GRDI-AMR specification package 13.4.4

Data Collection Template 13.4.4
Field and Term Reference Guides 13.4.4
Curation Standard Operating Procedure (SOP) 13.4
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 13.4
New Term Request Standard Operating Procedure (SOP) 2.0

Updates:

Field	Change
environmental_material	Corrected picklist IDs
genome_sequence_filename	Updated label from assembly_filename

New automated exports available for NCBI_BioSample Enterics and NCBI_Antibiogram.

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Details can be found under release notes issue #98

GRDI-AMR specification package 13.3.3

Contents:

Data Collection Template 13.3.3
Field and Term Reference Guides 13.3.3
Curation Standard Operating Procedure (SOP) 13.3
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 13.3
New Term Request Standard Operating Procedure (SOP) 2.0

Updates:

Field	Change
specimen processing details	New field
environmental_site	New term IDs and definitions
sample_collection_end_date	New field
sample_processing_date	New field
sample_collection_start_time	New field
sample_collection_end_time	New field
sample_collection_time_of_day	New field
sample_collection_time_duration_value	New field
sample_collection_time_duration_unit	New field
sampling_weather_conditions	New field
presampling_weather_conditions	New field
precipitation_measurement_value	New field
precipitation_measurement_unit	New field
precipitation_measurement_method	New field

Updated curation guidance to support addition of new fields.

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Details can be found under release notes issue #94

GRDI-AMR specification package 12.2.2

Contents:

Data Collection Template 12.2.2
Field and Term Reference Guides 12.2.2
Curation Standard Operating Procedure (SOP) 12.2
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 12.2
New Term Request Standard Operating Procedure (SOP) 2.0

Updates:

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

Updated guidance to support addition of new fields.

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Details can be found under release notes issue #88

GRDI-AMR specification package 11.1.1

Contents:

Data Collection Template 11.1.1
Field and Term Reference Guides 11.1.1
Curation Standard Operating Procedure (SOP) 11.1.
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 11.1.
New Term Request Standard Operating Procedure (SOP) 2.0

Updates:

Field	Change
experimental _protocol_field	New field
experimental_specimen_role _type	New field, new picklist IDs
nucleic acid extraction method	New field
nucleic acid extraction kit	New field
sample_volume_measurement_value	New field
sample_volume_measurement_unit	New field, new picklist IDs
residual_sample_status	New field, new picklist IDs
sample_storage_duration_value	New field
sample_storage_duration_unit	New field, new picklist IDs
nucleic_acid_storage_duration_value	New field
nucleic_acid_storage_duration_unit	New field, new picklist IDs
DNA fragment length	New field
genomic target enrichment method	New field, new picklist IDs
genomic target enrichment method details	New field
amplicon pcr primer scheme	New field
amplicon size	New field
sequencing flow cell version	New field
quality control method name	New field
quality control method version	New field
quality control determination	New field, new picklist IDs
quality control issues	New field , new picklist IDs
quality control details	New field
raw sequence data processing method	New field
dehosting method	New field
sequence assembly software name	New field
sequence assembly software version	New field
consensus sequence software name	New field
consensus sequence software version	New field
breadth of coverage value	New field
depth of coverage value	New field
depth of coverage threshold	New field
genome completeness	New field
number of base pairs sequenced	New field
number of total reads	New field
number of unique reads	New field
minimum post-trimming read length	New field
number of contigs	New field
percent Ns across total genome length	New field
Ns per 100 kbp	New field
N50	New field
percent read contamination	New field
sequence assembly length	New field
consensus genome length	New field
reference genome accession	New field
deduplication method	New field
bioinformatics protocol	New field
read mapping software name	New field
read mapping software version	New field
taxonomic reference database name	New field
taxonomic reference database version	New field
taxonomic analysis report filename	New field
taxonomic analysis date	New field
read mapping criteria	New field

Updated guidance to support addition of new field.

