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Recent Releases of https://github.com/cidgoh/grdi_amr_one_health

https://github.com/cidgoh/grdi_amr_one_health - GRDI-AMR specification package 14.5.4

Data Collection Template 14.5.4 Field and Term Reference Guides 14.5.4 Curation Standard Operating Procedure (SOP) 14.5 DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 14.5 New Term Request Standard Operating Procedure (SOP) 2.0

Updates:

| Field | Change | | --- | --- | | sequencing_date | new field | | collection_method | new picklist ID | | sample_collected_by | new picklist IDs |

Details can be found under release notes issue #111 and release note tracking #107


Published by cbarcl01 12 months ago

https://github.com/cidgoh/grdi_amr_one_health - 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 NCBIBioSample Enterics and NCBIAntibiogram.

Details can be found under release notes issue #98


Published by cbarcl01 about 1 year ago

https://github.com/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


Published by cbarcl01 over 1 year ago

https://github.com/cidgoh/grdi_amr_one_health - 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


Published by cbarcl01 over 1 year ago

https://github.com/cidgoh/grdi_amr_one_health - 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


Published by cbarcl01 almost 2 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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


Published by cbarcl01 almost 2 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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


Published by cbarcl01 about 2 years ago

https://github.com/cidgoh/grdi_amr_one_health - GRDI-AMR specification package 9.10.10

Contents:

Data Collection Template 9.10.10 Field and Term Reference Guides 9.10.10 Curation Standard Operating Procedure (SOP) 9.10 DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 9.10 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


Published by cbarcl01 about 2 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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


Published by cbarcl01 about 2 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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


Published by cbarcl01 about 2 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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


Published by cbarcl01 over 2 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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


Published by cmrn-rhi over 2 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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 | | 'animalorplantpopulation' | New ID | | `antimicrobiallaboratorytypingplatform| New ID, Correction | |antimicrobialtestingstandard| Correction | |antimicrobialvendorname| New Menu | |collectiondevice| New ID/Definition | |environmentalmaterial| New ID | |foodproduct| New ID | |foodproductproperties| New ID | |host (food production name)| New ID | |samplecollectedby| New ID/Definition | |sequencinginstrument` | New Term |

Details can be found under release notes issue #32


Published by cmrn-rhi over 2 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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. |

Details can be found under release notes issue #23


Published by cmrn-rhi over 2 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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


Published by cmrn-rhi about 3 years ago

https://github.com/cidgoh/grdi_amr_one_health - GRDI-AMR specification package 5.3.2

:star2: NEW MULTISELECT FUNCTIONALITY - DETAILS BELOW :star2:

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


Published by cmrn-rhi about 3 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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. | | foodproductproperties | 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


Published by cmrn-rhi over 3 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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 ("purposeofsampling") - Manure digester equipment ("environmentalmaterial") - Manure digester facility ("environmentalsite") - Manure lagoon (Anaerobic lagoon) ("environmental_site")

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


Published by cmrn-rhi over 3 years ago

https://github.com/cidgoh/grdi_amr_one_health - 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


Published by cmrn-rhi over 3 years ago