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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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7.7.5 - release note tracking #32

Closed cmrn-rhi closed 1 year ago

cmrn-rhi commented 1 year ago

Template Fixes:

Specification Changes:

Field Change
AMR_testing_by New Menu
anatomical_part New ID
animal_or_plant_population New ID
antimicrobial_laboratory_typing_platform New ID, Correction
antimicrobial_testing_standard Correction
antimicrobial_vendor_name New Menu
collection_device New ID/Definition
environmental_material New ID
food_product New ID
food_product_properties New ID
host (food production name) New ID
sample_collected_by New ID/Definition
sequencing_instrument New Term

Version Tracking:

Excel Template, Reference Guides, Curation SOP

x = # = y = # = New terms and IDs z = # = New definitions, formatting changes/fixes

New Term SOP N/A unless indicated.

cmrn-rhi commented 1 year ago

Specification Change Details

Field Change
AMR_testing_by New Menu: Public Health Agency of Canada (PHAC) [GENEPIO:0100551], Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552], Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553], Health Canada (HC) [GENEPIO:0100554], Environment Canada (EC) [GENEPIO:0100555], Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]
anatomical_part New ID: Bird vent [UBERON:0012464]
'animal_or_plant_population' New ID: Beef cattle [FOODON:00004413]
antimicrobial_laboratory_typing_platform New ID: BIOMIC Microbiology System [ARO:3007569]; Correction: "Sensititre" typo in template
antimicrobial_testing_standard Correction: menu added to template.
antimicrobial_vendor_name New Menu: Becton Dickinson [ARO:3004405]; bioMérieux [ARO:3004406]; Omron [ARO:3004408]; Siemens [ARO:3004407]; Trek [ARO:3004409]
collection_device New ID/Definition: Scoop [GENEPIO:0002125]
environmental_material New ID: Canola straw [FOODON:00004430]
food_product New ID: Avocado [FOODON:00003600]
food_product_properties New ID: Food (cooked) FOODON:00001181; New Definition: Meat (skinless) [FOODON:00003468]
host (food production name) New ID: Dry cow [FOODON:00004411]
sample_collected_by New ID/Definition: University of Manitoba (UM) [GENEPIO:0004434]
sequencing_instrument New Term: Oxford Nanopore Flongle [GENEPIO:0004433]
cmrn-rhi commented 1 year ago

released as v7.7.5