[infectious-disease-ontology] r340 committed - fix bug that put some rdfs:commments as definitions
infectious-di...@googlecode.com
Author: alanruttenberg
Date: Sun Dec 5 15:24:31 2010
Log: fix bug that put some rdfs:commments as definitions
http://code.google.com/p/infectious-disease-ontology/source/detail?r=340
Modified:
/releases/2010-12-02/ido.obo
=======================================
--- /releases/2010-12-02/ido.obo Sat Dec 4 22:59:50 2010
+++ /releases/2010-12-02/ido.obo Sun Dec 5 15:24:31 2010
@@ -1,7 +1,7 @@
format-version: 1.2
-date: 05:12:2010 01:46
+date: 05:12:2010 18:08
saved-by: generate-ido-obo
-auto-generated-by:
http://purl.obolibrary.org/obo/obi/repository/trunk/src/tools/build/generate-obo.lisp
+auto-generated-by:
http://purl.obolibrary.org/obo/infectious-disease-ontology/repository/trunk/src/tools/generate-obo.lisp
default-namespace: IDO
idspace: RO http://www.obofoundry.org/ro/ro.owl# "OBO Relation ontology
official home on OBO Foundry"
idspace: ROP http://purl.org/obo/owl/OBO_REL# "Relation ontology proposed
terms"
@@ -23,6 +23,7 @@
idspace: VO http://purl.obolibrary.org/obo/VO "Vaccine Ontology"
idspace: SO http://purl.org/obo/owl/SO# "Sequence Ontology"
idspace: HPO http://purl.org/obo/owl/HP# "Human Phenotype Ontology"
+idspace: UBERON http://purl.org/obo/owl/UBERON# "Multi-species anatomy"
remark: This file is a subset of IDO adequate for indexing using the OLS
service. It does not include all logical assertions present in the OWL
file, which can be obtained at
http://purl.obolibrary.org/obo/ido/2010-12-02/ido-base.owl
@@ -272,7 +273,6 @@
name: Bacteria
is_a: OBI:0100026 ! organism
-
[Term]
id: GO:0085030
name: mutualism
@@ -291,7 +291,6 @@
def:"An interaction between two organisms living together in more or less
intimate association in a relationship in which one benefits and the other
is unaffected." [OBO:imported "http://purl.org/obo/owl/GO"]
is_a: GO:0044403 ! symbiosis, encompassing mutualism through parasitism
-
[Term]
id: span:ScatteredTemporalRegion
name: scattered_temporal_region
@@ -385,7 +384,7 @@
[Term]
id: IDO:0000481
name: infectious disease incidence proportion
-def:"An instance of infectious disease incidence proportion is measured by
dividing a measure of an instance of infectious disease incidence by the
number of members of the population in which the infectious disease course
had not begun at the beginning of the specified period of time over which
the incidence was measured." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the
proportion of members of the population not experiencing an infectious
disease course at the beginning of a specified period of time in whom the
infectious disease begins during the specified period of time. "
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -397,7 +396,7 @@
[Term]
id: IDO:0000480
name: infection incidence
-def:"A particular instance of infection incidence will depend on a type of
infectious agent\, a population\, and a period of time. Incidence is used
as a measure of risk. Actual measures of incidence are based only on
reported cases and usually specify a time interval and geographic
location. Other constraints may include population demographics. These
constraints will vary with the context of the incidence measure."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the number of
organisms in the population that become infected with an infectious agent
during a specified period of time." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -409,7 +408,7 @@
[Term]
id: IDO:0000483
name: infectious disease incidence rate
-def:"An instance of infectious disease incidence rate is measured by
dividing a measure of an instance of the infectious disease incidence
proportion by the length of the period of time over which the incidence was
measured." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the
infectious disease incidence proportion per unit time." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -420,13 +419,13 @@
[Term]
id: IDO:0000482
name: infection incidence proportion
-def:"An instance of infection incidence proportion is measured by dividing
a measure of an instance of infection incidence by the number of members of
the population not infected at the beginning of the specified period of
time over which the incidence was measured." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the
proportion of members of the population not experiencing an infectious
disease course at the beginning of a specified period of time in whom the
infectious disease begins during the specified period of time. "
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
id: IDO:0000485
name: infectious disease prevalence
-def:"Prevalence is sometimes defined as a proportion with total population
size in the denominator. A particular instance of infectious disease
prevalence will depend on a type of infectious disease\, a population\, and
a period of time. Actual measures of prevalence are based only on reported
cases and usually specify a time interval and geographic location. Other
constraints may include population demographics." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the number of
realizations of an infectious disease in the population at a specified
time." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -438,7 +437,7 @@
[Term]
id: IDO:0000484
name: infection incidence rate
-def:"An instance of infection incidence rate is measured by dividing a
measure of an instance of infection incidence proportion by the length of
the period of time over which the incidence was measured."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the infection
