Noctua Form MF Extensions

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This page describes how to add contextual information to a Molecular Function annotation with the Noctua Form Editor using a C. elegans gene as an example.

Contextual information may be added to any standard MF GO annotation to provide additional details about the biological context in which the MF occurs.

Note: add video

Getting started

Types of contextual information for MF annotations

  • There are currently five types of contextual information that can be added to an MF annotation:
    • 'part of' a Biological Process
    • 'occurs in' a Cellular Component
    • 'has input' a chemical entity or protein-containing complex
    • 'has output' a chemical entity or protein-containing complex
    • 'happens during' a biological phase or life cycle/developmental stage

Adding 'part of' BP and/or 'occurs in' CC MF contextual information

  • Adding BP and CC contextual information to an MF annotation can be done by filling in the BP and CC fields in the 'Create Activity' form
  • Note that the default relations of the 'Create Activity' form are 'part of' and 'occurs in' for BP and CC, respectively
  • Add each GO term using the autocomplete list
  • Add evidence
  • Add a reference

Adding 'has input', 'has output', 'happens during' MF contextual information

  • Click on the ‘more options’ icon on the far right of the MF annotation line
  • Scroll down to the 'Add an extension' menu option
  • Select the appropriate extension relation-value pair, e.g. Add 'has input' (GP/chemical)
  • A new line for the ‘has input’ entity, evidence code, and reference will appear
  • Type in ‘cpb-3’ and select the corresponding gene from the autocomplete menu
  • Add an ECO code
  • Add a reference

Repeat these steps to add ‘has output’ and/or ‘happens during’ contextual information, as needed.

Saving your annotation

  • Once you have finished entering the contextual information for an MF annotation, the Save button at the bottom of the form will turn blue, and you can click on it to save your work.
  • If the Save button is disabled, click on the red 'Why is the Save button disabled?' message at the bottom left of the form to see an error report that will guide you in how to fix your entry.

Previewing your annotation

  • As you enter information into the form editor, you can click on the Preview button at the bottom of the form to see a representation of the annotation as it will be seen in the graph editor.

Clearing all fields

  • If you would like to delete all of the information in the fields, click on the Clear button at the bottom of the form.

Suggestions for continuing

  • Naming a model
  • Making a model production

Additional helpful information

Back to Noctua Users Manual