A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.
License: MIT License
May request multiple terms in a single issue - delete the fields irrelevant to your request.
Associated Field(s): environmental_site
Label: Manure Storage Lagoon
Definition/Description: Large capacity, liquid manure storage
Definition Source: http://omafra.gov.on.ca/english/engineer/facts/10-051.htm
Synonyms or alternative labels:
Additional Comments (not an annotation):
Contributor Attribution: Andrew Scott (AAFC)
May request multiple terms in a single issue - delete the fields irrelevant to your request.
Associated Field(s): environmental_site
Label: Digester
Definition/Description: Aerobic/Anaerobic Digester for on-Farm digestion of manure
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):
Contributor Attribution: Andrew Scott (AAFC)
Enterococcus asini NCBI:txid57732
Enterococcus cecorum NCBI:txid44008
Enterococcus caccae NCBI:txid317735
Enterococcus canis NCBI:txid214095
Enterococcus durans NCBI:txid53345
Enterococcus dispar NCBI:txid44009
Enterococcus hirae NCBI:txid1354
Enterococcus malodoratus NCBI:txid71451
Enterococcus mundtii NCBI:txid53346
Enterococcus ratti NCBI:txid150033
Enterococcus saccharolyticus NCBI:txid41997
Enterococcus thailandicus NCBI:txid417368
Enterococcus villorum NCBI:txid112904
Associated Field(s): Organism
Term Label: Enterococcus species
Definition/Description: The requested picklist terms can be added to the existing 'sub-picklist' of Enterococcus [NCBITaxon:1350]. There are more Enterococcus species than these but these recommended species terms along with already included species can serve the purpose of commonly and somewhat rarely isolated Enterococcus species in our samples and also in the literature.
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):
Contributor Attribution:
ceftazidime-clavulanic_acid are incorrect and don't reflect the AMR tab layout. JD (ceftazidime-clavulanic_acid_measurement_sign) should be the one in JF (ceftazidime-clavulanic_acid_measurement) and JE is empty when it should have the measurement_units column imported.| Field | Change |
|---|---|
field |
Excel Template, Reference Guides, Curation SOP
x = # = N/A
y = # = N/A
z = # = Fixing some columns in the merged tab
New Term SOP N/A unless indicated.
Aeromonas salmonicida
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
Initial DataHarmonizer template for version 6.5.3
Not expected to have the multipage functionality at this point.
Currently it only allows "YYYY-MM-DD" but we'd like for it to accept "YYYY" and "YYYY-MM" as well.
Likely need to turn off the excel date format and encode this in VBA.
'Beef farm' or 'Beef feedlot'
Associated Field(s): environmental_site
Term Label: 'Beef farm' or 'Beef feedlot'
Definition/Description: This can be added as a sub-picklist of Farm [ENVO:00000078]
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):
Contributor Attribution:
- NB: curation team to add phenotype dropdowns (do we need a Notes field e.g. Susceptible, but dose dependent)
Need to confirm with @griffie:
AMR_phenotype picklist across specific antibiotic versions of the field (e.g., amikacin_resistance_phenotype, amoxicillin-clavulanic_acid_resistance_phenotype, ampicillin_resistance_phenotype, etc.)| Field | Change |
|---|---|
organism |
New picklist values as requested in issues |
collection_method |
Added IDs to picklist values |
collection_device |
Added IDs and updated definition to picklist values |
specimen_processing |
Added IDs to picklist values |
environmental_site |
Added IDs to picklist values |
environmental_material |
Added IDs and updated definition to picklist values |
body_product |
Added IDs and updated definition to picklist values |
anatomical_part |
Added IDs to picklist values |
Excel Template, Reference Guides, Curation SOP
x = # = no changes
y = 9 = new picklist values
z = 8 = definitions for new picklist values
New Term SOP N/A unless indicated.
May request multiple terms in a single issue - delete the fields irrelevant to your request.
Associated Field(s): purpose_of_sampling
Label: Research > Survey
Definition/Description: Survey study conducted for research purposes outside of a mandated requirement.
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):
Contributor Attribution: Andrew Scott (AAFC)
Shewanella sp.
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
Associated Field(s): anatomical_part
Term Label: Nasopharynx
Definition/Description: The section of the pharynx that lies above the soft palate.
Definition Source: http://www.informatics.jax.org/accession/cwg
Synonyms or alternative labels: NP
Additional Comments (not an annotation): description of usage within a sample plan
Contributor Attribution: https://orcid.org/0000-0002-1825-0087
]_ instead of : as a separatorsample_collection_project_namesequencing_protocol on merge sheetbiosample_accession all lowercaseAMR_laboratory_typing_platform to the correct menu| 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 |
Excel Template, Reference Guides, Curation SOP
x = # =
y = # = New terms and IDs
z = # = New definitions, formatting changes/fixes
New Term SOP N/A unless indicated.
