GRDI-AMR specification package 7.7.5

Contents:

Data Collection Template 7.7.5
Field and Term Reference Guides 7.7.5
Curation Standard Operating Procedure (SOP) 7.6
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 7.6
New Term Request Standard Operating Procedure (SOP) 1.2

Updates:

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

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Details can be found under release notes issue #32

GRDI-AMR specification package 7.6.4

Contents:

Data Collection Template 7.6.4
Field and Term Reference Guides 7.6.4
Curation Standard Operating Procedure (SOP) 7.6
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 7.6
New Term Request Standard Operating Procedure (SOP) 1.2

Updates:

All sheets have rows beneath "1502" hidden - limiting submissions to 1500 rows as that is currently the decided limit of the merge sheet to avoid slowdown.

Field	Change
AMR_laboratory_typing_platform	NEW/UPDATED picklist.
AMR_laboratory_typing_platform	Removed phenotype picklist options.
AMR_measurement_units	Removed field, replaced each antimicrobial specific columns.
AMR_measurement_sign	Removed field, replaced each antimicrobial specific columns.
AMR_phenotype	Removed field, replaced each antimicrobial specific columns.
AMR_testing_intermediate_breakpoint	Removed field, replaced each antimicrobial specific columns.
AMR_testing_resistant_breakpoint	Removed field, replaced each antimicrobial specific columns.
AMR_testing_standard	Removed field, replaced each antimicrobial specific columns.
AMR_testing_standard_version	Removed field, replaced each antimicrobial specific columns.
AMR_testing_susceptible_breakpoint	Removed field, replaced each antimicrobial specific columns.
AMR_testing_standard_details	Removed field, replaced each antimicrobial specific columns.
anatomical_part	NEW/UPDATED picklist.
anatomical_region	NEW field.
animal_or_plant_population	NEW/UPDATED picklist.
antimicrobial_agent_name	NEW/UPDATED picklist.
antimicrobial_measurement_sign	Reordered to be after the units column, added picklist.
antimicrobial_measurement_units	Added respective columns to each antimicrobial option with picklist.
available_data_types	NEW/UPDATED picklist.
body_product	NEW/UPDATED picklist.
collection_device	NEW/UPDATED picklist.
collection_method	NEW/UPDATED picklist.
environmental_material	NEW/UPDATED picklist.
environmental_site	NEW/UPDATED picklist.
food_packaging	NEW/UPDATED picklist.
food_product	New picklist IDs and definitions.
food_product_properties	NEW/UPDATED picklist.
geo_loc_name (state/province/region)	NEW/UPDATED picklist.
host_age_bin	NEW field.
host (common name)	NEW/UPDATED picklist.
host (food production name)	Removed unwanted blank spaces, NEW/UPDATED picklist.
host (scientific name)	NEW/UPDATED picklist.
isolated_by	NEW/UPDATED picklist.
organism	NEW/UPDATED picklist.
presampling_activity	NEW/UPDATED picklist.
production_stream	NEW field.
sample_collected_by	NEW/UPDATED picklist.
sample_collection_date_precision	NEW field.
sediment_depth	NEW field.
sequencing_instrument	NEW/UPDATED picklist.
water_temperature	NEW field.
weather_type	NEW/UPDATED picklist.

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Details can be found under release notes issue #23

GRDI-AMR specification package 6.4.2

Contents:

Data Collection Template 6.4.2
Field and Term Reference Guides 6.4.2
Curation Standard Operating Procedure (SOP) 6.4
New Term Request Standard Operating Procedure (SOP) 1.2

Updates:

Field	Change
antimicrobial_agent_name	NEW PICKLIST items: Enrofloxacin [CHEBI:35720], Norfloxacin [CHEBI:100246], Oxolinic acid [CHEBI:138856], Oxytetracycline [CHEBI:27701], Piperacillin [CHEBI:8232], Polymyxin B [ARO:3000454]
<enrofloxacin_fields>	NEW enrofloxacin fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
food_packaging_date	NEW field.
food_product_properties	NEW PICKLIST items: Food (canned) [FOODON:00002418], Food (dried) [FOODON:03307539], Food (fresh) [FOODON:00002457], and Food (frozen) [FOODON:03302148].
food_quality_date	NEW field.
<norfloxacin_fields>	NEW norfloxacin fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
<oxolinic-acid_fields>	NEW oxolinic acid fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
<oxytetracycline_fields>	NEW oxytetracycline fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
<piperacillin_fields>	NEW piperacillin fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
<polymyxin-b_fields>	NEW polymyxin b fields: resistance_phenotype, measurement_sign, measurement, testing_standard, testing_standard_version, testing_standard_details,susceptible_breakpoint, intermediate_breakpoint, and resistant_breakpoint.
sequencing_instrument	Several GENEPIO term IDs deprecated after rehoming in OBI, see issue #18 for details.

