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GRDI-AMR specification package 4.2.1
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@cmrn-rhi cmrn-rhi released this 16 Nov 17:53
· 165 commits to main since this release
v4.2.1
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Learn about vigilant mode.

Contents:

Data Collection Template 4.2.1
Field and Term Reference Guides 4.2.1
Curation Standard Operating Procedure (SOP) 4.2
New Term Request Standard Operating Procedure (SOP) 1.1

UPDATES:

  • FIX: Added the following fields to the Strain and Isolate Information and Merged tabs:
    • ceftazidime_testing_standard
    • ceftazidime_testing_standard_version
    • ceftazidime_testing_standard_details
    • ceftazidime_susceptible_breakpoint
    • ceftazidime_intermediate_breakpoint
    • ceftazidime_resistant_breakpoint
    • ceftazidime-clavulanic_acid_resistance_phenotype
    • ceftazidime-clavulanic_acid_measurement_sign
    • ceftazidime-clavulanic_acid_measurement
Field Change
animal_source_of_food FOODON:03411563 label updated from "Poultry" to "Poultry or game bird".
anatomical_part Picklist updates.
collection_device Picklist updates.
collection_method Picklist updates.
environmental_material "Bulk tank" ENVO:03501407 removed (incorrect ID assignment) and new ID has been requested. "Animal manure" ENVO:00003031 ID changed to AGRO:00000079. "Poultry litter" ENVO:00003860 ID changed to AGRO:00000080. More terms received IDs and definitions.
environmental_site Picklist updates.
food_product "Meat scrap" FOODON:03309475 removed due to synonymy with "Meat trim" FOODON:03309475 which was already present in this list.
food_product_properties Picklist updates.
host (common name) Picklist updates.
host (food production name) FOODON:03411563 label updated from "Poultry" to "Poultry or game bird". "Whether" changed to "Wether sheep" FOODON:00004306. Picklist updates.
organism Removed "strain" level terms, added species, added subspecies, made sure all existing categories had an overarching class. Details on added/removed terms available under #9 .
sequencing_platform Picklist updates.
taxonomic_identification_process NEW recommended field GENEPIO:0100583 and associated picklist added.
taxonomic_identification_process_details NEW free text recommended field GENEPIO:0100584 added.
weather_type Picklist updates.

More details can be found under release notes issue #9

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