Releases: cidgoh/GRDI_AMR_One_Health
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.
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.
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.
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.
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.
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.
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 |
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 |
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
, andceftazidime-clavulanic_acid_measurement_units
.
More details can be found under release notes issue #34
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 |
Details can be found under release notes issue #32