incidence proportion per unit time." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -456,13 +455,13 @@
[Term]
id: IDO:0000487
name: infectious disease lifetime prevalence
-def:"Prevalence is sometimes defined as a proportion with total population
size in the denominator. A particular instance of infectious disease
lifetime prevalence will depend on a type of infectious disease and a
population. Actual measures of prevalence are based only on reported cases
and usually specify a geographic location. Other constraints may include
population demographics." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the number of
organisms in the population who have\, at any point during their lives\,
been bearers of an infectious disease and experienced realization of the
disease." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
id: IDO:0000486
name: infection prevalence
-def:"Prevalence is sometimes defined as a proportion with total population
size in the denominator. A particular instance of infection prevalence
will depend on a type of infectious agent\, a population\, and a period of
time. Actual measures of prevalence are based only on reported cases and
usually specify a time interval and geographic location. Other constraints
may include population demographics." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the number of
organisms in the population infected with an infectious agent at a
specified time." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -474,13 +473,13 @@
[Term]
id: IDO:0000489
name: infectious disease mortality rate
-def:"A particular instance of infectious disease mortality rate will
depend on a type of infectious disease and a population. Actual measures
of mortality rate are based only on reported cases and usually specify a
geographic location. Other constraints may include population
demographics. Mortality rate is typically expressed in units of deaths per
1000 individuals per year." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the per
capita number of deaths in the population resulting from an infectious
disease over a specified period of time." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
id: IDO:0000488
name: infectious agent seroprevalence
-def:"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." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the number of
organisms in the population that have antibody specific for an infectious
agent in their serum at a specified time." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -492,7 +491,7 @@
[Term]
id: IDO:0000596
name: infectious agent
-def:"The term infectious agent refers to infectious organisms and prion
proteins." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An organism that has an infectious disposition." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000528 ! pathogen
is_a: OBI:0100026 ! organism
@@ -726,7 +725,7 @@
[Term]
id: IDO:0000479
name: infectious disease incidence
-def:"A particular instance of infectious disease incidence will depend on
a type of infectious disease\, a population\, and a period of time.
Incidence is used as a measure of risk. Actual measures of incidence are
based only on reported cases and usually specify a time interval and
geographic location. Other constraints may include population
demographics. These constraints will vary with the context of the
incidence measure." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population and is the number of
realizations of an infectious disease for which the infectious disease
course begins during a specified period of time." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -870,19 +869,19 @@
[Term]
id: IDO:0000494
name: infectious disease sporadicity
-def:"Sporadic quality of infectious disease is relational to previous
prevalence of the disease." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population by virtue of the
fact that realizations of an infectious disease occur in the population
with a fluctuating prevalence." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
id: IDO:0000493
name: infectious disease hyper-endemicity
-def:"Hyper-endemic infectious diseases may have high endemic levels only
in certain seasons. A hyper-endemic disease affects all age groups
equally." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An infectious disease endemicity that inheres in an organism
population in virtue of the fact that the infectious disease endemic level
for an infectious disease is persistently high in the population. "
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000490 ! infectious disease endemicity
[Term]
id: IDO:0000492
name: infectious disease endemic rate
-def:"Infectious disease endemic rate is relational to previous infectious
disease incidence rates of the disease." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An infectious disease incidence rate that is typical for an
infectious disease in an organism population. " [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000483 ! infectious disease incidence rate
[Term]
@@ -894,13 +893,13 @@
[Term]
id: IDO:0000491
name: infectious disease endemic level
-def:"Infectious disease endemic level is relational to previous
prevalences of the disease." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An infectious disease prevalence that is typical for an infectious
disease in an organism population. " [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000485 ! infectious disease prevalence
[Term]
id: IDO:0000490
name: infectious disease endemicity
-def:"A particular instance of infectious disease endemicity will depend on
a type of infectious agent and a population. The population may be
specified by temporal\, geographic\, or demographic constraints.
