[infectious-disease-ontology] r348 committed - move OGMS sypmtom to under entity rather than under quality
infectious-di...@googlecode.com
Author: lindsay...@utsouthwestern.edu
Date: Thu Sep 1 15:46:33 2011
Log: move OGMS sypmtom to under entity rather than under quality
http://code.google.com/p/infectious-disease-ontology/source/detail?r=348
Modified:
/trunk/src/ontology/ido-core/ido-external-derived.owl
/trunk/src/ontology/ido-core/ido-external.owl
=======================================
--- /trunk/src/ontology/ido-core/ido-external-derived.owl Fri Dec 3
19:41:27 2010
+++ /trunk/src/ontology/ido-core/ido-external-derived.owl Thu Sep 1
15:46:33 2011
@@ -32,26 +32,26 @@
<rdfs:label xml:lang="en">Archaea</rdfs:label>
</owl:Class>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000045">
- <rdfs:label>disorder</rdfs:label>
<obi:IAO_0000115 xml:lang="en">A material entity which is clinically
abnormal and part of an extended organism. Disorders are the physical basis
of disease.</obi:IAO_0000115>
+ <rdfs:label>disorder</rdfs:label>
<obi:IAO_0000111>disorder</obi:IAO_0000111>
</owl:Class>
<owl:Class rdf:about="http://purl.org/obo/owl/NCBITaxon#NCBITaxon_10239">
- <rdfs:label>Viruses</rdfs:label>
<rdfs:label xml:lang="en">Viruses</rdfs:label>
+ <rdfs:label>Viruses</rdfs:label>
</owl:Class>
<owl:Class rdf:about="http://purl.org/obo/owl/NCBITaxon#NCBITaxon_33154">
- <obi:IAO_0000412 rdf:resource="http://purl.org/obo/owl/NCBITaxon"/>
- <obi:IAO_0000111 xml:lang="en">Fungi/Metazoa group</obi:IAO_0000111>
+ <rdfs:label xml:lang="en">Fungi/Metazoa group</rdfs:label>
<rdfs:subClassOf>
<owl:Class
rdf:about="http://purl.org/obo/owl/NCBITaxon#NCBITaxon_2759"/>
</rdfs:subClassOf>
- <rdfs:label xml:lang="en">Fungi/Metazoa group</rdfs:label>
+ <obi:IAO_0000111 xml:lang="en">Fungi/Metazoa group</obi:IAO_0000111>
+ <obi:IAO_0000412 rdf:resource="http://purl.org/obo/owl/NCBITaxon"/>
</owl:Class>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000020">
- <obi:IAO_0000111>symptom</obi:IAO_0000111>
- <obi:IAO_0000115 xml:lang="en">A quality of a patient that is observed
by the patient and is hypothesized by the patient to be a realization of a
disease.</obi:IAO_0000115>
+ <obi:IAO_0000115 xml:lang="en">A quality of a patient that is observed
by the patient or a processual entity experienced by the patient, either of
which is hypothesized by the patient to be a realization of a
disease.</obi:IAO_0000115>
<rdfs:label>symptom</rdfs:label>
+ <obi:IAO_0000111>symptom</obi:IAO_0000111>
</owl:Class>
<owl:Class rdf:about="http://purl.org/obo/owl/NCBITaxon#NCBITaxon_2759">
<rdfs:label xml:lang="en">Eukaryota</rdfs:label>
@@ -75,65 +75,70 @@
<obi:IAO_0000111>extended organism</obi:IAO_0000111>
</owl:Class>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000063">
+ <rdfs:label>disease course</rdfs:label>
<obi:IAO_0000115 xml:lang="en">The totality of all processes through
which a given disease instance is realized.</obi:IAO_0000115>
<obi:IAO_0000111>disease course</obi:IAO_0000111>
- <rdfs:label>disease course</rdfs:label>
</owl:Class>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0006955">
+ <obi:IAO_0000115 xml:lang="en">Any immune system process that
functions in the calibrated response of an organism to a potential internal
or invasive threat.</obi:IAO_0000115>
<obi:IAO_0000111 xml:lang="en">immune response</obi:IAO_0000111>
<rdfs:label xml:lang="en">immune response</rdfs:label>
- <obi:IAO_0000115 xml:lang="en">Any immune system process that
functions in the calibrated response of an organism to a potential internal
or invasive threat.</obi:IAO_0000115>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0044403">
- <obi:IAO_0000111 xml:lang="en">symbiosis, encompassing mutualism
through parasitism</obi:IAO_0000111>
<obi:IAO_0000115 xml:lang="en">An interaction between two organisms
living together in more or less intimate association. The term host is
usually used for the larger (macro) of the two members of a symbiosis. The
