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: during
name: during
def: "added_during, present_during, happens_during or exists_during." [BFO:cjm, PomBase:mah]
is_transitive: true

[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 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 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 process during which the modification is observed (note that the modification may have been added during this process (if this is known use the added_during relation) or during a preceding process)." [PomBase:al]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: absent_during
name: absent_during
def: "identifies a biological process during which the modification is not observed (note that the modification may have been removed during this process (if this is known use the removed_during relation) or during a preceding process)" [PomBase:al]
property_value: local_domain MOD:00000 ! protein modification

[Typedef]
id: occupancy
name: occupancy
def: "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

[Typedef]
id: level_fluctuates_during
name: level_fluctuates_during
def: "identifies a biological process during which the modification site occupancy is observed to vary" [PomBase:mah]
synonym: occupancy_fluctuates_during
comment: would usually be used with a GO term for the cell cycle or one of its phases