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Import Genotype

Overview

Import Genotype Wizard can be used in following scenarios:

First Page of Import Genotype Wizard

This wizard can be activated using [ Task > Genotype > Manage Genotype > Record > Import Genotype ]. It has following options:
The first page of the import wizard changes as per the selected option (above) but the second page is same for all the options.

Following three examples are for [ Import Genotype with/without parent ] option.

Example 1 - Import Genotype without parent

This example illustrates steps on importing Genotypes without their parents but with their aliases from a source file. Following (dummy) example is used in this page for illustration only.
Genotype GenotypeAlias* Genotype Note Crop^ OrganisationName
Genotype1     Wheat NSW DPI
Genotype1     Wheat NSW DPI
Genotype3 GA3,G_03   Wheat NSW DPI
Genotype10     Wheat NSW DPI
Genotype11 XYZ89   Wheat QLD DPI&F
Genotype12     Wheat QLD DPI&F
^If the source file does not have Genus (or crop) column, then the genus for the genotypes in the source file must be selected in the Import Wizard.
*If Genotype Alias does not exist in the source file, then genotype alias is not imported.

Click here to read important note on importing data.

Illustrative snapshot:
First page of Import Genotype without parent (Click it to change its size)
  1. Select the [ Import Genotype with/without parent ] option.
  2. Select source file to import genotype.
  3. Tick this check box if the source file has repeated Genotype or some of the genotype in the source file may already exist in the database.
    • This is recommended option for other than bulk importing genotypes.
    • This option is slow because:
      • it needs to filter the genotype if the source has one or more genotypes repeated.
      • it also loads existing genotypes (in the source file) from database as their information may need to be updated.
  4. Since the source file has "Crop" column, the Genus is set to [ .All Genus ] in order to use the Genus (or crop) in the source file while importing genotypes..
  5. Toolbar in the import wizard.
  6. Mapping of column names in spreadsheet with column name of the database.
    • GenotypeAliasName (or GenotypeAlias): This column has aliases of a genotype separated by comma (eg GA3,GA_03).
Once column mapping is completed, click on [ Preview ] to move to next step where you can view the genotypes, fix any error and save them into database.

Example 2 - Import Genotype with Female and Male Parent

This example illustrates steps on importing Genotypes with their parents andwith their aliases from a source file. Following (dummy) example is used in this page for illustration only. In following example Genotype3 and Genotype1 are the female and male parent of Genotype10 respectively.

Genotype Selection History Aliases# FemaleParent MaleParent Comment*
Genotype1          
Genotype1 SH1        
Genotype3   GA3,G_03      
Genotype10     Genotype3 Genotype1  
Genotype11 SH3 XYZ89      
Genotype12          
#Aliases is mapped to Genotype Alias Name in the database
*Comment is mapped to GenotypeNote in the database

Note: Click here to read important note on importing data.

How does the import process work?
Katmandoo first imports all the genotypes and save into database to obtain unique Genotype Id. Then Female ParentId and Male Parent Id are updated for the genotypes that have parent name in the source file.

Illustrative snapshot:
First page of Import Genotype with parent (Click it to change its size)
  1. Select the [ Import Genotype with/without parent ] option.
  2. Select source file to import genotype.
  3. Tick this check box if the source file has repeated Genotype or some of the genotype in the source file may already exist in the database.
    • This is recommended option for other than bulk importing genotypes.
    • This option is slow because:
      • it needs to filter the genotype if the source has one or more genotypes repeated.
      • it also loads existing genotypes (in the source file) from database as their information may need to be updated.
  4. Since the source file does not have Genus (or Crop) column, the genus is selected for the genotypes in the source file.
  5. Toolbar in the import wizard.
  6. Mapping of column names in spreadsheet with column name of the database.
    • Please note the mapping of column in source file with the columns in the database.
Once column mapping is completed, click on [ Preview ] to move to next step where you can view the genotypes, fix any error and save them into database.

