Breeding Analytics

Phenotypic Data Manager

This tool was developed to enable a breeder to do data exploration and data cleaning prior to analysis. The key features include a descriptive statistics table, outlier identification, and the ability to tag trait data (individually or in bulk) as suppressed, good, bad, or questionable. Raw data visualization is also possible through box plots, histograms, scatter plots, and heatmaps. Once the data is cleaned, the status of the occurrence/experiment is changed to TRAIT DATA QUALITY CHECKED, and the Analyze button is activated to launch the Analysis Request Manager.

Analysis Request Manager

The tool features a new data browser that lists all single occurrence analysis requests and their statuses. One job is created for each trait to be analyzed, where a READY status indicates availability of job outputs. The following job outputs are generated: Table of Residuals, Analysis Parameters, Residual Plots, and Heat Maps.

Users can choose to reanalyze, void, or finalize a job. The request status is set to CLOSED when at least one job is FINALIZED and no other job has the status of PROCESSING or READY. A closed request generates the downloadable report from the data browser. Operational Analytics – Phase 1 and the refactored analysis framework has also been fully implemented in this milestone.

Statistical Design Models

The Partially Replicated (P-Rep) design was updated to remove the requirement to replicate 20% of test entries. Further, users are now allowed to generate this design without replicated test entries. Other validation rules were also documented and improved to allow the upload of unspecified designs in Experiment Manager.

Molecular Data Analysis (New)

The tool enabled key analytical pipelines for EBS-supported molecular analyses. For its initial release, a data browser for genotyping requests is supported. This lists genotyping requests with the status DESIGN CREATED from the Genotyping Service Manager. The foundational features include viewing the genotype data matrix and downloading cleaned genotype data that includes samples with missing data of less than or equal to 5% and markers with a call rate of 95% or higher.

Interoperability (BrAPI)

Core Breeding is now connected to Query the Breeding Management System (QBMS) via Breeding API (BrAPI). This is aligned with the efforts to enable interoperability among plant breeding databases.

Breeding Analytics Platform

A new domain user interface was launched, which adopts the Core Breeding standard. The version is displayed at the bottom left of the page and as users point the cursor to the domain name on the menu bar. The development process, technology stack, data dictionary and library upgrades have also been employed for the development of all the BA tools moving forward.

Core Breeding

Dashboard

New users can access the EBS User Guides via the Learn More button in the pop-up welcome window.

Experiment Creation

The tool was improved to support the upload of unspecified designs and planting arrangement files generated outside EBS. The former is enabled for breeding trial experiments, while the latter is available when using the Entry Order option for all experiment types, excluding breeding trials. Downloadable prescribed templates are provided for both features. Crop-specific sample design files can also be downloaded when uploading design arrays for EBS-supported designs. Planting protocols are now easier to specify with improved auto-computed plot values, while the Finalize button was replaced by the Complete Creation button.

Experiment Manager

Enhanced occurrence management through permissions-based access, uploading revised planting mapping coordinates, and a new delete occurrence feature are supported in this tool. Regeneration of breeding trial designs is enabled to allow breeders to update designs that were already randomized or uploaded. The provision for custom data filters was developed for easier navigation in the data browser, while new trait data collection files are available for download. The tool also allows data managers to configure the files that can be downloaded from this tool.

Data Collection

The tool allows for a more seamless data collection process with the tool’s integration with the Field Book application through the Core Breeding BrAPI (Breeding API). Trait calculations were improved, where auto-computed traits are generated and recalculated as changes are made. Similar to the Experiment Manager, this tool also enabled the feature to upload new trait data collection files from external applications. The tool was optimized for a faster processing, while the data browser was improved for a better display.

Harvest Manager

The tool expanded on the functionalities available in the Harvest Data tab to optimize the harvest process. Plots and crosses can be filtered by range or by harvest status, to which bulk updates can be applied. A new button was enabled to revert failed harvests back to a ready status, while harvesting thousands of records are delegated to the background. A permissions-based access is configured in the Occurrence tab and more informative harvest remarks are displayed in the Creation tab.

Planting Instructions Manager

Package log records are reflected per transaction, while notifications are enabled for background processes. Information on reserved seeds for packages are displayed in the data browser and upon viewing and replacing entries.

Germplasm

New core capabilities are supported in the tool for EBS administrators. Merging germplasm records, creating germplasm relation data, and updating germplasm attribute and other information can be processed in the Merge, Create, and Update tabs, respectively. Prescribed templates are provided in these new tabs. The Merge tab also catches any possible conflicts in the merge records, which can be resolved in the Conflict Resolution page. The Search tab’s download functionality was improved to allow export of multiple selected records, while a separate page is opened when viewing more germplasm information. The performance of the tool was also optimized to handle large datasets.

Seed Search

Search results are returned and listed in the browser following the input order, while seed records are saved following its current sort order. Information on the reserved seeds for a package is displayed in the search results data browser. The facility and seed container is also reflected in the Working List page.

List Manager

List management features were enhanced in this tool. Combining two or more lists of the same type is now possible via the new merge button, while filtering seed lists is also supported in the data browser. Creating copies of all or selected list items is enabled through the Replicate Items button in the Manage Items tab. A download button is featured in the data browser and the standard germplasm names are provided when searching for list items using the Input List.

Inventory Manager

The tool was optimized to handle large processes, thereby avoiding gateway timeout errors. The upload of seed lots with no associated packages is now supported.

Cross Manager

The Add Parents and Add Crosses tabs feature a new download button that generates a CSV file of the entries’ germplasm attributes.

Core System

Shipment Manager

Developments revolved around improving the process for outgoing seed shipment. The Items tab displays the Germplasm Health Test (GHT) column for IITA and CIMMYT, while IRRI users can expect the Routine Seed Health Test (RSHT) data to be auto-populated for shipment entries. Printouts were configured and system-generated shipment names are generated. The tool also operates on a Role-Based Access Control (RBAC) basis.

Printout

The tool’s integration with other domains were improved. This involves enhanced templates for Core Breeding and Printout tool access for Service Management. New standard printout templates were also developed, while connecting templates to specific domains, tools, and program is supported. Data from multiple occurrences can now be fetched for the templates, provided that these use GraphQL. A new button in the Templates tab enables sending a printing order directly to a printer.

Tenant Management

Functionalities were improved based on feedback. New looks for the domain entry points are featured in the EBS landing page. A diagram of EBS crop implementations and their respective teams are provided in the Hierarchy and versions of the domains and its tools are also displayed for reference.

Contact Relationship Manager

Linking institutions and addresses to user profiles were enhanced as part of the tool’s core improvements. Creating multiple addresses for an institution and designating one as the primary address for a user profile was enabled to allow for an easier management of users and their connections.

Messaging

Notifications were improved to include alerts for breeders and laboratory managers after a genotyping request is submitted. Notifications will also be received by breeders upon edit or approval of such request.

More information on the EBS Milestone 7 is available here.

For questions or concerns, please file a support ticket via this link.. We look forward to hearing from you!