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Genotype and Alias

Overview

In Katmandoo Genotype uniquely identifies each individual organism in the database based on combination of Genus, Genotype Name and Selection History.

Detail

Genotype Name

Genotype Name uniquely identifies a genotype and it can not be changed once the  genotype has dependant data.

Double Quote ( " ) and Pipe (  |  ) must not be used in the genotype name as it is used as seperator by the DiGGer that is used by Katmandoo to generate trial design.

While adding new genotype (either using Setup Form or Import Genotype Wizard), genotype is validated using Smart-Genotype-Name Checking process. Suppose Genotype Name is "ABC_2_E" then the validation processes are:

Selection History

Though Selection History is part of the Alternate Key, it is optional.

If the Selection History of the new Genotype is given, system checks duplicate Genotype Name with Selection History and Genus otherwise duplicate checking uses Genotype Name and Genus only.

Pedigree

Pedigree of the Genotype.

While importing data, if the source file has Pedigree in Purdy Naming format, then the pedigree is parsed to generated ancestors of the genotypes. In this case the pedigree textvalue is not saved into database, rather it is generated dynamically.

But if the pedigree in the source is not in Purdy Naming format, then the pedigree is treated as a textvalue and saved into [ pedigree ] column of Genotype table in the database.

Visit importing genotype with pedigree for more info on importing genotype with Pedigree in Purdy Naming format.

Species Name

Species of the genotype. It is optional.

Female and Male Parent

Female and Male Parent of the Genotype. Visit importing genotype with genotype parent for more info on importing genotype with parent.

Origin Organisation

Origination of the genotype ie the organisation that owns the Genotype.

Table Structure

Column Name Description
GenotypeId (PK) Identification Number that identifies a Genotype
GenusId (AK) Id that identifies the Genus of the Genotype
GenotypeName (AK) Name that uniquely identifies a Genotype
SelectionHistory (AK) (optional) Selection History of the Genotype
OriginId (FK) Id that identifies owner of the Genotype
FemaleParentId Genotype Id that identifies the Female Parent of the genotype
MaleParentId Genotype Id that identifies the Male Parent of the genotype

Pre-requisite to add a genotype

The following information must exist before a Genotype can be added into the database.
Note: Although Unknown Organisation can be used it is preferable to add the Organisation before adding a new genotype. This avoids changing at a later date.

Navigator

The Genotype Navigator allows the user to quickly find the genotypes of the genus that can be used in the selected Sub-system. The nodes of the navigator are generated using the Genus Names which are retrieved from the database. The nodes are sorted into genus name order.

Important Note: Katmandoo automatically selects the node that was selected last time (ie before closing the navigator or Katmadoo).

Use [ Task > Genotype > Manage Genotype ] to activate the genotype navigator.
Illustrative snapshot:
Genotype Navigator (Click it to change its size)
  1. Click it to close the navigator as well as the genotype mainform.
  2. Filter value "*" means display all the genus (that user has permission to use) and genotypes as well as 0-9 and A-Z nodes.
  3. Genus node of the Navigator. Click it to dispay all the Genotypes of the Genus.
  4. ".ALL Demo Genotypes" node of the genus "Demo". Click it to dispay all the Genotypes of the Genus (ie Demo in this snapshot).
  5. OR click on one of these nodes to display genotypes starting with the node text
    • Click on "A" to display all the genotypes with genotype name starting from "A".
Important Note: ".ALL Genus" node (not shown in the snapshot) is displayed when logged-in user has System Administrative permission (eg dba) and the database has more than one genus. When ".All Genus" node is clicked, all the genotypes of the genus in the navigator are listed, but add/edit/repeat operations are disabled in the form.

Main Form

To display genotypes in the Genotype Main Form, follow the steps below:
Illustrative snapshot:
Main Form of Genotype (Click it to change its size)
  1. Genotype Navigator with the loaded Genus and species nodes.
    • Click here for an illustration of the navigator template.
  2. Genotype Main Form displaying the Genotypes of the selected species. 
    • Click here for an illustration of the main form template.
  3. Genotype subform displays Virtual column information of the selected Genotype in the Genotype Main Form (Belara in the snapshot). 
  4. Genotype Toolbar (new)
  5. Alias of selected genotype.
  6. Trait performance of the selected genotype.

Setup Form

To add/edit a Genotype, follow the steps below :
Illustrative snapshot (of First Page):
First page of the Setup Form of Genotype (Click it to change its size)
  1. Genotype Name which is disabled when the Genotype has has dependant data. Click here for information on editing restricted value.
  2. Pedigree of the Genotype. Since the Pedigree was parsed using Purdy Naming convention, it is generated dynamically using its female and male parent and their ancestors (if data is available).
  3. Either type the new species name in the text box or select a from the existing species list.
  4. Organisation that is the owner of the Genotype.
  5. Click it to select the Genotype Color which will be used to display Genotype in Genotype Graphical Display.
  6. To select a female parent, uncheck the "N/A" checkbox to enable the Female Parent combobox, and select the parent from the list.
  7. Click it to display Search Genotype that can be used to find/load genotype to use as parent.
  8. To select a male parent, uncheck the "N/A" checkbox to enable the Male Parent combobox, and select the parent from the list.
Illustrative snapshot (of Second Page):
First page of the Setup Form of Genotype (Click it to change its size)
  1. Genotype Notes (maximum 6600 characters).
  2. Virtual column name (in second step of the wizard). Click here for information on the Virtual column data entry data grid.
    • Important Note: If there is not any virtual column for GenotypeFactor table, then this datagrid is disabled.
  3. A value for the displayed Virtual column can be entered on this part of the data grid.
  4. Alias of the selected Genotype.

Alias of Genotype

A genotype alias name is part of alternate key in GenotypeAlias table and it can be used to represent the genotype. A genotype can have one or more aliases and an alias can be associated with one or more genotypes.

Please use [ Record > Update Genotype Alias ] to make any changes on genotype alias.
Please use [ Record > Delete Genotype Alias ] to delete the selected genotype alias.

GenotypeAliasName can be used to import Genotype Alias can be imported while import genotype. The aliases of a genotypes can be separated by comma (default) in GenotypeAliasName.


Alias is used while importing data find the genotype used in the source file if the genotype name used in the source file does not exist as Genotype name.

Merge Genotype

To merge data of a genotype into another genotype, use [ Record > Merge Genotype ] in the  Genotype main form.
Illustrative snapshot:
Merge Genotype
  1. Read this important note!
  2. Master Genotype is the one that will hold data of the Slave Genotype.
  3. Master GenotypeId replaces all the Slave GenotypeIds in the database.
  4. Slave Genotype is saved as an alias of Master Genotype.
  5. Slave GenotypeId.
  6. Authorised token.
  7. User must enter the exact authorised token (case-sensitive) to merge data.
    • Tips: Copy the token to a text file. Next time, copy the token from the text file and pasting here.
  8. After carefully entering all the required information, click [ Merge... ] button. 
IMPORTANT NOTE: 

Export / Import

Export
Import

See Also