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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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13.3.3 - release note tracking #94

Closed cbarcl01 closed 3 weeks ago

cbarcl01 commented 1 month ago

Template Fixes:

Specification Changes:

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

Version Tracking:

Excel Template, Reference Guides, Curation SOP

x = # = y = # = <value/ID changes> z = # = <def/format/example changes>

New Term SOP N/A unless indicated.

Template To-Dos

cbarcl01 commented 1 month ago

95

The following picklist terms have been added to 'presampling activity'

Term Ontology ID
Wastewater treatment process ENVO:06105300
Wastewater filtration GENEPIO:0100881
Wastewater grit removal GENEPIO:0100882
Wastewater microbial treatment GENEPIO:0100883
Wastewater primary sedimentation GENEPIO:0100884
Wastewater secondary sedimentation GENEPIO:0100885
cbarcl01 commented 1 month ago

93 and #92

The following terms have been added to 'environmental_site'

Term Ontology ID
Ditch ENVO:00000037
Drainage ditch ENVO:00000140
Irrigation ditch ENVO:00000139
Plumbing drain ENVO:01000924
Wastewater treatment plant ENVO:00002272

as required for test IRIDA dataset for RZ

cbarcl01 commented 4 weeks ago

91

The following field has been added

Field Ontology ID
specimen processing details GENEPIO:0100311
cbarcl01 commented 4 weeks ago

Resolve issues with multiselect functionality in excel template see details

cbarcl01 commented 4 weeks ago

Additional precipitation fields as requested by working group

Field Ontology ID
sampling_weather_conditions GENEPIO:0100779
presampling_weather_conditions GENEPIO:0100780
precipitation_measurement_value GENEPIO:0100911
precipitation_measurement_unit GENEPIO:0100912
precipitation_measurement_method GENEPIO:0100913
cbarcl01 commented 4 weeks ago
Field Ontology ID
sample collection end date GENEPIO:0101071
sample processing date GENEPIO:0100763
sample collection start time GENEPIO:0101072
sample collection end time GENEPIO:0101073
sample collection time of day GENEPIO:0100765
sample collection time duration value GENEPIO:0100766
sample collection time duration unit GENEPIO:0100767
cbarcl01 commented 3 weeks ago

PR #96