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cidgoh / GRDI_AMR_One_Health

A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.
MIT License
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12.2.2 - release note tracking #88

Closed cbarcl01 closed 2 months ago

cbarcl01 commented 3 months ago

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

cbarcl01 commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

NTR #87

cbarcl01 commented 3 months ago

NTR #86

cbarcl01 commented 3 months ago

NTR #85

cbarcl01 commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

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 commented 2 months ago

Preparing release for 10/07/2024

cbarcl01 commented 2 months ago

PR #90