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cidgoh / GRDI_AMR_One_Health

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.
MIT License
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8.9.8 - release note tracking #56

Closed cbarcl01 closed 7 months ago

cbarcl01 commented 7 months ago

Template Fixes:

Specification Changes:

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

Version Tracking:

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.

Template To-Dos

cbarcl01 commented 7 months ago
Organism ID
Aeromonas rivipollensis NCBITaxon:948519
Aeromonas salmonicida NCBITaxon:645
Citrobacter gillenii NCBITaxon:67828
Clostridium sporogenes NCBITaxon:1509
Exiguobacterium NCBITaxon:33986
Exiguobacterium oxidotolerans NCBITaxon:223958
Exiguobacterium sp. NCBITaxon:44751
Kluyvera NCBITaxon:579
Kluyvera intermedia NCBITaxon:61648
Photobacterium NCBITaxon:657
Photobacterium sp. NCBITaxon:660
Pseudoalteromonas NCBITaxon:53246
Pseudoalteromonas tetraodonis NCBITaxon:43659
Psychrobacter NCBITaxon:497
Psychrobacter faecalis NCBITaxon:180588
Psychrobacter sp. NCBITaxon:56811
Shewanella NCBITaxon:22
Shewanella pealeana NCBITaxon:70864
Shewanella putrefaciens NCBITaxon:24
Shewanella sp. NCBITaxon:50422
cbarcl01 commented 7 months ago
collection_method ID
Water filtration GENEPIO:0100931
Scooping GENEPIO:0100932
Sediment collection GENEPIO:0100933
Soil coring GENEPIO:0100934
cbarcl01 commented 7 months ago
collection_device ID Definition
Box corer GENEPIO:0100928 A specimen collection device that is used to collect soft sediments in lakes or oceans.
PONAR grab sampler GENEPIO:0100929 A specimen collection device that is used to collect sediment samples from hard bottoms.
Soil sample probe GENEPIO:0100930 A specimen collection device that is used to collect a soil sample from the ground.
cbarcl01 commented 7 months ago
specimen_processing ID
Isolated from single source GENEPIO:0100926
cbarcl01 commented 7 months ago
environmental_site ID
Breeding ground ENVO:03501441
Beef farm ENVO:03501443
Beef cattle feedlot ENVO:03501444
Benthic zone ENVO:03501440
Roost (bird) ENVO:03501439
Slough ENVO:03501438
Urban area ENVO:03501437
cbarcl01 commented 7 months ago
environmental_material ID Definition
Fecal slurry ENVO:03501436
Influent ENVO:03501442 Contaminated or untreated water which is flowing into a wastewater treatment plant for processing.
cbarcl01 commented 7 months ago
body_product ID Definition
Digestive tract substance GENEPIO:0100898 Undigested food material, microbiota, and other materials found in the digestive tract.
Caecal content GENEPIO:0100899 Undigested food material, microbiota, and other materials found in the cecum
Intestinal content GENEPIO:0100900 Undigested food material, microbiota, and other materials found in the intestine
Stomach content GENEPIO:0100901 Undigested food material, microbiota, and other materials found in the stomach
Fecal composite GENEPIO:0004512
Feces (fresh) GENEPIO:0004513
Feces (environmental) GENEPIO:0004514
cbarcl01 commented 7 months ago
anatomical_part ID
Mantle (bird) GENEPIO:0100927
cbarcl01 commented 7 months ago

Newest release v.8.9.8