Difference between revisions of "PAMGO 2007 RESOLVED ISSUES"

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This page has a summary of all the issues that were not resolved before the terms were integrated in the Gene Ontology. It is still open for discussion
 
This page has a summary of all the issues that were not resolved before the terms were integrated in the Gene Ontology. It is still open for discussion
 +
 +
==Proposed New Terms==
 +
 +
===Proposed Tree I===
 +
(Note: based upon the tree under “GO:0009628 Response to abiotic stimulus”)
 +
 +
GO:0044003 : modification of host morphology or physiology
 +
 +
children required:
 +
Modulation by symbiont of host response to abiotic stimulus
 +
            Modulation by symbiont of host response to temperature stimulus
 +
                        Modulation by symbiont of host response to cold
 +
                        Modulation by symbiont of host response to heat
 +
            Modulation by symbiont of host response to water
 +
            Modulation by symbiont of host response to osmotic stress
 +
            Modulation by symbiont of host response to pH
 +
            Modulation by symbiont of host response to gravity
 +
 +
===Specific requests for tree I===
 +
 +
===Term modification===
 +
====GO:0044003 : modification of host morphology or physiology====
 +
 +
Requested change: add “by symbiont” to the end of the term
 +
 +
===Term request:===
 +
====Modulation by symbiont of host response to abiotic stimulus====
 +
 +
Ontology:
 +
biological process
 +
 +
Synonyms:
 +
None
 +
 +
Definition:
 +
Any process by which an organism modulates a change in the state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
 +
Comment:
 +
None
 +
 +
===Term request:===
 +
====Modulation by symbiont of host response to temperature stimulus====
 +
 +
Ontology:
 +
biological process
 +
 +
Synonyms:
 +
exact: Modulation by symbiont of host response to thermal stimulus
 +
 +
Definition:
 +
Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
 +
Comment:
 +
None
 +
 +
===Term request===
 +
====Modulation by symbiont of host response to cold====
 +
 +
Ontology:
 +
biological process
 +
 +
Synonyms:
 +
related: freezing tolerance
 +
 +
Definition:
 +
Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
 +
Comment:
 +
None
 +
 +
===Term request===
 +
====Modulation by symbiont of host response to heat====
 +
 +
Ontology:
 +
biological process
 +
 +
Synonyms:
 +
narrow: response to heat shock
 +
 +
Definition:
 +
Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
 +
Comment:
 +
None
 +
 +
===Term request===
 +
====Modulation by symbiont of host response to water====
 +
 +
Ontology:
 +
biological process
 +
 +
Synonyms:
 +
None
 +
 +
Definition:
 +
Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
 +
Comment:
 +
None
 +
 +
===Term request
 +
Modulation by symbiont of host response to osmotic stress
 +
 +
Ontology
 +
biological process
 +
Synonyms
 +
exact: osmotic response
 +
exact: osmotic stress response
 +
Definition
 +
Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
 +
Comment
 +
None
 +
 +
Term request
 +
Modulation by symbiont of host response to pH
 +
 +
Ontology
 +
biological process
 +
Synonyms
 +
None
 +
Definition
 +
Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
 +
Comment
 +
None
 +
 +
Term request
 +
Modulation by symbiont of host response to gravitational stimulus
 +
 +
Ontology
 +
biological process
 +
Synonyms
 +
exact: response to gravitational stimulus
 +
Definition
 +
Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
 +
Comment
 +
None
 +
 +
Proposed Tree II
 +
(Note: based upon the tree under GO:0044464 “cell part”)
 +
 +
GO:0043657 : host cell
 +
 +
children required:
 +
Host cell part
 +
Host cell membrane
 +
Host cell  endomembrane system
 +
GO:0020002 Host cell  plasma membrane
 +
                GO:0043656 - intracellular region of host
 +
Host intracellular part
 +
Host intracellular organelle
 +
Host intracellular membrane-bound organelle
 +
Host cell nucleus
 +
Host cell mitochondrion
 +
Host cell plastid
 +
Host cell chloroplast
 +
GO:0020003 : parasitophorous vacuole
 +
                        GO:0030430 host cell cytoplasm
 +
Host cell cytoplasm part
 +
GO:0043658 : host symbiosome
 +
GO:0020030 : infected host cell surface knob
 +
GO:0020036 : Maurer's cleft
 +
GO:0043493 : phage terminase complex
 +
Host cell mitochondrion Host cell plastid
 +
Host cell chloroplast
 +
Host cell chloroplast part
 +
Host cell chloroplast thy  mem
 +
GO:0020003 : parasitophorous vacuole
 +
 +
Specific requests for tree II:
 +
 +
Term request
 +
Host cell part
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
None
 +
Definition
 +
Any constituent part of a host cell, the basic structural and functional unit of all organisms.
 +
Comment
 +
None
 +
 +
Term request
 +
Host cell membrane
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
None
 +
Definition
 +
Double layer of lipid molecules that encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
 +
Comment
 +
None
 +
 +
Term request
 +
Host cell  endomembrane system
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
None
 +
