Manage occurrences
- Rica Aicel Mariano
Before mapping an occurrence to a location and preparing for data collection, breeders must ensure that all information is correct. The Experiment Manager helps breeders find specific occurrences, view their information, and manage them. Let’s start by finding your occurrence!
Find an occurrence
There are two ways to find a specific occurrence: by sorting the table headers or by using the filter experiment button.
Search using table headers
The occurrences shown in the experiment manager table are grouped according to their experiments.
Filter the occurrences shown by typing a value in the blank header field. You may also use the wildcard ( % ) symbol if you don’t know the exact experiment name (e.g. RICE%).
After filters are applied, occurrences are sorted with respect to experiment names (e.g. when sorting by Year (ascending)). For example, an experiment named Breeding done in 2020 will still appear before an experiment named Grain Quality done in 2019.
You can also sort the occurrences shown (ascending or descending) by clicking on the header name.
Note that Status refers to the status of an occurrence (which may be status:CREATED, status:MAPPED, or status:PLANTED).
Search using Filter Experiments
If you are looking for occurrences under a specific experiment, you can use Filter Experiments.
On the upper right of the experiment manager table, find and click on the Filter () button from the toolbar.
Wait for the filter experiments tab to appear on the left side of your screen. Once the Data Filters tab is open, provide values to any of the following filters.
Near the bottom of the tab, you can toggle off () to apply the filters on all experiments or toggle on () for the experiments made by you. Click Apply once satisfied with the filters.
After the filters are applied, review the filtered occurrences.
You can reset the table or remove filters by clicking the Reset () button from the toolbar in the upper right corner of the browser.
Great job! You’ve successfully filtered your occurrences. Let’s choose an occurrence and make sure it contains the correct information.
View an occurrence
Each occurrence will have basic information, entry, and plot data based on the information provided during the experiment creation process. By viewing the information in each occurrence, you ensure that your experiments are accurate before you commit them and plant them in the field.
On the left side of the selected occurrence, click the View () icon.
You will be redirected to a new page that shows the information for that occurrence. Refer to the drop-down buttons below for information tabs.
Shows the basic information of an occurrence
Aside from the basic information, it also shows the occurrence status, number and percentage of tasks completed, traits collected, and seeds harvested. Users can also download design arrays, data collection files, planting instructions, and printouts for plot and harvest tags.
Shows the entries of the occurrence
The table shows entry information such as germplasm, generation, parentage, entry no., entry code, entry type, entry role, entry class, seed name, package label, package quantity, and package unit. You can also replace the entries in this tab.
Shows the plots of an occurrence
The table shows plot information such as plot no., plot code, entry no., entry code, germplasm code, germplasm state, germplasm type, rep, design X, design Y, PA X, and PA Y.
Shows the protocol information of the occurrence
The tab shows protocol subtabs such as planting, pollination (for generation nursery, cross parent nursery, and intentional crossing nursery), traits, management, and harvest.
Shows the crossing information of an occurrence
This tab is only shown for occurrences that have crosses. The table shows the cross and cross list name, harvest status, female and male parent names and parentages, cross method, female and male seed source, and cross remarks. You may also view the cross combinations in the Crosses tab.
Shows the layout of the planting arrangement of an occurrence
The design layout can viewed based on entry number, plot number, plot code, and block number.
Once you are done checking the occurrence information, click ← on your browser (or click the Experiment Manager header) until you are back at the Experiment Manager table.
Great job! After viewing your occurrence information, you can choose to either edit some basic information or proceed to map your occurrence.
Save entries or plots as list
On the left side of the selected occurrence, click the View () icon.
From either the Entry or Plot tab, tick the checkbox () of the items to be added to the list. You can also click the topmost checkbox to select all items.
Click the Save as New List () from the toolbar.
From the modal window, provide a name and other information about your new list. Give your list a meaningful name that helps you quickly identify what records are included and for which experiment it will be used.
You may indicate the list type from the Type dropdown menu.
Click Submit to finish saving your list. You can now access it in the List Manager.
Replace an entry in the occurrence
In the Experiment Manager data browser, go to the row of your selected occurrence. Then, click > Entry tab on the left side of the row.
From the Entry browser, tick the checkbox of the entry to be replaced.
You cannot replace an entry if at least one plot from the occurrence was harvested. A pop-up message will appear to remind them of this limitation.
Click Edit, then Replace occurrence entry from the toolbar.
On the modal window, choose whether you’d like to replace the entry with a check, filler, package, or germplasm. Then, click Next.
Tick the options button beside the entry you want to use as a replacement. You may view the dropdown menu below for the specific steps in replacing entries according to selected options. Once done, click Next.
Tick the options button of the check you want to use as a replacement.
Make sure you choose one that has enough package quantity.
Tick the options button of the filler package you want to use as a replacement.
Make sure you choose one that has enough package quantity.
Tick the options button of the package you want to use as a replacement.
Make sure you choose one that has enough package quantity.
Select the type of values that you want to search from the dropdown menu.
After that, type in the value that you want to search. Then, click Search.
You will be greeted with the list of germplasm from the search results. Click the options button of the germplasm and click Next.
Replaced entries in crossing experiments will be reflected in the cross records in Experiment Manager and Cross Manager when viewing the crosses, and in Harvest Manager when updating cross harvest data.
In another modal window, you will see the information about the original entry and the replacement entry. Then, click Confirm.
A pop-up window will appear indicating the successful replacement of the entry. The new entry will also appear in your Entry browser.
