Difference between revisions of "PAMGO 2007 RESOLVED ISSUES"

From GO Wiki
Jump to: navigation, search
(Proposed Tree VI)
 
(29 intermediate revisions by 3 users not shown)
Line 1: Line 1:
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
+
[[Category:Content_PAMGO]]
 +
This page has a summary of all resolved issues. Proposed new terms and changes made are ready for  incorporation in the Gene Ontology. For new topics open for discussion, see PAMGO Summary_2007 which will redirect you to a page titled "Topics for Discussion".
  
==Proposed New Terms==
+
== The other organism string==
 +
 
 +
There was a consensus to replace the phrases "by organism" and "other organism" with the specific words "symbiont" and "host" where appropriate. Another excellent point raised had to do with the fact that, not all users will immediately know that the word symbiont is used by PAMGO to refer to mutualists, pathogens and commensalists. Resolutions in item 1 and 2.
 +
 
 +
 
 +
Action Item 1 Most of these changes have been made by Jane already. If you come across any that still needs modification, please add to the below....preferably GO ID and term.
 +
 
 +
Action Item 2 Add narrow synonyms to all terms where the symbiont is the acting organism Example: "Acquisition of nutrients by symbiont" will have the following narrow synonyms
 +
 
 +
        "acquisition of nutrients by pathogen..................."
 +
        "acquisition of nutrients by mutualist..................."
 +
        "acquisition of nutrients by commensalist..................."
 +
 
 +
Also include in COMMENT field that when the symbiont is the acting organism, genes annotated to the term can be from pathogens, mutualists or commensalists.
 +
 
 +
 
 +
==Secretory systems==
 +
 
 +
All issues resolved. However in a conversation with Magdalen, she had mentioned that there was a discussion with GO members to obsolete the MF terms associated with the secretory systems. From the last check, they are still in there.
 +
 
 +
Action item 1
 +
 
 +
Obsolete the following
 +
 
 +
GO:0015428 protein secretor activity
 +
 
 +
GO:0015447 type II protein secretor activity
 +
 
 +
GO:0015448 type III protein (virulence-related) secretor activity
 +
 
 +
GO:001544 type IV protein (DNA-protein) secretor activity
 +
 
 +
GO:0015323 type V protein secretor activity
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
==Magdalen's Proposed New Terms==
  
 
===Proposed Tree I===
 
===Proposed Tree I===
Line 24: Line 69:
  
 
Requested change: add “by symbiont” to the end of the term
 
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:===
 
===Term request:===
 
====Modulation by symbiont of host response to abiotic stimulus====
 
====Modulation by symbiont of host response to abiotic stimulus====
Line 151: Line 202:
 
GO:0043657 : host cell
 
GO:0043657 : host cell
  
children required under:
+
children required under this term:
Host cell part
+
 
 +
        Host cell part
 
             Host cell membrane
 
             Host cell membrane
 
                   Host cell  endomembrane system
 
                   Host cell  endomembrane system
Line 191: Line 243:
  
 
Definition:
 
Definition:
Any constituent part of a host cell, the basic structural and functional unit of all organisms.
+
Any constituent part of a host cell.
  
 
Comment:
 
Comment:
Line 206: Line 258:
  
 
Definition:
 
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.
+
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:
 
Comment:
Line 281: Line 333:
  
 
Definition:
 
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.
+
A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated.  
  
 
Comment:
 
Comment:
Line 296: Line 348:
  
 
Definition:
 
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.  
+
A semiautonomous, self replicating organelle as found in host cells that occurs in varying numbers, shapes, and sizes in the cell cytoplasm.  
  
 
Comment:
 
Comment:
Line 311: Line 363:
  
 
Definition:
 
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.  
+
Any member of a family of organelles as found in the cytoplasm of host cells, which are membrane-bounded and contain DNA.
  
 
Comment:
 
Comment:
Line 412: Line 464:
  
 
Definition:
 
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.
+
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:
 
Comment:
Line 420: Line 472:
  
 
GO:0052158: modulation by symbiont of host resistance gene-dependent defense response
 
GO:0052158: modulation by symbiont of host resistance gene-dependent defense response
 +
 
GO:0052037: negative regulation by symbiont of host defense response
 
GO:0052037: negative regulation by symbiont of host defense response
  
Child to go under both:
+
Child to go under both terms:
 
     Negative regulation by symbiont of host resistance gene-dependent defense response
 
     Negative regulation by symbiont of host resistance gene-dependent defense response
  
Line 452: Line 505:
  
 
Child required:
 
Child required:
negative regulation by symbiont of defense-related host reactive oxygen species production
+
    negative regulation by symbiont of defense-related host reactive oxygen species production
  
 
===Term request===
 
===Term request===
Line 513: Line 566:
 
None
 
None
  
Term request
+
===Term request===
Negative regulation by symbiont of host defense-related protein level
+
====Negative regulation by symbiont of host defense-related protein level====
  
 
Ontology:
 
