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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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10.0.0 - release note tracking #78

Closed cbarcl01 closed 3 months ago

cbarcl01 commented 3 months ago

Template Fixes:

Specification Changes:

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

Version Tracking:

Excel Template, Reference Guides, Curation SOP

x = 10 = New sequencing_assay_type field y = 0 = New picklist IDs and labels z = 0 = Edit to excel template to fix format issue

New Term SOP N/A unless indicated.

Template To-Dos

cbarcl01 commented 3 months ago

Format issue for food_packaging showing incorrect icklist in excel template #73

cbarcl01 commented 3 months ago

NTR shrimp #74

Field Change
animal_source_of_food Shrimp [FOODON:03411237]
cbarcl01 commented 3 months ago

NTR scallop #75

Field Change
animal_source_of_food Scallop (Pectinidae) [NCBITaxon:6566]
food_product Scallop [FOODON:03411489]
cbarcl01 commented 3 months ago

NTR Weep fluid collection (pouring) #77

Field Change
collection method Weep fluid collection (pouring) [GENEPIO:0101003]
cbarcl01 commented 3 months ago

Christine Liu NTR #76

Field Change
host (common name) Sablefish [NCBITaxon:229290], Coho Salmon [NCBITaxon:8019]
host (scientific name) Anoplopoma fimbria [NCBITaxon:229290], Oncorhynchus kisutch [NCBITaxon:8019]
organism Shewanella oncorhynchi [NCBITaxon:2726434], Psychrobacter nivimaris [NCBITaxon:281738], Photobacterium indicum[NCBITaxon:81447]
sequenced_by McGill University [GENEPIO:0101083]
cbarcl01 commented 3 months ago
Field Change
environmental_site Barn [ENVO:03501257]
cbarcl01 commented 3 months ago
Field Change
environmental_material Broom [ENVO:03501431]
environmental_material Cleaning equipment [ENVO:03501430] - ID update
environmental_material Barley straw [FOODON:00004559] - ID update
cbarcl01 commented 3 months ago
Field Change
anatomical_part Foot [UBERON:0002387]
cbarcl01 commented 3 months ago
Field Change
food_product Chicken thigh [FOODON:02020219], Chicken thigh (skinless, with bone) [FOODON:02020227], Barley seed [FOODON:00003394], Canola seed [FOODON:00004560]
cbarcl01 commented 3 months ago
Field Change
sequencing_assay_type amplicon sequencing assay [OBI:0002767], 16S ribosomal gene sequencing assay [OBI:0002763], whole genome sequencing assay [OBI:0002117], whole metagenome sequencing assay [OBI:0002623], whole virome sequencing assay [OBI:0002768]