[infectious-disease-ontology] r357 committed - added the term "human pathogenicity disposition"
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infectious-di...@googlecode.com
Mar 9, 2013, 2:55:35 PM3/9/13
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Revision: 357
Author: lindsay...@utsouthwestern.edu
Date: Sat Mar 9 11:55:21 2013
Log: added the term "human pathogenicity disposition"
http://code.google.com/p/infectious-disease-ontology/source/detail?r=357
Modified:
/trunk/src/ontology/ido-core/IDO-editors-worksheet.xls
/trunk/src/ontology/ido-core/ido-base.owl
=======================================
--- /trunk/src/ontology/ido-core/IDO-editors-worksheet.xls Sun Nov 7
11:39:43 2010
+++ /trunk/src/ontology/ido-core/IDO-editors-worksheet.xls Sat Mar 9
11:55:21 2013
Binary file, no diff available.
=======================================
--- /trunk/src/ontology/ido-core/ido-base.owl Tue May 22 20:19:19 2012
+++ /trunk/src/ontology/ido-core/ido-base.owl Sat Mar 9 11:55:21 2013
@@ -523,6 +523,32 @@
+ <!-- http://purl.obolibrary.org/obo/IDO_0000428 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000428">
+ <rdfs:label xml:lang="en">enterotoxin disposition</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000427"/>
+ <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
+ <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
+ <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">An exotoxin disposition to damage
cells of the host intestinal mucosa.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/IDO_0000429 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000429">
+ <rdfs:label xml:lang="en">endotoxin disposition</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000426"/>
+ <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+ <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">A toxin disposition that inheres in
a protein or protein complex that is released from a pathogen only upon
cytolysis.</obo:IAO_0000115>
+ <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/IDO_0000430 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000430">
@@ -630,8 +656,8 @@
<rdfs:comment>The disposition is realized in an adherence to host
process.</rdfs:comment>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">A disposition borne by a biological
macromolecule that is the disposition to participate in adherence to a
host.</obo:IAO_0000115>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">A disposition borne by a biological
macromolecule that is the disposition to participate in adherence to
host.</obo:IAO_0000115>
</owl:Class>
@@ -656,10 +682,10 @@
<rdfs:label xml:lang="en">antimicrobial disposition</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
<obo:IAO_0000115 xml:lang="en">A disposition to kill or inhibit
the development or reproduction of microorganisms.</obo:IAO_0000115>
+ <rdfs:comment>The disposition is realized in the killing or
inhibition of microorganisms.</rdfs:comment>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
- <rdfs:comment>The disposition is realized in the killing or growth
inhibition of microorganisms.</rdfs:comment>
<rdfs:comment>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.</rdfs:comment>
</owl:Class>
@@ -724,11 +750,11 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000444">
<rdfs:label xml:lang="en">protective resistance</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
- <rdfs:comment>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.</rdfs:comment>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">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:IAO_0000115>
<rdfs:comment>The disposition is realized in a process that
mitigates damage to the bearer and has the part as a
participant.</rdfs:comment>
+ <rdfs:comment>Examples include the following: CCR5 mutations
protect T cells from HIV invasion. A tumor cell's resistance to
chemotherapy protects the cell from damage by the drug (although this harms
the patient). An insect's resistance to insecticide protects it from
the insecticide.</rdfs:comment>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
</owl:Class>
@@ -810,9 +836,9 @@
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<rdfs:comment>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.</rdfs:comment>
- <rdfs:comment>The disposition is realized in processes that create
a disorder.</rdfs:comment>
<obo:IAO_0000115 xml:lang="en">A disposition to initiate processes
that result in a disorder.</obo:IAO_0000115>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
+ <rdfs:comment>A pathogenic disposition is realized in processes
that create a disorder.</rdfs:comment>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">pathogenicity</obo:IAO_0000118>
</owl:Class>
@@ -841,7 +867,7 @@
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">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, (3) to initiate
processes that result in a disorder in the host, and (4) to become part of
that disorder.</obo:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">A pathogenic disposition that
inheres in an organism and is a disposition for that organism (1) to be
transmitted to a host, (2) to establish itself in the host, (3) to initiate
processes that result in a disorder in the host, and (4) to become part of
that disorder.</obo:IAO_0000115>
</owl:Class>
@@ -920,9 +946,9 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000458">
<rdfs:label xml:lang="en">contagiousness</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