Incrementing up one point for any number of changes.
x.y.zVersion Tracking tab (note: the latest version should be consistent across the SOPs, reference guides and templates)x.y.z (same as template)x.y (same as template, minus "z" changes since those don't come up in the protocol")x.y (independent versioning since changes to the specification/template doesn't impact this protocol)GRDI-AMR specification package #.#.#v#.#.# (create a new tag)Data Collection Template #.#.#
Field and Term Reference Guides #.#.#
Curation Standard Operating Procedure (SOP) #.#.#
DataHarmonizer Download and Operation Instructions (SOP) #.#
New Term Request Standard Operating Procedure (SOP) #.#
Release Notes - referencing applicable GitHub #issue release notes
More details can be found under release notes issue #
Make a document and video/gif guide showing how to do different updates on the template.
Photobacterium sp.
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
- NB: we likely need a "domesticated farm animal" term in the
animal_or_plant_populationfield pick list
May request multiple terms in a single issue - delete the fields irrelevant to your request.
Associated Field(s):
Label:
Definition/Description:
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):
Contributor Attribution: {Optional - ORCiD is preferred}
Exiguobacterium sp.
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
Here's my term requests: https://docs.google.com/spreadsheets/d/1JkOzRE7P4dsYrIKvzY_9i3O0-GIF4ojxCTqiW-o6DHU/edit#gid=2022130952
Some xxx_by fields in DH and the excel template say Environment Canada when they should read Environment and Climate Change Canada.
Identified by Gabriel at CFIA
Make a video tutorial on how to use the template that users and watch/review.
Can use this as a basis for the training "test" and possible additional walkthrough/troubleshooting materials.
Likely we won't be able to get this going properly until early 2023.
Exiguobacterium oxidotolerans
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
| 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. |
Excel Template, Reference Guides, Curation SOP
New Term SOP to be update as well.
| 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 |
Excel Template, Reference Guides, Curation SOP
x = 9 = New field ID and label
y = 0 = New picklist IDs and labels
z = 0 = Minor edits to guidance and fixed typo in definitions
New Term SOP N/A unless indicated.
Set the spreadsheet link sharing so that "Anyone with the link" can at least "View" or "Comment" if not "Edit".
<issue #> in the spreadsheet title has been replaced with the number of this issue.
Required columns (yellow highlight) have been provided for all of the requested terms.
Clostridium sporogenes
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
Associated Field(s): AMR_laboratory_typing_platform
Term Label:
Antibiotic resistance not defined [GENEPIO:0002040]
Intermediate antimicrobial phenotype [ARO:3004300]
Indeterminate antimicrobial phenotype [GENEPIO:0100585]
Nonsusceptible antimicrobial phenotype [ARO:3004303]
Resistant antimicrobial phenotype [ARO:3004301]
Susceptible antimicrobial phenotype [ARO:3004302]
Susceptible dose dependent antimicrobial phenotype [ARO:3004304]
Not Applicable [GENEPIO:0001619]
Not Collected [GENEPIO:0001620]
Not Provided [GENEPIO:0001668]
Missing [GENEPIO:0001618]
Restricted Access [GENEPIO:0001810]
Ontology ID or PURL:
Associated Field(s): AMR_laboratory_typing_platform
Term Label:
BIOMIC - Giles Scientific USA
Microscan [ARO:3004400]
Phoenix [ARO:3004401]
Sensitire [ARO:3004402]
Vitek System [ARO:3004403]
Not Applicable [GENEPIO:0001619]
Not Collected [GENEPIO:0001620]
Not Provided [GENEPIO:0001668]
Missing [GENEPIO:0001618]
Restricted Access [GENEPIO:0001810]
Definition/Description:
Synonyms or alternative labels:
Additional Comments (not an annotation):
Contributor Attribution:
Pseudoalteromonas tetraodonis
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
Shewanella pealeana
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
host (food production name) field terms: "Nursing pig [FOODON:00004297 ]" and "Tom (Gobbler) [FOODON:00004304 ]".| Field | Change |
|---|---|
food_product |
New picklist IDs and definitions. |
host (food production name) |
Removed unwanted blank spaces. |
Excel Template, Reference Guides, Curation SOP
x = 7 = N/A
y = 6 = New IDs
z = 4 = New definitions, minor fixes
New Term SOP N/A unless indicated.
