Duplicate variable name :GLys_M_pct

[cpommier]

It causes issue with file annotation.
Affects:

1	1	1	1	1	1	1
CO_321:0501073	GLys_M_pct	GLYS_pct	...	CO_321:0500170	GLys Protein Measurement	Measurement
CO_321:0001457	GLys_M_pct	...	CO_321:0000990	GLys Measurement	Measurement	Standard method for grain lysine content.

Propositions:
1- keep only CO_321:0501073
2- rename CO_321:0501073 from GLys_M_pct to GLys_Mp_pct

what do you think @ShresthaR ? Do you have Jean Luc or Clay github ID to double check with them ?

Same for :

1	1	1
CO_321:0501087	GWid_M_mm	detailled method
CO_321:0001468	GWid_M_mm	"standard" method

and

1	1	1
CO_321:0501007	BYDInc_E_pct	detailled method
CO_321:0001068	BYDInc_E_pct	"standard" method

and

1	1	1
CO_321:0001365	SN_Calc_Spksm2	detailled method
CO_321:0001599	SN_Calc_Spksm2	"standard" method

[dwaring87]

Hi @cpommier, I work with Jean-Luc and Clay and added the T3 ontology terms. It looks like we introduced some duplicates when we initially added the T3 terms. At some point I found the first two you mention and removed the duplicates in the file we use to manage our traits and we're now using the original variables, but it looks like I never pushed those changes back to this repo.

Since we're no longer using the newer duplicates I think it's safe to remove them:

---

• Remove variable: 501073 (trait=967, method=500170, scale=410)
  • replaced by variable: 1457 (trait=967, method=990, scale=410)
• Remove method: 500170
  • replaced by method: 990

---

• Remove variable: 501087 (trait=500038, method=500178, scale=428)
  • replaced by variable: 1468 (trait=980, method=1003, scale=428)
• Remove trait: 500038
  • replaced by trait: 980
• Remove method: 500178
  • replaced by method: 1003

---

• Keep variable: 501007 (trait=96, method=500104, scale=410)
  • this cannot be replaced by variable: 1068 (trait=96, method=316, scale=410)
  • the method of the T3 variable is specifically for the season average of a time series
  • we can rename the T3 variable's name (we don't use the variable names) so there is no longer a conflict

---

• Both of the spike number variables existed before our additions, T3 uses #1599

[cpommier]

Thank you very much for the feedback @dwaring87, and nice to meet you.
We will work on that one once we have merged #17 . I will ping you for validation in the pull request.