Elena de la Calle
Philippe Rocca-Serra
https://orcid.org/0000-0002-5111-7263
https://orcid.org/0000-0003-0351-6523
The COVID-19 Epidemiology and Monitoring Ontology (CEMO) provides a model for describing, sharing and integrating of COVID-19 epidemiological data for outbreak monitoring and research. This ontology is under development and URIs may not be stable.
16-05-2021
COVID-19 Epidemiology and Monitoring Ontology
This ontology is under development and URIs may not be stable.
CEMO
2023-03-18
realized in
projects to
projects onto temporal region
is about
denotes
is quality measurement of
caused by
process is result of
has participant
quality of
has quality
has role
has output
has member
has unit
has confidence level
DEPRECATED has left time boundary
true
DEPRECATED has right time boundary
true
DEPRECATED left boundary of
true
DEPRECATED right boundary of
true
DEPRECATED time boundary of
true
has value
The measure (R0) of the transmission potential of a disease such that the infection will be able to start spreading in a population or not. It is the average number of secondary infections produced by a typical case of an infection in a population where everyone is susceptible.
basic reproduction number
Length of time a person may transmit a microorganism; the duration of time a person is infectious
infectious period
A population of organisms that have been infected, but are no longer able to transmit the disease and to acquire the infection again.
recovered cases
DEPRECATED case
true
A period of time that must elapse before those exposed to or attacked by a contagious disease can be considered as incapable respectively of developing or transmitting the disease.
quarantine period
A count of individuals in a population who meet the criteria of some case definition during some time interval.
number of cases new this week
A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death.
total number of deaths
A data item that is the output of some infection case count.
total number of cases
number of cases removed from isolation this week
A hospital-wide nosocomial infection rate/100 admissions for a given period (month, quarter, or year) is commonly calculated. In this rate, a patient who has two infections is actually counted twice.
hospital-wide nosocomial infection rate per 100 admissions
Represents the proportion of deaths among all infected individuals, including all asymptomatic and undiagnosed subjects.
infection fatality rate
Quantity of members of a population that have an infection.
quantity of infected population
The proportion of a population that need to be immune in order for an infectious disease to become stable in that community.
herd immunity threshold
number of cases with mild symptoms
cumulative cases
DEPRECATED epidemiological core concepts
true
virus factor
virus factor disposition
quality of person
onset of symptom to hospitalization
Number of cases of a disease or another health-related condition, closely grouped in time and place.
cluster size
number of cases with exposure events
testing rate
rate of infectious contacts
initial infection case
The risk of infection is related to the extrinsic risk factors (use of devices such as ventilator, central line intravascular catheter, urinary catheter, surgical operation).
device-specific rates and procedure-specific rates
infected person diagnosed by antigen capture test
cases by exposure in a healthcare setting
percentage of asymptomatic of confirmed cases
total number of cases removed from isolation
number of cases exposed by local (one or cluster) case
Hospital-wide patient infection rate/100 admissions are used to avoid the pitfall of multiple infections in the same patient. This rate may be calculated for a given period: month, quarter, and year. In this rate, a patient with two infections is counted only once.
hospital-wide patient infection rate per 100 admissions
percentage of cases icu
percent increase in mortality
percentage cases female sex
undetected cases
risk factor
Represents the killing power of a disease, as the ratio of deaths to cases. The time interval is not specified. Not to be confused with mortality rate.
case fatality rate
susceptible person
Not all contacts will become infected and the average number of secondary cases per infectious case will be lower than the basic reproduction number. The effective reproductive number (R) is the average number of secondary cases per infectious case in a population made up of both susceptible and non-susceptible hosts.
effective reproduction number
health systems indicators
daily deaths
exposed contacts
average rate of infectious contacts
new daily case rates
weighted prevalence
Number of new cases of a specified disease during a specified time interval per 100 populations at risk during the same time interval.
attack rate
health status indicators
median age of cases died
The proportion of reported cases that actually have the health-related event under surveillance.
predictive value positive (pvp)
cumulative case rates
duration of infection
quality of infection process
percentage cases died
number of cases currently in icu
total number of cases ever hospitalized
median age of cases hospitalized
number of cases hospitalized this week
Male-to-female ratio of confirmed case-patients
male-to-female ratio
Time for a given quantity to double in size or number at a constant growth rate.
epidemic doubling time
per capita mobility
incidence of sever outcomes
suspected cases
positive contacts
rate of cases with at least one comorbidity
proportion of cases attributed to travel
Indicates epidemic growth rate as the median percent change in daily numbers of new cases.
percent daily change
1
timecourse of infection
timeline of infection
infection course
number of cases exposed by international travel
infectious process
cumulative death rates
Vaccination effort needed to eliminate an infection from a population.
critical vaccination coverage
period from infectious to confirmed
prevalence of sars-cov-2 seropositivity
number of cases currently in hospital
initial exposed case
number of cases by testing
percentage cases removed
number of tests
Number of exposed persons developing the disease within the range of incubation period following exposure to a primary case.