Definition
 +
A collection of membranous structures involved in transport within the host cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
 +
Comment
 +
None
 +
 +
Term request
 +
Host intracellular part
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
None
 +
Definition
 +
Any constituent part of the living contents of a host cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
 +
Comment
 +
None
 +
 +
Term request
 +
Host intracellular organelle
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
None
 +
Definition
 +
Organized structure of distinctive morphology and function, occurring within the host cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
 +
Comment
 +
None
 +
 +
Term request
 +
Host intracellular membrane-bound organelle
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
None
 +
Definition
 +
Organized structure of distinctive morphology and function, as found in host cells, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
 +
Comment
 +
None
 +
 +
Term request
 +
Host cell nucleus
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
None
 +
Definition
 +
A membrane-bounded organelle in the host cell in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
 +
Comment
 +
None
 +
 +
Term request
 +
Host cell mitochondrion
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
exact: mitochondria
 +
Definition
 +
A semiautonomous, self replicating organelle as found in host cells that occurs in varying numbers, shapes, and sizes in the cell cytoplasm. It is notably the site of tissue respiration.
 +
Comment
 +
None
 +
 +
Term request
 +
Host cell plastid
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
None
 +
Definition
 +
Any member of a family of organelles as found in the cytoplasm of host cells, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
 +
Comment
 +
None
 +
 +
Term request
 +
Host cell chloroplast
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
None
 +
Definition
 +
A chlorophyll-containing plastid as found within host cells with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
 +
Comment
 +
None
 +
 +
Term request
 +
Host cell cytoplasm part
 +
 +
Ontology
 +
cellular component
 +
Synonyms
 +
exact: cytoplasm component
 +
Definition
 +
Any constituent part of the host cell cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
 +
Comment
 +
None
 +
 +
Proposed Tree III
 +
GO:0052043 - modification by symbiont of host cellular component
 +
 +
children required:
 +
            Modification by symbiont of host chloroplast
 +
                        Modification by symbiont of host chloroplast part
 +
                                    Modification by symbiont of host chloroplast thylakoid
 +
            Modification by symbiont of host mitochondrian
 +
 +
Terms Requested for Tree III
 +
 +
Term request
 +
Modification by symbiont of host chloroplast
 +
 +
Ontology
 +
biological process
 +
Synonyms
 +
None
 +
Definition
 +
The process by which an organism effects a change in the structure or function of host cell chloroplasts. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
Comment
 +
None
 +
 +
Term request
 +
Modification by symbiont of host chloroplast part
 +
 +
Ontology
 +
biological process
 +
Synonyms
 +
None
 +
Definition
 +
The process by which an organism effects a change in the structure or function of a component of the host cell chloroplast. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
Comment
 +
None
 +
 +
Term request
 +
Modification by symbiont of host chloroplast thylakoid
 +
 +
Ontology
 +
biological process
 +
Synonyms
 +
None
 +
Definition
 +
The process by which an organism effects a change in the structure or function of the host cell chloroplast thylakoid. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
Comment
 +
None
 +
 +
Term request
 +
Modification by symbiont of host mitochondrion
 +
 +
Ontology
 +
biological process
 +
Synonyms
 +
None
 +
Definition
 +
The process by which an organism effects a change in the structure or function of the host cell mitochondria. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
Comment
 +
None
 +
 +
Proposed Tree IV
 +
 +
GO:0052158: modulation by symbiont of host resistance gene-dependent defense response
 +
GO:0052037: negative regulation by symbiont of host defense response
 +
 +
Child to go under both:
 +
                Negative regulation by symbiont of host resistance gene-dependent defense response
 +
 +
Term request for Tree IV
 +
Ontology
 +
biological process
 +
Synonyms
 +
narrow: inhibition by symbiont of host resistance gene-dependent defense response
 +
exact: down regulation by symbiont of defense response in host by specific elicitors
 +
exact: down-regulation by symbiont of host gene-4-gene resistance
 +
exact: downregulation by symbiont of pathogen-race/host plant cultivar-specific resistance in symbiont
 +
exact: suppression by symbiont of host resistance gene-dependent defense response
 +
Definition
 +
Any process by which an organism stops, prevents or reduces the frequency, rate or extent of the resistance gene-dependent defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
 +
Comment
 +
None