- <rdfs:comment>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.</rdfs:comment>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+ <rdfs:comment>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 day-to-day activities of
the host.</rdfs:comment>
<rdfs:comment>The disposition is realized in a horizontal
transmission process.</rdfs:comment>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">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:IAO_0000115>
@@ -1193,7 +1219,7 @@
<rdfs:comment>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.</rdfs:comment>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">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:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">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 and in whom the infectious disease begins during the
specified period of time. </obo:IAO_0000115>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">cumulative incidence of infectious
disease</obo:IAO_0000118>
</owl:Class>
@@ -1206,10 +1232,10 @@
<rdfs:label xml:lang="en">infection incidence
proportion</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
<rdfs:comment>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.</rdfs:comment>
+ <obo:IAO_0000115 xml:lang="en">A quality that inheres in an
organism population and is the proportion of members of the population not
infected at the beginning of a specified period of time who become infected
during the specified period of time. </obo:IAO_0000115>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">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:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">cumulative incidence of
infection</obo:IAO_0000118>
</owl:Class>
@@ -1655,10 +1681,10 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000520">
<rdfs:label xml:lang="en">communicability period</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/span#TemporalInterval"/>
- <obo:IAO_0000115 xml:lang="en">A continuous temporal interval
during which contagiousness inhering in the bearer of a host
role.</obo:IAO_0000115>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">A continuous temporal interval
during which an infectious agent host bears a contagiousness
disposition.</obo:IAO_0000115>
</owl:Class>
@@ -2154,12 +2180,13 @@
<!-- http://purl.obolibrary.org/obo/IDO_0000562 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000562">
- <rdfs:label xml:lang="en">antibiotic</rdfs:label>
+ <rdfs:label xml:lang="en">antibacterial</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#MaterialEntity"/>
+ <obo:IAO_0000118>antibiotic</obo:IAO_0000118>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">A material entity bearing an
antiviral disposition.</obo:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">A material entity bearing an
antibacterial disposition.</obo:IAO_0000115>
</owl:Class>
@@ -2250,7 +2277,7 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">An organism that is host to an
infectious agent has no symptoms of the infectious disease associated with
the infectious agent.</obo:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">An organism that is host to an
infectious agent and has no symptoms of the infectious disease associated
with the infectious agent.</obo:IAO_0000115>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
</owl:Class>
@@ -2582,11 +2609,8 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000598">
<rdfs:label xml:lang="en">host living with infected household
contact</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000597"/>
- <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">A host exposure to environment with
infectious agent where the environment is a household that also has an
infected host</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Alan Ruttenberg 2010/05/20-
Tentative definition. Needs review by Bjoern</obo:IAO_0000116>
- <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
</owl:Class>
@@ -2598,9 +2622,6 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000597"/>
<obo:IAO_0000115 xml:lang="en">A host exposure to environment with
infectious agent where the environment is an area in which an infectious
agent is endemic</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Alan Ruttenberg 2010/05/20-
Tentative definition. Needs review by Bjoern</obo:IAO_0000116>
- <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
- <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
</owl:Class>
@@ -2610,9 +2631,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000600">
<rdfs:label xml:lang="en">release of infectious human pathogen in
laboratory</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000597"/>
- <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
- <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">A host exposure to environment with
infectious agent where the exposure is accidental; the environment is a
laboratory, and the infectious agent is infectious in
humans.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Alan Ruttenberg 2010/05/20-
Tentative definition. Needs review by Bjoern</obo:IAO_0000116>
</owl:Class>
@@ -2624,9 +2642,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000601">
<rdfs:label xml:lang="en">host coming into contact with vector of
infectious agent</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000597"/>
- <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
- <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">A host exposure to environment with