secondary attack rate
number of schools with exposure events
length of icu stay
non-pharmaceutical interventions
Average number of cases that will result from an index case.
reproductive rate
recovered person
quality of infection
The time interval between symptom onset in a primary case and a secondary case, which is considered a reasonable approximation of the generation interval and is more practical to observe
serial interval
number of tested specimens
growth rate
number of cases exposed by local unknown exposure
exposition interval
odds ratio for being an infected contact
patient
percentage of cases which are detected
infected person diagnosed by PCR
average daily number of new infections generated per case (rt)
untraceable contacts
Proportion of confirmed cases that were hospitalized.
hospitalization rate
median age of cases
other indicators
number of deaths new this week
Number of daily contacts the infected person has; average number of opportunities a person has to spread the infection each day the person is infectious.
opportunity
number of cases with no symptoms
exposed individuals
susceptible individuals
DEPRECATED interpretation
true
service coverage indicators
DEPRECATED distribution
true
infected person diagnosed by serology
environmental risk factor
rate of community transmission
number of cases with missing exposure information
case
infected person
risk factors indicators
new daily death rates
DEPRECATED descriptive epidemiology
true
DEPRECATED etiology
true
number of active cases
relative change in new infections
daily cases
cumulative excess mortality
Number of points of interets within a geographical area.
points of interest (pois)
prevalence of comorbidities cases
The time lag from a primary infection to a secondary infection caused by the primary infection.
generation interval
Proportion of confirmed cases that suffered complications.
complication rate
percentage of cases
number of cases with school exposure events
percentage of laboratory findings
protection rate
Percent of positive specimens.
rate cases by testing
new daily cases
host risk factor
exposure
Confirmed and infected cases under quarantine.
quarantined cases
quantitative quality
Any person meeting the laboratory criteria for COVID-19.
confirmed cases
fertility rate
datum label
data item
information content entity
measurement datum
identifier
virulence factor
virulence factor disposition
contagiousness
Likelihood any contact passes on an exposure.
transmission probability
infectivity
The ratio of the number of cases of the disease in relation to the total number of individuals infected; a quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal.
virulence
Average susceptibility of the population; the share of the population capable of being infected.
susceptibility
Cumulative incidence of infection during a specified period of time.
incidence proportion
incidence rate
infection rate
A quality that inheres in an organism population and is the infection incidence proportion per unit time.
infection incidence rate
organism population
infected population
diseased population
infectious agent population
susceptible population
The time that passes between being exposed to something that can cause disease (such as radiation or a virus) and having symptoms.
incubation period
infection
immune population
host exposure to infectious agent
infection source
source of infection
latent time
Period of time starting with the establishing of an infection in a host and ending when the host becomes contagious.
latency period
eukaryota
person
sequence identity of sample
gene sequence identity
Population groups with an increased likelihood of a disease or other health issue
at-risk population
geographic location
Epidemiology, Geographic Location
The dose of pathogens received by the exposed individual.
infectious dose
The rate of population recovering from and infection.
recovery rate
A data item that refers to the number of new events that have occurred in a specific time interval divided by the population at risk at the beginning of the time interval. The result gives the likelihood of developing an event in that time interval.
incidence proportion ratio
It measures the frequency of all current cases (Old & New) existing during a defined period of time (e.g. annual prevalence) expressed in relation to a defined population.
period prevalence
planned process
evaluant role
assay
population
cohort role
organism
clinical history
disease
1
timecourse of disease
timeline of disease
disease course
clinical data item
geographic distribution
spatial pattern
morbidity
population size
sample size
Statistical sample size is a count evaluating the number of individual experimental units.
study group population size
The probability that a test will produce a true negative result when used on non-effected subjects as compared to a reference or "gold standard". The specificity of a test can be determined by calculating: number of true negative results divided by the sum of true negative results plus number of false positive results.
diagnostic specificity
odds ratio
confidence interval
cohort
Ability to identify every single case of disease.
sensitivity
Compares the risk of a health event (disease, injury, risk factor, or death) among one group with the risk among another group. Also called risk ratio.
relative risk
Ratio formed by the total number of all individuals who have an attribute or disease at a particular time or during a particular period divided by the populations at risk of having the attribute or disease at this point of time or midway through the period.
prevalence
mortality rate
risk difference
transmission
unit
Numerical expression of the quantity of virus in a given volume of fluid.
viral load
Percentage reduction in disease incidence attributable to vaccination.
vaccine efficacy
neonatal mortality rate
birth rate
DEPRECATED chronoid
true
DEPRECATED concrete
true
DEPRECATED event
true
DEPRECATED individual
true
DEPRECATED left time boundary
true
DEPRECATED occurrent
true
DEPRECATED process
true
DEPRECATED processual structure
true
DEPRECATED right time boundary
true
DEPRECATED space
true
DEPRECATED space time entity
true
DEPRECATED temporal region
true
DEPRECATED time
true
DEPRECATED time boundary
true
Type of prevalence where the data have been collected for one point of time.
point prevalence