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