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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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9.0.0 - release note tracking #65

Closed cbarcl01 closed 8 months ago

cbarcl01 commented 8 months ago

Template Fixes:

Specification Changes:

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

Version Tracking:

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.

Template To-Dos

cbarcl01 commented 8 months ago

Request from Cathy - see issue #64

Added terms

food_product IDs
coconut meat FOODON:00003856
food_product_properties IDs
Food (chunks) FOODON:00004555
Food (diced) FOODON:00004549
Food (grated) FOODON:00004552
Food (pulped) FOODON:00004554
Food (sliced) FOODON:00002455
Food (shredded) FOODON:00004553
cbarcl01 commented 8 months ago

68 NFR available_data_types_details

cbarcl01 commented 8 months ago

New picklist term to add for field available_data_types GENEPIO:0101024 Metagenomic sequencing

cbarcl01 commented 8 months ago

Addition of units fields for depth and temperature values to be consistent with other specs. Additional fields are:

PIcklists for water_depth_units are and sediment_depth_units are the same:

depth_units IDs
centimeter (cm) UO:0000015
meter (m) UO:0000008
kilometer (km) UO:0010066
inch (in) UO:0010011
foot (ft) UO:0010013

Picklists for air_temperature_units and water_temperature_units are the same:

temperature_units IDs
degree Fahrenheit (F) UO:0000195
degree Celsius (C) UO:0000027
cbarcl01 commented 8 months ago

Add term udder under anatomical part

cbarcl01 commented 8 months ago

Actioned release v9.0.0