format-version: 1.2
date: 13:07:2012 17:15
saved-by: midori
default-namespace: PSI-MOD_extension_relations
ontology: PSI-MOD_extension_relations

[Typedef]
id: required_for
name: required_for
def: "Indicates that a modification is required for a GO function or process." [PomBase:mah]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: added_by
name: added_by
def: "Identifies a gene product that adds the modification." [PomBase:mah]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: removed_by
name: removed_by
def: "Identifies a gene product that removes the modification." [PomBase:mah]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: removed_during
name: removed_during
def: "Identifies a biological phase or process during which the modification is removed." [PomBase:al]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: added_during
name: added_during
def: "Identifies a biological phase or process during which the modification is actively added." [PomBase:al]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: present_during
name: present_during
def: "Identifies a biological phase or process during which the modification is observed, where it is not known whether the modification was added during the indicated phase or process (if this is known use the added_during relation) or during a preceding phase or process." [PomBase:al]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: absent_during
name: absent_during
def: "Identifies a biological phase or process during which the modification is not observed, where it is not known whether the modification was removed during the indicated phase or process (if this is known use the removed_during relation), or during a preceding phase or process." [PomBase:al]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: occupancy
name: occupancy
def: "A number representing what proportion of copies of the protein have the modification." [PomBase:mah]
comment: Use a decimal value, rounded to something sensible like 2 or 3 digits.
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: level_fluctuates_during
name: level_fluctuates_during
def: "Identifies a biological phase or process during which the modification site occupancy is observed to vary." [PomBase:mah]
synonym: "occupancy_fluctuates_during" EXACT [PomBase:mah]
comment: This qualifier would most commonly be used with a GO term for the cell cycle or one of its phases.
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: affected_by
name: affected_by
def: "Identifies a gene product that influences the modification, where the experiment does not distinguish between direct action (e.g. adds or removes a modification) and indirect effects." [PomBase:mah]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: increased_during
name: increased_during
def: "Identifies a biological phase or process during which the modification is present to a greater extent than in a preceding phase or process, where the experiment does not distinguish between increased addition and decreased removal of the modification (if this is known use the added_during or removed_during relation)." [PomBase:mah]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: decreased_during
name: decreased_during
def: "Identifies a biological phase or process during which the modification is present to a lower extent than in a preceding phase or process, where the experiment does not distinguish between decreased addition and increased removal of the modification (if this is known use the added_during or removed_during relation)." [PomBase:mah]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: decreased_in_presence_of
name: decreased_in_presence_of
def: "Identifies a substance, where the modification is present to a lower extent in the presence than in the absence of the substance." [PomBase:mah]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: increased_in_presence_of
name: increased_in_presence_of
def: "Identifies a substance, where the modification is present to a greater extent in the presence than in the absence of the substance." [PomBase:mah]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: multiplicity
name: multiplicity
def: "The number of sites simultaneously modified on a peptide." [PMID:24501219, PMID:25159151, PomBase:mah]
comment: Applicable to peptide-based proteomic methods. Use an integer.
property_value: local_domain MOD:00000 ! protein modification