Week 5
From LMU BioDB 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 (each member of the group receives the same grade).
- Group oral presentation about the database you reviewed: due on Thursday, October 8, at midnight PDT. (Wednesday night/Thursday morning), 25 points (each member of the group receives the same grade).
- 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 (this will be graded individually).
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 gain and 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 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. Each member of the group will receive the same grade for the manuscript 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 and confidential 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 (LionShare) for your review and presentation slides (which should only be shared with your group members, Dr. Dahlquist, and Dr. Dionisio).
Specifically, the requirements for confidentiality from NAR's instructions to reviewers are as follows:
- The review process is strictly confidential. Referees should not discuss the manuscript with anyone not directly involved in the review process. Referees may consult with colleagues or other experts in the field only upon approval from the Executive Editor. Under no circumstances should the Referees disclose, copy, share or distribute any of the manuscript files or any of their comments. In the event of queries, the Referees must not contact the Authors directly but must raise the queries with the Executive Editor.
Review of a Database Article from NAR
Your group will submit a joint review paper as a PDF or Word document. Please submit your review via LionShare. Your review will be reviewed by Dr. Dahlquist and then submitted to the NAR Database Issue editor, who will send the "comments for the authors" to the article authors. A manuscript review consists of several parts:
- Confidential comments for the editor
- These comments are only seen by the editor. They are typically used to add any information about why you accepted/rejected the manuscript that would not be appropriate to show the authors.
- Comments for the authors
- These are (obviously) seen by the authors. The NAR Instructions to reviewers states that: "Referees should approach each manuscript with an impartial and positive but critical mind. Comments to the Authors must be constructive, clearly identifying the manuscript’s strengths and weaknesses, and providing tangible suggestions for improvement. Offensive language is not acceptable. Referees will not be able to edit their report once it is submitted, so should not include anything in the Comments for the Authors that they would not wish the Authors to read." Thus, while it is OK and expected that you should be critical of the article, you should be careful to word your criticisms in a polite and diplomatic way. The comments to the authors generally is written in three parts:
- "An introductory paragraph placing the manuscript in a broader context, describing the contribution of the manuscript to the field, summarizing the manuscript’s main findings and claims, and giving the Referee’s overall impression of the manuscript." The summary and specific comments that your group submits will be longer because you need to include all of the answers to the questions listed below.
- Specific comments which should be further divided into
- Major comments
- Minor comments
- Suggestions to improve the manuscript. These may include:
- addition/deletion of references
- changes to the text to improve presentation, quality of English, length etc.
- These are (obviously) seen by the authors. The NAR Instructions to reviewers states that: "Referees should approach each manuscript with an impartial and positive but critical mind. Comments to the Authors must be constructive, clearly identifying the manuscript’s strengths and weaknesses, and providing tangible suggestions for improvement. Offensive language is not acceptable. Referees will not be able to edit their report once it is submitted, so should not include anything in the Comments for the Authors that they would not wish the Authors to read." Thus, while it is OK and expected that you should be critical of the article, you should be careful to word your criticisms in a polite and diplomatic way. The comments to the authors generally is written in three parts:
- Finally, a determination whether the article should be accepted, revised or, rejected. This recommendation is not placed in the comments seen by the authors because it is the editor that makes the final decision. Specifically, NAR has the following categories of recommendations:
- Accept: as is
- Accept: after minor revision
- Reconsider: If substantially revised
- Reconsider: If more data added
- Reconsider: If data re-analyzed
- Reconsider: If conclusions modified
- Reconsider: If English corrected
- Reconsider: If completely rewritten
- Reject: Scientifically Flawed
- Reject: too specialized
- Reject: because insufficient new information
The specific instructions to the reviewers for the database issue provided by the editor are as follows:
- The main issues concern the scientific quality of the database, the adequacy of the description that is presented in the manuscript and the general utility of the database to the scientific community. Reviewers are expected to read the manuscript, explore the database through the web and to judge its content for completeness, usefulness and timeliness. One issue that is arising most often is whether the database is a professional database in the sense that it is well curated and maintained, or whether it is really just a hobby database that is incomplete and unlikely to be maintained for a long period of time. The former usually qualifies for inclusion in the issue, whereas the latter should not be accepted. A key question to ask yourself is whether this database will be useful to workers in the field that it covers such that you would direct a colleague unfamiliar with the field to use it for information purposes.
- In the event that the database appears well curated and maintained, then the primary focus of your review should be on the presentation. Based on the description in the article, could a naive user quickly navigate the website and gather useful information? Are search options sensible? Is it convenient to browse and download the data? For the most part we are looking for reviews that will be used constructively to improve the manuscript, wherever that is the appropriate course of action.
- For detailed guidelines, please consult the Referee Information page on our website http://www.oxfordjournals.org/our_journals/nar/referee_info.html
The review that your group will write, has to follow the format described above and 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. It may be appropriate to address these points either as part of the general summary section of your review or as part of either the major/minor revisions section, or suggestions to improve the manuscript.
- Scientific quality of the database
- What is the purpose of the database?
- What biological information does it contain?
- Does the content of the database appear to completely cover its content domain?
- What species are covered in the database?
- Is the database content useful?
- What biological questions can it be used to answer?
- Is the database content timely?
- Is there a need in the scientific community for such a database at this time?
- Is this content covered by other databases already?
- Adequacy of the description of the database
- Are the points listed above adequately covered in the manuscript?
- 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?
- Based on all of the above is it a "professional" or "hobby" database?
- General utility of the database to the scientific community
- How often is the database updated?
- When was the last update?
- Are there links to other databases?
- Which ones?
- Is it convenient to browse the data?
- Is it convenient to download the data?
- In what file formats are the data provided?
- Evaluate the “user-friendliness” of the database. Could a naive user (i.e., you) quickly navigate the website and gather useful information?
- Is the web site well-organized?
- Does it have a help section or tutorial?
- Are search options sensible?
- Run a sample query. Do the results make sense?
- Would you direct a colleague unfamiliar with the field to use it for information purposes?
- How often is the database updated?
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 12-15 minute PowerPoint presentation based on their assigned database in class on Thursday, October 8.
- You will need to prepare ~12-15 slides (assume 1 slide per minute of presentation).
- Please follow the Presentation Guidelines 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 guidelines shown here in the four areas:
- Content and message
- Organization
- Visuals/slides
- Speaking style/delivery
- Your PowerPoint slides must be uploaded and shared with the instructors via Please submit your review via LionShare by midnight Thursday (Wednesday night/Thursday morning).
- You can update your slides before your presentation, but we 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:
- What is the speakers’ take-home message? (One short sentence)
- What is the best point about the presentation’s organization? What needs improvement? Give one specific example for each.
- What is the best point about the presentation’s visuals (slides)? What needs improvement? Give one specific example for each.
- What is the best point about the presentation’s delivery (speaking style)? What needs improvement? Give one specific example for each for each presenter.
- 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.
