diff --git a/midas-data.owl b/midas-data.owl index df3f984..2e1919b 100644 --- a/midas-data.owl +++ b/midas-data.owl @@ -17,11 +17,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:apollo_sv="http://purl.obolibrary.org/obo/apollo_sv.owl/"> - + An ontology of midas data types. https://creativecommons.org/licenses/by/4.0/ Testing automated release process by editing the midas-data-edit.owl file. - 2025-11-21 + 2026-05-28 @@ -361,10 +361,20 @@ + + + + + Practices involved in preventing the transmission of diseases by hand. + Hand Hygiene + + + + - + An action specification giving the number of vaccinations possible in a population during a specific time interval. Vaccination Capacity 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. @@ -384,13 +394,51 @@ One property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating. -While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations. - +While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations. simulation time series + + + + + A plan specification whose objective specification is an infectious disease control objective specification. + Control Strategy + A plan with the goal of preventing or mitigating the effects of infections in a population due to one or more pathogens. + InfectiousDiseaseControlMeasure + The essential goal of an infectious disease control strategy is to protect the susceptible organisms in a population. + infectious disease control strategy + + + + + + + + + A place closure control strategy whose action specification is realized in a school closure process. + School Closure + A control measure in which schools are closed in an attempt to reduce transmission of disease. + SchoolClosureControlStrategy + school closure control strategy + + + + + + + + + An individual treatment control strategy that has as part an action specification that is realized in a vaccination process. + vaccination + An individual treatment control strategy that administers one or more vaccines to individuals in a population with the goal of inducing resistance to infection with a particular pathogen in those individuals. + vaccination control strategy + + + + @@ -401,6 +449,7 @@ While in many pieces of fiction the order in which the purely intentional entiti A treatment of an individual with antigenic material from a pathogen that has the goal of inducing resistance of the individual to infection with the pathogen. Vaccination vaccination + true @@ -431,6 +480,76 @@ While in many pieces of fiction the order in which the purely intentional entiti + + + + + A census about a particular medical treatment of a population. + Treatment Census + A census of a population that determines for a particular treatment whether each organism in the population has undergone that treatment. + PopulationTreatmentCensus + population treatment census + + + + + + + + + vaccination control strategy, antiviral control strategy + An infectious disease control strategy that immediately targets individuals. + Mathias Brochhausen + individual treatment + An infectious disease control strategy that immediately targets individuals. + IndividualTreatmentControlMeasure + individual treatment control strategy + + + + + + + + + A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders. + William R. Hogan + Border Control + A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders. + BorderControlMeasure + border control strategy + + + + + + + + + An infectious disease control strategy that has an action specification that is realized in closing facilities where organisms congregate during times when the facilities normally would be open. + William R. Hogan + Place Closure + An infectious disease control strategy that attempts to prevent infection of susceptible host organisms in a population by preventing potentially infectious contacts (for a particular pathogen) among the organisms in the population. + PlaceClosureControlMeasure + place closure control strategy + + + + + + + + + A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one ecosystem to another ecosystem + William R. Hogan + Travel Restriction + A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one geographical region to another + TravelRestrictionControlMeasure + travel restriction control strategy + + + + @@ -457,6 +576,49 @@ While in many pieces of fiction the order in which the purely intentional entiti + + + + + A place-closure control strategy that decides on a case-by-case basis whether to close places of a certain type, as opposed to blanket policy that closes all places of a certain type at the same time. + Close Individual Places + A place-closure control strategy that decides on a