Items corresponding to entire populations or subpopulations. Might be geographically or temporally temporally limited.

population

This is a repository for COVID-19 in South Africa containing datasets on testing, cases, recoveries, deaths, transmission types, vaccination and hospital surveillance data. It also contains Jupyter notebooks with analysis and visualization code, forecasting modeling for COVID-19. The repository also stores python scrips for data processing and scraper. The code is licensed under the MIT license.

non-collection specific

(Simple) Released

Comma-separated values: a delimited text file format for tabular data.

Portable Document Format (PDF), a fixed-layout document format.

Plain text file with no specific encoding or markup.

Province

District

Republic of South Africa

English

CC BY-SA 4.0

ORCID

Dr. Vukosi Marivate

Data Science for Social Impact Research Group at University of Pretoria

Herkulaas Combrink

Python is a high-level, interpreted programming language known for its readability and broad applicability in web development, data science, and automation.

Python

R is a programming language and software environment for statistical computing and graphics, widely used among statisticians and data miners.

Coronavirus COVID-19 (2019-nCoV) Data Repository and Dashboard for South Africa

A data set that is a collection of case records

infection case list

Infection Case List

A species of BETACORONAVIRUS causing atypical respiratory disease (COVID-19) in humans. The organism was first identified in 2019 in Wuhan, China. The natural host is the Chinese intermediate horseshoe bat, RHINOLOPHUS affinis.

Severe acute respiratory syndrome coronavirus 2

SARS-CoV2

Information about diagnostic tests, results, including serology tests, PCR, and other tests

diagnostic tests

Tests

An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.

host organism

Host

Actions of groups of people in response to outbreaks.

behavior

Behavior

Homo sapiens

A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.

disease

Disease

A disease whose physical basis is an infectious disorder

infectious disease

Infectious Disease

A Coronavirus infection that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.

COVID-19

a data set that is about the human daily movement behavior of the individual huamns in a given population. 

human daily movement data set

Human Movement

A service that has some information content entity as input and output.

data service

Data Service

viral Infectious disease

Viruses Infection

Tools for initial stages of data processing, usually prior to modeling. Includes pre-processing, cleaning, exploratory analysis.

data preparation

Data Preparation

 A count of simulated or physical individuals in a population.

Population count

Population Count

A population mortality dataset that compares deaths in the population during one time interval to deaths in the population during a previous time interval and reports an estimate of how many more or less deaths occurred in the later time interval.

excess mortality dataset

Excess Mortality

A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon.

mortality data

Mortality

a dataset that is about two or more hospital stays involving two or more patients.

hospital stay dataset

Hospitalization

Descriptors of the behavior of an outbreak

modeling

Modeling

Projections of outbreak behavior into some future time, determined relative to a defined starting point. Might include retrospective projects or projections for current activitiy (known as "now-casting").

forecasting

Forecasting

A respiratory tract infection caused by a virus. Viruses represent the most common causes of upper and lower respiratory tract infections and include rhinoviruses, influenza viruses, parainfluenza viruses, and respiratory syncytial virus.

viral respiratory tract infection

Viral Respiratory Tract Infection

A census that is the specific outcome of a population demographic survey.

population demographic census

Population Demographic

Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.

Viruses

Information about capacity, including hospital beds, PPE supplies, nursing home capacity, testing sites, therapeutics, etc.

health system capacity

Health System Capacity

a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem.

control strategy census

Control Strategy

a population treatment census that is about one or more vaccinations of organisms in a population

vaccination administration census

Vaccination Administration

A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval.

cumulative death count

Cumulative Death Count

A count of individuals in a population who meet the criteria of some case definition during some time interval.

count of disease cases

Case Count

A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval.

incident hospitalization count

Incident Hospitalization

modeling purpose

Modeling Purpose

The method or type of model used to achieve the purpose.

modeling method

Modeling Method

A count of recovery that occured in a population in a given temporal region

count of recovered in a population

Recovery Count

a statistical model is an information content entity which is a formalization of relationships between variables in the form of mathematical equations. A statistical model describes how one or more random variables are related to one or more other variables. The model is statistical as the variables are not deterministically but stochastically related.

