diff --git a/src/ontology/midas-data.owl b/src/ontology/midas-data.owl new file mode 100644 index 0000000..e21ce65 --- /dev/null +++ b/src/ontology/midas-data.owl @@ -0,0 +1,2081 @@ + + + + + An ontology of midas data types. + Testing automated release process by editing the midas-data-edit.owl file. + 2024-02-27 + + + + + + + + + + + + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + + + + + + + example of usage + example of usage + + + + + + + + has curation status + has curation status + + + + + + + + definition + definition + textual definition + + + + + + + + editor note + editor note + + + + + + + + definition editor + definition editor + term editor + term editor + + + + + + + + alternative term + alternative term + + + + + + + + definition source + definition source + + + + + + + + imported from + + + + + + + + elucidation + + + + + + + + term replaced by + + + + + + + + STATO alternative term + + + + + + + + Unique Apollo Label + + + + + + + + + + + + + + Creator + + + + + + + + + + + + + + + + + + + + dc:type + + + + + + + + + + + + + + + + + + + + + + + + + + database_cross_reference + + + + + + + + has exact synonym + has_exact_synonym + + + + + + + + has_obo_namespace + + + + + + + + id + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + + + + + + + label + label + + + + + + + + + + + + + + An action specification giving the number of vaccinations possible in a population during a specific time interval. + The counts of individuals that could be vaccinated in a population location per time step unit in the absence of any vaccine supply constraints. It represents the capacity of medical system to vaccinate individuals. + vaccination administration capacity + + + + + + + + + A census that is the specific outcome of a population demographic survey. + Mathias Brochhausen + A census that is the specific outcome of a population demographic survey. + population demographic census + + + + + + + + + An algorithm that models the progress of a transmissible disease in a population. + An algorithm that models the progress of a transmissible disease in a population. + disease transmission model + disease transmission model + + + + + + + + + An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon. + An organism, virus, or prion that can infect another organism. + pathogen + pathogen + + + + + + + + + An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. + An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. + host + host + + + + + + + + + A data set that is a collection of case records. + Matthew Diller + William R. Hogan + A data set that is a collection of case records. + CaseList + infection case list + + + + + + + + + population mortality data set + 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. + Matthew Diller + William R. Hogan + 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 + + + + + + + + + climate data set + A data set that is an aggregate of data items that are about an environmental system process (e.g., hydrological precipitation) or a participant in an environmental system process. + Matt Diller + William R. Hogan + climate data set + + + + + + + + + abiotic ecosystem data set + A data set that is about some abiotic ecosystem or abiotic ecosystem element. + William R. Hogan + abiotic ecosystem dataset + data set about an abiotic ecosystem or abiotic ecosystem element + A data set that is about an abiotic ecosystem or some abiotic ecosystem element. + abiotic ecosystem data set + + + + + + + + + census of treatment facility + A census that counts the number of treatment facilities of some kind in a particular geographical region. + William R. Hogan + census of treatment facilities + treatment facilities census + treatment facility census + A census that counts the number of treatment facilities of some kind in a particular geographical region. + NOTE: this class counts the facilities themselves, not patients (people) in those facilities. For example, how many hospitals in a state. Not how many patients are in a hospital or hospitals in a state. + treatment facility census + + + + + + + + + dataset about hospital stays + The datasets at this link are rdf:type this class: https://www.opendataphilly.org/dataset/covid-hospitalizations + a dataset that is about two or more hospital stays involving two or more patients. + William R. Hogan + hospital discharge dataset + hospitalization dataset + The dataset may be limited to stays in one hospital, but hospital discharge datasets as compiled by state departments of health typically contain stays from multiple hospitals (typically every hospital) in the geographical region over which they have jurisdiction + hospital stay dataset + + + + + + + + + human daily movement behavior data set + https://www.google.com/covid19/mobility/ + a data set that is about the human daily movement behavior of the individual huamns in a given population. + William R. Hogan + human daily movement data set + + + + + + + + + potentially infectious contact process data set in a population + a data set that is about one or more potentially infectious contact processes in a population of host organisms. + William R. Hogan + contact data set + potentially infectious contact data set + + + + + + + + + infectious disease control strategy census + a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem. + William R. Hogan + control strategy census + + + + + + + + + school closure infectious disease control strategy census + an infectious disease control strategy census that is about school closure infectious disease control strategies implemented in a particular geographical region. + William R. Hogan + This class represents datasets about strategies for school closure. Datasets about individual actual school closures go elsewhere. + school closure control strategy census + + + + + + + + + population vaccination census + vaccine / immunization registry data, vaccination / immunization records extracted from an EHR + a population treatment census that is about one or more vaccinations of organisms in a population. + William R. Hogan + vaccination census + vaccination administration census + + + + + + + + + dataset about excess mortality in a population + 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. + William R. Hogan + Often used during epidemics or pandemics to estimate the death toll. + excess mortality dataset + + + + + + + + + census of supplies of vaccine products + A control strategy inventory census that counts available vaccine doses of one or more similar vaccines. + William R. Hogan + vaccine availability + Motivated my MIDAS coordination center indexing of COVID-19 data, software, etc. + +By "similar vaccines" we typically mean same pathogen, but could be similar in other ways (requiring refrigeration of a certain kind). + census of vaccination supplies + + + + + + + + + census of facilities that conduct clinical laboratory tests + A census of facilities that conduct clinical laboratory testing. + William R. Hogan + testing availability + The census might also include information about each facility such as operating hours, address, accessibility, and so on. + laboratory testing facility census + + + + + + + + + laboratory testing capacity action specification + An action specification giving the number of laboratory tests of a certain type that it is possible to perform in a given population during a specific time interval. + William R. Hogan + laboratory testing capacity + + + + + + + + + data set about Earth's atmospheric weather + A data set about the Earth's atmospheric weather + William R. Hogan + weather data set + + + + + + + + + A disease surveillance data set that is about some wastewater disease surveillance. + Matthew Diller + sewage surveillance data + wastewater surveillance data set + + + + + + + + + A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic. + William R. Hogan + A count of cases from the beginning of the epidemic until recently. + The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. + cumulative epidemic case count + + + + + + + + + A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic. + William R. Hogan + A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week. + Incident case counts are measured according to regular intervals, typically day or week. + The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin. + incident epidemic case count + + + + + + + + + A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic infection count + + + + + + + + + A count of infections in a population where the infections are an occurrent part of the same epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic infection count + + + + + + + + + A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic death count + + + + + + + + + A count of deaths in a population where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic death count + + + + + + + + + A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic hospitalization count + + + + + + + + + A count of hospitalizations in a population where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic hospitalization count + + + + + + + + + A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is the region occupied by the entire epidemic. + William R. Hogan + cumulative epidemic vaccination count + + + + + + + + + A count of vaccinations in a population where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the region occupied by the entire epidemic. + William R. Hogan + incident epidemic vaccination