Creating a Biological Process (BP) only annotation

• Click on the arrow to the left of the ‘Create Activity’ icon.
• Select ‘Create New BP Annotation’.
• Using C. elegans as an example:
  • Type in gene name: skn-1
  • Select the WBGene entry from the dropdown list
  • Gene products link out to respective gene product pages via dbxrefs.yaml
• Note that the BP only form automatically fills in the root Molecular Function GO term (GO:0003674). This is done because the GO-CAM data model requires an MF annotation in order to associate a gene with a BP.

• Select the appropriate relation between the root MF term and the GO BP term based on the experimental evidence you have in the paper. For example, a mutant phenotype may simply warrant ‘causally upstream of or within’.

• Add the BP
  • Search for ‘innate immune response’
  • Autocomplete options are presented in a pop-up window
  • Terms link out to AmiGO
  • Enter the appropriate evidence code from using ECO term names
  • Search for ‘mutant phenotype’
  • GO codes are indicated with bold three-letter GO code
  • Add a reference. Two options:
    • Cut and paste a DB and id, e.g. PMID:30442878 OR
    • Click on the +/lines symbol
• Add the CC
  • If applicable, add that the BP ‘occurs in’ a GO CC. Note that this is different from saying that the MF ‘occurs in’ a GO CC, which is the statement made in an Activity Unit.
  • Search for ‘nucleus’
  • Autocomplete options are presented in a pop-up window
  • Terms link out to AmiGO
  • Evidence code autocomplete using ECO term names
  • Search for ‘direct assay’
  • GO codes are indicated with bold three-letter GO code
  • Add a reference. Two options: - Cut and paste a DB and id, e.g. PMID:30442878 OR - Click on the +/lines symbol - Pop-up appears with a select drop-down of dbs for references: PMID, DOI, GO_REF - Select PMID - Add identifier: 30442878
• Adding contextual information to a BP only annotation can be done as for Activity Units but note that contextual information cannot be added to the root MF term.