COVID-19 Epidemiology and Monitoring Ontology
type: Ontology
version IRI: cemo.owl
imports: bfo.owl
contributor: https://orcid.org/0000-0001-8149-5890
contributor: 0000-0002-8691-772X
contributor: Elena de la Calle
contributor: Philippe Rocca-Serra
contributor: https://orcid.org/0000-0002-5111-7263
contributor: https://orcid.org/0000-0003-0351-6523
creator: http://orcid.org/0000-0003-0169-8159
description: 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.
issued: 16-05-2021
license: https://creativecommons.org/publicdomain/zero/1.0/
comment: This ontology is under development and URIs may not be stable.
label: CEMO
version info: 2023-03-18

realized in
type: ObjectProperty
domain: BFO_0000017
range: BFO_0000015

projects onto temporal region
type: ObjectProperty
type: FunctionalProperty
IAO_0000118: projects to

is about
type: ObjectProperty

denotes
type: ObjectProperty
sub property of: is about

is quality measurement of
type: ObjectProperty

process is result of
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000015
IAO_0000118: caused by

has participant
type: ObjectProperty

quality of
type: ObjectProperty

has quality
type: ObjectProperty
range: BFO_0000019

has role
type: ObjectProperty
domain: BFO_0000004
range: BFO_0000023

has output
type: ObjectProperty
domain: BFO_0000015
range: information content entity

has member
type: ObjectProperty
domain: population
range: person

has unit
type: ObjectProperty

has confidence level
type: ObjectProperty
range: confidence interval

DEPRECATED has left time boundary
type: ObjectProperty
inverse of: DEPRECATED left boundary of
deprecated: true

DEPRECATED has right time boundary
type: ObjectProperty
inverse of: DEPRECATED right boundary of
deprecated: true

DEPRECATED left boundary of
type: ObjectProperty
deprecated: true

DEPRECATED right boundary of
type: ObjectProperty
deprecated: true

DEPRECATED time boundary of
type: ObjectProperty
deprecated: true

has value
type: DatatypeProperty
domain: information content entity

basic reproduction number
type: Class
subclass of: quantitative quality
subclass of: Restriction
  on property: quality of
  some values from: BFO_0000008
description: 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.

infectious period
type: Class
subclass of: BFO_0000038
subclass of: quantitative quality
description: Length of time a person may transmit a microorganism; the duration of time a person is infectious

recovered cases
type: Class
subclass of: quantitative quality
description: A population of organisms that have been infected, but are no longer able to transmit the disease and to acquire the infection again.

DEPRECATED case
type: Class
deprecated: true

quarantine period
type: Class
subclass of: quantitative quality
description: 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.

number of cases new this week
type: Class
subclass of: quantitative quality
description: A count of individuals in a population who meet the criteria of some case definition during some time interval.

total number of deaths
type: Class
subclass of: quantitative quality
description: 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 cases
type: Class
subclass of: quantitative quality
description: A data item that is the output of some infection case count.

number of cases removed from isolation this week
type: Class
subclass of: quantitative quality

hospital-wide nosocomial infection rate per 100 admissions
type: Class
subclass of: quantitative quality
description: 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.

infection fatality rate
type: Class
subclass of: quantitative quality
description: Represents the proportion of deaths among all infected individuals, including all asymptomatic and undiagnosed subjects.

quantity of infected population
type: Class
subclass of: quantitative quality
description: Quantity of members of a population that have an infection.

herd immunity threshold
type: Class
subclass of: quantitative quality
description: The proportion of a population that need to be immune in order for an infectious disease to become stable in that community.

number of cases with mild symptoms
type: Class
subclass of: quantitative quality

cumulative cases
type: Class
subclass of: quantitative quality

DEPRECATED epidemiological core concepts
type: Class
deprecated: true

virus factor disposition
type: Class
subclass of: BFO_0000016
IAO_0000118: virus factor

quality of person
type: Class
subclass of: BFO_0000019

onset of symptom to hospitalization
type: Class
subclass of: quantitative quality

cluster size
type: Class
subclass of: quantitative quality
description: Number of cases of a disease or another health-related condition, closely grouped in time and place.