Infectious diseases that are typical or common to a particular population
are referred to as endemic." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an organism population in virtue of the
fact that infections of the type that causes an infectious disease are
maintained in the population via intra-population transmission or by
transmission from a local reservoir." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -1000,7 +999,7 @@
[Term]
id: IDO:0000443
name: antiparasitic disposition
-def:"In the term name\, we are using parasite in the medical sense of
eukaryotic organisms that are parasitic in humans." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
+def:"A disposition to kill or inhibit the development or reproduction of
eukaryotic parasites." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
@@ -1012,7 +1011,7 @@
[Term]
id: IDO:0000444
name: protective resistance
-def:"The disposition is realized in a process that mitigates damage to the
bearer and has the part as a participant.; This mitigation sometimes takes
the form of protection. CCR5 mutations protect T cells from HIV invasion.
If a patient's tumor is resistant to chemotherapy\, then the patient is
resistant to something beneficial\, but the tumor is resistant to something
damaging. In this case protective resistance inheres in the tumor's cells
and in the tumor\, but not in the patient. In some cases\, the quality
that confers the protective resistance will confer other dispositions that
damage the entity\, such as is the case with sickle cell trait."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A disposition that inheres in a material entity in virtue of the fact
that the entity has a part (e.g. a gene product)\, which itself has a
disposition to mitigate damage to the entity." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
@@ -1066,13 +1065,13 @@
[Term]
id: IDO:0000448
name: immunity to infectious agent
-def:"We don't specify that immunity results from prior exposure\, because
we want to include innate immunity. In addition\, for adaptive immunity\,
there could be some low level immunity even in a primary immune response."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A resistance to infectious agent that inheres in an organism in
virtue of immune system components in the extended organism."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000446 ! resistance to infectious agent
[Term]
id: IDO:0000449
name: sterilizing immunity to infectious agent
-def:"Sterilizing immunity is typically conferred by neutralizing
antibodies." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An immunity to infectious agent that results in elimination of the
infectious agent from the host." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000448 ! immunity to infectious agent
[Term]
@@ -1170,7 +1169,7 @@
[Term]
id: IDO:0000433
name: antiseptic role
-def:"The role is realized in the killing and/or growth inhibition of
microorganisms on the anatomical entity. " [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by a material entity in virtue of the fact that it has
an antimicrobial disposition and is applied to an anatomical entity of a
living organism. " [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
[Term]
@@ -1188,7 +1187,7 @@
[Term]
id: IDO:0000434
name: primary infection role
-def:"The role is realized in a process by which the infectious disorder is
established in the host." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by an infectious disorder in virtue of the fact that (1)
the host has at least two distinct infectious disorders\, where neither
arose from the other through metastasis\, (2) at the time the infectious
disorder was established in the host\, the host had no infectious
disorder\, and (3) the infectious disorder increases the host's
susceptibility to infectious disorders." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
[Term]
@@ -1200,13 +1199,13 @@
[Term]
id: IDO:0000431
name: infectious agent portal of exit role
-def:"The role is realized in a process by which an infectious agent exists
a host." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by an anatomical entity in virtue of the fact that it
serves as the site through which an infectious agent exits a host."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
[Term]
id: IDO:0000432
name: disinfectant role
-def:"The role is realized in the killing and/or growth inhibition of
microorganisms on the non-living entity." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by a material entity in virtue of the fact that it has
an antimicrobial disposition and is applied to a non-living entity. "
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
[Term]
@@ -1224,13 +1223,13 @@
[Term]
id: IDO:0000437
name: adhesion disposition
-def:"The disposition is realized in an adherence to host process."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A disposition borne by a biological macromolecule that is the
disposition to participate in adherence to host." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
id: IDO:0000438
name: invasion disposition
-def:"A molecule with the invasion disposition is referred to as an
invasion factor or invasin." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A disposition borne by a biological macromolecule that is the
disposition to facilitate breach of host epithelial barriers or entry into
and survival in host cells." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
@@ -1242,7 +1241,7 @@
[Term]
id: IDO:0000435