count + + + + + + + + + An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization. + William R. Hogan + An intent to be vaccinated in the future. + intent to be vaccinated + + + + + + + + + An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system. + William R. Hogan + An intention to give a vaccine to someone or an animal. + intent to vaccinate + + + + + + + + + A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab. + William R. Hogan + vaccination with nirsevimab + + + + + + + + + An antigen capable, on its own, of inducing an immune response. + immunogenicity + http://purl.obolibrary.org/obo/chebi/213/chebi.owl + PMID:19152635 + PMID:19328011 + PMID:19397283 + chebi_ontology + CHEBI:60816 + + Europe PMC + immunogen + + + + + + + + + a clinical trial is a medical interventional study where participants are assigned prospectively to an intervention or interventions according to a protocol to evaluate the safety and efficacy of the intervention(s) on biomedical or other health related outcomes. The Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, preventive care, etc. + Oliver He, Asiyah Yu Lin, Qingliang Li + interventional trial + https://clinicaltrials.gov/ct2/search/map + https://en.wikipedia.org/wiki/Clinical_trial + https://prsinfo.clinicaltrials.gov/definitions.html + https://www.who.int/ictrp/en/ + http://purl.obolibrary.org/obo/cto.owl + clinical trial + + + + + + + + + A Coronavirus infection that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2. + http://purl.obolibrary.org/obo/doid/releases/2022-08-29/doid.owl + ICD10CM:U07.1 + MESH:D000086382 + NCI:C171133 + SNOMEDCT_US_2021_09_01:840539006 + UMLS_CUI:C5203670 + url:https://www.cdc.gov/coronavirus/2019-ncov/about/index.html + url:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049 + url:https://www.ncbi.nlm.nih.gov/pubmed/?term=32007143 + url:https://www.ncbi.nlm.nih.gov/pubmed/?term=32007145 + url:https://www.who.int/emergencies/diseases/novel-coronavirus-2019 + 2019 Novel Coronavirus (2019-nCoV) + 2019-nCoV infection + COVID19 + SARS-CoV-2 infection + Wuhan coronavirus infection + Wuhan seafood market pneumonia virus infection + disease_ontology + DOID:0080600 + COVID-19 + + + + + + + + + A viral infectious disease that results in infection of primates, rodents and humans, located in skin, has_material_basis_in Monkeypox virus, which is transmitted by contact with the animal's blood, body fluids, rash, or with the body fluids of a sick person, transmitted by fomites, and transmitted by respiratory droplets. The infection has symptom fever, has symptom muscle ache, has symptom headache, and has symptom lymphadenopathy. + http://purl.obolibrary.org/obo/doid/releases/2022-08-29/doid.owl + + GARD:10722 + ICD10CM:B04 + ICD9CM:059.01 + MESH:D045908 + NCI:C128421 + SNOMEDCT_US_2021_09_01:240466002 + UMLS_CUI:C0276180 + url:http://www.cdc.gov/ncidod/monkeypox/factsheet2.htm + disease_ontology + DOID:3292 + + + mpox + + + + + + + + + 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. + http://purl.obolibrary.org/obo/doid/releases/2022-08-29/doid.owl + + MESH:D004194 + NCI:C2991 + SNOMEDCT_US_2021_09_01:64572001 + UMLS_CUI:C0012634 + url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ + disease_ontology + DOID:4 + + + disease + + + + + + + + + software + + Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit. + see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert + PERSON: Melanie Courtot + GROUP: OBI + http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl + software + + + + + + + + + data set + Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). + + + A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. + 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type + 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000042 + OBI_0000042 + group:OBI + http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl + dataSets + data set + + + + + + + + + A disease whose physical basis is an infectious disorder. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + tranmissible disease + http://purl.obolibrary.org/obo/ido/2017-11-03/ido.owl + The disposition is realized in an infectious disease course. + infectious disease + + + + + + + + + A quality that inheres in an organism population and is the number of organisms in the population that have antibod +y specific for an infectious agent in their serum at a specified time. + Albert Goldfain + Alexander Diehl + Lindsay Cowell + Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious +agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics. + infectious agent seroprevalence + + + + + + + + + mumps infectious disease + + + + + + + + + respiratory syncytial virus infectious disease + + + + + + + + + West Nile fever + + + + + + + + + measles + + + + + + + + + malaria + + + + + + + + + dengue disease + + + + + + + + + Ebola hemorrhagic fever + + + + + + + + + influenza + + + + + + + + + AIDS + + + + + + + + + tuberculosis + + + + + + + + + Zika virus infectious disease + + + + + + + + + vector-borne disease + + + + + + + + + http://purl.obolibrary.org/obo/doid/releases/2022-08-29/doid.owl + Monkeypox virus + + + + + + + + + West Nile virus + + + + + + + + + Measles morbillivirus + + + + + + + + + Human orthopneumovirus + + + + + + + + + unidentified influenza virus + + + + + + + + + Influenza A virus + + + + + + + + + Influenza B virus + + + + + + + + + Human immunodeficiency virus 1 + + + + + + + + + Human immunodeficiency virus 2 + + + + + + + + + Dengue virus + + + + + + + + + Human immunodeficiency virus + + + + + + + + + Mycobacterium tuberculosis + + + + + + + + + Ebolavirus + + + + + + + + + Mumps orthorubulavirus + + + + + + + + + SARS-CoV-2 + GC_ID:1 + 2019-nCoV + COVID-19 virus + HCoV-19 + Human coronavirus 2019 + SARS-2 + SARS-CoV2 + SARS2 + ncbi_taxonomy + Severe acute respiratory syndrome coronavirus 2 + + + + + + + + + Plasmodium + + + + + + + + + Zika virus + + + + + + + + + GC_ID:1 + human + ncbi_taxonomy + Homo sapiens + + + + + + + + + + data service + Data analysis service such statistical abalysis or storage service such data backup. + + A service that has some information content entity as input and output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Carlo Torniai + http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl + Information content entity was used as specified input and output since it was more appropriate then data item or dataset. + data service + + + + + + + + + A social identity information content entity that is about whether some person identifies as some ethnicity. + S. Clint Dowland + http://purl.obolibrary.org/obo/omrse/releases/2022-09-06/omrse.owl + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + Ethnicity is separate from but related to racial identity. It refers more to identifying with a particular culture than with individuals similar in physical appearance. It includes things like Hispanic ethnicity (which spans many nations) and national cultural identities like Irish and ethnic groups within nations such as Catalan and Armenian. + ethnic identity information content entity + + + + + + + + + A social identity information content entity that is about whether some person identifies as some gender. + S. Clint Dowland + http://purl.obolibrary.org/obo/omrse/releases/2022-09-06/omrse.owl + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + gender identity information content entity + + + + + + + + + A social identity information content entity that is about whether some person identifies as some race. + S. Clint Dowland + http://purl.obolibrary.org/obo/omrse/releases/2022-09-06/omrse.owl + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + racial identity information content entity + + + + + + + + + An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. + http://purl.obolibrary.org/obo/pato/releases/2022-08-31/pato.owl + quality + PATO:0001894 + + phenotypic sex + + + + + + + + + A collection of discontinuous sequences. + http://purl.obolibrary.org/obo/so/2021-11-22/so.owl + SO:ke + sequence collection + sequence + SO:0001260 + sequence collection + + + + + + + + + + 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. + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + adapted from Wikipedia: +http://en.wikipedia.org/wiki/Statistical_model + +last accessed: 14/01/2014 + http://purl.obolibrary.org/obo/stato.owl + statistical model + statistical model + + + + + + + + + A medical diagnosis associated with a given outbreak or dataset related to that outbreak. Usually will refer to an ICD, NCIT, UMLS, or similar code. + + diagnosis + true + + + + + + + + + Level of details of the location: ADMIN0, ADMIN1, Country, State, … (can be multiple). + List comes from GEONAMES class like: "Dependent political entity" or "First-order administrative division", but it also contains common terms (from https://en.wikipedia.org/wiki/Administrative_division for example) to help with the data entry + geographical resolution + + + + + + + + + Expertise-driven estimates from epidemiologists, modelers, or others with domain knowledge + expert assessment / opinion + + + + + + + + + Descriptors of the data found in the dataset - broadly categorizing the entries that might be annotated with this model + digital object type + + + + + + + + + A collection of links to other data items, often found in external repositories. No claims are made as to the format or consistency of the items associated with those links. + Probably should link to some external