smaller (micro) member is called the symbiont organism. Microscopic
symbionts are often referred to as endosymbionts. The various forms of
symbiosis include parasitism, in which the association is disadvantageous
or destructive to one of the organisms; mutualism, in which the association
is advantageous, or often necessary to one or both and not harmful to
either; and commensalism, in which one member of the association benefits
while the other is not affected. However, mutualism, parasitism, and
commensalism are often not discrete categories of interactions and should
rather be perceived as a continuum of interaction ranging from parasitism
to mutualism. In fact, the direction of a symbiotic interaction can change
during the lifetime of the symbionts due to developmental changes as well
as changes in the biotic/abiotic environment in which the interaction
occurs.</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">symbiosis, encompassing mutualism
through parasitism</obi:IAO_0000111>
<rdfs:label xml:lang="en">symbiosis, encompassing mutualism through
parasitism</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0042101">
<rdfs:label xml:lang="en">T cell receptor complex</rdfs:label>
- <obi:IAO_0000111 xml:lang="en">T cell receptor
complex</obi:IAO_0000111>
<obi:IAO_0000115 xml:lang="en">A protein complex that contains a
disulfide-linked heterodimer of T cell receptor (TCR) chains, which are
members of the immunoglobulin superfamily, and mediates antigen
recognition, ultimately resulting in T cell activation. The TCR heterodimer
is associated with the CD3 complex, which consists of the nonpolymorphic
polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA
splice variant of zeta) or Fc epsilon chains.</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">T cell receptor
complex</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0019814">
- <obi:IAO_0000111 xml:lang="en">immunoglobulin complex</obi:IAO_0000111>
<obi:IAO_0000115 xml:lang="en">A protein complex that in its canonical
form is composed of two identical immunoglobulin heavy chains and two
identical immunoglobulin light chains, held together by disulfide bonds and
sometimes complexed with additional proteins. An immunoglobulin complex may
be embedded in the plasma membrane or present in the extracellular space,
in mucosal areas or other tissues, or circulating in the blood or
lymph.</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">immunoglobulin complex</obi:IAO_0000111>
<rdfs:label xml:lang="en">immunoglobulin complex</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/CL#CL_0000738">
- <rdfs:label xml:lang="en">leukocyte</rdfs:label>
<obi:IAO_0000115 xml:lang="en">An achromatic cell of the myeloid or
lymphoid lineages capable of ameboid movement, found in blood or other
tissue.</obi:IAO_0000115>
+ <rdfs:label xml:lang="en">leukocyte</rdfs:label>
<obi:IAO_0000111 xml:lang="en">leukocyte</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/TRANS#TRANS_0000000">
- <rdfs:label xml:lang="en">transmission process</rdfs:label>
<obi:IAO_0000115 xml:lang="en">A process that is the means during
which the pathogen is transmitted directly or indirectly from its natural
reservoir, a susceptible host or source to a new host.</obi:IAO_0000115>
<obi:IAO_0000111 xml:lang="en">transmission process</obi:IAO_0000111>
+ <rdfs:label xml:lang="en">transmission process</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0006959">
- <obi:IAO_0000111 xml:lang="en">humoral immune
response</obi:IAO_0000111>
<obi:IAO_0000115 xml:lang="en">An immune response mediated through a
body fluid.</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">humoral immune
response</obi:IAO_0000111>
<rdfs:label xml:lang="en">humoral immune response</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0085031">
- <obi:IAO_0000115 xml:lang="en">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.</obi:IAO_0000115>
