External: Import germplasm, search germplasm and pedigree viewer v1.0
- Kristen Lind |
- 11 steps |
- 36 seconds
Skills Required
This part of the training assumes that you have completed the "using the germplasm template" module. If you haven't, please go back to that section to review. [Using the germplasm template.](https://scribehow.com/shared/External_Germplasm_template_v09__UYj8o_IITpaO8NhXmOovZw)
Learning Targets
In this section of training, you will learn how to:
- Import a germplasm file.
- Search germplasm.
- View pedigree connections. (Note that adding pedigree connections using GIDs is a later training module.)
Upload Germplasm Data with Completed Template
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Once you have a complete germplasm data file you want to upload, head to "import data" in DeltaBreed and click on the purple "choose a file" button.
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Choose the file, then click "upload & validate".
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List Name is required. You can also add a list description (optional).
The import summary gives you important information about the data that you are going to import. Double check your number of entries, new germplasm count and pedigree connections to make sure that they match the file you are uploading.
In this example, there are duplicate names that are detected. These germplasm will become independent database entries with new GIDs (DeltaBreed system assigned identification numbers) if the import is confirmed. The use case for this feature is a breeding program that has a naming system where there are two germplasm with the same name, but the program would want them to be represented by DeltaBreed with different GIDs. \
Click "Confirm" to import. If you are unhappy with your import, you can "Abort" and choose another file.
Jobs page in DeltaBreed
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After you click confirm, you can look at the "Jobs" page in DeltaBreed to check the progress up your data upload.
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This page will keep you updated on your upload progress. You can use the "refresh" button to check on any new job progress. Yellow denotes "in progress", green means "finished" and red denotes that there was an "error". You can see more details in the "details" link to the right of the status message column.
Germplasm details
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Back in the "germplasm" screen, the data has been uploaded successfully. Note that the GIDs (that system assigned value) is now assigned.
Now you can view several different pieces of information from this same screen.
You can search for germplasm using GID, Name, Breeding Method, etc.
You can look at specific details about each germplasm though the "Show Details".
You can click on the lists tab and see the details of that specific list or import.
You can also manage germplasm through the purple "manage germplasm" button. (See more below.)
Manage Germplasm
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You can manage your germplasm (import and download germplasm) through the purple "Manage Germplasm". Note that you can download entire germplasm lists under this tab.\
You can also sort germplasm information by clicking on the title of the column you'd like to sort. (See the orange arrow in the screen below.) You can use this same sort feature when searching for ontology terms and for a specific experiment and observations in the UI screen.
View Specific Germplasm Details
Let's take a closer look at a specific germplasm using the "show details" link and the germplasm view screen.
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In the germplasm screen, click on "show details" on the right of the germplasm you wish to view. From here you will be able to view both pedigree connections as well as any genotyping details about your specific germplasm (beta feature only, look for improvements in this feature in future versions).
Pedigrees
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To look at pedigree connections, choose a germplasm and click on the pedigree tab.