Revision as of 10:43, 11 July 2007

This page has a summary of all the issues that were not resolved before the terms were integrated in the Gene Ontology. It is still open for discussion

Proposed New Terms

Proposed Tree I

(Note: based upon the tree under “GO:0009628 Response to abiotic stimulus”)

GO:0044003 : modification of host morphology or physiology

children required: Modulation by symbiont of host response to abiotic stimulus

            Modulation by symbiont of host response to temperature stimulus
                        Modulation by symbiont of host response to cold
                        Modulation by symbiont of host response to heat
            Modulation by symbiont of host response to water
            Modulation by symbiont of host response to osmotic stress
            Modulation by symbiont of host response to pH
            Modulation by symbiont of host response to gravity

Specific requests for tree I

Term modification

GO:0044003 : modification of host morphology or physiology

Requested change: add “by symbiont” to the end of the term

Term request:

Modulation by symbiont of host response to abiotic stimulus

Ontology: biological process

Synonyms: None

Definition: Any process by which an organism modulates a change in the state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None

Term request:

Modulation by symbiont of host response to temperature stimulus

Ontology: biological process

Synonyms: exact: Modulation by symbiont of host response to thermal stimulus

Definition: Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None

Term request

Modulation by symbiont of host response to cold

Ontology: biological process

Synonyms: related: freezing tolerance

Definition: Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None

Term request

Modulation by symbiont of host response to heat

Ontology: biological process

Synonyms: narrow: response to heat shock

Definition: Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None

Term request

Modulation by symbiont of host response to water

Ontology: biological process

Synonyms: None

Definition: Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None

===Term request Modulation by symbiont of host response to osmotic stress

Ontology biological process Synonyms exact: osmotic response exact: osmotic stress response Definition Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment None

Term request Modulation by symbiont of host response to pH

Ontology biological process Synonyms None Definition Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment None

Term request Modulation by symbiont of host response to gravitational stimulus

Ontology biological process Synonyms exact: response to gravitational stimulus Definition Any process by which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment None

Proposed Tree II (Note: based upon the tree under GO:0044464 “cell part”)

GO:0043657 : host cell

children required: Host cell part Host cell membrane Host cell endomembrane system GO:0020002 Host cell plasma membrane

               GO:0043656 - intracellular region of host

Host intracellular part Host intracellular organelle Host intracellular membrane-bound organelle Host cell nucleus Host cell mitochondrion Host cell plastid Host cell chloroplast GO:0020003 : parasitophorous vacuole

                       		GO:0030430 host cell cytoplasm 

Host cell cytoplasm part GO:0043658 : host symbiosome GO:0020030 : infected host cell surface knob GO:0020036 : Maurer's cleft GO:0043493 : phage terminase complex Host cell mitochondrion Host cell plastid Host cell chloroplast Host cell chloroplast part Host cell chloroplast thy mem GO:0020003 : parasitophorous vacuole