case-by-case basis whether to close places of a certain type, as opposed to blanket policy that closes all places of a certain type at the same time. + closeIndividualPlacesIndependently + close individual places independently strategy + + + + + + + + + An individual treatment control strategy that has as part an action specification that is realized in anti-infective treatment. + William R. Hogan + anti-infective treatment + An anti-infective individual treatment control strategy that uses anti-infective medications to treat infected hosts in an attempt to limit their infectiousness and/or infectious period. + DrugTreatmentControlStrategy + anti-infective control strategy + anti-infective individual treatment control strategy + + + + + + + + + An infectious disease control strategy that has a vector control action specification as part. + William R. Hogan + Vector Control + An infectious disease control strategy that attempts to reduce infections in a population of a particular host species by limiting infection acquisitions from a second host species, called the 'vector'. + VectorControlMeasure + Typically, the strategy is to limit the population of the second host species, which is called the "vector" for the infection. + vector control strategy + + + + @@ -467,6 +629,20 @@ While in many pieces of fiction the order in which the purely intentional entiti Treatment with a drug. DrugTreatment drug treatment + true + + + + + + + + + An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts. + William R. Hogan + An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts. + VoluntaryHouseholdQuarantineControlMeasure + voluntary household quarantine control strategy @@ -486,6 +662,34 @@ While in many pieces of fiction the order in which the purely intentional entiti + + + + + infectious disease control strategy to prevent infection acquisition by individuals traveling from one ecosystem to another ecosystem + An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem. + William R. Hogan + Travel-related Control Strategy + An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem. + travel-related infectious disease control strategy + + + + + + + + + travel recommendation infectious disease control strategy + A travel-related infectious disease control strategy that has an action specification that is realized by making recommendations to travelers to either (1) avoid travel to an ecosystem with an ongoing infection such as an epidemic, (2) take precautions when traveling to such an ecosystem, (3) receive certain vaccinations prior to traveling to such an ecosystem, or (4) take certain medications when traveling to such an ecosystem + William R. Hogan + Travel Recommendation + A travel-related infectious disease control strategy that recommends to travelers to either (1) avoid travel to a region with an ongoing infection such as an epidemic, (2) take precautions when traveling to such a region, (3) receive certain vaccinations prior to traveling to such a region, or (4) take certain medications when traveling to such a region + travel recommendation control strategy + + + + @@ -516,6 +720,20 @@ While in many pieces of fiction the order in which the purely intentional entiti + + + + + An infectious disease control strategy that identifies and treats contacted organisms in a host population. + Matthew Diller + William R. Hogan + Contact Tracing + An infectious disease control strategy that identifies and treats contacted organisms in a host population. + contact tracing + + + + @@ -557,7 +775,6 @@ While in many pieces of fiction the order in which the purely intentional entiti Treatment Facility 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 @@ -571,7 +788,7 @@ While in many pieces of fiction the order in which the purely intentional entiti 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. + A dataset that is about two or more hospital stays involving two or more patients. William R. Hogan Hospitalization hospital discharge dataset @@ -588,7 +805,7 @@ While in many pieces of fiction the order in which the purely intentional entiti 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. + A data set that is about the human daily movement behavior of the individual huamns in a given population. William R. Hogan Human Movement human daily movement data set @@ -601,7 +818,7 @@ While in many pieces of fiction the order in which the purely intentional entiti 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. + 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 @@ -615,9 +832,9 @@ While in many pieces of fiction the order in which the purely intentional entiti 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. + 