number of cases with exposure events
type: Class
subclass of: quantitative quality

testing rate
type: Class
subclass of: quantitative quality

rate of infectious contacts
type: Class
subclass of: quantitative quality

initial infection case
type: Class
subclass of: quantitative quality

device-specific rates and procedure-specific rates
type: Class
subclass of: quantitative quality
description: 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).

infected person diagnosed by antigen capture test
type: Class
subclass of: person

cases by exposure in a healthcare setting
type: Class
subclass of: quantitative quality

percentage of asymptomatic of confirmed cases
type: Class
subclass of: quantitative quality

total number of cases removed from isolation
type: Class
subclass of: quantitative quality

number of cases exposed by local (one or cluster) case
type: Class
subclass of: quantitative quality

hospital-wide patient infection rate per 100 admissions
type: Class
subclass of: quantitative quality
description: 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.

percentage of cases icu
type: Class
subclass of: quantitative quality

percent increase in mortality
type: Class
subclass of: quantitative quality

percentage cases female sex
type: Class
subclass of: quantitative quality

undetected cases
type: Class
subclass of: quantitative quality

risk factor
type: Class
subclass of: BFO_0000016

case fatality rate
type: Class
subclass of: quantitative quality
subclass of: Restriction
  on property: quality of
  some values from: person
description: 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.

susceptible person
type: Class
subclass of: person

effective reproduction number
type: Class
subclass of: quantitative quality
description: 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.

health systems indicators
type: Class
subclass of: other indicators
disjoint with: health status indicators

daily deaths
type: Class
subclass of: quantitative quality

exposed contacts
type: Class
subclass of: quantitative quality

average rate of infectious contacts
type: Class
subclass of: quantitative quality

new daily case rates
type: Class
subclass of: quantitative quality

weighted prevalence
type: Class
subclass of: quantitative quality

attack rate
type: Class
subclass of: quantitative quality
description: Number of new cases of a specified disease during a specified time interval per 100 populations at risk during the same time interval.

health status indicators
type: Class
subclass of: other indicators

median age of cases died
type: Class
subclass of: quantitative quality

predictive value positive (pvp)
type: Class
subclass of: quantitative quality
description: The proportion of reported cases that actually have the health-related event under surveillance.

cumulative case rates
type: Class
subclass of: quantitative quality

duration of infection
type: Class
subclass of: quantitative quality

quality of infection process
type: Class
subclass of: BFO_0000019

percentage cases died
type: Class
subclass of: quantitative quality

number of cases currently in icu
type: Class
subclass of: quantitative quality

total number of cases ever hospitalized
type: Class
subclass of: quantitative quality

median age of cases hospitalized
type: Class
subclass of: quantitative quality

number of cases hospitalized this week
type: Class
subclass of: quantitative quality

male-to-female ratio
type: Class
subclass of: quantitative quality
description: Male-to-female ratio of confirmed case-patients

epidemic doubling time
type: Class
subclass of: quantitative quality
description: Time for a given quantity to double in size or number at a constant growth rate.

per capita mobility
type: Class
subclass of: quantitative quality

incidence of sever outcomes
type: Class
subclass of: quantitative quality

suspected cases
type: Class
subclass of: quantitative quality

positive contacts
type: Class
subclass of: quantitative quality

rate of cases with at least one comorbidity
type: Class
subclass of: quantitative quality

proportion of cases attributed to travel
type: Class
subclass of: quantitative quality

percent daily change
type: Class
subclass of: quantitative quality
description: Indicates epidemic growth rate as the median percent change in daily numbers of new cases.

