Adding contextual information to a basic Activity Unit

  • Click on ‘Create Activity’
  • Using C. elegans as an example:
    • Type in gene name: mpk-1 (explain that returned entities are what is in gpi file and therefore in NEO)
    • Autocomplete options are presented in a pop-up window
    • Gene products link out to respective gene product pages via dbxrefs.yaml
  • Add an MF
    • Search for ‘protein kinase activity’
    • 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:31296532 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: 31296532
  • Add an input to the MF
    • Click on the ‘more options’ icon on the far right of the annotation line
    • Scroll down to the Add option
    • Select Add ‘has input’ (GP/Chemical)
    • A new line for the ‘has input’ entity and evidence will appear
    • Type in ‘ced-3’ and select the gene from the autocomplete menu
    • 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:31296532 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: 31296532
    • Repeat steps i - vii to add ‘has output’ and/or ‘happens during’ contextual information, as needed.
  • Add that MF is ‘part of’ a BP
    • Search for ‘DNA damage response, detection of DNA damage’
    • Autocomplete options are presented in a pop-up window

    • Terms link out to AmiGO

    • Evidence code autocomplete 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:31296532 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: 31296532

  • Add that the first BP is ‘part of’ a second BP

    • Click on the ‘more options’ icon on the far right of the annotation line
    • Scroll down to the Add option
    • Select Add ‘part of’ (Biological Process)
    • A new line for the ‘part of’ BP and evidence will appear

    • Type in ‘apoptotic process’ and select the GO term from the autocomplete menu

    • Evidence code autocomplete 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:31296532 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: 31296532
    • Repeat steps i - vii to add more ‘part of’ BPs, as needed.

  • Add that MF ‘occurs in’ a CC

    • 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:31296532 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: 31296532
  • Add that a CC is ‘part of’ a cell
    • Click on the ‘more options’ icon on the far right of the annotation line
    • Scroll down to the Add option
    • Select Add ‘part of’ (Cell Type)
    • A new line for the ‘part of’ cell type and evidence will appear

    • Type in ‘germ cell’ and select the WBbt:0006796 from the autocomplete menu

    • 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:31296532 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: 31296532
    • Repeat steps i - vii to add ‘part of’ for tissue and organism contextual information, as needed. Note that organismal contextual information is not needed except for when relevant to multi-species processes.