About

The Germplasm List manager allows you to:

browse for germplasm lists
import a list of existing germplasm
edit list metadata, lock/unlock the germplasm list
customize the list view
import list updates in batch
reorder entries
remove entries
add entries from a specific list to a different list
delete and clone lists
export list data and labels
move a list to a different folder
export list data and labels
calculate Coefficient of Parentage

Browse Germplasm Lists

Click on the Browse link. You will see the list tree browser
Select one or more germplasm lists
Click OK

The lists selected are opened in different tabs.

Select Entries

When a list is open, you can select a few entries by checking the boxes. If you need to select all entries in a list, click on the checkbox to select all pages.

Search Germplasm Lists

You will see a paginated table of all of the available lists in the system with the corresponding information (List Name, Parent folder, Description, List Owner, List type, #of Entries, Status -locked/unlocked-, Notes, List Date).

You can add and combine filters using any of these columns using the corresponding "Search by" functionality (List Name filter added by default).

Search by: List type> Harvest

Apply the filter

Create a List using the LIST BUILDER option

You can use the LIST BUILDER option to create a new list.

Click on the Show LIST BUILDER button

Open a list (s), select the entries of interest, and drag the chosen entries to the list builder section.

To SAVE the list, Scroll down on the List Builder page and click the SAVE button. Select or create a folder to house the new list. Name the germplasm list and Save. The germplasm list will be available from the germplasm list filter or Browse options.

Actions

Import List

Actions > Import List

Download the template. This template has the Observation and Entry Details sheets

Observation: You should provide the file with either the GID, GUID, or the DESIGNATION of the germplasm to include in the list. If you provide multiple values for a record, the system will use the following order: GUID, GID, DESIGNATION for retrieval. The ENTRY_CODE information is optional.

Entry Details: contains the information about the available entry details for the crop (VARIABLE, ALIAS, DESCRIPTION, PROPERTY, SCALE, METHOD, DATA TYPE, EXPECTED VALUES). The import process validates that the values defined for the different variables do not conflict with the defined scale for such variables.

Note: Users with the corresponding permissions can define “Entry detail” variables type via Ontology Manager (see v28 Manage Ontologies | Add & Edit Variable ). Once the user creates a new entry detail variable, it will be available in the template for the list importation and can be added to an existing list (v28 Germplasm Lists | Add and Remove Entry Details )

Browse for the file to be imported and click on Next.

Example:

The import list process is able to read in the variables assigned to the different entries by variable name or alias. In addition, the import validates that the values defined for the different entry details do not conflict with the defined scale and prevent the import otherwise.

Variables popup is displayed indicating if the entry details variables exist in the list (for updating existing list process), new to the list (used in updating existing list process too), or not found in the ontology.

Click Next

The system uses the information provided in GID and/or GUID and/or DESIGNATION to show a review table where you can see which records 1) have a single match 2) multiple matches and 3) have no match.

You can use these criteria to filter the records and click on GID MATCHES to get the details pop-up of the corresponding germplasm.

Note: You can skip the entries with multiple matches and/or entries without matches

Click on Next

For multiple matches, the Select match popup is displayed.

Select the match desired or omit the entry by clicking on Omit button
Click on Next

When the system cannot find a germplasm record that matches the criteria for one or more file records the Select match for mapping entries is displayed.

Click on the mapping action for a record

Then you will be prompted with a germplasm search popup where the user can search the entire germplasm database to find the germplasm (one and only one) to be mapped.

Select one germplasm and click on Select. The system marks the record as matched (✓)

And the system retrieves or shows the GID and DESIGNATION of the matched germplasm in the table.

Next

A confirmation message is displayed with a summary of the List importation process:

Confirm

Now you need to define the usual list metadata (name, description, etc.) and its parent folder.

Save

The system will auto-enumerate ENTRY_NO using the order of the excel file, and the list will become available for management.

Customize the list view

You will be able to customize your lists by enabling them to add and remove any germplasm information.

List Selection

Click on a list.

The system opens a new tab in the germplasm list section with the corresponding list entries having the following default columns (ENTRY_NO, GID, DESIGNATION, LOTS, AVAILABLE, UNIT).