name: secondary infection role
-def:"The role is realized in a process by which the infectious disorder is
established in the host." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by an infectious disorder in virtue of the fact that (1)
the host has at least two distinct infectious disorders\, where neither
arose from the other through metastasis\, (2) at the time the infectious
disorder was established in the host\, the host had a primary infectious
disorder\, and (3) establishment of the infectious disorder occurs because
of increased susceptibility to infectious disorders conferred by the
primary infectious disorder." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
[Term]
@@ -1260,7 +1259,7 @@
[Term]
id: IDO:0000436
name: infectious disease
-def:"The disposition is realized in an infectious disease course."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A disease whose physical basis is an infectious disorder."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: OGMS:0000031 ! disease
[Term]
@@ -1284,7 +1283,7 @@
[Term]
id: IDO:0000430
name: infectious agent portal of entry role
-def:"The role is realized in a process by which an infectious agent enters
a host." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by an anatomical entity in virtue of the fact that it
serves as the site through which an infectious agent enters a host."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
[Term]
@@ -1360,7 +1359,7 @@
[Term]
id: IDO:0000439
name: antimicrobial disposition
-def:"Some instances might be functions\, depending on whether the bearer
is something that exists and is used for the purpose (alcohol) or something
that was designed for the purpose (pine sol). Entities that kill
microorganisms are referred to as microbicidal; entities that inhibit the
growth of microorganisms are referred to as microbistatic.; The disposition
is realized in the killing or growth inhibition of microorganisms."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A disposition to kill or inhibit the development or reproduction of
microorganisms." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
@@ -1409,7 +1408,7 @@
[Term]
id: IDO:0000576
name: innate immunity to infectious agent
-def:"The disposition is realized in an innate immune response."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"An immunity to infectious agent that inheres in an organism in virtue
of germline encoded components that directly recognize components of
potential pathogens." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000448 ! immunity to infectious agent
[Term]
@@ -1421,25 +1420,25 @@
[Term]
id: IDO:0000464
name: infectivity
-def:"This quality is measured by the proportion of exposed who become
infected." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an infectious agent and is the liklihood
that the infectious disposition will be realized upon exposure of a
susceptible organism." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
id: IDO:0000578
name: humoral immunity to infectious agent
-def:"The disposition is realized in a humoral immune
response.; "Circulating body fluid" refers to blood\, lymph\, and
hemolymph." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An immunity to infectious agent that inheres in an organism in virtue
of components of its circulating body fluid." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000448 ! immunity to infectious agent
[Term]
id: IDO:0000579
name: leukocyte-mediated immunity to infectious agent
-def:"The disposition is realized in a leukocyte-mediated immune response."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"An immunity to infectious agent that inheres in an organism in virtue
of its leukocytes." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000448 ! immunity to infectious agent
[Term]
id: IDO:0000466
name: virulence
-def:"This quality is measured by the proportion of clinically apparent
cases that are severe or fatal." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an infectious agent and is the degree to
which realizations of the infectious disease caused by the infectious agent
become severe or fatal. " [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -1451,7 +1450,7 @@
[Term]
id: IDO:0000467
name: susceptibility
-def:"Low susceptibility is often referred to as resistance. In this
sense\, resistance is a quality." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an entity and is the degree to which it can
be harmed by another entity." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -1475,7 +1474,7 @@
[Term]
id: IDO:0000463
name: infectious agent transmissibility
-def:"The transmissibility quality varies with both the type of organism
being transmitted and the type of organism to which transmission is
happening." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A quality that inheres in an infectious agent and is the likelihood
that the infectious agent will undergo a horizontal transmission process."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Quality ! quality
[Term]
@@ -1582,7 +1581,7 @@
[Term]
id: IDO:0000587
name: genetic resistance to infectious agent
-def:"The resistance of individuals to HIV invasion oonferred by particular
CCR5 alleles is an example. Resistance against malaria conferred by the
sickle cell gene is another." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A resistance to infectious agent that inheres in an organism in
virtue of a specific allele or combination of alleles in its genome."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000446 ! resistance to infectious agent