infectious agent where the environment contains an infectious agent
vector.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Alan Ruttenberg 2010/05/20-
Tentative definition. Needs review by Bjoern</obo:IAO_0000116>
</owl:Class>
@@ -2638,10 +2653,7 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000602">
<rdfs:label xml:lang="en">host exposure to substance that might
have infectious agent</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000597"/>
- <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">A host exposure to environment with
infectious agent where the environment contains a material entity that has
been assessed to confer a risk of infection.</obo:IAO_0000115>
- <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000116 xml:lang="en">Alan Ruttenberg 2010/05/20-
Tentative definition. Needs review by Bjoern</obo:IAO_0000116>
</owl:Class>
@@ -2668,7 +2680,7 @@
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">An establishment in host process in
which an organism establishes itself in a host.</obo:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">An establishment of localization in
host process in which an organism establishes itself in a
host.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Establishment of one organism in
the extended organism of another (the host) involves at least one of (1)
movement of the organism to a location within the host in which the
organism can persist, or (2) adherence or attachment of the organism to
part of the host.</obo:IAO_0000116>
</owl:Class>
@@ -3344,6 +3356,26 @@
+ <!-- http://purl.obolibrary.org/obo/IDO_0000666 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000666">
+ <rdfs:label xml:lang="en">human pathogenicity
disposition</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000450"/>
+ <obo:IAO_0000115>A disposition to initiate processes that result
in a disorder in a human organism.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/IDO_0000667 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000667">
+ <rdfs:label xml:lang="en">parasitic disposition</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
+ <obo:IAO_0000115>A disposition to participate in a process of
symbiosis in which the bearer derives a growth, survival, or fitness
advantage from symbiosis while the other symbiont's growth, survival,
or fitness is reduced.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/IDO_0001002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0001002">
@@ -3464,12 +3496,6 @@
- <!-- http://www.geneontology.org/formats/oboInOwl#ObsoleteClass -->
-
- <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
-
-
-
<!-- http://www.ifomis.org/bfo/1.1/snap#Disposition -->
<owl:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
Author: lindsay...@utsouthwestern.edu
Date: Sat Mar 9 11:55:21 2013
Log: added the term "human pathogenicity disposition"
http://code.google.com/p/infectious-disease-ontology/source/detail?r=357
Modified:
/trunk/src/ontology/ido-core/IDO-editors-worksheet.xls
/trunk/src/ontology/ido-core/ido-base.owl
=======================================
--- /trunk/src/ontology/ido-core/IDO-editors-worksheet.xls Sun Nov 7
11:39:43 2010
+++ /trunk/src/ontology/ido-core/IDO-editors-worksheet.xls Sat Mar 9
11:55:21 2013
Binary file, no diff available.
=======================================
--- /trunk/src/ontology/ido-core/ido-base.owl Tue May 22 20:19:19 2012
+++ /trunk/src/ontology/ido-core/ido-base.owl Sat Mar 9 11:55:21 2013
@@ -523,6 +523,32 @@
+ <!-- http://purl.obolibrary.org/obo/IDO_0000428 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000428">
+ <rdfs:label xml:lang="en">enterotoxin disposition</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000427"/>
+ <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
+ <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
+ <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">An exotoxin disposition to damage
cells of the host intestinal mucosa.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/IDO_0000429 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000429">
+ <rdfs:label xml:lang="en">endotoxin disposition</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000426"/>
+ <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+ <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">A toxin disposition that inheres in
a protein or protein complex that is released from a pathogen only upon
cytolysis.</obo:IAO_0000115>
+ <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/IDO_0000430 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000430">
@@ -630,8 +656,8 @@
<rdfs:comment>The disposition is realized in an adherence to host
process.</rdfs:comment>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">A disposition borne by a biological
macromolecule that is the disposition to participate in adherence to a
host.</obo:IAO_0000115>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">A disposition borne by a biological
macromolecule that is the disposition to participate in adherence to
host.</obo:IAO_0000115>
</owl:Class>
@@ -656,10 +682,10 @@
<rdfs:label xml:lang="en">antimicrobial disposition</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
<obo:IAO_0000115 xml:lang="en">A disposition to kill or inhibit
the development or reproduction of microorganisms.</obo:IAO_0000115>
+ <rdfs:comment>The disposition is realized in the killing or
inhibition of microorganisms.</rdfs:comment>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