If the list has associated Entry details variables they are displayed in its corresponding field and their values are populated in the list table.

And you can filter and sort some columns.

In the example displayed, GID, DESIGNATION, and LOTS are hyperlinks to the corresponding germplasm details.

Add and Remove Entry Details

Select an Entry detail variable and click on the remove link.

A confirmation message is displayed.

Confirm

The Entry detail variable and the values are not displayed anymore.

Click on Add button
Select an Entry detail from the variable dropdown
Save

You can add values manually for the Entry details variables

Click on a cell and add values. It could be typing a text, adding a number, selecting a categorical value, adding a date depending on the variable data type.

Add and Remove Columns

Using the Columns button you will be able to search, add and remove columns in the germplasm list table. NAMES, PASSPORT, and ATTRIBUTES are also included.

Open an F1CRT list type
Click on the Columns button
Select FEMALE PARENT NAME, MALE PARENT NAME, LOCATION NAME
Click on Apply button

The new columns added are populated with their corresponding values.

Note: The changes are saved automatically, if you close the list tab and re-open the list, you will see the changes applied previously.

For removing columns:

Click on the Columns button
Uncheck the column (s) desired
Click on the Apply button

The columns selected are not displayed anymore.

Define the level of the pedigree to consider for CROSS string

You can define the generation to be considered for the CROSS string (up to 10 levels).

Click on the Columns button
Add the Cross Column
Click on the Apply button

Click on the Cross expansion icon and specify the level desired.

Apply

Edit List Metadata

Click on the Edit List Metadata icon

The Edit list Metadata popup is displayed.

Edit the List Name, Description, and Notes

Save. A success message is displayed and the changes are applied.

Lock / Unlock a Germplasm List

You can unlock and lock the germplasm lists for restricting actions over the list. It can be done by clicking on the icon.

Note: When a list is locked the Edit List Metadata icon is not available. The Columns button is not displayed, and the options available under the Actions button are: i) Add entries to another list, ii) Clone list, and iii) Export list data and labels (See next section).

Create New List

You can create a new list from existing list (s) using the list builder option.

Click on the Show List Builder button.

Open germplasm list(s) and select entries of interest. You can select entries from multiple lists.
Drag the selected entries to the LIST BUILDER section.
To save the new list, Select the SAVE button at the bottom of the List Builder window.
Select or create a folder to house the new list. Name the germplasm list and Save. The germplasm list can be accessed from the Browse Lists or Search options.
To reset the list before saving, Select the Reset button at the bottom of the List Builder window.

Germplasm List Actions

Import list update

Using this action you will be able to update a germplasm list, update the ENTRY_CODE and ENTRY_DETAILS variables adding them, or edit the existing values. The action can be done for all entries or some of the germplasm list.

Open a germplasm list
Actions > Import list update

The Import list update popup is displayed.

You can download the template which has ENTRY_NO and ENTRY_CODE columns in the Observation sheet and a tab with the available entry details variables (VARIABLE, ALIAS, DESCRIPTION, PROPERTY, SCALE, METHOD, DATA TYPE, EXPECTED VALUES)

Download the germplasm list import update template
Specify the entry number you what to update under the ENTRY_NO column
Fill the file up with valid data
Browse for the file and click on Next

The import list process is able to read the variables assigned to the different entries by variable name or alias. In addition, the import validates that the values defined for different do not conflict with the defined scale and prevent the import otherwise.

Example:

The Variables popup is displayed, in a similar way that in the import list process, the status of the variable is indicated, if the variable imported already exists in the list, if the variable is new to the list, or not found in the ontology.

Click on Next
A confirmation message is displayed, click on Confirm.

The updates are displayed in the list table:

Note: For ENTRY_CODE you need to add the column using the Columns button and apply the change.

Reorder entries

Triggering this action, you will be able to manipulate the entry number order of the list entries under the condition that the sequential nature of the list (1 to N) is always preserved.