Example 3 - Import Genotype with Pedigree

This example illustrates steps on importing Genotypes with Pedigree and their aliases from a source file. Following (dummy) example is used in this page for illustration only. In following example pedigree Genotype3/Genotype1 means Genotype3 and Genotype1 are the female and male parent of Genotype10 respectively.

Genotype Selection History Aliases# Pedigree% Comment*
Genotype1        
Genotype1 SH1      
Genotype3   GA3,G_03    
Genotype10 SH2   Genotype3/Genotype1  
Genotype11 SH3 XYZ89  Genotype10,SH2/Genotype1  
Genotype12        
#Aliases is mapped to Genotype Alias Name in the database
*Comment is mapped to GenotypeNote in the database
%The pedigree must follow Purdy Naming convention in order to parse Pedigree and save genotype parents in the pedigree.

Click here to read important note on importing data.

How does the import process work?
Katmandoo first parse the pedigree using Purdy Naming Convention and save the parsed genotypes into database to obtain unique Genotype Id. Then Female ParentId and Male Parent Id are updated for the genotypes that have pedigree in the source file.

Illustrative snapshot:
First page of Import Genotype with Pedigree (Click it to change its size)
  1. Select the [ Import Genotype with/without parent ] option.
  2. Select source file to import genotype.
  3. Tick this check box if the source file has repeated Genotype or some of the genotype in the source file may already exist in the database.
    • This is recommended option for other than bulk importing genotypes.
    • This option is slow because:
      • it needs to filter the genotype if the source has one or more genotypes repeated.
      • it also loads existing genotypes (in the source file) from database as their information may need to be updated.
  4. Since the source file does not have Genus (or Crop) column, the genus is selected for the genotypes in the source file.
  5. Toolbar in the import wizard.
  6. Maping of column names in spreadsheet with column name of the database.
    • Please note the mapping of column in source file with the columns in the database.
Once column mapping is completed, click on [ Preview ] to move to next step where you can view the genotypes, fix any error and save them into database.

Alert dialogs that appear during import process

These dialogs appears during the import genotype process.

Genotype Alias column mapping dialog

This is to notify user that comma is used as separator between the genotype aliases. If a genotype alias has comma then wrap the alias within double quote ie change x123,ym to "x123,ym" so that "x123,ym" is treated as a single genotypes rather than x123 and ym. 

Genotype Alias Mapping Alert

Genotype Pedigree and Selection History columns mapping dialog

This is to notify user that Pedigree as well as Selection History columns are mapped.

If user clicks on [ Yes ] then Pedigree is parsed without using data from the Selection History column ie Katmandoo uses Selection History in conjuction with Genotype only.

If user clicks on [ No ] then Katmandoo will not save the Genotype parents into database. In case a genotype parent does not exist in database, then the import process will fail. 

Genotype Pedigree and Selection History Mapping Alert

Genotype Pedigree column mapping dialog

This is to notify user that Pedigree is parsed first and the parsed Genotype Parents are saved before proceeding to import Genotypes. Incase there is problems processing the genotypes, the saved Genotype Parents can not be rolled-back (ie deleted from database).

If user clicks on [ Yes ] then parsed Genotype parents are saved into database first in order to obtain unique GenotypeId.

If user clicks on [ No ] then Katmandoo will not parse Genotype Pedigree but rather treat it as a text value and save in Pedigree column of Genotype table in the database

Genotype Pedigree Mapping Alert

Second (Preview) Page of Import Genotype Wizard

The default order of columns displayed can be changed by editing the column list of the Misc Group GenotypeSetupDataGrid.

Illustrative snapshot (for [ Import Genotype ] option):
First page of Import Genotype (Click it to change its size)
  1. These 4 rows (HasError = Checked) has problem with genotype.
  2. Click it to display only those rows that have error (this preview option is visible only when there is error in the dat being imported).
  3. Move mouse over the error icon to display the error message.
  4. If the genotype name is valid and you would like to store in database, the error from the selected row can be removed by clicking this button.
  5. Click it to save imported genotypes into database (after you have fixed all the errors).
Tips:

See Also