[Term]
@@ -1605,25 +1604,25 @@
[Term]
id: IDO:0000585
name: collective pathogenic disposition
-def:"The disposition is realized in processes that create a disorder."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A collective disposition to initiate processes that result in a
disorder." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000455 ! collective disposition
[Term]
id: IDO:0000458
name: contagiousness
-def:"The disposition is realized in a horizontal transmission process.;
Highly contagious infections\, those with a relatively high likelihood of
spread\, are referred to as contagious and are those for which spread is
likely as a result of data-to-day activities of the host."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A disposition that inheres in a host of infectious agent and is a
disposition to transmit infectious agents to organisms of the same Species
through casual contact with a high likelihood of realization."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
id: IDO:0000586
name: infection
-def:"The organism corresponding to the extended organism is host to the
infectious agents. By this definition\, parts of the host can be
considered part of the infection." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A part of an extended organism that itself has as part a population
of one or more infectious agents and that is (1) clinically abnormal in
virtue of the presence of this infectious agent population\, or (2) has a
disposition to bring clinical abnormality to immunocompetent organisms of
the same Species as the host (the organism corresponding to the extended
organism) through transmission of a member or offspring of a member of the
infectious agent popuation." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:MaterialEntity ! material_entity
[Term]
id: IDO:0000455
name: collective disposition
-def:"The disposition is realized in a process that has as part
realizations of some of the individual dispositions.; "... in virtue of the
individual dispositions of the contstituents" is intended to capture the
fact that the collective disposition results from the combination of the
individual dispositions. It is not necessary that every constituent of the
aggregate have a relevant individual disposition." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
+def:"A disposition that inheres in a collection of entities in virtue of
the individual dispositions of the constituents of that collection. "
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
@@ -1641,7 +1640,7 @@
[Term]
id: IDO:0000453
name: zoonotic disposition
-def:"An infectious disease associated with an infectious agent that bears
the zoonotic disposition is referred to as a zoonosis." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
+def:"An infectious disposition that is the disposition to be transmitted
from an infected\, non-human host to a human host." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000452 ! infectious disposition
[Term]
@@ -1653,7 +1652,7 @@
[Term]
id: IDO:0000454
name: reverse zoonotic disposition
-def:"An infectious disease associated with an infectious agent that bears
the reverse zoonotic disposition is referred to as a reverse zoonosis."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"An infectious disposition that is the disposition to be transmitted
from an infected\, human host to a non-human host." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000452 ! infectious disposition
[Term]
@@ -1665,19 +1664,19 @@
[Term]
id: IDO:0000580
name: passive immunity to infectious agent
-def:"The disposition is realized in a neutralizing process carried out by
the antibodies.; Passive immunity results from a passive immunization.; The
protective antibodies are typically introduced by injection\, breast
feeding\, or by passing from the placenta to the fetus." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
+def:"An immunity to infectious agent that inheres in an organism in virtue
of antibodies not produced by that organism." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000448 ! immunity to infectious agent
[Term]
id: IDO:0000452
name: infectious disposition
-def:"The disposition is realized in a process that has as part a
transmission process\, an establishment in host process\, and a process in
which an entity becomes part of a disorder. The infectious disposition has
a complementary disposition that inheres in an organism and is the
capability to be host to an entity with an infectious disposition and to
undergo processes intiated by that entity that result in a disorder."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A pathogenic disposition that inheres in an organism and is the
disposition for that organism (1) to be transmitted to a host\, (2) to
establish itself in the host\, and (3) to become part of a disorder in the
host." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000450 ! pathogenic disposition
[Term]
id: IDO:0000450
name: pathogenic disposition
-def:"The use of 'initiates' is intended to convey that a pathogenic
disposition is realized when processes resulting in a disorder begin
because of some action on the part of the bearer of the disposition. By
this interpretation of 'initiates'\, disorder-causing entities such as
glass\, UV light\, and toxins do not have a pathogenic disposition.; The
disposition is realized in processes that create a disorder."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A disposition to initiate processes that result in a disorder."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