dataset. + catalog + + + + + + + + + An interactive display, usually in the form of a web page, that provides a summary of the current state of some dataset, usually from multiple perspectives. May include both counrs and forecats. + link to some existing ontological term? + dashboard + + + + + + + + + Code that allows users to change input and obtain modified output (interactive) + http://purl.obolibrary.org/obo/IAO_0000010 + link to some external entity? + Software + true + + + + + + + + + A collection of data presented in a formatted and defined manner, along with metadata enabling interpretation of that data. Might be one of the elements in a catalog or repository + http://purl.obolibrary.org/obo/IAO_0000100 + is there some existing external definition to tie this to? + Dataset + true + + + + + + + + + The goal or purpose of a modeling study. + modeling purpose + + + + + + + + + The method or type of model used to achieve the purpose. + modeling method + + + + + + + + + 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 + + + + + + + + + data on occurrences of different pathogen species, strains, clades, or variants + variant cases + + + + + + + + + The subject of the digital object - what it is about. + topic + + + + + + + + + An environmental dataset about natural cover of land surface such as forest, plains, rock, etc. or about human land development. + land cover / land use + + + + + + + + + Information about capacity, including hospital beds, PPE supplies, nursing home capacity, testing sites, therapeutics, etc. + health system capacity + + + + + + + + + An environmenal dataset about air contaminants that threaten human health. + air quality + + + + + + + + + An environmental dataset about destruction of entities in an ecosystem including living things and human-built sructures and artifacts by overwhelming natural phenomena such as hurricanes, tornadoes, tsunamis, earthquakes, and volcano eruptions. + natural disasters + + + + + + + + + + Code for facilitating access to modeling data from a remote source. + http://purl.obolibrary.org/obo/OBI_0001530 + Data retrieval/API + true + + + + + + + + + Construction and/or visualization of phylogenetic trees based on sequence data + phylogenetics + + + + + + + + + Analysis and comparison of DNA, RNA, or other sequence data. Includes all types of analysises, including alignment, cleaning, and other comparisons. + http://purl.obolibrary.org/obo/SO_0001260 + Sequence data + true + + + + + + + + + Papers describing modeling studies + modeling studies + + + + + + + + + A collection of information in various types of structured or non-structured formats + repository + + + + + + + + + A catalog focused on a specific disease + disease-specific collection + + + + + + + + + Information about diagnostic tests, results, including serology tests, PCR, and other tests + diagnostic tests + + + + + + + + + Data on impact of outbreak on humanitarian efforts + aid/responses + + + + + + + + + Data describing human behavior in terms of shopping gathering, transit, etc. + http://w3id.org/midas-metadata/midas79 + Behavior + true + + + + + + + + + Counts of cases, deaths, etc. Often includes multiple types of counts as not compatible with more specific labels. Information about diagnostic tests, results, including serology tests, PCR, and other tests. Can include various methods of estimation, including the COVID-19 Forecast and Scenario Hubs + case counts + + + + + + + + + Associated with the 2019-2020 COVID-19 outbreak. + http://purl.obolibrary.org/obo/DOID_0080600 + COVID-19 + ICD Code U07.1 + true + + + + + + + + + Forecasts based on SIR (Susceptible, Infected, Recovered) models or any of the many variants of this basic famework. + compartmental models + + + + + + + + + Information about population counts, and counts for subgroups + http://purl.obolibrary.org/obo/APOLLO_SV_00000159 + Demographics + true + + + + + + + + + includes social, economic, also mental health impact + socio-economic impacts + + + + + + + + + Events that were cancelled due to an outbreak + event cancellations + + + + + + + + + Increases in deaths potentially attributable to an outbreak + http://purl.obolibrary.org/obo/APOLLO_SV_00000608 + Excess mortality + true + + + + + + + + + Expertise-driven estimates from epidemiologists, modelers, or others with domain knowledge + http://w3id.org/midas-metadata/midas04 + expert opinion forecasts + true + + + + + + + + + The "domain" of the entity - specifically, the focus of the data contained therein. + biological scale + + + + + + + + + Health systems/providers participating in some aspect of relevant data + http://purl.obolibrary.org/obo/APOLLO_SV_00000595 + Health systems + true + + + + + + + + + Includes diagnosed