12.2.2 - release note tracking

[cbarcl01]

Template Fixes:

Specification Changes:

Field	Change
animal_source_of_food	New picklist IDs
food_product	New picklist IDs, change picklist IDs, new definitions
label claim	New field
taxonomic_identification_process	New picklist IDs
environmental_material_constituent	New field
collection_device	Change picklist ID

Version Tracking:

Excel Template, Reference Guides, Curation SOP

x = 12 = New field
y = 2 = New IDs
z = 1 = <def/format/example changes>

New Term SOP N/A unless indicated.

Template To-Dos

• Update picklist value labels/IDs/descriptions
  • Excel Template
  • DataHarmonizer Template (GRDI-enums)
• Update field labels/IDs/descriptions
  • Excel Template
  • DataHarmonizer Template (GRDI-slots)

[cbarcl01]

New terms requested by Sandeep Tamber.

From conversation with Emma:

Can we add to food_product list:

1. Under shellfish:

• Mussel [FOODON:03411223]
• Oyster [FOODON:03411224]

2. Under produce:

• Karela (Bitter melon) [FOODON:00004367]

Can we add to taxonomic_identification_process?

1. Matrix Assisted Laser Desorption Ionization imaging mass spectrometry assay (MALDI) [OBI:0003099]

[cbarcl01]

From conversation with Emma:

We might need to separate out label claims from food product properties. There is a need for requesting things like antibiotic-free in addition to organic. Distinguishing between them will also be more in-line with the US One health Biosample.

New field: label claim [FOODON:03602001]

[cbarcl01]

Need to capture what an environmental material is composed of (for example a plastic pipe vs a lead pipe etc). Suggestion environmental material constituent.

NOTE: Added new field as string (not picklist).

[cbarcl01]

NTR #87

[cbarcl01]

NTR #86

[cbarcl01]

NTR #85

[cbarcl01]

Update term for 'collection tube'. Currently references an uberon term which is not appropriate for use so need to usenew term 'sample collection tube' GENEPIO:0101196

[cbarcl01]

Resolved changes to missing FOODON IDs. Some IDs were included in GRDI but had not yet been surfaced in EBI OLS. This was mostly due to a modelling change in food characteristics that had happened in FOODON. Details can be found in this spreadsheet.

[cbarcl01]

Update Fields experimental_specimen_role_type and specimen_processing to ensure IDs are consistent with processing vs the role.

From Gabriel: the ids are slightly different technical replicates for example has the same number, but the prefix is different: one with OBI and another one with EFO, is that correct?

From Charlie: Biological replicate, based on the definition the EFO term is a better fit for 'experimental_specimen_role_type'. It looks like the biological and technical replicate terms under 'specimen_processing' have been left there as a legacy of earlier templates, when there was no other place to capture this info. In other specifications we have changed this to 'Biological replicate processing' and 'Technical replicate processing', to better reflect the field.

[cbarcl01]

Preparing release for 10/07/2024

[cbarcl01]

PR #90