Correct picklist term as requested by CFIA/ACIA. The 'sequenced_by' field is “Environment Canada (EC)” when it should state "Environment and Climate Change Canada (ECCC)". This needs to be updated across reference guide, DH and template.
Correct "sample storage method" definition and example, as well as the "packaging field" definition and example.
| Field | Change |
|---|---|
specimen_processing |
New ID and updated definition for Isolated from single source |
collection_device |
Updated definition's for PONAR grab sampler, Soil sample probe |
collection_method |
Updated definition's for scoping, Sediment collection, soil coring |
sample_storage_method |
Corrected definition |
sample_storage_medium |
Corrected definition |
Excel Template, Reference Guides, Curation SOP
x = # = none
y = # = none
z = # = Updated definitions and IDs for existing picklist.
New Term SOP N/A unless indicated.
Psychrobacter faecalis
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
Incrementing up one point for any number of changes.
x.y.zVersion Tracking tab (note: the latest version should be consistent across the SOPs, reference guides and templates)x.y.z (same as template)x.y (same as template, minus "z" changes since those don't come up in the protocol")x.y (independent versioning since changes to the specification/template doesn't impact this protocol)GRDI-AMR specification package #.#.#v#.#.# (create a new tag)Data Collection Template #.#.#
Field and Term Reference Guides #.#.#
Curation Standard Operating Procedure (SOP) #.#.#
DataHarmonizer Download and Operation Instructions (SOP) #.#
New Term Request Standard Operating Procedure (SOP) #.#
Release Notes - referencing applicable GitHub #issue release notes
More details can be found under release notes issue #
Shewanella putrefaciens
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
Cattle / Beef cattle / Dairy cattle
Associated Field(s):
Term Label: Cattle / Beef cattle / Dairy cattle
Definition/Description:
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):
Contributor Attribution:
Label: Nasopharynx
Definition/Description: The section of the pharynx that lies above the soft palate.
Definition Source: http://www.informatics.jax.org/accession/cwg
Synonyms or alternative labels: NP
Additional Comments (not an annotation):
description of usage within a sample plan
Contributor Attribution: https://orcid.org/0000-0002-1825-0097
Strain and Isolate Information and Merged tabs:
ceftazidime_testing_standardceftazidime_testing_standard_versionceftazidime_testing_standard_detailsceftazidime_susceptible_breakpointceftazidime_intermediate_breakpointceftazidime_resistant_breakpointceftazidime-clavulanic_acid_resistance_phenotypeceftazidime-clavulanic_acid_measurement_signceftazidime-clavulanic_acid_measurementPurpose_of_sequencing field now draws from the purpose_of_sequencing picklist instead of the purpose_of_sampling picklist. No impact users at this time since both lists contained the same entities.| Field | Change |
|---|---|
animal_source_of_food |
FOODON:03411563 label updated from "Poultry" to "Poultry or game bird" |
food_product |
"Meat scrap" FOODON:03309475 removed due to synonymy with "Meat trim" FOODON:03309475 which was already present in this list. |
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 |
host (food production name) |
FOODON:03411563 label updated from "Poultry" to "Poultry or game bird". "Whether" changed to "Wether sheep" FOODON:00004306 |
organism |
Still discussing with workgroup. |
taxonomic_identification_process |
New recommended field GENEPIO:0100583 and associated picklist added. |
taxonomic_identification_process_details |
New free text recommended field GENEPIO:0100584 added. |
| Field | Change |
|---|---|
food_product |
"Chicken meat (ground or minced, extra lean)" FOODON:03000392 ID corrected to FOODON:03000396. |
Apologies for the lack of template structure, but this may be more of a discussion with input from others rather than a direct request.
Issues #24 and #25 get at an important concept I've been thinking about - "production streams".
How do we most cleanly and efficiently differentiate between "production streams", like beef|dairy cattle production and layer|broiler chicken production?
I see that this difference is captured in host (food production name), but I wonder if a separate field may be more useful, since the concept modifies both environment and host. Additionally, some terms would be repeated if we simply prepended the stream (e.g., beef heifers, dairy heifers).
It looks like the HSO ontology (https://github.com/SVA-SE/HSO) has struggled with this too. Their terms in the livest sheet of this workbook have been marked EOL, and two more documents discuss their work:
I'm eager to hear what others think, as I'm approaching this from the analysis side rather than the data entry side.
.xslx to .xslm to allow for VBA macro coding (e.g., additional validation functionality, multiselect).taxonomic_identification_process column of the Strain and Isolate Information tab.Field Reference Guide.| 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. |
- NB: curation team to get lists of agency lab names
Aeromonas rivipollensis
organism
Just received a metadata from DFO sequencing with many bacteria absent in the pick list
No response
No response
No response
No response
No response
New term requests to be imported from FOODON
Psychrobacter sp.