<rdfs:label xml:lang="en">commensalism</rdfs:label>
<obi:IAO_0000111 xml:lang="en">commensalism</obi:IAO_0000111>
+ <obi:IAO_0000115 xml:lang="en">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.</obi:IAO_0000115>
+ </rdf:Description>
+ <rdf:Description
rdf:about="http://purl.org/obo/owl/UBERON#UBERON_0000178">
+ <obi:IAO_0000115 xml:lang="en">Circulating body substance which
consists of blood plasma and hemoglobin-carrying red blood cells. Excludes
blood analogues (see UBERON:0000179 haemolymphatic fluid).</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">blood</obi:IAO_0000111>
+ <rdfs:label xml:lang="en">blood</rdfs:label>
</rdf:Description>
<owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000412"/>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0051093">
- <obi:IAO_0000111 xml:lang="en">negative regulation of developmental
process</obi:IAO_0000111>
- <obi:IAO_0000115 xml:lang="en">Any process that stops, prevents or
reduces the rate or extent of development, the biological process whose
specific outcome is the progression of an organism over time from an
initial condition (e.g. a zygote, or a young adult) to a later condition
(e.g. a multicellular animal or an aged adult).</obi:IAO_0000115>
<rdfs:label xml:lang="en">negative regulation of developmental
process</rdfs:label>
+ <obi:IAO_0000115 xml:lang="en">Any process that stops, prevents or
reduces the rate or extent of development, the biological process whose
specific outcome is the progression of an organism over time from an
initial condition (e.g. a zygote, or a young adult) to a later condition
(e.g. a multicellular animal or an aged adult).</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">negative regulation of developmental
process</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0044406">
- <rdfs:label xml:lang="en">adhesion to host</rdfs:label>
<obi:IAO_0000115 xml:lang="en">The attachment of an organism to its
host via adhesion molecules, general stickiness etc., either directly or
indirectly. The host is defined as the larger of the organisms involved in
a symbiotic interaction.</obi:IAO_0000115>
+ <rdfs:label xml:lang="en">adhesion to host</rdfs:label>
<obi:IAO_0000111 xml:lang="en">adhesion to host</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0002250">
+ <obi:IAO_0000111 xml:lang="en">adaptive immune
response</obi:IAO_0000111>
<rdfs:label xml:lang="en">adaptive immune response</rdfs:label>
<obi:IAO_0000115 xml:lang="en">An immune response based on directed
amplification of specific receptors for antigen produced through a somatic
diversification process, and allowing for enhanced response to subsequent
exposures to the same antigen (immunological memory).</obi:IAO_0000115>
- <obi:IAO_0000111 xml:lang="en">adaptive immune
response</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0048525">
<obi:IAO_0000115 xml:lang="en">Any process that stops, prevents, or
reduces the frequency, rate or extent of the viral life cycle, the set of
processes by which a virus reproduces and spreads among
hosts.</obi:IAO_0000115>
@@ -162,64 +167,64 @@
<obi:IAO_0000111 xml:lang="en">developmental process</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0050777">
+ <rdfs:label xml:lang="en">negative regulation of immune
response</rdfs:label>
<obi:IAO_0000115 xml:lang="en">Any process that stops, prevents, or
reduces the frequency, rate or extent of the immune response, the
immunological reaction of an organism to an immunogenic
stimulus.</obi:IAO_0000115>
<obi:IAO_0000111 xml:lang="en">negative regulation of immune
response</obi:IAO_0000111>
- <rdfs:label xml:lang="en">negative regulation of immune
response</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0085030">
- <obi:IAO_0000111 xml:lang="en">mutualism</obi:IAO_0000111>
<rdfs:label xml:lang="en">mutualism</rdfs:label>
<obi:IAO_0000115 xml:lang="en">An interaction between two organisms