Ontology:
Line 547: Line 600:
  
 
Children required:
 
Children required:
Modulation of growth or development of symbiont within host
+
      Modulation of growth or development of symbiont within host
Positive regulation 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  
+
          Negative regulation of  growth or development of symbiont within host
 +
 
 
===Term request===
 
===Term request===
  
Line 562: Line 616:
  
 
Definition:
 
Definition:
Any process by which the symbiont modulates the increase in size or mass of an organism, or the progression of an organism from an initial condition to a later condition, occurring 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
+
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
+
===Term request===
Positive regulation of growth or development of symbiont within host  
+
====Positive regulation of growth or development of symbiont within host====
  
 
Ontology:
 
Ontology:
Line 581: Line 635:
  
 
Definition:
 
Definition:
Any process by which the symbiont activates, maintains or increases the increase in size or mass of an organism, or the progression of an organism from an initial condition to a later condition, occurring 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
+
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===
 
===Term request===
Line 602: Line 656:
  
 
Definition:
 
Definition:
Any process by which the symbiont stops, prevents or reduces the increase in size or mass of an organism, or the progression of an organism from an initial condition to a later condition, occurring 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
+
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===
 
===Proposed Tree VIII===
Line 608: Line 662:
  
 
Children required:
 
Children required:
Negative regulation by symbiont of host apoptosis
+
      Negative regulation by symbiont of host apoptosis
Positive regulation by symbiont of host apoptosis
+
      Positive regulation by symbiont of host apoptosis
  
 
===Term request===
 
===Term request===
Line 652: Line 706:
 
Comment:
 
Comment:
 
None
 
None
 +
 +
==New Terms Added Oct. 15, 2007==
 +
 +
Additions and other edits, mainly from Magdalen's list above [midori]
 +
 +
===New terms:===
 +
*GO:0033635 modulation by symbiont of host response to abiotic stimulus
 +
*GO:0033636 modulation by symbiont of host response to temperature stimulus
 +
*GO:0033637 modulation by symbiont of host response to cold
 +
*GO:0033638 modulation by symbiont of host response to heat
 +
*GO:0033639 modulation by symbiont of host response to water
 +
*GO:0033640 modulation by symbiont of host response to osmotic stress
 +
*GO:0033641 modulation by symbiont of host response to pH
 +
*GO:0033642 modulation by symbiont of host response to gravitational stimulus
 +
*GO:0033643 host cell part
 +
*GO:0033644 host cell membrane
 +
*GO:0033645 host cell endomembrane system
 +
*GO:0033646 host intracellular part
 +
*GO:0033647 host intracellular organelle
 +
*GO:0033648 host intracellular membrane-bound organelle
 +
*<strike>GO:0033649</strike> host cell nucleus - already had GO:0042025, so I merged GO:0033649 into it, and used the new definition
 +
*GO:0033650 host cell mitochondrion
 +
*GO:0033651 host cell plastid
 +
*GO:0033652 host cell chloroplast
 +
*GO:0033653 host cell chloroplast part
 +
*GO:0033654 host cell chloroplast thylakoid membrane
 +
*GO:0033655 host cell cytoplasm part
 +
*GO:0033656 modification by symbiont of host chloroplast
 +
*GO:0033657 modification by symbiont of host chloroplast part
 +
*GO:0033658 modification by symbiont of host chloroplast thylakoid
 +
*GO:0033659 modification by symbiont of host mitochondrion
 +
*GO:0033660 negative regulation by symbiont of host resistance gene-dependent defense response
 +
*GO:0033661 negative regulation by symbiont of defense-related host reactive oxygen species production
 +
*GO:0033662 modulation by symbiont of host defense-related protein level
 +
*GO:0033663 negative regulation by symbiont of host defense-related protein level
 +
*GO:0033664 positive regulation by symbiont of host defense-related protein level
 +
*GO:0033665 modulation of growth or development of symbiont within host
 +
*GO:0033666 positive regulation of growth or development of symbiont within host
 +
*GO:0033667 negative regulation of growth or development of symbiont within host
 +
*GO:0033668 negative regulation by symbiont of host apoptosis
 +
*GO:0033669 positive regulation by symbiont of host apoptosis
 +
 +
===Other changes:===
 +
*renamed GO:004403 to 'modification by symbiont of host morphology or physiology'
 +
*moved to is_a host cell cytoplasm part GO:0033655
 +
**GO:0043658 host symbiosome
 +
**GO:0020030 infected host cell surface knob
 +
**GO:0020036 Maurer's cleft
 +
**GO:0043493 phage terminase complex
 +
**GO:0020003 parasitophorous vacuole
 +
*added relationship GO:0043658 is_a GO:0033648 host intracellular membrane-bound organelle
 +
*moved host cell plasma membrane GO:0020002 to is_a host cell membrane GO:0033644
 +
*moved intracellular region of host GO:0043656 to is_a host cell part GO:0033643
 +
*moved GO:0030430 host cell cytoplasm to is_a host intracellular part GO:0033646
 +
*moved host cell nucleus GO:0042025 to is_a host intracellular membrane-bound organelle GO:0033648

Latest revision as of 12:46, 1 July 2014

This page has a summary of all resolved issues. Proposed new terms and changes made are ready for incorporation in the Gene Ontology. For new topics open for discussion, see PAMGO Summary_2007 which will redirect you to a page titled "Topics for Discussion".

