Finding COVID-19 Information

Featured

Last Updated 6/23/2020

Organizations across the globe have put together resources for finding and accessing information about COVID-19. Here is a growing list:

ASCO Coronavirus Resources
Information for cancer patients and physicians from the American Society of Clinical Oncology.

CDC COVID-19 (2019 Novel Coronavirus) Research Guide
A guide to articles, search strategies, statistics, and websites on COVID-19.

Centre for Evidence-Based Medicine Oxford COVID-19 Evidence Service
A selection of clinical questions answered using the highest level evidence available.

Coronavirus Disease 2019 (COVID-19)—For Beginners to Experts
A University of British Columbia resource compiling international resources, database search strategies, and other information.

The COVID-19 & Cancer Consortium
A consortium of over 100 cancer centers and organizations  collecting data about cancer patients who have been infected with COVID-19.

COVID-19 Health System Response Monitor
Offers a cross-country analysis of health system responses and key policy lessons from COVID-19. Focuses primarily on European countries.

COVID-19 Live Literature Searches
The Australian Library and Information Association has developed PubMed searches for COVID-related information and link to results on this page. 

COVID-19 Open Research Dataset (CORD-19)
A free resource of over 29,000 scholarly articles, including over 13,000 with full text, about COVID-19 and the coronavirus family of viruses.

COVID-19 Resource Center
The ECRI Institute offers evidence assessments and other resources for healthcare professionals and patients.

Dimensions
An openly accessible application that contains publications, data sets, and clinical trials on COVID-19. 

Johns Hopkins University Coronavirus Resource Center
Along with its global map tracking COVID-19 cases, Hopkins now offers breakdowns at the US county level and visualizations of epidemiological trends.

Kaiser Family Foundation – Coronavirus (COVID-19)
State-by-state news, tools, and trackers.

LitCovid
A curated literature hub of COVID-19 articles in PubMed, from the National Library of Medicine.

NIH COVID-19 Treatment Guidelines
Frequently updated guidelines based on published and preliminary data and clinical expertise.

Public Health England
A collection of open-access resources compiled by the PHE Knowledge and Library Services Team.

Society of Critical Care Medicine Emergency Resources: COVID-19
Guidelines, strategy documents, checklists, online training, and more.

Synapse – COVID-19
MSK-authored COVID-19 publications.

WHO: Global research on coronavirus disease (COVID-19)
A WHO database of the latest COVID-19 findings.

Journals and Publishers

Journals and publishers are offering portals to their COVID-19 content, some free to all and some available via the Library through remote access:

CellPress
Cochrane
BMJ Best Practice
EBSCO
Elsevier
The Lancet
The New England Journal of Medicine
Ovid
Proquest
Springer
Wiley

Do you need other specific COVID-19 information? Please ASK US!

Covidence: Better SR Data Quality & Integrity

The Covidence systematic review (SR) data management software is essentially a research electronic data capture tool, similar to REDCap. In a SR, however, the “study population” consists not of patients, but rather of literature database search results (i.e., references), while the “survey” administered to each “study subject” consists of the inclusion and exclusion criteria. 

Different than in a typical clinical study, a unique feature of the systematic review study design is that all the information captured is done so in duplicate (ideally), by two human screeners/reviewers working independently of each other. In other words, the same “survey” is administered twice to the same “study subject” and the two data captures are then compared to identify any disagreements.

This is where REDCap differs in its functionality from Covidence. Covidence not only documents the decisions of the two reviewers but it also compares them, and then automatically separates out any conflicts that need to be resolved – providing built-in quality control.

In fact, Covidence requires that reviewers address all screening discrepancies before allowing them to move on to the next stage of the review. In the full-text review stage, where explanations for exclusions must be provided, even if both reviewers vote similarly to exclude an item, Covidence will flag any exclusion reason discrepancies and force the team to resolve the conflicts before being allowed to proceed.

Data integrity features are also prominent in Covidence. For example, reviewers have the ability to reverse a decision (ie. make changes to collected data), however, if the second reviewer has already voted on that item, both reviewers will have to re-screen the record from the beginning in order to re-capture both reviewers’ judgements (i.e., this undoes all of the votes associated with the reference from that stage).

Also, in order to minimize the introduction of bias into the review process, the individual decisions made by the two reviewers are blinded to the team so that if a conflict has to be resolved by a third party, the third party will not be influenced by knowing who made which decision (as they may unconsciously side with the more senior reviewer, etc.). Even though a specific batch of records cannot be assigned to/linked to a particular reviewer, a particular task in the review process can, however, be assigned to a specific team member (for example, resolving conflicts may be set to be solely handled by the project PI).

Another feature of Covidence that leads to better data is its quality assessment and data extraction process. If two reviewers are assessing each study for bias, a comparison of assessments and consensus of judgements will be needed to complete this stage. The data extraction completed by two reviewers independently is also followed by a consensus step. If the consensus step is skipped, data will appear blank in the data export as it is only the “consensus judgements of data extraction” that can be exported to Excel. In other words, if the data is not first “cleaned” by the team, they will literally not be able to get it out of Covidence.

Although Covidence does not include any data visualization or data/statistical analysis functionality, it does allow you to export the data in a spreadsheet. “The goal of this format is to facilitate import of data extracted in Covidence into statistical programs such as Stata, R, or SPSS.”