- <rdfs:comment>The disposition is realized in the killing or growth
inhibition of microorganisms.</rdfs:comment>
<rdfs:comment>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.</rdfs:comment>
</owl:Class>
@@ -724,11 +750,11 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000444">
<rdfs:label xml:lang="en">protective resistance</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
- <rdfs:comment>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.</rdfs:comment>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">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:IAO_0000115>
<rdfs:comment>The disposition is realized in a process that
mitigates damage to the bearer and has the part as a
participant.</rdfs:comment>
+ <rdfs:comment>Examples include the following: CCR5 mutations
protect T cells from HIV invasion. A tumor cell's resistance to
chemotherapy protects the cell from damage by the drug (although this harms
the patient). An insect's resistance to insecticide protects it from
the insecticide.</rdfs:comment>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
</owl:Class>
@@ -810,9 +836,9 @@
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<rdfs:comment>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.</rdfs:comment>
- <rdfs:comment>The disposition is realized in processes that create
a disorder.</rdfs:comment>
<obo:IAO_0000115 xml:lang="en">A disposition to initiate processes
that result in a disorder.</obo:IAO_0000115>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
+ <rdfs:comment>A pathogenic disposition is realized in processes
that create a disorder.</rdfs:comment>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">pathogenicity</obo:IAO_0000118>
</owl:Class>
@@ -841,7 +867,7 @@
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">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, (3) to initiate
processes that result in a disorder in the host, and (4) to become part of
that disorder.</obo:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">A pathogenic disposition that
inheres in an organism and is a disposition for that organism (1) to be
transmitted to a host, (2) to establish itself in the host, (3) to initiate
processes that result in a disorder in the host, and (4) to become part of
that disorder.</obo:IAO_0000115>
</owl:Class>
@@ -920,9 +946,9 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000458">
<rdfs:label xml:lang="en">contagiousness</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
- <rdfs:comment>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.</rdfs:comment>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+ <rdfs:comment>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 day-to-day activities of
the host.</rdfs:comment>
<rdfs:comment>The disposition is realized in a horizontal
transmission process.</rdfs:comment>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">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:IAO_0000115>
@@ -1193,7 +1219,7 @@
<rdfs:comment>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.</rdfs:comment>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">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:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">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 and in whom the infectious disease begins during the
specified period of time. </obo:IAO_0000115>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">cumulative incidence of infectious
disease</obo:IAO_0000118>
</owl:Class>
@@ -1206,10 +1232,10 @@
<rdfs:label xml:lang="en">infection incidence
proportion</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
<rdfs:comment>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.</rdfs:comment>
+ <obo:IAO_0000115 xml:lang="en">A quality that inheres in an
organism population and is the proportion of members of the population not
infected at the beginning of a specified period of time who become infected
during the specified period of time. </obo:IAO_0000115>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">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:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">cumulative incidence of
infection</obo:IAO_0000118>
</owl:Class>
@@ -1655,10 +1681,10 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000520">
<rdfs:label xml:lang="en">communicability period</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/span#TemporalInterval"/>
- <obo:IAO_0000115 xml:lang="en">A continuous temporal interval
during which contagiousness inhering in the bearer of a host
role.</obo:IAO_0000115>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">A continuous temporal interval
during which an infectious agent host bears a contagiousness
disposition.</obo:IAO_0000115>
</owl:Class>
@@ -2154,12 +2180,13 @@
<!-- http://purl.obolibrary.org/obo/IDO_0000562 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000562">
- <rdfs:label xml:lang="en">antibiotic</rdfs:label>
+ <rdfs:label xml:lang="en">antibacterial</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#MaterialEntity"/>
+ <obo:IAO_0000118>antibiotic</obo:IAO_0000118>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">A material entity bearing an
antiviral disposition.</obo:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">A material entity bearing an
antibacterial disposition.</obo:IAO_0000115>
</owl:Class>
@@ -2250,7 +2277,7 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">An organism that is host to an
infectious agent has no symptoms of the infectious disease associated with