Contents

The other organism string

There was a consensus to replace the phrases "by organism" and "other organism" with the specific words "symbiont" and "host" where appropriate. Another excellent point raised had to do with the fact that, not all users will immediately know that the word symbiont is used by PAMGO to refer to mutualists, pathogens and commensalists. Resolutions in item 1 and 2.


Action Item 1 Most of these changes have been made by Jane already. If you come across any that still needs modification, please add to the below....preferably GO ID and term.

Action Item 2 Add narrow synonyms to all terms where the symbiont is the acting organism Example: "Acquisition of nutrients by symbiont" will have the following narrow synonyms

        "acquisition of nutrients by pathogen..................."
        "acquisition of nutrients by mutualist..................."
        "acquisition of nutrients by commensalist..................."

Also include in COMMENT field that when the symbiont is the acting organism, genes annotated to the term can be from pathogens, mutualists or commensalists.


Secretory systems

All issues resolved. However in a conversation with Magdalen, she had mentioned that there was a discussion with GO members to obsolete the MF terms associated with the secretory systems. From the last check, they are still in there.

Action item 1

Obsolete the following

GO:0015428 protein secretor activity

GO:0015447 type II protein secretor activity

GO:0015448 type III protein (virulence-related) secretor activity

GO:001544 type IV protein (DNA-protein) secretor activity

GO:0015323 type V protein secretor activity






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

New Terms Added Oct. 15, 2007

Additions and other edits, mainly from Magdalen's list above [midori]

New terms:

  • GO:0033635 modulation by symbiont of host response to abiotic stimulus
  • GO:0033636 modulation by symbiont of host response to temperature stimulus
  • GO:0033637 modulation by symbiont of host response to cold
  • GO:0033638 modulation by symbiont of host response to heat
  • GO:0033639 modulation by symbiont of host response to water
  • GO:0033640 modulation by symbiont of host response to osmotic stress
  • GO:0033641 modulation by symbiont of host response to pH
  • GO:0033642 modulation by symbiont of host response to gravitational stimulus
  • GO:0033643 host cell part
  • GO:0033644 host cell membrane
  • GO:0033645 host cell endomembrane system
  • GO:0033646 host intracellular part
  • GO:0033647 host intracellular organelle
  • GO:0033648 host intracellular membrane-bound organelle
  • GO:0033649 host cell nucleus - already had GO:0042025, so I merged GO:0033649 into it, and used the new definition
  • GO:0033650 host cell mitochondrion
  • GO:0033651 host cell plastid
  • GO:0033652 host cell chloroplast
  • GO:0033653 host cell chloroplast part
  • GO:0033654 host cell chloroplast thylakoid membrane
  • GO:0033655 host cell cytoplasm part
  • GO:0033656 modification by symbiont of host chloroplast
  • GO:0033657 modification by symbiont of host chloroplast part
  • GO:0033658 modification by symbiont of host chloroplast thylakoid
  • GO:0033659 modification by symbiont of host mitochondrion
  • GO:0033660 negative regulation by symbiont of host resistance gene-dependent defense response
  • GO:0033661 negative regulation by symbiont of defense-related host reactive oxygen species production
  • GO:0033662 modulation by symbiont of host defense-related protein level
  • GO:0033663 negative regulation by symbiont of host defense-related protein level
  • GO:0033664 positive regulation by symbiont of host defense-related protein level
  • GO:0033665 modulation of growth or development of symbiont within host
  • GO:0033666 positive regulation of growth or development of symbiont within host
  • GO:0033667 negative regulation of growth or development of symbiont within host
  • GO:0033668 negative regulation by symbiont of host apoptosis
  • GO:0033669 positive regulation by symbiont of host apoptosis

Other changes:

  • renamed GO:004403 to 'modification by symbiont of host morphology or physiology'
  • moved to is_a host cell cytoplasm part GO:0033655
    • GO:0043658 host symbiosome
    • GO:0020030 infected host cell surface knob
    • GO:0020036 Maurer's cleft
    • GO:0043493 phage terminase complex
    • GO:0020003 parasitophorous vacuole
  • added relationship GO:0043658 is_a GO:0033648 host intracellular membrane-bound organelle
  • moved host cell plasma membrane GO:0020002 to is_a host cell membrane GO:0033644
  • moved intracellular region of host GO:0043656 to is_a host cell part GO:0033643
  • moved GO:0030430 host cell cytoplasm to is_a host intracellular part GO:0033646
  • moved host cell nucleus GO:0042025 to is_a host intracellular membrane-bound organelle GO:0033648