13.4.4 - release note tracking

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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13.4.4 - release note tracking #98

Open cbarcl01 opened 3 months ago

cbarcl01 commented 3 months ago

Template Fixes:

Specification Changes:

Field	Change
`environmental_material`	New picklist IDs, updated picklist IDs

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

[x] Update picklist value labels/IDs/descriptions
- [x] Excel Template
- [x] DataHarmonizer Template (GRDI-enums)
[x] Update field labels/IDs/descriptions
- [x] Excel Template
- [x] DataHarmonizer Template (GRDI-slots)

cbarcl01 commented 3 months ago

New wastewater treatment terms

environmental_material	ID
Sludge	ENVO:00002044
Primary sludge	ENVO:00002057
Secondary sludge	ENVO:00002058

cbarcl01 commented 2 weeks ago

Term AGRO:00000080 coded twice under different names under field environmental_material.

Pig manure [AGRO:00000080]: should be Pig manure [ENVO:00003860]. Poultry litter [AGRO:00000080] is correct.

See #100

cbarcl01 commented 2 weeks ago

Resolve Time and Date field errors in DH from PGP 5.4.1

cbarcl01 commented 2 weeks ago

assembly_filename label changed to genome_sequence_filename [GENEPIO:0101715] to be consistent with other specs.

cbarcl01 commented 2 weeks ago

NCBI_BioSample Enterics automated export and NCBI_Antibiogram export available in DH PGP.