Phenotypic Data Manager

Owned by Rica Aicel Mariano
Last updated: Dec 13, 2024
8 min read

 

After collecting and uploading trait data, breeders must evaluate them and look for probable outliers and questionable data before sending them for analysis. The Phenotypic Data Manager allows you to:

  • View, filter, and sort plot data;

  • View the descriptive statistics of all numeric traits of the active occurrence;

  • Detect possible outliers;

  • Suppress and unsuppressed plot data; and

  • Generate box plots, histograms, scatter plots, and heatmaps per trait.

Get started

There are two ways of accessing the Phenotypic Data Manager: through the Experiment Manager tool and the Breeding Analytics domain.

Reminder:

  • You should have BA user access and if you have challenges, contact admin.

  • The tool only accepts occurrences that have the plantedTRAIT DATA COLLECTED status.

  • You can only choose one occurrence at a time.

  1. On the Experiment Manager browser, tick the checkbox () parallel to the selected occurrence.

  2. On the upper right of the table, click the Access Breeding Tool button () then select Phenotypic Data Manager from the dropdown menu.

  1. Open the Breeding Analytics domain link and log in using your EBS credentials.

 

  1. After that, click the left navigation button (image-20240506-062526.png) and find the Phenotypic Data Manager tool.

 

  1. You will be redirected to the Phenotypic Data Manager page which displays the trait data from the selected occurrence. Table, Box Plot, Histogram, Scatter Plot, and Heatmap tabs are available to visualize more about the occurrence. To know more about the tabs, you may check generate visualizations.

 

However, you may still switch to another occurrence by clicking the dropdown menu.

 

  1. The Phenotypic Data Manager browser will display the list of all experiments under your program with their experiment types and statuses. To select the occurrence for evaluating trait data, click the Expand button (>) beside the experiment.

 

  1. Once you have the occurrence in mind, click the radio button () on the left side of the occurrence and click Explore from the upper right corner of the browser.

 

Navigate the Phenotypic Data Manager

The Phenotypic Data Manager tool allows users to view, sort, and verify the data uploaded to your occurrence.

Let’s look at the action items and their functions on the page.

PDM Data Browser

Some occurrences with no plot trait data might be available on this data browser. This is due to data issues in the tool. While these occurrences can be selected on the data browser, they cannot be opened because there is no plot trait data to show.

To resolve this, please let us know by reporting the issue as a bug as soon as you encounter it.

1. Explore button

Component

Name

Function

Component

Name

Function

1

Explore

The main button for users to proceed with quality-checking their data in the Phenotypic Data Manager.

2. Expand All/Collapse All

Component

Name

Function

Component

Name

Function

1

Expand All

Shows all the occurrences per experiment in the data browser.

2

Collapse All

Hides all the occurrences in the data browser. Only the experiment names are displayed.

3. Data Columns and Filters

Component

Name

Function

Component

Name

Function

1

Data Column

Displays the data type each column. Users can click on one of these columns to sort the data in ascending or descending order.

2

Search

Searches and filters specific data that the users want to see. They can click the remove filter () button beside to reset the search.

4. Experiment and Occurrence

Component

Name

Function

Component

Name

Function

1

Experiment name

Displays the experiment name. Users can click the dropdown button beside the experiment name to see the occurrences under it.

2

Occurrence

Displays the occurrences under a certain experiment and their relevant data. Users can also see the status of the occurrence. To select the occurrence for quality-checking, click the radio button () beside it.

5. Pagination

Component

Name

Function

Component

Name

Function

1

 

 

Go to page

Located at the bottom left side of the trait table, it allows the user which page to go to view

2

Rows per page

Located at the bottom right side of the trait table, this drop down button allows user to selected number of rows to view per page

 

Quality Control

 

1. Analyze button

Component

Name

Function

Component

Name

Function

1

Analyze

The main button for users to send their quality-checked trait data for single-occcurrence analysis.

2. Select Occurrence

Component

Name

Function

Component

Name

Function

1

Select occurrence

Allows user to select which occurrence to view by using the dropdown box.

3. Main tabs

Component

Name

Function

Component

Name

Function

1

 

 

Table

 

View the stats table of the data

2

 

 

Box Plot

 

Visualize data in the form of box plots

3

 

 

Histogram

 

View data in the form of histograms

4

 

 

Scatter Plot

 

Visualize data in the form of scatter plots

5

 

 

Heatmap

 

View data in the form of heat maps

4. Key Columns and Cells

Component

Name

Function

Component

Name

Function

1

Quality Controlled

trait data columns for all plots are checked for quality control

2

Not Quality Controlled

trait data columns for all plots are for review

3

Possible Outliers

trait data identified as outliers based on 1.5 IQR in the trait table. The cell is colored orange.

4

Suppressed Data

trait data identified by users as suppressed. The cell is colored gray.

5

Bad Data

trait data identified as invalid. It may be data that do not conform with the set data type or are not within the set range of values. The cell is colored red.

6

Missing Data

missing data during collection. The cell is empty and colored blue

5. View Traits

Component

Name

Function

Component

Name

Function

1

Trait(s)

A drop down button on the top left of the trait table. The user selects the trait columns to view.

2

Pin/Unpin

Allows users to freeze and unfreeze the first few columns of the trait table. It eases the viewing of trait data without scrolling past the columns.

6. Main Toolbar

Component

Name

Function

Component

Name

Function

1

Comments

This icon, when hovered, displays the comments the user inputs while saving the transanction.

2

Check for updates

This button allows user to check for any updates made to the trait values of the selected occurrence

3

Edit

Edit button allows the user to do trait(s) changes by suppressing, changing the QC code, or resetting to last saved

4

Filter

User can filter to show possible outliers only or suppressed data only or both

5

Save

Used to save the transaction and mark the trait(s) as quality checked

6

Settings

This is the settings button for the trait table

7

Refresh

This button allows user to refresh the trait table

7. Trait Table columns

Component

Name

Function

Component

Name

Function

1

Data Column

Displays the data type each column. Users can click on one of these columns to sort the data in ascending or descending order.

2

Search

Searches and filters specific data that the users want to see. They can click the remove filter () button beside to reset the search.

8. Pagination

Component

Name

Function

Component

Name

Function

1

Go to page

Located at the bottom left side of the trait table, it allows the user which page to go to view

2

Rows per page

Located at the bottom right side of the trait table, this drop down button allows user to selected number of rows to view per page

Great job! Now that you are familiar with the Phenotypic Data Manager browser, you can start evaluating your trait data.