living together in more or less intimate association in a relationship in
which both organisms benefit from each other.</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">mutualism</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0051234">
<obi:IAO_0000111 xml:lang="en">establishment of
localization</obi:IAO_0000111>
- <rdfs:label xml:lang="en">establishment of localization</rdfs:label>
<obi:IAO_0000115 xml:lang="en">The directed movement of a cell,
substance or cellular entity, such as a protein complex or organelle, to a
specific location.</obi:IAO_0000115>
+ <rdfs:label xml:lang="en">establishment of localization</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0032991">
- <rdfs:label xml:lang="en">macromolecular complex</rdfs:label>
<obi:IAO_0000111 xml:lang="en">macromolecular complex</obi:IAO_0000111>
+ <rdfs:label xml:lang="en">macromolecular complex</rdfs:label>
<obi:IAO_0000115 xml:lang="en">A stable assembly of two or more
macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in
which the constituent parts function together.</obi:IAO_0000115>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/CARO#CARO_0000000">
- <rdfs:label xml:lang="en">anatomical entity</rdfs:label>
<obi:IAO_0000115 xml:lang="en">Biological entity that is either an
individual member of a biological species or constitutes the structural
organization of an individual member of a biological
species.</obi:IAO_0000115>
<obi:IAO_0000111 xml:lang="en">anatomical entity</obi:IAO_0000111>
+ <rdfs:label xml:lang="en">anatomical entity</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0051704">
- <obi:IAO_0000115 xml:lang="en">Any process by which an organism has an
effect on another organism of the same or different
species.</obi:IAO_0000115>
<rdfs:label xml:lang="en">multi-organism process</rdfs:label>
+ <obi:IAO_0000115 xml:lang="en">Any process in which an organism has an
effect on another organism of the same or different
species.</obi:IAO_0000115>
<obi:IAO_0000111 xml:lang="en">multi-organism process</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0043093">
- <obi:IAO_0000115 xml:lang="en">A cytokinesis process that involves a
set of conserved proteins including FtsZ, and results in the formation of
two similarly sized and shaped cells; the process by which prokaryotic
cells divide.</obi:IAO_0000115>
- <rdfs:label xml:lang="en">cytokinesis by binary fission</rdfs:label>
+ <obi:IAO_0000115 xml:lang="en">A cytokinesis process that involves a
set of conserved proteins including FtsZ, and results in the formation of
two similarly sized and shaped cells; the process in which prokaryotic
cells divide.</obi:IAO_0000115>
<obi:IAO_0000111 xml:lang="en">cytokinesis by binary
fission</obi:IAO_0000111>
+ <rdfs:label xml:lang="en">cytokinesis by binary fission</rdfs:label>
</rdf:Description>
<owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0044411">
+ <rdfs:label xml:lang="en">entry into host through host
barriers</rdfs:label>
<obi:IAO_0000115 xml:lang="en">Penetration by an organism into its
host organism via active breaching of the physical barriers of the host
organism. The host is defined as the larger of the organisms involved in a
symbiotic interaction.</obi:IAO_0000115>
<obi:IAO_0000111 xml:lang="en">entry into host through host
barriers</obi:IAO_0000111>
- <rdfs:label xml:lang="en">entry into host through host
barriers</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/ENVO#ENVO_00002036">
- <obi:IAO_0000115 xml:lang="en">A spatial region having environmental
qualities which may sustain an organism or a community of
organisms.</obi:IAO_0000115>
- <rdfs:label xml:lang="en">habitat</rdfs:label>
<obi:IAO_0000111 xml:lang="en">habitat</obi:IAO_0000111>
+ <rdfs:label xml:lang="en">habitat</rdfs:label>
+ <obi:IAO_0000115 xml:lang="en">A spatial region having environmental
qualities which may sustain an organism or a community of
organisms.</obi:IAO_0000115>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/CL#CL_0000000">