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 + Control Strategy Census control strategy census @@ -628,9 +845,9 @@ While in many pieces of fiction the order in which the purely intentional entiti 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. + An infectious disease control strategy census that is about school closure infectious disease control strategies implemented in a particular geographical region. William R. Hogan - School Closure + School Closure Census This class represents datasets about strategies for school closure. Datasets about individual actual school closures go elsewhere. school closure control strategy census @@ -640,10 +857,10 @@ While in many pieces of fiction the order in which the purely intentional entiti - + 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. + A population treatment census that is about one or more vaccinations of organisms in a population. William R. Hogan Vaccination Administration vaccination census @@ -669,7 +886,7 @@ While in many pieces of fiction the order in which the purely intentional entiti - + 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 @@ -749,6 +966,19 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations. + Matthew Diller + Lockdown + The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services. + lockdown infectious disease control measure + + + + @@ -797,6 +1027,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si William R. Hogan Nirsevimab Vaccination vaccination with nirsevimab + true @@ -2512,8 +2743,8 @@ agent seroprevalence will depend on a type of infectious agent and a population. A genus in the family FILOVIRIDAE consisting of several distinct species of Ebolavirus, each containing separate strains. These viruses cause outbreaks of a contagious, hemorrhagic disease (HEMORRHAGIC FEVER, EBOLA) in humans, usually with high mortality. + Ebolavirus Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus - Ebolavirus @@ -2571,7 +2802,18 @@ agent seroprevalence will depend on a type of infectious agent and a population. A genus of FLAVIVIRIDAE causing parenterally-transmitted HEPATITIS C which is associated with transfusions and drug abuse. Hepatitis C virus is the type species. Hepatitis C virus Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus - Hepacivirus hominis + Orthohepacivirus hominis + + + + + + + + + Small proteinaceous infectious particles which resist inactivation by procedures that modify NUCLEIC ACIDS and contain an abnormal isoform of a cellular protein which is a major and necessary component. The abnormal (scrapie) isoform is PrPSc (PRPSC PROTEINS) and the cellular isoform PrPC (PRPC PROTEINS). The primary amino acid sequence of the two isoforms is identical. Human diseases caused by prions include CREUTZFELDT-JAKOB SYNDROME; GERSTMANN-STRAUSSLER SYNDROME; and INSOMNIA, FATAL FAMILIAL. + prion + Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus @@ -2669,8 +2911,9 @@ agent seroprevalence will depend on a type of infectious agent and a population. A genus of protozoa that comprise the malaria parasites of mammals. Four species infect humans (although occasional infections with primate malarias may occur). These are PLASMODIUM FALCIPARUM; PLASMODIUM MALARIAE; PLASMODIUM OVALE, and PLASMODIUM VIVAX. Species causing infection in vertebrates other than man include: PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; P. vinckei, and PLASMODIUM YOELII in rodents; P. brasilianum, PLASMODIUM CYNOMOLGI; and PLASMODIUM KNOWLESI in monkeys; and PLASMODIUM GALLINACEUM in chickens. + Plasmodium Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus - Plasmodium + Plasmodium <genus> @@ -2913,12 +3156,42 @@ agent seroprevalence will depend on a type of infectious agent and a population. - A computer application that requires with an active internet connection and that uses HTTP as its primary communications protocol. + A computer application that requires an active internet connection and that uses HTTP as its primary communications protocol. Web Application + + + + + The practice of keeping a safe space between yourself and other people. + Social Distancing + + + + + + + + + A barrier device that covers the nose and mouth, used in infection control. + Protective Face Mask + + + + + + + + + Masks, shields, gloves, gowns, boots, or other equipment used to provide coverage against infectious agents or environmental hazards. + Personal Protective Equipment + + + + @@ -2981,6 +3254,27 @@ agent seroprevalence will depend on a type of infectious agent and a population. + + + + + A test whose operational purpose is to determine the presence or absence of