To learn more about Covidence, register for an upcoming workshop or Ask Us

A Document Delivery Milestone: 400,000 ILLiad Requests

We’re celebrating a milestone here on the library team; the counter has tipped from 399,999 to 400,000 requests in ILLiad. This means that since 2009, the ILL team at the MSK Medical Library has processed 400k requests for books, articles, standards, dissertations, meeting abstracts, conference papers, tables of contents, and more for researchers at MSK and on the flip side, for libraries all over the world who request items from our collection.

https://pixabay.com/images/id-1614223/

We’ve learned some tricks here and there to fill these requests. One blog [now defunct] referred to our specialization as Forensic Bibliographic Reconstruction and I, for one, take that as a huge compliment. Most requests come to us replete with all the fields filled, others take more research. I’ve seen requests for “The Smith Article from last week” or “Not sure.” Sometimes it can be more of a scavenger hunt or a wild goose chase. We usually get the article in the user’s hands.

We provide this service at no cost to the user, anyone with an MSK email and ID number, and as long as it’s relevant to work done at MSK. We’ve processed requests for physics, psychology, nutrition, medicine, physical therapy, chemistry, administration, HR, etc. But sometimes there are things we just can’t get.

With libraries around the world currently shut down or in various stages of quarantine, getting articles to users has been trickier. We are learning just how many items are only available from the shelves of shuttered libraries. The partnerships and channels of interlibrary loan have become more important than ever.    

I’m happy to use this opportunity to announce that ILLiad will soon be getting a new look! The webpages are being redesigned to be easier to use, especially on mobile devices. We’re currently working to make ordering and receiving articles easier for our user community. More details will follow in the coming weeks.

If you’d like to know more about our service or place a request, visit us at https://illiad.mskcc.org/illiad/Logon.html. We’re happy to answer any questions at ill@mskcc.org.

RDM and COVID-19 (Part 4): Data Repositories and Publishers

This is the final post of a 4 part series of posts on Research Data Management and COVID-19. Click here for part 1, part 2, and part 3.

Generalist Data Repositories and Publishers have created some impressive collaborative, open access resources to support COVID-19 research. Even some traditionally for-pay companies have been contributing to the effort. Many of these repositories allow researchers to contribute their own data as well as provide platforms to enhance discoverability of datasets, code, and on-going projects. In late April, NIH hosted a webinar in which representatives from several generalist repositories spoke about their efforts to promote sharing, discovery, and citation guidance for COVID-19 data and code. The recorded webinar is available to the public: NIH/NLM Sharing, Discovering, and Citing COVID-19 Data and Code in Generalist Repositories Webinar. Here are a few of the COVID-19 resources advanced by generalist repositories:

  • Figshare: As a discipline agnostic data repository, Figshare provides a free platform (after creating a login) for researchers to store their datasets regardless of the data format. In response to COVID-19, they have created a subset of open datasets based on tags applied by data submitters and curated by Figshare staff. In addition to traditional numerical and quantity-based datasets, they encourage submission of code, presentations slides, conference posters, and other formats of information which might not typically be viewed as ‘data’, particularly since many conferences and meetings were canceled in light of the global pandemic.
    Figshare - Digital Science
  • Mendeley: This data repository provided by the publisher Elsevier, has also created a COVID-19 hub. They index numerous repositories, curating an aggregate of datasets including those deposited in their own repository. Access to the Elsevier Coronavirus Research Hub is free with registration to individual researchers wishing to use Mendeley to organize their own researh. Alternatively, COVID-19 datasets indexed in Mendeley are freely accessible to the public without an account. You can search or view them here.Mendeley Elsevier
  • Zenodo: Part of the CERN Against COVID-19 project, Zenodo, has allocated additional dedicated server space for COVID-19 research and beefed up its overall storage infrastructure in anticipation of expanded computing needs researchers. Their main ‘Coronavirus Disease Research Community’ page contains a simple but powerful search interface to discover information about COVID-19 projects and datasets. The database is powered by Elasticsearch and populated in part by the OpenAIRE harvesting gateway to bring in records for datasets from across the European research community. Zenodo has also added a librarian to their staff specifically dedicated to curating COVID-19 datasets.
    Zenodo
  • GitHub: The open code repository and versioning tool, GitHub, has aggregated public COVID-19 projects to aid in discoverability and reduce collaboration barriers. Based on tags added by contributors to their own repos, GitHub has a weekly ingest to add projects to their covid-19-repo-data. The README page of this repository contains additional documenation about how to view, search, and use code and data in this collection.
    GitHub
  • Dryad: Although Dryad, another public platform for storing and sharing research data, does not have a particular COVID-19 portal, they have engaged in specific initiatives related to supporting open science during this pandemic. Dryad supports building standards for COVID-19 data in an effort to prepare the data for future use. They are also offering guidance for researchers in appropriate handling of Protected Health Information (PHI), since many researcher have shifted to working with human subjects for the first time.Dryad Digital Repository | DataONE
  • Vivli: For clinical trial, Vivli has created a COVID-19 portal to encourage data submission and sharing from participant-level clinical trials. A challenging aspect to this has been maintaining a balance between openness, speed, and privacy. Vivli is waiving fees for submission and sharing of COVID-19 datasets.
    Vivli - Center for Global Clinical Research Data

We hope the resources highlighted in this series of Research Data Management and COVID-19 will keep any interested researchers busy exploring and potentially contributing to the global effort to understand, treat, and eradicate COVID-19!

Just remember that if you decide to take part in this tremendous collaborative effort, all data included in a publication must be cited. If you’re unsure of how to do that or would like guidance in finding datasets, using data tools, or sharing your data, please reach out to Anthony Dellureficio, Associate Librarian for Data Management Services.