cases, deaths, hospitalizations. Also known as line lists. + http://purl.obolibrary.org/obo/APOLLO_SV_00000397 + Individual cases reported + true + + + + + + + + + Models based on simulated actions of individuals and interactions between those individuals + agent-based models + + + + + + + + + Impacts of outbreak on human movement + http://purl.obolibrary.org/obo/APOLLO_SV_00000602 + Mobility + true + + + + + + + + + Aggregate descriptions of multiple factors invovling susceptibility to outbreaks + risk factors + + + + + + + + + Numbers of deaths + http://purl.obolibrary.org/obo/APOLLO_SV_00000542 + Deaths + true + + + + + + + + + Information about vaccination, lockdowns, school closures, other interventions + http://purl.obolibrary.org/obo/APOLLO_SV_00000604 + Public health interventions and policies + true + + + + + + + + + Descriptors of the behavior of an outbreak + modeling + + + + + + + + + Where tests are available, how mmany tests, etc. + http://purl.obolibrary.org/obo/APOLLO_SV_00000610 + Testing availability + true + + + + + + + + + Places where outbreaks are transmitted. + http://purl.obolibrary.org/obo/APOLLO_SV_00000603 + Transmission settings + true + + + + + + + + + Reports of policy violations + regulatory complaints + + + + + + + + + Counts of inpatients by region, facilty, etc. + http://purl.obolibrary.org/obo/APOLLO_SV_00000600 + Hospitalizations + true + + + + + + + + + Policies undertaken to slow spread or otherwise combat outbreaks + Interventions + true + + + + + + + + + + Tools for initial stages of data processing, usually prior to modeling. Includes pre-processing, cleaning, exploratory analysis. + data preparation + + + + + + + + + Predicted value of key outbreak parameters, including (but not limited to) fatality rate, R_0, etc. + parameter estimation + + + + + + + + + Estimates of understanding potential impacts of aspects of human behavior on transmission risk , often under different scenarios. + http://purl.obolibrary.org/obo/APOLLO_SV_00000174 + Need a clearer distinction to distinguish from other parameter estimation. + Transmission modeling + true + + + + + + + + + Models of interactions between entities that might impact outbreak progression. + network modeling + + + + + + + + + Collections of entities from the research literature, or derived from the literature. + literature + + + + + + + + + Data regarding the availability or administration of vaccinations. + http://purl.obolibrary.org/obo/APOLLO_SV_00000609 + Vaccinations + true + + + + + + + + + Information about the edudcational institutions that either paused in-person instruction or closed entirely in repsonse to an outbreak. + http://purl.obolibrary.org/obo/APOLLO_SV_00000605 + School closures + true + + + + + + + + + Information about population mobility: Flights , trains, general travel, cruise ships, etc. + http://purl.obolibrary.org/obo/APOLLO_SV_00000602 + Mobility + true + + + + + + + + + Information about media, coverage about a topic + media + + + + + + + + + Population data divided by age ranges + age-stratified + + + + + + + + + Groups of people relevant to specific locations - schools, nursing homes, prisons, etc. + location-specific + true + + + + + + + + + Name of the location in English at country or ADMIN1 level corresponding from GEONAMES (if more than 10 different countries possible "Earth" can be used). + Also have Continent and Earth information as some data set have data for multiple countries but in the same continent. + geographical scope + + + + + + + + + Estimates of parameter values based on expert opinion + http://w3id.org/midas-metadata/midas04 + expert assessments of parameter values + true + + + + + + + + + Actions of groups of people in response to outbreaks. + behavior + + + + + + + + + Items referring to sequence-level data, including genomics, microbiomics, proteomics, etc. + molecular + + + + + + + + + data about high-risk areas, and places where transmission is likely to happen. + http://purl.obolibrary.org/obo/APOLLO_SV_00000603 + Transmission settings + true + + + + + + + + + Frequency of interactions between individuals in different settings, at different times... + contact rates + + + + + + + + + Rates of compliance with policies/interventions including mask wearing, facility closures, large events, etc. + policy adherence + + + + + + + + + Claims of false or unsubstantiated rumors about any aspect of an outbreak. + conspiracy theories + + + + + + + + + Estimates of reluctance to being vaccinated. + vaccine hesitancy + + + + + + + + + Datasets discussing outbreaks on social media sites + social media + + + + + + + + + Items corresponding to entire populations or subpopulations. Might be geographically or temporally temporally limited. + population + + + + + + +