a substance, organism, or condition. + Screening Test + + + + + + + + + + Public communication via television, radio, newspapers, pamphlets, telephone, and other media to influence health or social behaviors. + Media Campaign + + + + @@ -3051,6 +3345,16 @@ agent seroprevalence will depend on a type of infectious agent and a population. + + + + + Place into enforced isolation. + Quarantine + + + + @@ -3794,7 +4098,7 @@ last accessed: 14/01/2014 - + Events that were cancelled due to an outbreak Event Cancellations event cancellations @@ -3887,7 +4191,7 @@ last accessed: 14/01/2014 - + Aggregate descriptions of multiple factors invovling susceptibility to outbreaks Risk Factors risk factors @@ -3957,7 +4261,7 @@ last accessed: 14/01/2014 - + Reports of policy violations Regulatory Complaints regulatory complaints @@ -4307,7 +4611,7 @@ last accessed: 14/01/2014 - + A range of activities focused on preventing, managing, and mitigating health issues in wild animal populations, including disease prevention, public health considerations, etc. Wildlife Health Interventions diff --git a/src/ontology/imports/apollo-sv_import.owl.zip b/src/ontology/imports/apollo-sv_import.owl.zip index 128013f..1bec8f6 100644 Binary files a/src/ontology/imports/apollo-sv_import.owl.zip and b/src/ontology/imports/apollo-sv_import.owl.zip differ diff --git a/src/ontology/imports/mondo_import.owl.zip b/src/ontology/imports/mondo_import.owl.zip index cf2d14f..1fe40f8 100644 Binary files a/src/ontology/imports/mondo_import.owl.zip and b/src/ontology/imports/mondo_import.owl.zip differ diff --git a/src/ontology/imports/ncbitaxon_import.owl.zip b/src/ontology/imports/ncbitaxon_import.owl.zip index c5b188e..fc408e2 100644 Binary files a/src/ontology/imports/ncbitaxon_import.owl.zip and b/src/ontology/imports/ncbitaxon_import.owl.zip differ diff --git a/src/ontology/imports/ncit_import.owl.zip b/src/ontology/imports/ncit_import.owl.zip index 0ec6a53..1f939f9 100644 Binary files a/src/ontology/imports/ncit_import.owl.zip and b/src/ontology/imports/ncit_import.owl.zip differ diff --git a/src/ontology/imports/seed.txt b/src/ontology/imports/seed.txt index cfd480f..584cc07 100644 --- a/src/ontology/imports/seed.txt +++ b/src/ontology/imports/seed.txt @@ -41,6 +41,22 @@ APOLLO_SV:00000064 APOLLO_SV:00000617 APOLLO_SV:00000497 APOLLO_SV:00000628 +APOLLO_SV:00000550 +APOLLO_SV:00000229 +APOLLO_SV:00000286 +APOLLO_SV:00000621 +APOLLO_SV:00000322 +APOLLO_SV:00000486 +APOLLO_SV:00000228 +APOLLO_SV:00000231 +APOLLO_SV:00000487 +APOLLO_SV:00000086 +APOLLO_SV:00000123 +APOLLO_SV:00000136 +APOLLO_SV:00000187 +APOLLO_SV:00000194 +APOLLO_SV:00000304 +APOLLO_SV:00000308 NCBITaxon:2 NCBITaxon:11676 NCBITaxon:666 @@ -93,6 +109,7 @@ NCBITaxon:2697049 NCBITaxon:10255 NCBITaxon:11089 NCBITaxon:12059 +NCBITaxon:36469 MONDO:0012268 MONDO:0018076 MONDO:0005812 @@ -179,4 +196,10 @@ NCIT:C171586 NCIT:C15719 NCIT:C173755 NCIT:C14419 +NCIT:C18227 +NCIT:C173748 +NCIT:C173747 +NCIT:C71902 +NCIT:C181548 +NCIT:C173636 IAO:0000115 \ No newline at end of file diff --git a/src/ontology/midas-data-edit.owl b/src/ontology/midas-data-edit.owl index 71ad5b2..1b09ba7 100644 --- a/src/ontology/midas-data-edit.owl +++ b/src/ontology/midas-data-edit.owl @@ -320,10 +320,20 @@ + + + + + Practices involved in preventing the transmission of diseases by hand. + Hand Hygiene + + + + - + Vaccination Capacity @@ -338,11 +348,39 @@ + + + + + Control Strategy + + + + + + + + + School Closure + + + + + + + + + vaccination + + + + Vaccination + true @@ -365,6 +403,51 @@ + + + + + Treatment Census + + + + + + + + + individual treatment + + + + + + + + + Border Control + + + + + + + + + Place Closure + + + + + + + + + Travel Restriction + + + + @@ -383,11 +466,47 @@ + + + + + Close Individual Places + + + + + + + + + anti-infective treatment + + + + + + + + + Vector Control + + + + Drug Treatment + true + + + + + + + + @@ -401,6 +520,24 @@ + + + + + Travel-related Control Strategy + + + + + + + + + Travel Recommendation + + + + @@ -419,6 +556,15 @@ + + + + + Contact Tracing + + + + @@ -478,7 +624,7 @@ - Control Strategy + Control Strategy Census @@ -487,7 +633,7 @@ - School Closure + School Closure Census @@ -495,7 +641,7 @@ - + Vaccination Administration @@ -513,7 +659,7 @@ - + Vaccination Supplies @@ -564,6 +710,15 @@ + + + + + Lockdown + + + + @@ -596,6 +751,7 @@ Nirsevimab Vaccination + true @@ -2113,6 +2269,7 @@ agent seroprevalence will depend on a type of infectious agent and a population. A genus in the family FILOVIRIDAE consisting of several distinct species of Ebolavirus, each containing separate strains. These viruses cause outbreaks of a contagious, hemorrhagic disease (HEMORRHAGIC FEVER, EBOLA) in humans, usually with high mortality. + Ebolavirus Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus @@ -2176,6 +2333,7 @@ agent seroprevalence will depend on a type of infectious agent and a population. Small proteinaceous infectious particles which resist inactivation by procedures that modify NUCLEIC ACIDS and contain an abnormal isoform of a cellular protein which is a major and necessary component. The abnormal (scrapie) isoform is PrPSc (PRPSC PROTEINS) and the cellular isoform PrPC (PRPC PROTEINS). The primary amino acid sequence of the two isoforms is identical. Human diseases caused by prions include CREUTZFELDT-JAKOB SYNDROME; GERSTMANN-STRAUSSLER SYNDROME; and INSOMNIA, FATAL FAMILIAL. + prion Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus @@ -2266,6 +2424,7 @@ agent seroprevalence will depend on a type of infectious agent and a population. A genus of protozoa that comprise the malaria parasites of mammals. Four species infect humans (although occasional infections with primate malarias may occur). These are PLASMODIUM FALCIPARUM; PLASMODIUM MALARIAE; PLASMODIUM OVALE, and PLASMODIUM VIVAX. Species causing infection in vertebrates other than man include: PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; P. vinckei, and PLASMODIUM YOELII in rodents; P. brasilianum, PLASMODIUM CYNOMOLGI; and PLASMODIUM KNOWLESI in monkeys; and PLASMODIUM GALLINACEUM in chickens. + Plasmodium Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus @@ -2480,6 +2639,30 @@ agent seroprevalence will depend on a type of infectious agent and a population. + + + + + + + + + + + + + + + + + + + + + + + + @@ -2530,6 +2713,22 @@ agent seroprevalence will depend on a type of infectious agent and a population. + + + + + + + + + + + + + + + + @@ -2586,6 +2785,14 @@ agent seroprevalence will depend on a type of infectious agent and a population. + + + + + + + + @@ -3326,7 +3533,7 @@ last accessed: 14/01/2014 - + Events that were cancelled due to an outbreak Event Cancellations event cancellations @@ -3418,7 +3625,7 @@ last accessed: 14/01/2014 - + Aggregate descriptions of multiple factors invovling susceptibility to outbreaks Risk Factors risk factors @@ -3488,7 +3695,7 @@ last accessed: 14/01/2014 - + Reports of policy violations Regulatory Complaints regulatory complaints @@ -3837,7 +4044,7 @@ last accessed: 14/01/2014 - + A range of activities focused on preventing, managing, and mitigating health issues in wild animal populations, including disease prevention, public health considerations, etc. Wildlife Health Interventions diff --git a/src/ontology/midas-data.owl b/src/ontology/midas-data.owl index df3f984..2e1919b 100644 --- a/src/ontology/midas-data.owl +++ b/src/ontology/midas-data.owl @@ -17,11 +17,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:apollo_sv="http://purl.obolibrary.org/obo/apollo_sv.owl/"> - + An ontology of midas data types. https://creativecommons.org/licenses/by/4.0/ Testing automated release process by editing the midas-data-edit.owl file. - 2025-11-21 + 2026-05-28 @@ -361,10 +361,20 @@ + + + + + Practices involved in preventing the transmission of diseases by hand. + Hand Hygiene + + + + - + An action specification giving the number of vaccinations possible in a population during a specific time interval. Vaccination Capacity 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. @@ -384,13 +394,51 @@ One property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating. -While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations. - +While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations. simulation time series + + + + + A plan specification whose objective specification is an infectious disease control objective specification. + Control Strategy + A plan with the goal of preventing or mitigating the effects of infections in a population due to one or more pathogens. + InfectiousDiseaseControlMeasure + The essential goal of an infectious disease control strategy is to protect the susceptible organisms in a population. + infectious disease control strategy + + + + + + + + + A place closure control strategy whose action specification is realized in a school closure process. + School Closure + A control measure in which schools are closed in an attempt to reduce transmission of disease. + SchoolClosureControlStrategy + school closure control strategy + + + + + + + + + An individual treatment control strategy that has as part an action specification that is realized in a vaccination process. + vaccination + An individual treatment control strategy that administers one or more vaccines to individuals in a population with