statistical model

Statistical Model

A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval.

cumulative case count

Cumulative Case Count

A count of recovery in a population that is the total number of recovery that occur during a reference temporal interval

cumulative recovered count

Cumulative Recovered Count

A social identity information content entity that is about whether some person identifies as some gender.

gender identity information content entity

Gender

age-stratified

Age-Stratified

A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval.

cumulative vaccination count

Cumulative Vaccination

Vaccine preventable diseases are those infectious diseases that can be prevented by vaccination

vaccine-preventable Disease

Vaccine-Preventable Disease

A treatment that consists of the administration of antigenic material to stimulate an individual's immune system to develop adaptive immunity to a pathogen.

vaccination

Vaccination

Computer methods for creating images, diagrams or animations.

Graphics Visualization

A census that counts the number of treatment facilities of some kind in a particular geographical region.

treatment facility census

Treatment Facility

An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon.

pathogen

Pathogen

A Bayesian model is a statistical model where inference is based on using Bayes theorem to obtain a posterior distribution for a quantity (or quantities) of interest for some model (such as parameter values) based on some prior distribution for the relevant unknown parameters and the likelihood from the model.

Bayesian model

Bayesian Model

A collection of information in various types of structured or non-structured formats.

repository

The 'about' property contains mixed types: DefinedTerm objects represent subject matter/topics, while Place objects represent geographical scope or applicability

about-property-structure

Apache 2.0

Schema.org vocabulary for structured data on the web

Schema.org

A structured data markup specification for describing datasets in the life sciences, extending schema.org Dataset

Bioschemas Dataset Profile

Dublin Core Metadata Initiative Terms - refined elements for precise resource description

DCMI Metadata Terms

W3C Data Catalog Vocabulary for describing data catalogs

Data Catalog Vocabulary

DataCite metadata schema for research data citation

DataCite Metadata Schema

W3C Provenance Ontology for describing provenance information

PROV Ontology

Provenance, Authoring and Versioning ontology for metadata about web resources

PAV Ontology

Custom MIDAS vocabulary for epidemiological data and modeling

MIDAS Metadata Vocabulary

OBO Foundry ontologies for life sciences and biomedical research

Open Biological and Biomedical Ontology

GeoNames Ontology

Health Level 7 Fast Healthcare Interoperability Resources

HL7 FHIR

Systematized Nomenclature of Medicine Clinical Terms

SNOMED Clinical Terms

LOINC database for laboratory and clinical observations

Logical Observation Identifiers Names and Codes

JSON Schema (Draft 2020-12) defining the structure of MIDAS Catalog JSON-LD metadata records

MIDAS Catalog JSON-LD Schema

Landing page where users can browse and download dataset files in various formats.

Identifier	URL: https://github.com/dsfsi/covid19za
Type	Repository
Topics/About	Behavior Human Movement Control Strategy Vaccination Vaccination Administration Cumulative Vaccination Data Preparation Data Service Disease Infectious Disease Vaccine-Preventable Disease COVID-19 Viruses Infection Viral Respiratory Tract Infection COVID-19 Graphics Visualization Health System Capacity Treatment Facility Host Homo sapiens Modeling Modeling Method Statistical Model Bayesian Model Modeling Purpose Forecasting Pathogen Viruses SARS-CoV2 Population Count Case Count Cumulative Case Count Hospitalization Incident Hospitalization Infection Case List Mortality Cumulative Death Count Excess Mortality Recovery Count Cumulative Recovered Count Tests Population Demographic Age-Stratified Gender
Language	English
License	CC BY-SA 4.0
Rights	https://github.com/dsfsi/covid19za/blob/master/README.md
Accessible For Free	TRUE
Biological Scale	population
Geographical Scope	Republic of South Africa
Geographical Resolution	Province, District
Start Date	2020/02/11
End Date	2022/12/23
Software Language	Python, R
File Format	CSV, PDF, TXT
Version	12
HTTP Status Code	200
HTTP Checked On	2026/07/12