@@ -1839,13 +1838,13 @@
[Term]
id: IDO:0000417
name: infectious agent transporter role
-def:"The role is realized in a process that transfers an infectious
organism from one location to another." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by a material entity in virtue of the fact that an
infectious agent is located in or on the entity and the entity has the
capability to transfer (either actively or passively) the infectious agent
from one location to another. " [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
[Term]
id: IDO:0000418
name: infectious agent vector role
-def:"The role is realized in a transmission process. A bearer of a vector
role is also a bearer of a host role." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An infectious agent transporter role that is borne by an organism
active in the transfer of an infectious agent to an organism of another
Species and in which the agent is infectious." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000417 ! infectious agent transporter role
[Term]
@@ -1857,7 +1856,7 @@
[Term]
id: IDO:0000410
name: intermediate host role
-def:"The role is realized in developmental processes of the host's partner
in symbiosis." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A symbiont host role borne by an organism in virtue of the fact that
its partner in symbiosis utilizes the host to undergo a developmental stage
transition\, and the host is required for continuation of the partner's
life cycle." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000408 ! symbiont host role
[Term]
@@ -1869,19 +1868,19 @@
[Term]
id: IDO:0000411
name: paratenic host role
-def:"The role is realized in developmental processes of the host's partner
in symbiosis." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A symbiont host role borne by an organism in virtue of the fact that
its partner in symbiosis utilizes the host to undergo a developmental stage
transition\, but the host is not required for continuation of the partner's
life cycle. " [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000408 ! symbiont host role
[Term]
id: IDO:0000414
name: infectious agent host role
-def:"By this definition\, vectors and other organisms that may not be
infected are bearers of the infectious agent host role." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
+def:"A pathogen host role borne by an organism in virtue of the fact that
its extended organism contains an infectious agent." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000415 ! pathogen host role
[Term]
id: IDO:0000413
name: parasite host role
-def:"The partner in symbiosis bears the parasite role.; The role is
realized in processes that result in the parasite's growth\, survival\, or
fitness advantage or in the host's growth\, survival\, or fitness
reduction." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A symbiont host role borne by an organism in virtue of the fact that
its partner in symbiosis derives from the host a growth\, survival\, or
fitness advantage while the host's growth\, survival\, or fitness is
reduced." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000408 ! symbiont host role
[Term]
@@ -1893,7 +1892,7 @@
[Term]
id: IDO:0000415
name: pathogen host role
-def:"Bearing the infectious agent host role implies bearing the pathogen
host role\, but the reverse is not true. See comment for infectious agent
host role." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A host role borne by an organism in virtue of the fact that its
extended organism contains a pathogen." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000629 ! host role
[Term]
@@ -1911,7 +1910,7 @@
[Term]
id: IDO:0000640
name: acquired immunodeficiency
-def:"Causes of acquired immunodeficiences include infection and drug
treatments (e.g. chemotherapy)." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An immunodeficiency that is not caused by a genetic predisposition."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000617 ! immunodeficiency
[Term]
@@ -2019,13 +2018,13 @@
[Term]
id: IDO:0000422
name: biological vehicle of infectious agent role
-def:"Examples include blood\, serum\, tissue\, or fresh produce."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"An infectious agent vehicle role borne by an entity in virtue of the
fact that the entity is living or contains living cells other than those
that have the infectious disposition." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000421 ! infectious agent vehicle role
[Term]
id: IDO:0000421
name: infectious agent vehicle role
-def:"Drinking water bears the infectious agent vehicle role\, but does not
bear either of the subtype roles." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An infectious agent transporter role borne by an entity in virtue of
the fact that the entity is not a complete organism." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000417 ! infectious agent transporter role
[Term]
@@ -2037,7 +2036,7 @@
[Term]
id: IDO:0000427
name: exotoxin disposition
-def:"The disposition is realized in a direct enzymatic process that
damages host cells or extracellular matrix." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A toxin disposition to damage cells or extracellular matrix by a
direct enzymatic process." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000426 ! toxin disposition
[Term]
@@ -2049,13 +2048,13 @@
[Term]
id: IDO:0000425
name: virulence factor disposition