the goal of inducing resistance to infection with a particular pathogen in those individuals. + vaccination control strategy + + + + @@ -401,6 +449,7 @@ While in many pieces of fiction the order in which the purely intentional entiti A treatment of an individual with antigenic material from a pathogen that has the goal of inducing resistance of the individual to infection with the pathogen. Vaccination vaccination + true @@ -431,6 +480,76 @@ While in many pieces of fiction the order in which the purely intentional entiti + + + + + A census about a particular medical treatment of a population. + Treatment Census + A census of a population that determines for a particular treatment whether each organism in the population has undergone that treatment. + PopulationTreatmentCensus + population treatment census + + + + + + + + + vaccination control strategy, antiviral control strategy + An infectious disease control strategy that immediately targets individuals. + Mathias Brochhausen + individual treatment + An infectious disease control strategy that immediately targets individuals. + IndividualTreatmentControlMeasure + individual treatment control strategy + + + + + + + + + A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders. + William R. Hogan + Border Control + A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders. + BorderControlMeasure + border control strategy + + + + + + + + + An infectious disease control strategy that has an action specification that is realized in closing facilities where organisms congregate during times when the facilities normally would be open. + William R. Hogan + Place Closure + An infectious disease control strategy that attempts to prevent infection of susceptible host organisms in a population by preventing potentially infectious contacts (for a particular pathogen) among the organisms in the population. + PlaceClosureControlMeasure + place closure control strategy + + + + + + + + + A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one ecosystem to another ecosystem + William R. Hogan + Travel Restriction + A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one geographical region to another + TravelRestrictionControlMeasure + travel restriction control strategy + + + + @@ -457,6 +576,49 @@ While in many pieces of fiction the order in which the purely intentional entiti + + + + + A place-closure control strategy that decides on a case-by-case basis whether to close places of a certain type, as opposed to blanket policy that closes all places of a certain type at the same time. + Close Individual Places + A place-closure control strategy that decides on a case-by-case basis whether to close places of a certain type, as opposed to blanket policy that closes all places of a certain type at the same time. + closeIndividualPlacesIndependently + close individual places independently strategy + + + + + + + + + An individual treatment control strategy that has as part an action specification that is realized in anti-infective treatment. + William R. Hogan + anti-infective treatment + An anti-infective individual treatment control strategy that uses anti-infective medications to treat infected hosts in an attempt to limit their infectiousness and/or infectious period. + DrugTreatmentControlStrategy + anti-infective control strategy + anti-infective individual treatment control strategy + + + + + + + + + An infectious disease control strategy that has a vector control action specification as part. + William R. Hogan + Vector Control + An infectious disease control strategy that attempts to reduce infections in a population of a particular host species by limiting infection acquisitions from a second host species, called the 'vector'. + VectorControlMeasure + Typically, the strategy is to limit the population of the second host species, which is called the "vector" for the infection. + vector control strategy + + + + @@ -467,6 +629,20 @@ While in many pieces of fiction the order in which the purely intentional entiti Treatment with a drug. DrugTreatment drug treatment + true + + + + + + + + + An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts. + William R. Hogan + An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts. + VoluntaryHouseholdQuarantineControlMeasure + voluntary household quarantine control strategy @@ -486,6 +662,34 @@ While in many pieces of fiction the order in which the purely intentional entiti + + + + + infectious disease control strategy to prevent infection acquisition by individuals traveling from one ecosystem to another ecosystem + An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem. + William R. Hogan + Travel-related