diff --git a/midas-data.owl b/midas-data.owl index e21ce65..a9d20b4 100644 --- a/midas-data.owl +++ b/midas-data.owl @@ -17,10 +17,10 @@ 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. Testing automated release process by editing the midas-data-edit.owl file. - 2024-02-27 + 2024-04-30 @@ -296,6 +296,19 @@ + + + + + A treatment that consists of the administration of antigenic material to stimulate an individual's immune system to develop adaptive immunity to a pathogen. + Mathias Brochhausen + 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 + + + + @@ -339,7 +352,7 @@ 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 + host organism @@ -577,152 +590,184 @@ By "similar vaccines" we typically mean same pathogen, but could be si - + - - - A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic. + + + An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization. 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 + An intent to be vaccinated in the future. + intent to be vaccinated - + - - - A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic. + + + 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 - 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 + An intention to give a vaccine to someone or an animal. + intent to vaccinate - + - - - 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. + + + A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab. William R. Hogan - cumulative epidemic infection count + vaccination with nirsevimab - + - - - 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. + + + A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval. William R. Hogan - incident epidemic infection count + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative vaccination 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. + + + A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval. William R. Hogan - cumulative epidemic death count + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident vaccination 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. + A count of infections in a population that is the total number of infections that occur during a reference temporal interval. William R. Hogan - incident epidemic death count + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative infection 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. + A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval. William R. Hogan - cumulative epidemic hospitalization count + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident infection 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. + + + A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval. William R. Hogan - incident epidemic hospitalization count + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative 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. + + + A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval. William R. Hogan - cumulative epidemic vaccination count + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident hospitalization count - + - + + + A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval. + William R. Hogan + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative death count + + + + + + + + + A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval. + William R. Hogan + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident death 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. + A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval. William R. Hogan - incident epidemic vaccination count + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative case count - + - - - An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization. + + + A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval. William R. Hogan - An intent to be vaccinated in the future. - intent to be vaccinated + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident case count - + - - - 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. + + + guardian's intent to have a ward under their care vaccinated + An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role. William R. Hogan - An intention to give a vaccine to someone or an animal. - intent to vaccinate + The intent of a guardian to have a ward under their care vaccinated in the near future. + Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE. + intent to have a ward vaccinated - + - - - A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab. + + + An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child. William R. Hogan - vaccination with nirsevimab + Intent to have one's child vaccinated. + The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist. + intent to have a child vaccinated diff --git a/src/ontology/imports/apollo-sv_import.owl b/src/ontology/imports/apollo-sv_import.owl index 5936a7f..31891d0 100644 --- a/src/ontology/imports/apollo-sv_import.owl +++ b/src/ontology/imports/apollo-sv_import.owl @@ -27,7 +27,7 @@ 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). 2023-01-10 - 2024-02-23 + 2024-04-19 @@ -148,6 +148,18 @@ + + + + A treatment that consists of the administration of antigenic material to stimulate an individual's immune system to develop adaptive immunity to a pathogen. + Mathias Brochhausen + 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 + + + + @@ -187,7 +199,7 @@ 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 + host organism @@ -410,139 +422,171 @@ By "similar vaccines" we typically mean same pathogen, but could be si - + - - A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic. + + An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization. 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 + An intent to be vaccinated in the future. + intent to be vaccinated - + - - A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic. + + 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 - 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 + An intention to give a vaccine to someone or an animal. + intent to vaccinate - + - - 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. + + + A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab. William R. Hogan - cumulative epidemic infection count + vaccination with nirsevimab - + - - 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. + + A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval. William R. Hogan - incident epidemic infection count + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative vaccination 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. + + A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval. William R. Hogan - cumulative epidemic death count + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident vaccination 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. + + A count of infections in a population that is the total number of infections that occur during a reference temporal interval. William R. Hogan - incident epidemic death count + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative infection 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. + + A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval. William R. Hogan - cumulative epidemic hospitalization count + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident infection 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. + + A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval. William R. Hogan - incident epidemic hospitalization count + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative 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. + + A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval. William R. Hogan - cumulative epidemic vaccination count + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident 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 a proper part of the region occupied by the entire epidemic. + + A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval. William R. Hogan - incident epidemic vaccination count + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative death count - + - - An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization. + + A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval. William R. Hogan - An intent to be vaccinated in the future. - intent to be vaccinated + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident death count - + - - 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. + + A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval. William R. Hogan - An intention to give a vaccine to someone or an animal. - intent to vaccinate + The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + cumulative case count - + - - A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab. + + A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval. William R. Hogan - vaccination with nirsevimab + The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization. + incident case count + + + + + + + + guardian's intent to have a ward under their care vaccinated + An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role. + William R. Hogan + The intent of a guardian to have a ward under their care vaccinated in the near future. + Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE. + intent to have a ward vaccinated + + + + + + + + + An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child. + William R. Hogan + Intent to have one's child vaccinated. + The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist. + intent to have a child vaccinated diff --git a/src/ontology/imports/ncbitaxon_import.owl b/src/ontology/imports/ncbitaxon_import.owl index 0dd43f9..f3a1fff 100644 --- a/src/ontology/imports/ncbitaxon_import.owl +++ b/src/ontology/imports/ncbitaxon_import.owl @@ -7,7 +7,7 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - 2023-12-12 + 2024-03-26 diff --git a/src/ontology/imports/seed.txt b/src/ontology/imports/seed.txt index 7fa6206..3a2c9a0 100644 --- a/src/ontology/imports/seed.txt +++ b/src/ontology/imports/seed.txt @@ -1,4 +1,5 @@ APOLLO_SV:00000047 +APOLLO_SV:00000142 APOLLO_SV:00000159 APOLLO_SV:00000174 APOLLO_SV:00000237 @@ -20,19 +21,21 @@ APOLLO_SV:00000610 APOLLO_SV:00000613 APOLLO_SV:00000614 APOLLO_SV:00000618 -APOLLO_SV:00000622 -APOLLO_SV:00000623 -APOLLO_SV:00000631 -APOLLO_SV:00000632 -APOLLO_SV:00000633 -APOLLO_SV:00000634 -APOLLO_SV:00000629 -APOLLO_SV:00000630 -APOLLO_SV:00000635 -APOLLO_SV:00000636 +APOLLO_SV:00000648 +APOLLO_SV:00000649 +APOLLO_SV:00000646 +APOLLO_SV:00000647 +APOLLO_SV:00000644 +APOLLO_SV:00000645 +APOLLO_SV:00000642 +APOLLO_SV:00000643 +APOLLO_SV:00000640 +APOLLO_SV:00000641 APOLLO_SV:00000637 APOLLO_SV:00000638 APOLLO_SV:00000639 +APOLLO_SV:00000652 +APOLLO_SV:00000650 NCBITaxon:11676 NCBITaxon:5820 NCBITaxon:1773 diff --git a/src/ontology/midas-data-edit.owl b/src/ontology/midas-data-edit.owl index c9673f0..0e47a4c 100644 --- a/src/ontology/midas-data-edit.owl +++ b/src/ontology/midas-data-edit.owl @@ -264,6 +264,14 @@ + + + + + + + + @@ -416,106 +424,106 @@ - + - - + + - + - - + + - + - - + + - + - - + + - + - + - + - + - + - - + + - + - - + + - + - - + + - + - - + + - + - - + + - + - - + + - + - - + +