PAMGO 2007 RESOLVED ISSUES

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Revision as of 06:23, 29 September 2007 by Maria (talk | contribs) (Trudy=)

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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

Contents

Magdalen's 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 under: 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


Trudy

Other proposed terms look fine. Very minor detail----Rather than add at the end, to be consistent with what exists in GO alraedy, it should read modification by symbiont of host morphology or physiology

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 under this term:

       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 cell nucleus
                           Host cell mitochondrion
                           Host cell plastid
                                 Host cell chloroplast
                                       Host cell chloroplast part
                                             Host cell chloroplast thylakoid memb
                           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 thylakoid 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.

Comment: None

Term request

Host cell membrane

Ontology: cellular component

Synonyms: None

Definition: Double layer of lipid molecules as it 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 as it is found in the host cell in which chromosomes are housed and replicated.

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.

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.

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 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 terms:

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

Term request for Tree IV

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

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

Proposed Tree V

GO:0052164: modulation by symbiont of defense-related host reactive oxygen species production

Child required:

    negative regulation by symbiont of defense-related host reactive oxygen species production

Term request

negative regulation by symbiont of defense-related host reactive oxygen species production

Ontology: biological process

Synonyms:

narrow: inhibition by organism of defense-related host active oxygen species production

exact: downregulation by organism of defense-related host AOS production

exact: down regulation by organism of defense-related host metabolic burst

exact: down-regulation by organism of defense-related host oxidative burst

exact: negative regulation by organism of defense-related host reactive oxidative species production

exact: negative regulation by organism of defense-related host reactive oxygen intermediate production

exact: negative regulation by organism of defense-related host respiratory burst

exact: negative regulation by organism of defense-related host ROI production

exact: negative regulation by organism of defense-related host ROS production

Definition: Any process by which an organism stops, prevents or reduces the frequency, rate or extent of the production of reactive oxygen species as part of the defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None


Proposed Tree VI

GO:0052031 : modulation by symbiont of host defense response

Children required:

    Modulation by symbiont of host defense-related protein level
         Negative regulation by symbiont of host defense-related protein level
         Positive regulation by symbiont of host defense-related protein level

(Note that this would cover a multitude of different pathways)

Term request

Modulation by symbiont of host defense-related protein level

Ontology: biological process

Synonyms: None

Definition: The alternation by a symbiont of the levels of defense-related proteins in its host. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None

Term request

Negative regulation by symbiont of host defense-related protein level

Ontology: biological process

Synonyms: None

Definition: Any process by which the symbiont stops or reduces of the levels of defense-related proteins in its host. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None

Term request

Positive regulation by symbiont of host defense-related protein level

Ontology: biological process

Synonyms: None

Definition: Any process by which the symbiont activates, maintains or increases levels of defense-related proteins in its host. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None

Proposed Tree VII

GO:0044412: growth or development of symbiont within host

Children required:

     Modulation of growth or development of symbiont within host
          Positive regulation of growth or development of symbiont within host 
          Negative regulation of  growth or development of symbiont within host

Term request

Modulation of growth or development of symbiont within host

Ontology: biological process

Synonyms: exact: modulation of growth or development of organism within host broad: modulation of invasive growth

Definition: Any process by which the symbiont modulates the increase in its size or mass, or its progression from an initial condition to a later condition, within the cells or tissues of the host organism. This may (but not necessarily) include a filamentous growth form, and also can include secretion of proteases and lipases to break down. The host is defined as the larger of the organisms involved in the symbiotic interaction.

Term request

Positive regulation of growth or development of symbiont within host

Ontology: biological process

Synonyms:

exact: up-regulation of growth or development of organism within host

exact: upregulation of growth or development of organism within host

exact: up regulation of growth or development of organism within host

broad: positive regulation of invasive growth

Definition: Any process by which the symbiont activates, maintains or increases its size or mass or its progression from an initial condition to a later condition, within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction.

Term request

Negative regulation of growth or development of symbiont within host

Ontology: biological process

Synonyms:

exact: down-regulation of growth or development of organism within host

exact: downregulation of growth or development of organism within host

exact: down regulation of growth or development of organism within host

broad: negative regulation of invasive growth

narrow: inhibition of growth of development of organism within host

Definition: Any process by which the symbiont stops, prevents or reduces its increase in size or mass or its progression from an initial condition to a later condition, within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction.

Proposed Tree VIII

GO:0052150 : modulation by symbiont of host apoptosis

Children required:

     Negative regulation by symbiont of host apoptosis
     Positive regulation by symbiont of host apoptosis

Term request

Negative regulation by symbiont of host apoptosis

Ontology: biological process

Synonyms:

exact: down-regulation by organism of host apoptotic programmed cell death

exact: downregulation by organism of host apoptotic programmed cell death

exact: down regulation by organism of host apoptotic programmed cell death

narrow: inhibition by organism of host apoptotic programmed cell death

Definition: Any process by which an organism stops, prevents or reduces the frequency, rate or extent of programmed cell death in the host, where programmed cell death proceeds by apoptosis. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None

Term request

Positive regulation by symbiont of host apoptosis

Ontology: biological process

Synonyms:

exact: up-regulation by organism of host apoptotic programmed cell death

exact: upregulation by organism of host apoptotic programmed cell death

exact: up regulation by organism of host apoptotic programmed cell death

Definition: Any process by which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host, where programmed cell death proceeds by apoptosis. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Comment: None