Control Strategy + An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem. + travel-related infectious disease control strategy + + + + + + + + + travel recommendation infectious disease control strategy + A travel-related infectious disease control strategy that has an action specification that is realized by making recommendations to travelers to either (1) avoid travel to an ecosystem with an ongoing infection such as an epidemic, (2) take precautions when traveling to such an ecosystem, (3) receive certain vaccinations prior to traveling to such an ecosystem, or (4) take certain medications when traveling to such an ecosystem + William R. Hogan + Travel Recommendation + A travel-related infectious disease control strategy that recommends to travelers to either (1) avoid travel to a region with an ongoing infection such as an epidemic, (2) take precautions when traveling to such a region, (3) receive certain vaccinations prior to traveling to such a region, or (4) take certain medications when traveling to such a region + travel recommendation control strategy + + + + @@ -516,6 +720,20 @@ While in many pieces of fiction the order in which the purely intentional entiti + + + + + An infectious disease control strategy that identifies and treats contacted organisms in a host population. + Matthew Diller + William R. Hogan + Contact Tracing + An infectious disease control strategy that identifies and treats contacted organisms in a host population. + contact tracing + + + + @@ -557,7 +775,6 @@ While in many pieces of fiction the order in which the purely intentional entiti Treatment Facility 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 @@ -571,7 +788,7 @@ While in many pieces of fiction the order in which the purely intentional entiti 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. + A dataset that is about two or more hospital stays involving two or more patients. William R. Hogan Hospitalization hospital discharge dataset @@ -588,7 +805,7 @@ While in many pieces of fiction the order in which the purely intentional entiti 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. + A data set that is about the human daily movement behavior of the individual huamns in a given population. William R. Hogan Human Movement human daily movement data set @@ -601,7 +818,7 @@ While in many pieces of fiction the order in which the purely intentional entiti 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. + 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 @@ -615,9 +832,9 @@ While in many pieces of fiction the order in which the purely intentional entiti 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. + 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 + Control Strategy Census control strategy census @@ -628,9 +845,9 @@ While in many pieces of fiction the order in which the purely intentional entiti 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. + An infectious disease control strategy census that is about school closure infectious disease control strategies implemented in a particular geographical region. William R. Hogan - School Closure + School Closure Census This class represents datasets about strategies for school closure. Datasets about individual actual school closures go elsewhere. school closure control strategy census @@ -640,10 +857,10 @@ While in many pieces of fiction the order in which the purely intentional entiti - + 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. + A population treatment census that is about one or more vaccinations of organisms in a population. William R. Hogan Vaccination Administration vaccination census @@ -669,7 +886,7 @@ While in many pieces of fiction the order in which the purely intentional entiti - + 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 @@ -749,6 +966,19 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations. + Matthew Diller + Lockdown + The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services. + lockdown infectious disease control measure + + + + @@ -797,6 +1027,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si William R. Hogan Nirsevimab Vaccination vaccination with nirsevimab + true @@ -2512,8 +2743,8 @@ agent seroprevalence will depend on a type of infectious agent and a population. A genus in the family FILOVIRIDAE consisting of several distinct species of Ebolavirus, each containing separate strains. These viruses cause outbreaks of a contagious, hemorrhagic disease (HEMORRHAGIC FEVER, EBOLA) in humans, usually with high mortality. + Ebolavirus Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus - Ebolavirus @@ -2571,7 +2802,18 @@ agent seroprevalence will