Open a list
Select one, or more than one entry. It could be from different pages.
Action> Reorder entries

The Reorder entries popup is displayed. There are three options for reordering the entries on a list: i) at the beginning of the list, ii) at the end of the list, and iii) select a specific position.

Choose the option: Select a specific position and type a valid value
Click on Reorder

A success message is displayed and the entries selected are reordered starting at position 10 in the example shown.

Remove entries

With this action, you are able to remove the selected entries (and corresponding entry detail values) from the list and re-enumerate ENTRY_NO.

Open a list
Select one or more than one entry. It could be done from different pages.
Actions> Remove entries

A confirmation message is displayed:

Confirm

A success message is displayed, the entries are removed from the list, and the ENTRY_NO is re-enumerated.

Add entries

The user can add additional entries to the list.

Open a list
Actions> Add entries

The Germplasm Search is opened permitting you to search and select the germplasm of interest using the existing filters.

Select one or many entries
Click on Select

A success message is displayed, “Germplasm entries added to list successfully!”

The system adds the selected germplasm as new entry/es at the bottom of the list, populating the corresponding configured columns and letting the user define the values for the corresponding entry details

Add entries to another list

This action enables you to add entries from one list to another list.

Open a list
Select one or more entries
Actions> Add entries to another list

The popup Add entries to the list is displayed. The system presents the list tree where the user can define the destination list of the selected germplasm.

Select the destination list
Click on Add button

A confirmation message is displayed.

Confirm

A success message is shown, “Germplasm entries added to list successfully!”

The system adds the selected germplasm as new entry/es at the bottom of the destination list, populating the corresponding configured columns and letting the user define the values for the corresponding entry details.

Delete list

Open the list you want to delete
Actions> Delete list

A confirmation message is displayed:

Confirm

A success message is shown, “Successfully deleted list.” And the list is not displayed anymore.

Clone list

When you trigger this action, the system permits you to clone a list. The BMS creates a new list with the specified name conserving the elements, enumeration (ENTRY_NO), germplasm columns, and entry details (variables and values) of the original list.

Open a list
Actions> Clone list

Then the system presents the list tree popup where the user can define the name and folder location of the new list.

Save

A success message is displayed, “Germplasm list cloned successfully!”.

The cloned list is opened in a new list tab

Export list data and labels

This component from the Germplasm List module has the same features that the other printing labels implemented into the BMS, the presets options, output formats, and the “specify labels stock” options for PDF format.

Export list XLS gives you the opportunity to export a view of the thing you want to modify and import it back as an entry details update file.

Additionally, the ability to print labels for the list will help you to physically identify the lines that they are preparing for shipping or study.

For germplasm lists, you can choose and drag fields from the Germplasm Details and Names and Attributes and Entry Details into the Left Side Fields and Right Side Fields (PDF), or Selected fields (XLS and CSV) to add them to your export file. For PDF you can only add 5 fields per side

Open a list
Actions> Export list data and labels
Select Excel Data output format
Include column headings in XLS export?: Yes
Select fields from Germplasm Details, Names, Attributes, Entry details and drag them to Selected fields

Add a preset name and Save preset
Export

The excel file is exported and populated properly with all fields included.

Coefficient of Parentage

You will be able to calculate the coefficient of parentage for a given set of germplasm. This coefficient in turn determines a measure of relatedness between germplasm by traversing their corresponding pedigree trees and recursively identifying the common ancestors.

btype parameter configuration

Go to Manage Crop Settings > Parameters tab
Notice btype field is editable. Configure the btype parameter according to your crop by choosing any of the following: 0=cross fertilizing, 1=self fertilizing, 2=self Fertilizing with unknown source but known parents.

Coefficient of parentage calculation

Go to Manage lists
Open the list you are interested in
Select entries
Actions > Coefficient of parentage (Beta)

You will see a confirmation message about the calculation progress.

When the Coefficient of parentage calculation finishes the results are displayed in a matrix.

In the Name Selector, GID and PREFERRED NAME options are always available, plus other common name types if available for all the GIDs selected.

Download the results in CSV format by clicking in the Download button.

IBP Support Knowledge Base

v28 Germplasm Lists