- Migrate data from one format to another, and understand the benefits of standard data formats.
- Quality Assurance
- Use metadata and screening procedures to recognize artifacts, incompletion, or corruption of data sets.
- Metadata
- Interpret metadata from external sources, and annotate data so it can be used by external users.
- Data Curation and Re-use
- Recognize the role of curation throughout the data lifecycle in its value in effective reuse of data.
- Cultures of Practice
- Know the practices, values, and norms of discipline as they relate to managing, sharing, and curating data.
- Data Preservation
- Understand the technology, resource, and organizational components of preserving data.
- Data Analysis
- Understand the basic analysis tools of their discipline including workflow management tools.
- Data Visualization
- Use visualization tools of discipline, and understand the advantages of the different types of visualization.
- Ethics, including citation of data
- Understand intellectual property, privacy, and the ethos of the discipline around sharing and citing data.