Download occurrence files
You can download mapping and data collection files from one or more occurrences in the Experiment Manager.
Download from a single occurrence
From the data browser, click Download () beside one of the occurrences. Then, choose the type of file that you need to download. Mapping file, occurrence or location file, and data collection summary files are saved as .csv file. Trait files are saved as .trt file.
Your file will start to download and will be stored in your local drive upon completion.
You must have your trait data collected and uploaded before downloading the data collection summary files.
3. Another way to download your files is by viewing your occurrence and accessing the files from the Basic, Entry, Plot, and Crosses tabs. Click the Download button () from the toolbar to download your file.
If you download more than 1000 plots, it will be processed in the background and you will be brought back to the Experiment Manager browser. Click the Notifications () icon and select the topmost notification to start downloading the file.
You may view the cross combinations in the Crosses tab.
Download from multiple occurrences
Tick the checkboxes of the occurrences where you want to download your files.
From the toolbar, click Download (). Then, choose the type of file that you need to download.
Downloading the trait data collection file using this method will not proceed for occurrences with unsaved trait protocol. To check, you may view and set the traits in the Traits subtab in the Experiment Manager.
Your files will start to download and will be stored as a compressed (.zip) file in your local drive upon completion.
You must have your trait data collected and uploaded before downloading the data collection summary files.
Customize occurrence-level and plot-level files
The Experiment Manager tool allows you to select the information you want to view in your occurrence-level and plot-level data before downloading them as a CSV file.
For metadata and plot data
Tick the checkboxes ( ) of the occurrences where you want to download your files.
From the toolbar, click Download (). Then, select Metadata and plot data.
A new page will display the (a) Selected Occurrences section where you can view the selected occurrence(s) for downloading and the (b) Data section where you can select the variables that you want to include in your downloadable file.
In the Selected Occurrences section, click the View () button beside one of the occurrences. This will open the Basic tab wherein you can view the occurrence information. If you have selected more than one occurrence, you may type the occurrence name in the search area.
Meanwhile, the Data section is divided into two parts, the Data Categories and the Related Data. The Data Categories column contains the data categories that group related data together.
You can also expand each data category to view its related metadata and plot data.
Finally, you can arrange the data categories in your desired order.
On the other hand, the Related Data contains all the metadata and plot data. By default, all the variables are included in the downloadable file.
To exclude the metadata and plot data, you may click the ( x ) mark beside one or more of them.
You may also drag the metadata and plot data to arrange them in order or place them under Hidden Columns.
After selecting the metadata and plot data, click Export to proceed. The download will be processed in the background.
For bad, missing, and suppressed trait data values, you may replace them with”NA” before downloading. Click the gear icon () and toggle on () Replace Suppressed and Bad Data with NA.
To check if the download is successful, click the Notifications () icon from the toolbar and click the most recent update containing the downloaded file. After that, your CSV file will be saved immediately in your local storage.
For occurrence data collection
Tick the checkboxes ( ) of the occurrences where you want to download your files.
From the toolbar, click Download (). Then, select Occurrence data collection.
The modal window will display the (a) Selected Occurrences section where you can view the selected occurrence(s) for downloading and the (b) Data section where you can select the variables that you want to include in your downloadable file.
In the Selected Occurrences section, click the View () button beside one of the occurrences. This will open the Basic tab wherein you can view the occurrence information. If you have selected more than one occurrence, you may type the occurrence name in the search area.
Meanwhile, the Data section is divided into two parts, the Data Categories and the Related Data. The Data Categories column contains the data categories that group related data together.
You can also expand each data category to view its related occurrence data.
Finally, you can arrange the data categories in your desired order.
On the other hand, the Related Data contains all the occurrence data and management protocols. By default, all the variables are included in the downloadable file
To exclude the occurrence data, you may click the ( x ) mark beside one or more of them.
You may also drag the occurrence data to arrange them in order or place them under Hidden Columns.
After selecting the occurrence data, click Export to proceed. The download will be processed in the background.
To check if the download is successful, click the Notifications () icon from the toolbar and click the most recent update containing the downloaded file. After that, your CSV file will be saved immediately in your local storage.
Delete occurrence
If you encounter major issues or blockers during the management of occurrences, you may delete them in the Experiment Manager. However, you may only delete status:DRAFT, status:CREATED, status:MAPPED, or status:PLANTED occurrences that are not used for data collection.
Collaborators are not allowed to delete occurrences in the Experiment Manager
From the data browser, click from the left side of one of the occurrences
A modal window will appear to notify you of the deletion. To proceed, click Confirm.
The deletion will then proceed in the background. Click Notifications () to check if deletion is successful. Once done, your occurrence is now removed from the dashboard.
Share occurrence with collaborators
We can also share occurrences with different programs and collaborators as long as we are the creator of the experiment.
In the Experiment Manager table, click the checkboxes () of the occurrences. Then, click .
You will be directed to the Experiment Permissions browser with the list of selected occurrences. Tick the checkbox () of the occurrence that you want to share with collaborators.
Click Manage. You may choose between Selected in page or All in page.
On the Manage Permissions modal window, select the program(s) and/or the user(s) you wish to share your occurrence with.
You can change the permission by toggling between Read and Write. You may refer to the drop-down below for the permission options.
Click Add.
To revoke a shared list from a user and/or program, select the program and/or user on the right, click Remove, and click Confirm for the removal. When done, click Close to go back to the browser.
Great job! Let us now review and modify the information about our occurrences.