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1. Querying KnetMiner

  • Multispecies Selector
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6. KnetMiner Deployment (Advanced)

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4. Exercises

  • Exercise 1: Choosing the right search terms
  • Exercise 2: Exploratory analysis from gene list
  • Exercise 3: Exploring gene knowledge networks
  • Exercise 4: Exploring KnetMiner Map View

5. Use Cases

  • KnetMiner Plant Use Case
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  • 4. Exercises
  • Exercise 1: Choosing the right search terms

Exercise 1: Choosing the right search terms

Begin by opening the Wheat (Triticum aestivum) KnetMiner instance from the /Products page. Ensure that you are in Triticum Aestivum by checking the Multispecies selector at the top left of the website header.

Seed dormancy and germination are the underlying developmental processes that activate or prevent pre-harvest sprouting in many grains and other seeds. We can provide this knowledge as a list of keywords into the search box. The Concept Selector provides alternative synonyms or more specific keywords. It also highlights key concept types that match the keywords.


Exercise 1 query:

Keyword Search:

dormancy OR anthocyanin


Exercise steps

1. Copy/paste the keywords from “Exercise 1 query” above, into the Wheat (Triticum Aestivum) KnetMiner instance’s Keyword search box.
2. Using the Concept Selector shows that the keyword dormancy has BioProc, Trait, Protein, PlantOntologyTerm and Gene matches (note the various shapes along the left of the box) (Figure 1).
3. Click on the Trait category and pick a more specific trait keyword from the list by clicking the ‘Replace’ button. Alternatively, add the keyword with the ‘+’ button, or remove it with the ‘-’ button.


Figure 1 – Replacing dormancy with Entry Into Dormancy


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Updated on February 23, 2023
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