the infectious agent.</obo:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">An organism that is host to an
infectious agent and has no symptoms of the infectious disease associated
with the infectious agent.</obo:IAO_0000115>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
</owl:Class>
@@ -2582,11 +2609,8 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000598">
<rdfs:label xml:lang="en">host living with infected household
contact</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000597"/>
- <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">A host exposure to environment with
infectious agent where the environment is a household that also has an
infected host</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Alan Ruttenberg 2010/05/20-
Tentative definition. Needs review by Bjoern</obo:IAO_0000116>
- <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
</owl:Class>
@@ -2598,9 +2622,6 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000597"/>
<obo:IAO_0000115 xml:lang="en">A host exposure to environment with
infectious agent where the environment is an area in which an infectious
agent is endemic</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Alan Ruttenberg 2010/05/20-
Tentative definition. Needs review by Bjoern</obo:IAO_0000116>
- <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
- <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
</owl:Class>
@@ -2610,9 +2631,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000600">
<rdfs:label xml:lang="en">release of infectious human pathogen in
laboratory</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000597"/>
- <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
- <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">A host exposure to environment with
infectious agent where the exposure is accidental; the environment is a
laboratory, and the infectious agent is infectious in
humans.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Alan Ruttenberg 2010/05/20-
Tentative definition. Needs review by Bjoern</obo:IAO_0000116>
</owl:Class>
@@ -2624,9 +2642,6 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000601">
<rdfs:label xml:lang="en">host coming into contact with vector of
infectious agent</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000597"/>
- <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
- <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">A host exposure to environment with
infectious agent where the environment contains an infectious agent
vector.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Alan Ruttenberg 2010/05/20-
Tentative definition. Needs review by Bjoern</obo:IAO_0000116>
</owl:Class>
@@ -2638,10 +2653,7 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000602">
<rdfs:label xml:lang="en">host exposure to substance that might
have infectious agent</rdfs:label>
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000597"/>
- <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">A host exposure to environment with
infectious agent where the environment contains a material entity that has
been assessed to confer a risk of infection.</obo:IAO_0000115>
- <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
- <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
<obo:IAO_0000116 xml:lang="en">Alan Ruttenberg 2010/05/20-
Tentative definition. Needs review by Bjoern</obo:IAO_0000116>
</owl:Class>
@@ -2668,7 +2680,7 @@
<obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
<obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
<obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
- <obo:IAO_0000115 xml:lang="en">An establishment in host process in
which an organism establishes itself in a host.</obo:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">An establishment of localization in
host process in which an organism establishes itself in a
host.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Establishment of one organism in
the extended organism of another (the host) involves at least one of (1)
movement of the organism to a location within the host in which the
organism can persist, or (2) adherence or attachment of the organism to
part of the host.</obo:IAO_0000116>
</owl:Class>
@@ -3344,6 +3356,26 @@
+ <!-- http://purl.obolibrary.org/obo/IDO_0000666 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000666">
+ <rdfs:label xml:lang="en">human pathogenicity
disposition</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IDO_0000450"/>
+ <obo:IAO_0000115>A disposition to initiate processes that result
in a disorder in a human organism.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/IDO_0000667 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000667">
+ <rdfs:label xml:lang="en">parasitic disposition</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
+ <obo:IAO_0000115>A disposition to participate in a process of
symbiosis in which the bearer derives a growth, survival, or fitness
advantage from symbiosis while the other symbiont's growth, survival,
or fitness is reduced.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/IDO_0001002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0001002">
@@ -3464,12 +3496,6 @@
- <!-- http://www.geneontology.org/formats/oboInOwl#ObsoleteClass -->
-
- <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
-
-
-
<!-- http://www.ifomis.org/bfo/1.1/snap#Disposition -->
<owl:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#Disposition"/>
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