-def:"The virulence factor disposition is typically realized in processes
that improve survival of the pathogen in a host\, increase the likelihood
of transmission to a host\, or cause pathological processes in a host."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A disposition borne by a biological macromolecule produced by a
pathogen that is a disposition to undergo processes that increase the
pathogen's virulence." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
id: IDO:0000424
name: reservoir of infectious agent role
-def:"If the material entity bearing the reservoir role is an organism\,
then this organism also bears the host role. The organism may also bear
the vector role.; The role is realized in a process that has as part life
and multiplication processes of an infectious agent and a transmission
process. " [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by a material entity in virtue of the fact that it is a
habitat in which infectious agents can persist and multiply and from which
they can be transmitted in virtue of prevailing practices of potential
hosts." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
[Term]
@@ -2115,7 +2114,7 @@
[Term]
id: IDO:0000635
name: source of infection role
-def:"The role is realized in a process that has as part a transmission
process and a process by which the infectious agent or one of its offspring
becomes part of a disorder in the host." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by a material entity in virtue of the fact that it
contains a site from which an infectious agent is transmitted."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
[Term]
@@ -2275,31 +2274,31 @@
[Term]
id: IDO:0000408
name: symbiont host role
-def:"The relevant environmental resources may include nutrient resources\,
warmth\, or moisture.; The role is realized in processes in which the host
makes the relevant environmental resources available to its partner in
symbiosis. A bearer of a symbiont host role is bearer also of a symbiont
role." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A host role borne by an organism in virtue of the fact that its
extended organism contains a second organism and provides an environment
supportive for the survival\, growth\, maturation\, or reproduction of that
organism. " [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000629 ! host role
[Term]
id: IDO:0000409
name: definitive host role
-def:"The role is realized in developmental and reproduction processes of
the host's partner in symbiosis." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A symbiont host role borne by an organism in virtue of the fact that
its partner in symbiosis reaches developmental maturity or reproduces
sexually in the host. " [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000408 ! symbiont host role
[Term]
id: IDO:0000406
name: opportunistic infectious disposition
-def:"The disposition is realized in a process by which the bearer becomes
part of a disorder in an immunocompromised host.; This includes individuals
who are immunocompromised or who have damaged barriers that normally
protect against infection (e.g. skin)." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An infectious disposition to become part of a disorder only in
organisms whose defenses are compromised." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000452 ! infectious disposition
[Term]
id: IDO:0000407
name: primary infectious disposition
-def:"A pathogen with a primary infectious disposition can cause disease or
death in both immunocompromised and immunocompetent hosts.; A quote from
page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth
edition): "It is useful to distinguish "principal" pathogens\, which
regularly cause disease in some proportion of susceptible individuals with
apparently intact defense systems\, from other potentially pathogenic
microorganisms. ... even for most organisms classified as principal
pathogens\, for example\, Staphylococcus aureus and the pneumococcus\, some
impairment or local breakdown in normal host defense mechanisms must occur
for these bacteria to cause disease. ... Thus\, it seems clear that the
capacity of certain microorganisms to cause disease in seemingly
uncompromised human hosts on a regular basis reflects some fundamental
difference in their virulence capabilities from those of opportunists and
the more numerous commensal species that rarely\, if ever\, cause
disease."" [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An infectious disposition to become part of a disorder in organisms
that have intact defenses." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000452 ! infectious disposition
[Term]
id: IDO:0000405
name: pathogen role
-def:"Clostridium botulinum is an example of an entity with the capability
to bear the pathogen role but that does not have the capability to bear the
infectious agent role or the parasite role. The influenza viruses are
examples of organisms that can bear both the infectious agent and pathogen
roles." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by pathogen in virtue of the fact that it or one of its
products is sufficiently close to an organism towards which it has the
pathogenic disposition to allow realization of the pathogenic disposition."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
[Term]
@@ -2329,7 +2328,7 @@
[Term]
id: IDO:0000403
name: parasite role
-def:"The role is realized in processes that result in the parasite's
growth\, survival\, or fitness advantage or in the other organism's