Details can be found under release notes issue #18

GRDI-AMR specification package 5.3.2

🌟 NEW MULTISELECT FUNCTIONALITY - DETAILS BELOW 🌟

Contents:

Data Collection Template 5.3.2
Field and Term Reference Guides 5.3.2
Curation Standard Operating Procedure (SOP) 5.3
New Term Request Standard Operating Procedure (SOP) 1.1

Updates:

• Multiselect added (see applicable fields below) allowing users to select multiple items. Reselecting an item will remove it from the list provided it isn't the last item (which must be deleted to remove). Currently using ";" (semicolon) separator.
• File format changed from .xslx to .xslm to allow for VBA macro coding (e.g., additional validation functionality, multiselect).
  • Troubleshooting: If you experience "A potentially dangerous macro has been blocked" warning please disregard this. There is no malicious coding and no features that have not been requested and encoded by the GRDI-AMR workgroup.
  • Troubleshooting: If you are having difficult unblocking on a Windows OS, go to the file in explorer, right-click the file and select "Properties", at the bottom you should see "Security: This file came from another computer and might be blocked to help protect this computer." Select "Unblock" followed by "Apply".
• Date validation removed and all dat columns reformatted as "Text" to allow dates inputting as yyyy-mm-dd, yyyy-mm, and yyyy.
• Added an invalid data "warning" to the taxonomic_identification_process column of the Strain and Isolate Information tab.
• Leading whitespaces removed after indented items are selected from a list (single select and multiselect), they still appear when viewing the drop-down lists.
• Reference Guides updated: Colour-coding applied to "required" and "recommended" fields and tracking information for deprecated (for the purpose of normalization) labels and IDs (more information in Curation Standard Operating Procedure (SOP) 5.3).

Field	Change
environmental_site	Multiselect functionality added.
weather_type	Multiselect functionality added.
animal_or_plant_population	Multiselect functionality added.
environmental_material	Multiselect functionality added.
anatomical_material	Multiselect functionality added.
body_product	Multiselect functionality added.
anatomical_part	Multiselect functionality added.
food_product	Multiselect functionality added.
food_product_properties	Multiselect functionality added.
animal_source_of_food	Multiselect functionality added.
food_packaging	Multiselect functionality added.
purpose_of_sequencing	Multiselect functionality added.
experimental_intervention	Multiselect functionality added.
AMR_measurement	REMOVED UPON REQUEST.
AMR_phenotype	List now applied to all <antibiotic>_phenotype columns and added new terms: Indeterminate antimicrobial phenotype [GENEPIO:0100585], Susceptible dose dependent antimicrobial phenotype [ARO:3004304].

Details can be found under release notes issue #12

GRDI-AMR specification package 4.2.1

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

GRDI-AMR specification package 3.1.0

Contents:

Data Collection Template 3.1.0
Field and Term Reference Guides 3.1
Curation Standard Operating Procedure (SOP) 3.0
New Term Request Standard Operating Procedure (SOP) 1.1

UPDATES - New Terms (added under "Field"):

• Survey study ("purpose_of_sampling")
• Manure digester equipment ("environmental_material")
• Manure digester facility ("environmental_site")
• Manure lagoon (Anaerobic lagoon) ("environmental_site")

Status: "Awaiting Ontology ID" - curators are making term requests in the appropriate domain ontologies.

GRDI-AMR specification package 3.0.0

Initial release of the GRDI-AMR contextual data specification package

• Data Collection Template 3.0.0
• Field and Term Reference Guides 3.0
• Curation Standard Operating Procedure (SOP) 3.0
• New Term Request Standard Operating Procedure (SOP) 1.1