Everything you need to know about the data

We strongly believe not only in making data open, but also in making it useful to other people.

To that end, we've done our best to document where these data come from, what they mean, and any known limitations about how they should be used.

Think we're missing something? Please let us know at [email protected]

Data overview

Current version:
CViSB version 1.1.0
updated 22 March 2022
View all release notes

Where do our data come from?

The majority of our data is provided to CViSB through a partnership with the Kenema Government hospital (KGH) in Sierra Leone. KGH is home to Sierra Leone's only Lassa fever isolation ward, which was used during the 2014-2016 West African Ebola outbreak to treat Ebola as well. Read more about the isolation ward in the height of the Ebola outbreak .

Schema

Building off of schema.org's data models, we created schema to organize and standardize our patient, sample, dataset, experiment, and other related data.

Data dictionaries

... will be coming soon. In the meantime, peruse our schema, which contain information about how we define variables in our datasets.

Cohort definition

Patients are grouped into four cohorts: Ebola, Lassa, Control, or Unknown. People in the Ebola or Lassa group are not necessarily infected with the virus. Rather, they are either patients suspected of infection (pending diagnostic confirmation), or contacts of these patients who have suspected exposure to the virus. For specific analyses, you will need to decide how to define the cohort.

Outcome definition

Patients are grouped into five outcomes: survivor, dead, contact, control, or unknown.

  • Survivors are patients who were alive at least 10 days after presenting at a treatment center.
  • Dead are patients who have a confirmed death related to the virus.
  • Contacts are people who have been exposed to a patient infected with a virus.
  • Controls are healthy people who show no symptoms of infection.
  • Unknowns are people whose status is not known 10 or more days after presentation.

Limitations

Please note that this data is still based on work in progress and should be considered preliminary. If you intend to include any of these data in publications, please let us know – otherwise please feel free to download and use without restrictions. We have shared this data with the hope that people will download and use it, as well as scrutinize it so we can improve our methods and analyses. Please contact us if you have any questions or comments.

Citing the CViSB Data Portal

To reference data from the Center for Viral Systems Biology Data Portal, please cite the Center for Viral Systems Biology:

The Center for Viral Systems Biology, 2022, "Center for Viral Systems Biology data", https://data.cvisb.org/, V1.1.0.

Citing individual data sources

The data in the CViSB Data Portal is a mixture of data collected by our consortium, data contributed by our partners, and publicly available data on Lassa and Ebola. Some of the data has been published and others are works in progress. Individual data sources can be cited as:

Systems Serology data

Caroline Atyeo et al.Immunity2020, 53, 3, 524-532.e4.

rapid diagnostics data

Viral Hemorrhagic Fever Consortium / Kenema Government Hospital, 2022, https://data.cvisb.org/dataset/rapid-diagnostics-vhf. (unpublished)

vitals data

Viral Hemorrhagic Fever Consortium / Kenema Government Hospital, 2022, https://data.cvisb.org/dataset/vitals-vhf. (unpublished)

blood chemistry data

Viral Hemorrhagic Fever Consortium / Kenema Government Hospital, 2022, https://data.cvisb.org/dataset/blood-chemistry-vhf. (unpublished)

RT-PCR data

Viral Hemorrhagic Fever Consortium / Kenema Government Hospital, 2022, https://data.cvisb.org/dataset/rtpcr-vhf. (unpublished)

blood counts data

Viral Hemorrhagic Fever Consortium / Kenema Government Hospital, 2022, https://data.cvisb.org/dataset/blood-counts-vhf. (unpublished)

RT-PCR data

Caroline Atyeo et al.Immunity2020, 53, 3, 524-532.e4.