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How to: Setup Katmandoo for Multi-phase Trial

Overview

This page explains how to setup Katmandoo to store data of Multi-phase Trials.
Assumption: Sub-system (in this case "Wheat") and Genus ("Wheat") already exists in the database.

Click here to read important note on importing data.

Example (dummy) Table

Following (dummy) example is used in this page for illustration only. The Table 2 used Source Site Year, Site, Trial Type and Trial Number rather than Source Trial Acronym (used by Table 3). Both tables 2 & 3 has same data for a multi-phase trial. Grain samples that are milled in the lab are from two different trials as identified by "Source Site Year, Site, Trial Type and Trial Number" or "Source Trial Acronym".

Assumption:
  1. Source Trial (2007 / Biloela / S4 / 1) with Trial Acronym DCHA07BLLX4 already exist in database.
  2. The trial design of the source trial DCHA07BLLX4 already exist in database and SourceColumn/SourceRow/SourceBlock of the genotype in this table 2 or 3 matches with the Column/Row/Block of the DCHA07BLLX4.
  3. Trial Acronym Prefix for "S4" trial type is "DCH".
Table 1: Snapshot of the Source trial unit information (please refer to DemoTrial.xls for complete data).
SiteYear SiteName Location Postcode Trialtype TrialNumber Column Row Replicate Block
2007 Biloela Biloela 4715 S4 1 61 2 1 1
2007 Biloela Biloela 4715 S4 1 61 3 1 1
2007 Biloela Biloela 4715 S4 1 61 4 1 1
2007 Biloela Biloela 4715 S4 1 61 5 1 1
2007 Biloela Biloela 4715 S4 1 61 6 1 1
2007 Biloela Biloela 4715 S4 1 61 7 1 1
2007 Biloela Biloela 4715 S4 1 61 8 2 1
2007 Biloela Biloela 4715 S4 1 61 9 2 1
2007 Bithramere Bithramere 2340 S4 1 1 1 1 2
2007 Bithramere Bithramere 2340 S4 1 1 2 1 2
2007 Bithramere Bithramere 2340 S4 1 1 3 1 2
2007 Bithramere Bithramere 2340 S4 1 1 4 1 2
2007 Bithramere Bithramere 2340 S4 1 1 5 1 2
2007 Bithramere Bithramere 2340 S4 1 1 6 1 2
2007 Bithramere Bithramere 2340 S4 1 1 7 1 2

Table 2: Milling data with source field plot information including Source Site Year, Site Name, Trial Type and Trial Number.
Site Year SiteName Location Postcode TrialType Trial Number Milling Day Milling Seq Replicate Genotype FE_B Source Site Year Source Site Name Source Trial Type Name Source Trial Number Source Column Source Row Source Block
2008 Wagga Lab Wagga AI 2650 Milling 1 1 1 1 Oddball 0.76 2007 Biloela S4 1 61 2 1
2008 Wagga Lab Wagga AI 2650 Milling 1 1 2 1 Kennett 0.748 2007 Biloela S4 1 61 3 1
2008 Wagga Lab Wagga AI 2650 Milling 1 1 3 1 Zeditave 0.738 2007 Biloela S4 1 61 4 1
2008 Wagga Lab Wagga AI 2650 Milling 1 1 4 1 Encore 0.759 2007 Biloela S4 1 61 5 1
2008 Wagga Lab Wagga AI 2650 Milling 1 2 1 1 Woodman 0.747 2007 Biloela S4 1 61 6 1
2008 Wagga Lab Wagga AI 2650 Milling 1 2 2 1 Methane 0.747 2007 Biloela S4 1 61 7 1
2008 Wagga Lab Wagga AI 2650 Milling 1 2 3 1 Secret 0.754 2007 Biloela S4 1 61 8 1
2008 Wagga Lab Wagga AI 2650 Milling 1 2 4 2 Irradiation 0.739 2007 Bithramere S4 1 1 1 2
2008 Wagga Lab Wagga AI 2650 Milling 1 2 5 2 Secret 0.749 2007 Bithramere S4 1 1 2 2
2008 Wagga Lab Wagga AI 2650 Milling 1 3 1 2 Zeditave 0.746 2007 Bithramere S4 1 1 3 2
2008 Wagga Lab Wagga AI 2650 Milling 1 3 2 2 Sunbeam 0.731 2007 Bithramere S4 1 1 4 2
2008 Wagga Lab Wagga AI 2650 Milling 1 3 3 2 Oddball 0.756 2007 Bithramere S4 1 1 5 2
2008 Wagga Lab Wagga AI 2650 Milling 1 3 4 2 Pyjama 0.758 2007 Bithramere S4 1 1 6 2
2008 Wagga Lab Wagga AI 2650 Milling 1 3 5 2 Encore 0.739 2007 Bithramere S4 1 1 7 2


