Trait definition file improvement

[bedroesb]

Examples:

t_RIGW1.txt:

Variable ID	Variable Name	Trait	Method	Method Description	Scale
CO_356:1000001	BUD_DATE	Budbreak	BUD_DATE Method		Calendar date
CO_356:1000010	VER_50	Veraison	VER_50 Method		Calendar date
CO_356:1000011	FLO_50	Flowering	FLO_50 Method		Calendar date
CO_356:1000053	BERRY_TOTATERP	Concentrations of free and bound alpha-terpineol	SPE	Solid Phase Extraction	microg/kg

t_POPYOMICS-POP2-F.txt:

Variable ID	Variable Name	Trait	Method	Method Description	Reference Associated to the Method	Scale
CO_357:0000010	BF_score_BL	Budflush	Budflush scoring protocol	Visual assessment on the terminal bud or on the whole tree when terminal bud is not visible with a reference scoring scale	https://forgemia.inra.fr/urgi-is/ontologies/blob/develop/Tree/T4F_D21_submitted.pdf - pages 6-20 + 30-35 for broadleaves and 45-49 + 62-64 for conifers	Broadleaves budflush scoring scale
CO_357:0000010	BF_score_BL	Débourrement	Protocole score débourrement	Evaluation à l'oeil nu selon une échelle de notation de référence sur le bourgeon apical (ou supposé apical) ou sur l'arbre entier lorsque le bourgeon apical n'est pas visible	https://forgemia.inra.fr/urgi-is/ontologies/blob/develop/Tree/T4F_D21_submitted.pdf - pages 6-20 + 30-35 pour les feuillus et 45-49 + 62-64 pour les conifers	Note de débourrement feuillus
CO_357:0000016	BS_date	Budset date	Bud date protocol	Estimated date from polynomial regression of a time series of budflush or budset scores		Calendar day
CO_357:0000016	BS_date	Date d'aoûtement	Protocole date bourgeon	Estimation de la date d'après une régression polynomiale réalisée sur une série temporelle de scores de débourrement ou bourgeonement		Jour calendaire

t_VIB_study___40.txt:

Variable ID	Variable Name	Trait	Method	Method Description	Scale
188	cellDivisionZoneLengthLeaf	cellDivisionZoneLengthLeaf	cellDivisionZoneLengthLeaf	size of the cell division zone at the basis of a leaf	mm
195	finalLeafLength	finalLeafLength	finalLeafLength	length of a leaf at the end of its elongation	mm
60	leafArea	leafArea	leafArea	a leaf anatomy and morphology trait (TO:0000748) which is associated with the total area of a leaf (PO:0025034)	mm2
71	leafFreshWeight	leafFreshWeight	leafFreshWeight	a leaf weight trait (TO:0000505) which is associated with the measure of the wet weight of a leaf (PO:0025034)	g

t_BTH_Colmar_2000_SetB1.txt:

Variable ID	Variable Name	Trait	Method	Method Description	Scale
WIPO:0000074	GY_q/ha	Grain yield	Direct measure	Mesure directe # ModeOp Arvalis = Récolte machine  RDT 0%	q/ha
WIPO:0000217	r	Yield	r	Yield expressed as a percentage of the average yield of reference varieties.	%

[bedroesb]

NO Term Source REF / Term Accesion Number implementation YET

[cpommier]

@bedroesb Did you had the opportunity to test with the wheat data set ? I remember there was a problem with TDF generation with treatments n the source.

[PapoutsoglouE]

I understand that the endpoints that are currently driving this implementation don't have all mandatory attributes. With that in mind, the above looks solid.
Otherwise:

• implement othe term source ref/accession number columns, as stated
• for all of the above, the variable ID is essentially what various crop ontologies call "variable name" - see here for example. I can see the confusion... In general, when in doubt, it's a good idea to consult the current version of the standard itself. In turn, the variable name here is supposed to be more human-readable, since it is the only non-ID, free-text field for the variable itself. I don't know which BrAPI fields are being used for this, so it may or may not be worth adjusting.

• the time scale field is not being used as intended. Per the MIAPPE definition, it is the:

  Name of the scale or unit of time with which observations of this type were recorded in the data file (for time series studies).

  and possible values for it include date/time and growing degree days. Also bear in mind that it is not mandatory.

[bedroesb]

@cpommier yes, I've added an example of the wheat dataset. I rewrote the whole tdf generation part.

[bedroesb]

@PapoutsoglouE Updated the examples