Protocols

Protocols for updating GRDI-AMR-One-Health specification and repository resources.

New Fields

• Add to "Field Reference Guide" in the "GRDI Master Reference Guide" gSheet.
  • Indicate if release included label and ID under "Editor Note" column.
  • Flag changes and contact Rhiannon Cameron to update master specification.
• Add to Excel "Template".
  • Add to "Reference Guide"
  • Add to appropriate "group" tab
  • Add to "Merged Sheet" tab
  • Add vocabulary (if applicable) using the protocol below
  • TEST: Input valid values for an entire row in the applicable "group" tab and the "strain and isolate information" tab then double check that they appear on the "Merged Sheet" tab.
• Log changes in the active "release notes" issue.

New Vocabulary

• Add to "Term Reference Guide" in the "GRDI Master Reference Guide" gSheet.
• Add to Excel Template.
  • Add column for corresponding field under "Vocabulary" tab (if not already present)
    • Add missing data status terms (if applicable)
    • Name the range (or expand existing named change if it didn't automatically capture the new term(s)).
  • Add/Update field picklist in appropriate "group" tab.
    • If this field did not already have a picklist (or an invalid data check) add one:
      • Data > Data Validation > Error Alert > [check] Show error alert after invalid data is entered
        • Style: Warning
        • Title: Invalid Data
        • Error message:
          Please use a value from the picklist associated with this field.
          You can find valid input using the drop-down menu or in
          the “Vocabulary” tab.
    • Apply this from row 3-1522 (select range before, or apply after by copy/pasting updated cell) in the applicable column.
  • TEST: Input valid values for an entire row in the applicable "group" tab and the "strain and isolate information" tab then double check that they appear on the "Merged Sheet" tab.
• Log changes in the active "release notes" issue.

Repository Release Prep

• Upload updated "Excel Template".
  • Versioning x.y.z
• Upload updated "Reference Guides" (TSV & PDF).
  • Update the Version Tracking tab
  • Make sure "text wrap" is on before export so all contents are legible in the PDF
  • Do not include "Editor Note" column
  • Clean up formatting (if applicable) e.g. colour formatting for new IDs etc
  • Versioning x.y.z (same as template)
• Upload updated "Metadata Curation SOP" & "DataHarmonizer Curation SOP".
  • Versioning x.y (same as template, minus "z" changes since those don't come up in the protocol")
• Upload updated "New Term Request SOP".
  • Versioning x.y (independent versioning since changes to the specification/template doesn't impact this protocol)
• Draft a new release (Example):
  • Release title: GRDI-AMR specification package #.#.#
  • Choose a tag: v#.#.# (create a new tag)
  • Include "Contents:" section that lists the files and their individual version information

    Data Collection Template #.#.#
    Field and Term Reference Guides #.#.#
    Curation Standard Operating Procedure (SOP) #.#.#
    DataHarmonizer Download and Operation Instructions (SOP) #.#
    New Term Request Standard Operating Procedure (SOP) #.#

  • Include "Updates:" section with important information like "fixes", new fields, and a table of fields and their associated changes (e.g., picklist updates, ID/label changes, etc.).
  • Include Release Notes - referencing applicable GitHub #issue release notes

    More details can be found under release notes issue #__
    

  • Set as the latest release
  • Publish release
  • Notify curation team on the CIDGOH SLACK #grdi channel

Versioning

• x = changes to fields
• y = changes to values/ontology IDs
• z = changes definitions/formats/examples

Incrementing up one point for any number of changes.