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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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8.9.9 - release note tracking #59

Closed cbarcl01 closed 5 months ago

cbarcl01 commented 5 months ago

Template Fixes:

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.

Specification Changes:

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

Version Tracking:

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.

Template To-Dos

cbarcl01 commented 5 months ago
specimen_processing Change
Isolated from single source Updated ID - OBI:0002079 A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
cbarcl01 commented 5 months ago
collection_device Change
PONAR grab sampler Updated def - A specimen collection device that is designed to collect sediment samples from the hard bottoms of a body of water i.e. sand, gravel, consolidated marl or clay.
Soil sample probe Updated def - A specimen collection device designed to penetrate soil with a hollow tube to collect soil sample cores.
cbarcl01 commented 5 months ago
collection_method Change
Scooping Updated def - A specimen collection process that is used to dig out an amount of sample using a scoop.
Sediment collection Updated def - A specimen collection process that is used to collect a sediment sample.
Soil coring Updated def - A specimen collection process that is used to collect soil sample cores.
cbarcl01 commented 5 months ago

sample_storage_medium and sample_storage_method definitions had been altered due to formatting error. Corrected these to return to last correct definition.

cbarcl01 commented 5 months ago

Latest release v8.9.9