growth\, survival\, or fitness reduction.; In the medical community\, the
term 'parasite' is used with the narrower meaning of eukaryotic pathogen."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A symbiont role borne by an organism in virtue of the fact that it
derives a growth\, survival\, or fitness advantage from symbiosis while the
other symbiont's growth\, survival\, or fitness is reduced."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000400 ! symbiont role
[Term]
@@ -2341,13 +2340,13 @@
[Term]
id: IDO:0000402
name: commensal role
-def:"The role is realized in processes that result in the commensal's
growth\, survival\, or fitness advantage." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A symbiont role borne by an organism in virtue of the fact that it
derives a growth\, survival\, or fitness advantage from symbiosis\, but the
other symbiont is neither advantaged nor disadvantaged." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000400 ! symbiont role
[Term]
id: IDO:0000401
name: mutualist role
-def:"The role is realized in processes that result in the growth\,
survival\, or fitness advantage of either organism." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
+def:"A symbiont role borne by an organism in virtue of the fact that both
symbionts derive a growth\, survival\, or fitness advantage from
symbiosis." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000400 ! symbiont role
[Term]
@@ -2359,10 +2358,9 @@
[Term]
id: IDO:0000400
name: symbiont role
-def:"The role is realized in symbiosis." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"A role borne by an organism in symbiosis." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Role ! role
-
[Term]
id: IDO:0000658
name: host exposure to infectious agent
@@ -2414,7 +2412,7 @@
[Term]
id: IDO:0000655
name: transmissibility disposition
-def:"The disposition is realized in a transmission process."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A disposition to undergo a transmission process." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
@@ -2588,25 +2586,25 @@
[Term]
id: IDO:0000623
name: communicability
-def:"The disposition is realized in a direct\, horizontal transmission
process between members of the same Species." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An infectious disposition to be transmitted directly from one
organism to another of the same Species by horizontal transmission."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000452 ! infectious disposition
[Term]
id: IDO:0000624
-name: host range
+name: obsolete_host range
def:"A quality that inheres in an infection and is the likelihood that
infectious agents part of the infection will spread to other hosts.; A
generically dependent continuant that is the set of organism types whose
instances have as one of their canonical dispositions\, the disposition to
bear the host role for a colony of a certain type." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_obsolete: true
[Term]
id: IDO:0000625
name: establishment of localization in host
-def:"An organism begins bearing a particular host role as soon as the
extended organism contains the relevant material entity\, regardless of
that entity's location in the extended organism. An establishment process
is any process by which the entity reaches a location in the extended
organism in which it can persist and continue its lifecycle. For example\,
an organism is host to a virus as soon as any part of the extended organism
is occupied by virus particles. During an establishment process\, virus
particles enter host cells of the relevant type\, and viral DNA is
integrated into host DNA." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An establishment of localization process in which a material entity
reaches a site in an organism in which it can survive\, grow\, multiply\,
or mature." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
is_a: GO:0051234 ! establishment of localization
[Term]
id: IDO:0000621
name: acquired immunity to infectious agent
-def:"The disposition is realized in an immune response in which such
antigen receptors participate." [OBO:sourced "IDO consortium
http://www.infectiousdiseaseontology.org"]
+def:"An immunity to infectious agent that inheres in an organism in virtue
of antigen receptors encoded by somatically diversified genes in the
organism's genome and expressed by cells that have undergone selection
during a primary immune response in that organism." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: IDO:0000448 ! immunity to infectious agent
[Term]
@@ -2675,7 +2673,7 @@
[Term]
id: IDO:0000618
name: immunocompetence
-def:"The disposition inheres in a bearer in virtue of the fact that the
bearer has all canonical immune system components and none are disordered.
The disposition is realized in a successful immune response."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
+def:"A disposition that is the ability to mount a normal immune response."
[OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:Disposition ! disposition
[Term]
@@ -2715,7 +2713,7 @@
[Term]
id: IDO:0000509
name: organism population
-def:"The organism population may be delineated by spatio-temporal
proximity or by demographic criteria such as age." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
+def:"An aggregate of organisms of the same Species." [OBO:sourced "IDO
consortium http://www.infectiousdiseaseontology.org"]
is_a: snap:ObjectAggregate ! object_aggregate
[Term]