infection course
type: Class
subclass of: BFO_0000015
subclass of: Class
  intersection of: BFO_0000015
  intersection of: Restriction
    on property: process is result of
    all values from: infectious process
  intersection of: Restriction
    on property: has participant
    all values from: person
  intersection of: Restriction
    on property: projects onto temporal region
    qualified cardinality: 1
    on class: BFO_0000008
IAO_0000118: timecourse of infection
IAO_0000118: timeline of infection

number of cases exposed by international travel
type: Class
subclass of: quantitative quality

infectious process
type: Class
subclass of: BFO_0000015

cumulative death rates
type: Class
subclass of: quantitative quality

critical vaccination coverage
type: Class
subclass of: quantitative quality
description: Vaccination effort needed to eliminate an infection from a population.

period from infectious to confirmed
type: Class
subclass of: BFO_0000038
subclass of: quantitative quality

prevalence of sars-cov-2 seropositivity
type: Class
subclass of: quantitative quality

number of cases currently in hospital
type: Class
subclass of: quantitative quality

initial exposed case
type: Class
subclass of: quantitative quality

number of cases by testing
type: Class
subclass of: quantitative quality

percentage cases removed
type: Class
subclass of: quantitative quality

number of tests
type: Class
subclass of: quantitative quality

secondary attack rate
type: Class
subclass of: quantitative quality
subclass of: Restriction
  on property: quality of
  some values from: person
description: Number of exposed persons developing the disease within the range of incubation period following exposure to a primary case.

number of schools with exposure events
type: Class
subclass of: quantitative quality

length of icu stay
type: Class
subclass of: quantitative quality

non-pharmaceutical interventions
type: Class
subclass of: quantitative quality

reproductive rate
type: Class
subclass of: quantitative quality
description: Average number of cases that will result from an index case.

recovered person
type: Class
subclass of: person

quality of infection
type: Class
subclass of: BFO_0000019

serial interval
type: Class
subclass of: quantitative quality
description: 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

number of tested specimens
type: Class
subclass of: quantitative quality

growth rate
type: Class
subclass of: quantitative quality

number of cases exposed by local unknown exposure
type: Class
subclass of: quantitative quality

exposition interval
type: Class
subclass of: quantitative quality

odds ratio for being an infected contact
type: Class
subclass of: quantitative quality

patient
type: Class
subclass of: person

percentage of cases which are detected
type: Class
subclass of: quantitative quality

infected person diagnosed by PCR
type: Class
subclass of: person

average daily number of new infections generated per case (rt)
type: Class
subclass of: quantitative quality

untraceable contacts
type: Class
subclass of: quantitative quality

hospitalization rate
type: Class
subclass of: quantitative quality
description: Proportion of confirmed cases that were hospitalized.

median age of cases
type: Class
subclass of: quantitative quality

other indicators
type: Class
subclass of: BFO_0000019

number of deaths new this week
type: Class
subclass of: quantitative quality

opportunity
type: Class
subclass of: quantitative quality
description: 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.

number of cases with no symptoms
type: Class
subclass of: quantitative quality

exposed individuals
type: Class
subclass of: quantitative quality

susceptible individuals
type: Class
subclass of: quantitative quality

DEPRECATED interpretation
type: Class
deprecated: true

service coverage indicators
type: Class
subclass of: health status indicators
disjoint with: risk factors indicators

DEPRECATED distribution
type: Class
deprecated: true

infected person diagnosed by serology
type: Class
subclass of: person

environmental risk factor
type: Class
subclass of: risk factor

rate of community transmission
type: Class
subclass of: quantitative quality

number of cases with missing exposure information
type: Class
subclass of: quantitative quality

infected person
type: Class
subclass of: person
IAO_0000118: case

risk factors indicators
type: Class
subclass of: health status indicators

new daily death rates
type: Class
subclass of: quantitative quality

DEPRECATED descriptive epidemiology
type: Class
deprecated: true

DEPRECATED etiology
type: Class
deprecated: true

number of active cases
type: Class
subclass of: quantitative quality

relative change in new infections
type: Class
subclass of: quantitative quality

daily cases
type: Class
subclass of: quantitative quality

cumulative excess mortality
type: Class
subclass of: quantitative quality

points of interest (pois)
type: Class
subclass of: quantitative quality
description: Number of points of interets within a geographical area.