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
Incrementing up one point for any number of changes.
x.y.zVersion Tracking tabx.y.z (same as template)x.y (same as template, minus "z" changes since those don't come up in the protocol")x.y (independent versioning since changes to the specification/template doesn't impact this protocol)GRDI-AMR specification package #.#.#v#.#.# (create a new tag)Data Collection Template #.#.#
Field and Term Reference Guides #.#.#
Curation Standard Operating Procedure (SOP) #.#.#
DataHarmonizer Download and Operation Instructions (SOP) #.#
New Term Request Standard Operating Procedure (SOP) #.#
Release Notes - referencing applicable GitHub #issue release notes
More details can be found under release notes issue #
Citrobacter gillenii
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
https://docs.google.com/spreadsheets/d/1yuWm76EO7jYQi0GHEFLvEbuzO5gCTLKNcL8oTvgNYM8/edit?usp=sharing
Set the spreadsheet link sharing so that "Anyone with the link" can at least "View" or "Comment" if not "Edit".
<issue #> in the spreadsheet title has been replaced with the number of this issue.
Required columns (yellow highlight) have been provided for all of the requested terms.
Kluyvera intermedia
organism
Just received a template with many bacteria species absent from the picklist.
No response
No response
No response
No response
No response
host (common name) picklist terms (e.g. between term label and term ID).| Field | Change |
|---|---|
presampling_activity |
NEW PICKLIST IDs: Certified humane animal husbandry practices [GENEPIO:0100894], Conventional farming practices [GENEPIO:0100895] |
specimen_processing |
NEW PICKLIST Definition: Samples pooled [OBI:0600016] |
geo_loc_name (state/province/region) |
NEW PICKLIST IDs: Atlantic region (Canada) [wikidata:Q246972], Central region (Canada) [wikidata:Q1048064], Northern region (Canada) [wikidata:Q764146], Pacific region (Canada) [wikidata:Q122953299], Prairie region (Canada) [wikidata:Q1364746] |
environmental_site |
NEW PICKLIST IDs: Pigsty [ENVO:03501413], Dairy farm [ENVO:03501416] |
animal_or_plant_population |
NEW PICKLIST IDs/Definitions: Wildlife [FOODON:00004503], Wild bird [FOODON:00004505]; NEW PICKLIST ID: Seabird [FOODON:00004504] |
environmental_material |
NEW PICKLIST IDs/Definitions: Dead haul trailer [GENEPIO:0100896], Live haul trailer [GENEPIO:0100897]; NEW PICKLIST IDs: Bulk tank [ENVO:03501379], Nest [ENVO:03501432]; NEW PICKLIST LABEL: Contaminated water [ENVO:00002186] |
body_product |
NEW PICKLIST IDs: Digestive tract substance [GENEPIO:0100898], Caecal content [GENEPIO:0100899], Intestinal content [GENEPIO:0100900], Stomach content [GENEPIO:0100901]; NEW DEFINITIONS: Fecal composite, Feces (fresh), Feces (environmental) |
anatomical_part |
NEW PICKLIST ID: Fish vent [GENEPIO:0100902] |
food_product |
NEW PICKLIST ID: Compound feed premix [FOODON:00004323], Compound feed premix (medicated) [FOODON:00004324], Animal feed ingredient [FOODON:00004322], Potato [FOODON:03315354] |
food_product_properties |
NEW PICKLIST IDs: Meat (with bone) [FOODON:02010116], Meat (with skin) [FOODON:02010111] |
food_product_production_stream |
NEW FIELD changes: production_stream label changed to food_product_production_stream; slight adjustments to definition; updated example; REMOVED PICKLIST VALUES: Food animal production stream [FOODON:03000450], Food product production stream [FOODON:03000457]; NEW PICKLIST IDs: Beef cattle production stream [FOODON:03000452], Broiler chicken production stream [FOODON:03000455], Dairy cattle production stream [FOODON:03000453], Layer chicken production stream [FOODON:03000456], Egg production stream [FOODON:03000458], Meat production stream [FOODON:03000460], Milk production stream [FOODON:03000459], NEW PICKLIST LABEL & ID: Veal meat production stream [FOODON:03000461], |
host (common name) |
NEW PICKLIST ID: Seabird [FOODON:00004504] |
Excel Template, Reference Guides, Curation SOP
x = 8 = Field relabeled
y = 8 = New value/picklist IDs
z = 7 = New definitions
New Term SOP update.
production_stream -> food_product_production_stream field label
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