depend on a type of infectious agent and a population. A genus of FLAVIVIRIDAE causing parenterally-transmitted HEPATITIS C which is associated with transfusions and drug abuse. Hepatitis C virus is the type species. Hepatitis C virus Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus - Hepacivirus hominis + Orthohepacivirus hominis + + + + + + + + + Small proteinaceous infectious particles which resist inactivation by procedures that modify NUCLEIC ACIDS and contain an abnormal isoform of a cellular protein which is a major and necessary component. The abnormal (scrapie) isoform is PrPSc (PRPSC PROTEINS) and the cellular isoform PrPC (PRPC PROTEINS). The primary amino acid sequence of the two isoforms is identical. Human diseases caused by prions include CREUTZFELDT-JAKOB SYNDROME; GERSTMANN-STRAUSSLER SYNDROME; and INSOMNIA, FATAL FAMILIAL. + prion + Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus @@ -2669,8 +2911,9 @@ agent seroprevalence will depend on a type of infectious agent and a population. A genus of protozoa that comprise the malaria parasites of mammals. Four species infect humans (although occasional infections with primate malarias may occur). These are PLASMODIUM FALCIPARUM; PLASMODIUM MALARIAE; PLASMODIUM OVALE, and PLASMODIUM VIVAX. Species causing infection in vertebrates other than man include: PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; P. vinckei, and PLASMODIUM YOELII in rodents; P. brasilianum, PLASMODIUM CYNOMOLGI; and PLASMODIUM KNOWLESI in monkeys; and PLASMODIUM GALLINACEUM in chickens. + Plasmodium Definition from NIH National Library of Medecine, National Center for Biotechnology Information; Medical Subject Headings (MeSH) thesaurus - Plasmodium + Plasmodium <genus> @@ -2913,12 +3156,42 @@ agent seroprevalence will depend on a type of infectious agent and a population. - A computer application that requires with an active internet connection and that uses HTTP as its primary communications protocol. + A computer application that requires an active internet connection and that uses HTTP as its primary communications protocol. Web Application + + + + + The practice of keeping a safe space between yourself and other people. + Social Distancing + + + + + + + + + A barrier device that covers the nose and mouth, used in infection control. + Protective Face Mask + + + + + + + + + Masks, shields, gloves, gowns, boots, or other equipment used to provide coverage against infectious agents or environmental hazards. + Personal Protective Equipment + + + + @@ -2981,6 +3254,27 @@ agent seroprevalence will depend on a type of infectious agent and a population. + + + + + A test whose operational purpose is to determine the presence or absence of a substance, organism, or condition. + Screening Test + + + + + + + + + + Public communication via television, radio, newspapers, pamphlets, telephone, and other media to influence health or social behaviors. + Media Campaign + + + + @@ -3051,6 +3345,16 @@ agent seroprevalence will depend on a type of infectious agent and a population. + + + + + Place into enforced isolation. + Quarantine + + + + @@ -3794,7 +4098,7 @@ last accessed: 14/01/2014 - + Events that were cancelled due to an outbreak Event Cancellations event cancellations @@ -3887,7 +4191,7 @@ last accessed: 14/01/2014 - + Aggregate descriptions of multiple factors invovling susceptibility to outbreaks Risk Factors risk factors @@ -3957,7 +4261,7 @@ last accessed: 14/01/2014 - + Reports of policy violations Regulatory Complaints regulatory complaints @@ -4307,7 +4611,7 @@ last accessed: 14/01/2014 - + A range of activities focused on preventing, managing, and mitigating health issues in wild animal populations, including disease prevention, public health considerations, etc. Wildlife Health Interventions diff --git a/src/ontology/mirror/apollo-sv.owl.zip b/src/ontology/mirror/apollo-sv.owl.zip index 4b76169..07ff00b 100644 Binary files a/src/ontology/mirror/apollo-sv.owl.zip and b/src/ontology/mirror/apollo-sv.owl.zip differ diff --git a/src/ontology/mirror/mondo.owl.zip b/src/ontology/mirror/mondo.owl.zip index d767b9f..f669b91 100644 Binary files a/src/ontology/mirror/mondo.owl.zip and b/src/ontology/mirror/mondo.owl.zip differ diff --git a/src/ontology/mirror/ncbitaxon.owl.zip b/src/ontology/mirror/ncbitaxon.owl.zip index 91abb3b..9a3e3d0 100644 Binary files a/src/ontology/mirror/ncbitaxon.owl.zip and b/src/ontology/mirror/ncbitaxon.owl.zip differ diff --git a/src/ontology/mirror/ncit.owl.zip b/src/ontology/mirror/ncit.owl.zip index 0aa5298..dc1275c 100644 Binary files a/src/ontology/mirror/ncit.owl.zip and b/src/ontology/mirror/ncit.owl.zip differ