This page describes how to create a Biological Process annotation with the Noctua Form Editor using a C. elegans gene as an example.

Biological Process 'only' annotations can be made using the 'Create New BP Annotation' version of the Form Editor and use the 'causally upstream of or within' or 'causally upstream of' RO relations (and their positive and negative effect child relations) and, in accordance with GO-CAM model specifications, the root Molecular Function term.

If you'd like to make an annotation to express that a gene's Molecular Function is 'part of' a Biological Process, you should instead use the 'Create Activity' version of the Form Editor.

Note: add video

Getting started

From the Noctua landing page, click on the link to 'Create New Model in Form'
From within the form, click on the down arrow to the right of the ‘Create Activity’ icon in the upper left corner
Select ‘Create New BP Annotation’ from the dropdown menu

Add an entity

Type in the gene name: mpk-1
Select mpk-1 Cele WB:WBGene00003401 from the resulting autocomplete list

Note that the root Molecular Function term is pre-populated on the form and cannot be edited.

Select the appropriate relation

Select the appropriate relation between the root MF term and the GO BP term based on the available evidence.
- For example, a mutant phenotype that results in loss of a particular organismal feature or behavior, may simply warrant ‘causally upstream of or within, positive effect’ for the BP that describes the relevant process.

Add a Biological Process term

Begin typing ‘innate immune response’ in the Biological Process field
Select 'innate immune response' GO:0045087 from the resulting autocomplete list

Add an evidence code

Type in 'IMP'
Select 'mutant phenotype evidence used in manual assertion' ECO:0000315 from the resulting autocomplete list
- Note that, when applicable, the traditional three-letter GO codes are shown in bold in the autocomplete list

Add a PubMed reference

Click on the + sign on the lower right of the reference field
Select PMID from the dropdown list
Paste '27525822' in the Accession field
Check that the bibliographic information is correct
Click on the check mark

Note: you can also cut and paste a DB and id, e.g. PMID:31296532, in the reference field, but if you are cutting and pasting directly from PubMed, remember to remove the space between PMID and the accession.
Note: users can also use dois and internal GO_REFs as references.

Saving your annotation

Once you have finished entering the minimal information for an 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
Adding contextual information

Additional helpful information

Back to Noctua Users Manual

Noctua Form Biological Process

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