COVID-19 Knowledge Curation Taskforce
During the ongoing COVID-19 pandemic, UAB research and medical trainees, under the guidance of UAB Informatics Institute faculty members, have volunteered their time and effort into fighting this disease through the COVID-19 Knowledge Curation Taskforce. The primary goal of the taskforce is to prioritize impactful and essential resources relevant to COVID-19 research in order to accelerate interdisciplinary collaborations between biomedical data scientists, clinicians, basic scientists, and translational researchers.
To accomplish this goal, our student-run taskforce has been collecting, filtering, prioritizing, and curating journal publications, publicly available datasets, open-source software tools, and other online learning resources based on various major topics relating to COVID-19 as emerging data becomes available or updated. These efforts may help the biomedical research community find novel therapeutics, repurposed drugs, or vaccines. In the short term, we set out to complete the following aims:
Aim 1: Develop an online series of articles titled “COVID-19 TOP 10”, directed towards both the research community and the greater public. These articles have been curated and released weekly on the COVID-19 web portal.
Aim 2: Organize and curate online COVID-19 data sets into the U-BRITE data management infrastructure. These data sets have been carefully examined and reviewed for their quality, coverage, and value to COVID-19 epidemiology, prevention, treatment, disease biology studies, and drug/vaccine development.
Aim 3: Publish review articles pertaining to COVID-19. Several review articles, particularly those serving challenging problems with available data, are being planned for interdisciplinary researchers interested in data science solutions to the pandemic.
Aim 4: Assemble various tools in the U-BRITE data science pipelines for practical problem solving. A COVID-19 Hackathon has been scheduled for early June 2020 to bring trainees with expertise in biomedical domain science and data science together in solving real-world problems posed by participating faculty PIs.
Curator Members are expected to:
- Curate COVID-19 literature for 5-10hrs/week
- Learn and contribute to biomedical data science
- Develop problem-solving skills for data-driven COVID-19 research
Jake Chen – firstname.lastname@example.org
Taskforce Chairs & Committee Members
Eric Zhang – email@example.com – Chair
Tarun Mamidi – firstname.lastname@example.org – Co-Chair
Thi Tran-nguyen – email@example.com – Committee Member
Elias Awad – firstname.lastname@example.org – Committee Member
Maani Kamal- email@example.com – Committee Member
Knowledge Curation Members
Knowledge Curator Tools
Please email Jake Chen or Eric Zhang or Tarun Mamidi to request access to Microsoft Teams, AirTable and Box folder.
Weekly Zoom Meeting ID: 2870934194
(Weekly meetings currently set at 1 pm Wednesdays)
Join Microsoft Teams
Click here to join COVID-19 discussion on Microsoft Teams.
Click here to request access for Microsoft Teams for UABMC users.
Once you’ve joined the Teams channel, you can see all channels as in the image to the right.
You can select topics from any of these or even out of these, if they’re related to COVID-19. Please check other reviews so that the articles don’t overlap.
Click here to access the Box Folder.
Folder is named ‘Student Knowledge Curation’.
Please upload your headshot in the ‘Curator Headshots’ folder.
‘Top Ten List’ folder has the template of a review article. Please follow the same for your topic.
Review manuscripts – Please upload your manuscripts for review and copy the link to AirTable.
Please email/message Tarun Mamidi to request access on AirTable. Table is named ‘Student Reviews’. This tool is used as a spreadsheet database and to track progress of each student.
As shown in the below picture, we have 2 Tables –
- Student reviews – Data table and progress tracking
- Knowledge Curators – Info of all student curators
Under ‘Student reviews’ tab, are the ‘views’ you can choose from to look at the table. Please ask Tarun to create a view for you.
- Main view – This view is for viewing purpose only. No modifications should be made here.
- Student view – This view is same as the main one but without any filters. No modifications here too.
- Jake – This is used by Dr. Jake Chen to track progress of each student and give comments for each of their reports
- Your Name view – This is where you should be working.
For example, take see Tarun’s view to understand the table.
- Paper ID – this is the format for each of your review articles. Students can work on any number of articles as approved by Dr. Jake Chen.
- CoV – –
- CoV – –
- Authors – You need to tag yourself for all your articles. You can also tag others if you’re collaborating.
- Topic – Please select a topic that you’re working on. If you don’t find what you’re looking for, please contact Tarun Mamidi to add it to the list. In the meantime, please add it to ‘notes’ tab.
- Status – This has a variety of tags. Please follow below for explanation.
- New – New curator and haven’t picked a topic yet to work on.
- Active – Picked a topic and started working on the review article.
- Pending review – Once you’ve finished writing up, please mark this tag so that the reviewers can look into your work.
- Reviewed with comments – Once the reviewer goes through your review and gives comments in the ‘notes’ tab, they’ll change the status to this. It’s your turn to look in to the comments and make changes.
- Pre-article – This is a version of your article where you work on addressing the comments.
- Article review – initial revisions made and submitted for second/final round of review.
- Article revisions – Tagged by the reviewer after commenting.
- Ready for publication – Final version used for publication.
- Sway edits – Edits to be made to the sway page before publishing.
- Review document link – This is where you link your word document that you are working. This document should be uploaded in box folder and a link address (only web browser link) should be copied here. Please grant access to your document so that reviewers can comment on your work.
- Person reviewed – ( also contact via Teams chat or email) select Dr. Jake Chen (firstname.lastname@example.org) and Eric Zhang (email@example.com) to review your work and give comments accordingly.
- Notes – This is where the reviewer addresses their comments. Please don’t delete any of the stuff. Please keep adding new comments below. It’s good practices to not delete and track your changes.
- Sway page – Once your article is publication ready, please contact Elias Awad to create a sway page for your article. Link to this page should be copied here. Keep working with Eli for a final version.
- Additional attachments – Please add any additional material to share or support your document. This tab is typically empty for everyone.
Please contact any of the chairs if you have any questions.
Call for Participation
Seeking students who are interested in participating in COVID-19 data science. If you are interested contact Jake Chen.