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Details can be found under release notes issue #81

GRDI-AMR specification package 10.0.0

Contents:

Data Collection Template 10.0.0
Field and Term Reference Guides 10.0.0
Curation Standard Operating Procedure (SOP) 10.0
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 10.0
New Term Request Standard Operating Procedure (SOP) 2.0

Updates:

Field	Change
sequencing_assay_type	New field
host (common name)	New picklist IDs
host (scientific name)	New picklist IDs
organism	New picklist IDs
sequenced by	New picklist IDs
collection method	New picklist IDs
animal_source_of_food	New picklist IDs
food_product	New picklist IDs
environmental_site	New picklist IDs
environmental_material	New picklist IDs

Updated guidance to support addition of new field.

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Details can be found under release notes issue #78

GRDI-AMR specification package 9.0.0

Contents:

Data Collection Template 9.0.0
Field and Term Reference Guides 9.0.0
Curation Standard Operating Procedure (SOP) 9.0
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 9.0
New Term Request Standard Operating Procedure (SOP) 2.0

Updates:

Field	Change
food_product	New picklist IDs and definitions
food_product_properties	New picklist IDs and definitions
available_data_types_details	New field ID and definition
available_data_types	New picklist IDs and definitions
water_depth_units	New field ID, definition and picklists
sediment_depth_units	New field ID, definition and picklists
air_temperature_units	New field ID, definition and picklists
water_temperature_units	New field ID, definition and picklists
water_depth	Updated definition and example
sediment_depth	Updated definition and example
air_temperature	Updated definition and example
water_temperature	Updated definition and example

Updated guidance to support change in atomising out measurement and unit for environmental measures described above.

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Details can be found under release notes issue #65

GRDI-AMR specification package 8.9.9

Contents:

Data Collection Template 8.9.9
Field and Term Reference Guides 8.9.9
Curation Standard Operating Procedure (SOP) 8.9
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 8.9
New Term Request Standard Operating Procedure (SOP) 2.0

Updates:

Field	Change
specimen_processing	Updated definitions
collection_device	Updated definitions
collection_method	Updated definitions
sample_storage_method	Corrected definition
sample_storage_medium	Corrected definition

Additionally, corrected minor error where Environment Canada should be Environment and Climate Change Canada on template.

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Details can be found under release notes issue #59

GRDI-AMR specification package 8.9.8

Contents:

Data Collection Template 8.9.8
Field and Term Reference Guides 8.9.8
Curation Standard Operating Procedure (SOP) 8.9
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 8.9
New Term Request Standard Operating Procedure (SOP) 2.0

Updates:

Field	Change
organism	New IDs and definitions
collection_method	New IDs
collection_device	New IDs and definitions
specimen_processing	New IDs
environmental_site	New IDs
environmental_material	New IDs and definitions
body_product	New IDs and definitions
anatomical_part	New IDs

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Details can be found under release notes issue #56

GRDI-AMR specification package 8.8.7

Contents:

Data Collection Template 8.8.7
Field and Term Reference Guides 8.8.7
Curation Standard Operating Procedure (SOP) 8.8
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 8.8
New Term Request Standard Operating Procedure (SOP) 2.0

Updates:

Field	Change
presampling_activity	New IDs
specimen_processing	New Definitions
geo_loc_name (state/province/region)	New IDs
environmental_site	New IDs
animal_or_plant_population	New IDs/Definitions
environmental_material	New IDs/Definitions
body_product	New IDs
anatomical_part	New IDs
food_product	New IDs
food_product_properties	New IDs
food_product_production_stream	New field changes
host (common name)	New ID

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Details can be found under release notes issue #38

GRDI-AMR specification package 7.7.6

Contents:

Data Collection Template 7.7.6
Field and Term Reference Guides 7.7.6
Curation Standard Operating Procedure (SOP) 7.7
DataHarmonizer Download and Operation Instructions (SOP) 7.7
New Term Request Standard Operating Procedure (SOP) 1.2

UPDATES:

• Merged table headers were correct for ceftazidime-clavulanic_acid_measurement_sign, ceftazidime-clavulanic_acid_measurement, and ceftazidime-clavulanic_acid_measurement_units.

More details can be found under release notes issue #34