- <obi:IAO_0000111 xml:lang="en">cell</obi:IAO_0000111>
<obi:IAO_0000115 xml:lang="en">Anatomical structure that has as its
parts a maximally connected cell compartment surrounded by a plasma
membrane.</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">cell</obi:IAO_0000111>
<rdfs:label xml:lang="en">cell</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0040007">
<rdfs:label xml:lang="en">growth</rdfs:label>
- <obi:IAO_0000111 xml:lang="en">growth</obi:IAO_0000111>
<obi:IAO_0000115 xml:lang="en">The increase in size or mass of an
entire organism, a part of an organism or a cell.</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">growth</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0000003">
- <obi:IAO_0000115 xml:lang="en">The production by an organism of new
individuals that contain some portion of their genetic material inherited
from that organism.</obi:IAO_0000115>
<rdfs:label xml:lang="en">reproduction</rdfs:label>
+ <obi:IAO_0000115 xml:lang="en">The production by an organism of new
individuals that contain some portion of their genetic material inherited
from that organism.</obi:IAO_0000115>
<obi:IAO_0000111 xml:lang="en">reproduction</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0065007">
@@ -234,12 +239,12 @@
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0045087">
<obi:IAO_0000111 xml:lang="en">innate immune response</obi:IAO_0000111>
- <obi:IAO_0000115 xml:lang="en">Innate immune responses are defense
responses mediated by germline encoded components that directly recognize
components of potential pathogens.</obi:IAO_0000115>
<rdfs:label xml:lang="en">innate immune response</rdfs:label>
+ <obi:IAO_0000115 xml:lang="en">Innate immune responses are defense
responses mediated by germline encoded components that directly recognize
components of potential pathogens.</obi:IAO_0000115>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0016265">
- <rdfs:label xml:lang="en">death</rdfs:label>
<obi:IAO_0000115 xml:lang="en">A permanent cessation of all vital
functions: the end of life; can be applied to a whole organism or to a part
of an organism.</obi:IAO_0000115>
+ <rdfs:label xml:lang="en">death</rdfs:label>
<obi:IAO_0000111 xml:lang="en">death</obi:IAO_0000111>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0019815">
@@ -248,8 +253,8 @@
<obi:IAO_0000115 xml:lang="en">An immunoglobulin complex that is
present in the plasma membrane of B cells and that in its canonical form is
composed of two identical immunoglobulin heavy chains and two identical
immunoglobulin light chains and a signaling subunit, a heterodimer of the
Ig-alpha and Ig-beta proteins.</obi:IAO_0000115>
</rdf:Description>
<rdf:Description rdf:about="http://purl.org/obo/owl/GO#GO_0044409">
- <obi:IAO_0000111 xml:lang="en">entry into host</obi:IAO_0000111>
- <obi:IAO_0000115 xml:lang="en">Penetration by an organism into the
body, tissues, or cells of the host organism. The host is defined as the
larger of the organisms involved in a symbiotic
interaction.</obi:IAO_0000115>
<rdfs:label xml:lang="en">entry into host</rdfs:label>
+ <obi:IAO_0000115 xml:lang="en">Penetration by an organism into the
body, tissues, or cells of the host organism. The host is defined as the
larger of the organisms involved in a symbiotic
interaction.</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">entry into host</obi:IAO_0000111>
</rdf:Description>
</rdf:RDF>
=======================================
--- /trunk/src/ontology/ido-core/ido-external.owl Fri Dec 3 19:41:27 2010
+++ /trunk/src/ontology/ido-core/ido-external.owl Thu Sep 1 15:46:33 2011
@@ -60,7 +60,7 @@
<!-- http://purl.obolibrary.org/obo/OGMS_0000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000020">
- <rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
+ <rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/#Entity"/>
<IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
</owl:Class>