Specific requests for tree II:

Term request Host cell part

Ontology cellular component Synonyms None Definition Any constituent part of a host cell, the basic structural and functional unit of all organisms. Comment None

Term request Host cell membrane

Ontology cellular component Synonyms None Definition Double layer of lipid molecules that encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. Comment None

Term request Host cell endomembrane system

Ontology cellular component Synonyms None Definition A collection of membranous structures involved in transport within the host cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. Comment None

Term request Host intracellular part

Ontology cellular component Synonyms None Definition Any constituent part of the living contents of a host cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. Comment None

Term request Host intracellular organelle

Ontology cellular component Synonyms None Definition Organized structure of distinctive morphology and function, occurring within the host cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. Comment None

Term request Host intracellular membrane-bound organelle

Ontology cellular component Synonyms None Definition Organized structure of distinctive morphology and function, as found in host cells, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. Comment None

Term request Host cell nucleus

Ontology cellular component Synonyms None Definition A membrane-bounded organelle in the host cell in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. Comment None

Term request Host cell mitochondrion

Ontology cellular component Synonyms exact: mitochondria Definition A semiautonomous, self replicating organelle as found in host cells that occurs in varying numbers, shapes, and sizes in the cell cytoplasm. It is notably the site of tissue respiration. Comment None

Term request Host cell plastid

Ontology cellular component Synonyms None Definition Any member of a family of organelles as found in the cytoplasm of host cells, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid. Comment None

Term request Host cell chloroplast

Ontology cellular component Synonyms None Definition A chlorophyll-containing plastid as found within host cells with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma. Comment None

Term request Host cell cytoplasm part

Ontology cellular component Synonyms exact: cytoplasm component Definition Any constituent part of the host cell cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. Comment None

Proposed Tree III GO:0052043 - modification by symbiont of host cellular component

children required:

            Modification by symbiont of host chloroplast
                        Modification by symbiont of host chloroplast part
                                    Modification by symbiont of host chloroplast thylakoid
            Modification by symbiont of host mitochondrian

Terms Requested for Tree III

Term request Modification by symbiont of host chloroplast

Ontology biological process Synonyms None Definition The process by which an organism effects a change in the structure or function of host cell chloroplasts. The host is defined as the larger of the organisms involved in a symbiotic interaction. Comment None

Term request Modification by symbiont of host chloroplast part

Ontology biological process Synonyms None Definition The process by which an organism effects a change in the structure or function of a component of the host cell chloroplast. The host is defined as the larger of the organisms involved in a symbiotic interaction. Comment None

Term request Modification by symbiont of host chloroplast thylakoid

Ontology biological process Synonyms None Definition The process by which an organism effects a change in the structure or function of the host cell chloroplast thylakoid. The host is defined as the larger of the organisms involved in a symbiotic interaction. Comment None

Term request Modification by symbiont of host mitochondrion

Ontology biological process Synonyms None Definition The process by which an organism effects a change in the structure or function of the host cell mitochondria. The host is defined as the larger of the organisms involved in a symbiotic interaction. Comment None

Proposed Tree IV

GO:0052158: modulation by symbiont of host resistance gene-dependent defense response GO:0052037: negative regulation by symbiont of host defense response

Child to go under both:

               Negative regulation by symbiont of host resistance gene-dependent defense response

Term request for Tree IV Ontology biological process Synonyms narrow: inhibition by symbiont of host resistance gene-dependent defense response exact: down regulation by symbiont of defense response in host by specific elicitors exact: down-regulation by symbiont of host gene-4-gene resistance exact: downregulation by symbiont of pathogen-race/host plant cultivar-specific resistance in symbiont exact: suppression by symbiont of host resistance gene-dependent defense response Definition Any process by which an organism stops, prevents or reduces the frequency, rate or extent of the resistance gene-dependent defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. Comment None