prevalence of comorbidities cases
type: Class
subclass of: quantitative quality

generation interval
type: Class
subclass of: quantitative quality
description: The time lag from a primary infection to a secondary infection caused by the primary infection.

complication rate
type: Class
subclass of: quantitative quality
description: Proportion of confirmed cases that suffered complications.

percentage of cases
type: Class
subclass of: quantitative quality

number of cases with school exposure events
type: Class
subclass of: quantitative quality

percentage of laboratory findings
type: Class
subclass of: quantitative quality

protection rate
type: Class
subclass of: quantitative quality

rate cases by testing
type: Class
subclass of: quantitative quality
description: Percent of positive specimens.

new daily cases
type: Class
subclass of: quantitative quality

host risk factor
type: Class
subclass of: risk factor

exposure
type: Class
subclass of: BFO_0000015

quarantined cases
type: Class
subclass of: quantitative quality
description: Confirmed and infected cases under quarantine.

quantitative quality
type: Class
subclass of: BFO_0000019

confirmed cases
type: Class
subclass of: quantitative quality
description: Any person meeting the laboratory criteria for COVID-19.

fertility rate
type: Class
subclass of: quantitative quality

datum label
type: Class
subclass of: information content entity

data item
type: Class
subclass of: information content entity

information content entity
type: Class
subclass of: BFO_0000031

measurement datum
type: Class
subclass of: data item

identifier
type: Class
subclass of: information content entity

virulence factor disposition
type: Class
subclass of: virus factor disposition
IAO_0000118: virulence factor

contagiousness
type: Class
subclass of: BFO_0000016

transmission probability
type: Class
subclass of: quantitative quality
subclass of: Restriction
  on property: quality of
  some values from: person
description: Likelihood any contact passes on an exposure.

infectivity
type: Class
subclass of: BFO_0000019

virulence
type: Class
subclass of: quantitative quality
description: 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.

susceptibility
type: Class
subclass of: quantitative quality
description: Average susceptibility of the population; the share of the population capable of being infected.

incidence proportion
type: Class
subclass of: quantitative quality
subclass of: Restriction
  on property: quality of
  some values from: person
description: Cumulative incidence of infection during a specified period of time.

infection incidence rate
type: Class
subclass of: quantitative quality
subclass of: Restriction
  on property: quality of
  some values from: BFO_0000006
IAO_0000118: incidence rate
IAO_0000118: infection rate
description: A quality that inheres in an organism population and is the infection incidence proportion per unit time.

organism population
type: Class
equivalent class: population
subclass of: BFO_0000027

infected population
type: Class
subclass of: organism population

diseased population
type: Class
subclass of: organism population

infectious agent population
type: Class
subclass of: organism population

susceptible population
type: Class
subclass of: organism population

incubation period
type: Class
subclass of: BFO_0000038
subclass of: quantitative quality
description: The time that passes between being exposed to something that can cause disease (such as radiation or a virus) and having symptoms.

infection
type: Class
subclass of: BFO_0000040

immune population
type: Class
subclass of: organism population

host exposure to infectious agent
type: Class
subclass of: exposure

source of infection
type: Class
subclass of: BFO_0000040
IAO_0000118: infection source

latency period
type: Class
subclass of: BFO_0000038
subclass of: quantitative quality
IAO_0000118: latent time
description: Period of time starting with the establishing of an infection in a host and ending when the host becomes contagious.

eukaryota
type: Class
subclass of: organism

person
type: Class
subclass of: eukaryota

sequence identity of sample
type: Class
subclass of: quantitative quality

gene sequence identity
type: Class
subclass of: quantitative quality

at-risk population
type: Class
subclass of: quantitative quality
description: Population groups with an increased likelihood of a disease or other health issue

Epidemiology, Geographic Location
type: Class
subclass of: BFO_0000016
IAO_0000118: geographic location

infectious dose
type: Class
subclass of: quantitative quality
description: The dose of pathogens received by the exposed individual.

