Both variables and underlying traits need synonyms when they are added to the ontology, it would be good to let submitters request these.
Variables usually have two synonyms - one that is a combo of the trait, method, and scale synonyms, and another that is short and descriptive and ideally all caps. The second variable synonym is often what breeders will use in day to day operations. Because they should be unique within the scope of the specific ontology, some tools like HIDAP even use just the synonym to track measurements in place of the trait name and id.
A couple examples:
In Cassava
[Term]
id: CO_334:0000293
name: Branch height
def: "Branch height" [CO:curators]
synonym: "branching" EXACT []
synonym: "BrnchHt" EXACT []
xref: TO:1000008
is_a: CO_334:0000329 ! Plant branch morphological trait
[Term]
id: CO_334:0000106
name: first apical branch height measurement in cm
def: "Height of first apical branch (ground level to point of first Apical branch, 9 months after planting) in cm." [CO:curators]
synonym: "BrnchHt_Meas_cm" EXACT []
synonym: "brnht" EXACT []
relationship: variable_of CO_334:0000293 ! Branch height
relationship: variable_of CO_334:0010352 ! Measurement :First Apical Branch Height_method
relationship: variable_of CO_334:0100558 ! cm
In Sweetpotato
[Term]
id: CO_331:0000203
name: number of storage root damages
namespace: SweetpotatoTrait
def: "Root with structural damages" []
synonym: "RtDam" EXACT []
is_a: CO_331:1000010 ! Morphological_trait
created_by: W. Grueneberg
[Term]
id: CO_331:0000206
name: Storage root damages estimating 1-9
namespace: SweetpotatoTrait
def: "Root with structural damages. 1= No damage, 2= Very minor, 3= Minor, 4= Minor to moderate, 5= Moderate, 6= Moderate to heavy, 7= Heavy, 8= Heavy to severe damage, 9= Severe damage" []
synonym: "DAMR" EXACT []
synonym: "RtDam_Et_1to9" EXACT []
is_a: CO_331:1000003 ! Variables
relationship: variable_of CO_331:0000203 ! number of storage root damages
relationship: variable_of CO_331:0000881 ! storage root damage
relationship: variable_of CO_331:0000882 ! rtsdam 9 pt. scale
I'm getting a 500 error when I try to add a new issue, so instead I'm reopening this one. A few more new fields are requested by attendees of the RTBFoods workshop:
New optional xref field for referencing documentation external to the ontology
New method definition field to provide details of the method, separate from the existing trait definition
Clarification in form that the detailed trait name should include the entity (specific plant tissue) and attribute
Both variables and underlying traits need synonyms when they are added to the ontology, it would be good to let submitters request these.
Variables usually have two synonyms - one that is a combo of the trait, method, and scale synonyms, and another that is short and descriptive and ideally all caps. The second variable synonym is often what breeders will use in day to day operations. Because they should be unique within the scope of the specific ontology, some tools like HIDAP even use just the synonym to track measurements in place of the trait name and id.
A couple examples:
In Cassava
In Sweetpotato