Table 3: Milling data with source field plot information including Source Trial Acronym.
Site Year SiteName Location Postcode TrialType Trial Number Milling Day Milling Seq Replicate Genotype FE_B Source TrialAcronym Source Column Source Row Source Block
2008 Wagga Lab Wagga AI 2650 Milling 1 1 1 1 Oddball 0.76 DCHA07BLLX4 61 2 1
2008 Wagga Lab Wagga AI 2650 Milling 1 1 2 1 Kennett 0.748 DCHA07BLLX4 61 3 1
2008 Wagga Lab Wagga AI 2650 Milling 1 1 3 1 Zeditave 0.738 DCHA07BLLX4 61 4 1
2008 Wagga Lab Wagga AI 2650 Milling 1 1 4 1 Encore 0.759 DCHA07BLLX4 61 5 1
2008 Wagga Lab Wagga AI 2650 Milling 1 2 1 1 Woodman 0.747 DCHA07BLLX4 61 6 1
2008 Wagga Lab Wagga AI 2650 Milling 1 2 2 1 Methane 0.747 DCHA07BLLX4 61 7 1
2008 Wagga Lab Wagga AI 2650 Milling 1 2 3 1 Secret 0.754 DCHA07BLLX4 61 8 1
2008 Wagga Lab Wagga AI 2650 Milling 1 2 4 2 Irradiation 0.739 DCHA07BTHR2 1 1 2
2008 Wagga Lab Wagga AI 2650 Milling 1 2 5 2 Secret 0.749 DCHA07BTHR2 1 2 2
2008 Wagga Lab Wagga AI 2650 Milling 1 3 1 2 Zeditave 0.746 DCHA07BTHR2 1 3 2
2008 Wagga Lab Wagga AI 2650 Milling 1 3 2 2 Sunbeam 0.731 DCHA07BTHR2 1 4 2
2008 Wagga Lab Wagga AI 2650 Milling 1 3 3 2 Oddball 0.756 DCHA07BTHR2 1 5 2
2008 Wagga Lab Wagga AI 2650 Milling 1 3 4 2 Pyjama 0.758 DCHA07BTHR2 1 6 2
2008 Wagga Lab Wagga AI 2650 Milling 1 3 5 2 Encore 0.739 DCHA07BTHR2 1 7 2

Required columns to import data

Following table list required columns for each import options:

Import Option Minimum required columns in the source file
Import Genotype Crop and Genotype
Import Location Location Name and Postcode
Import Site Location Name, Postcode and Site Name
Import Site Year Site Name and Site Year
Import Trial Site Name, Site Year, Trial Type and Trial Number

OR

TrialAcronym
Import Trial Design Site Name, Site Year, Trial Type, Trial Number, Genotype, Unit Position*, Replicate

OR

TrialAcronym, Genotype, Unit Position*, Replicate
Import Raw Data Site Name, Site Year, Trial Type, Trial Number, Genotype, Unit Position*, Replicate, FE_B**

OR

TrialAcronym, Genotype, Unit Position*, Replicate, FE_B**
*In this example Unit Positions are: Column, Row, Block, Milling Day, Milling Sequence, Source Column, Source Row, Source Block

Step 1 - Import Genotype

Click here for steps to import Genotype.

Step 2 - Import Location, Site and Site Year

Click here for steps to import Location, Site and Site Year.

Step 3 - Import Trial Type

Click here for steps to import Trial Type.

Step 4 - Fix Trial Acronym Prefix

Click here for steps to fix Trial Acronym Prefix.

Step 5 - Import Trial

Click here for steps to import Trial.

Step 6 - Setup Unit Position

Use steps outlined in Unit Position Virtual Column to add following unit positions in order to store multi-phase trial data in Katmandoo.
*In order to use source trial unit, the unit position name of the source trial unit must match prefixed with "Source". In this example, the source unit position names must be SourceColumn, SourceRow, SourceBlock because the unit position names for the source trial unit are Column, Row and Block respectively.

Step 7 - Import Trial Design

Click here for steps to import Trial Design with Source trial unit information.

Step 8 - Import Raw Data

Click here for steps to import raw data.

See Also