recovery rate
type: Class
subclass of: quantitative quality
description: The rate of population recovering from and infection.

incidence proportion ratio
type: Class
subclass of: quantitative quality
subclass of: Restriction
  on property: quality of
  some values from: person
description: 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.

period prevalence
type: Class
subclass of: quantitative quality
description: 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.

planned process
type: Class
subclass of: BFO_0000015

evaluant role
type: Class
subclass of: BFO_0000023

assay
type: Class
subclass of: planned process

population
type: Class
subclass of: BFO_0000040

cohort role
type: Class
subclass of: BFO_0000023

organism
type: Class
subclass of: BFO_0000040

clinical history
type: Class
subclass of: clinical data item

disease
type: Class
subclass of: BFO_0000016

disease course
type: Class
subclass of: BFO_0000015
subclass of: Class
  intersection of: BFO_0000015
  intersection of: Restriction
    on property: process is result of
    all values from: infectious process
  intersection of: Restriction
    on property: has participant
    all values from: person
  intersection of: Restriction
    on property: projects onto temporal region
    qualified cardinality: 1
    on class: BFO_0000008
IAO_0000118: timecourse of disease
IAO_0000118: timeline of disease

clinical data item
type: Class
subclass of: data item

spatial pattern
type: Class
subclass of: BFO_0000019
IAO_0000118: geographic distribution

morbidity
type: Class
subclass of: quantitative quality

study group population size
type: Class
subclass of: quantitative quality
IAO_0000118: population size
IAO_0000118: sample size
description: Statistical sample size is a count evaluating the number of individual experimental units.

diagnostic specificity
type: Class
subclass of: quantitative quality
description: 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.

odds ratio
type: Class
subclass of: quantitative quality
subclass of: Restriction
  on property: quality of
  some values from: person

confidence interval
type: Class
subclass of: data item

cohort
type: Class
subclass of: population

sensitivity
type: Class
subclass of: quantitative quality
description: Ability to identify every single case of disease.

relative risk
type: Class
subclass of: quantitative quality
subclass of: Class
  intersection of: Restriction
    on property: quality of
    some values from: BFO_0000008
  intersection of: Restriction
    on property: quality of
    some values from: person
description: 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.

prevalence
type: Class
subclass of: quantitative quality
description: 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.

mortality rate
type: Class
subclass of: quantitative quality

risk difference
type: Class
subclass of: quantitative quality

transmission
type: Class
subclass of: BFO_0000015

unit
type: Class
subclass of: datum label

viral load
type: Class
subclass of: quantitative quality
description: Numerical expression of the quantity of virus in a given volume of fluid.

vaccine efficacy
type: Class
subclass of: quantitative quality
description: Percentage reduction in disease incidence attributable to vaccination.

neonatal mortality rate
type: Class
subclass of: quantitative quality

birth rate
type: Class
subclass of: quantitative quality

DEPRECATED chronoid
type: Class
deprecated: true

DEPRECATED concrete
type: Class
deprecated: true

DEPRECATED event
type: Class
deprecated: true

DEPRECATED individual
type: Class
deprecated: true

DEPRECATED left time boundary
type: Class
deprecated: true

DEPRECATED occurrent
type: Class
deprecated: true

DEPRECATED process
type: Class
deprecated: true

DEPRECATED processual structure
type: Class
deprecated: true

DEPRECATED right time boundary
type: Class
deprecated: true

DEPRECATED space
type: Class
deprecated: true

DEPRECATED space time entity
type: Class
deprecated: true

DEPRECATED temporal region
type: Class
deprecated: true

DEPRECATED time
type: Class
deprecated: true

DEPRECATED time boundary
type: Class
deprecated: true

point prevalence
type: Class
subclass of: quantitative quality
subclass of: Restriction
  on property: quality of
  some values from: BFO_0000008
description: Type of prevalence where the data have been collected for one point of time.