3.1.1 - release note tracking

pha4ge / Wastewater_Contextual_Data_Specification

A data specification for harmonizing Wastewater pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via metadata template(s), supported by field and reference guides as well as different curation and new term request SOPs.

MIT License

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3.1.1 - release note tracking #7

Closed cbarcl01 closed 3 weeks ago

cbarcl01 commented 2 months ago

Template Fixes:

Specification Changes:

Field	Change
`INSDC sequence read accession`	new field
`INSDC assembly accession`	new field
`genome sequence file name`	new field
`genome sequence file path`	new field
`proximal environmental site`	new field
`environmental site`	new picklist IDs and defs
`presampling activity`	new picklist IDs and defs
`sequenced by laboratory name`	new field
`sample collected by laboratory name`	new field
`sample collector contact name`	new field

Version Tracking:

Excel Template, Reference Guides, Curation SOP

x = 3 = new fields y = 1 = new picklist IDs z = 1 = new defs and changes to DH template

New Term SOP N/A unless indicated.

Template To-Dos

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

cbarcl01 commented 2 months ago

New fields

Field	ID	Change
INSDC sequence read accession	GENEPIO:0101203	replaces previous fields
INSDC assembly accession	GENEPIO:0101204	replaces previous fields
genome sequence file name	GENEPIO:0101715	new field
genome sequence file path	GENEPIO:0101716	new field

cbarcl01 commented 2 months ago

New fields

Field	ID	change
proximal environmental site	GENEPIO:0101205	new field

cbarcl01 commented 2 months ago

New picklist terms

`environmental site`	ID
Influent pump station	ENVO:03501465
Grit chamber	ENVO:03501467
Communitor	ENVO:03501472
Primary clarifer	ENVO:03501468
Aeration tank	ENVO:03501469
Secondary clarifer	ENVO:03501471
Sludge dryer	ENVO:03501473
Commercial building	ENVO:01001222
Office	ENVO:01001221
Restaurant	ENVO:01000934
Shopping mall	ENVO:03501207

cbarcl01 commented 1 month ago

Add mapping document.

Edit: Deferred to next release.

cbarcl01 commented 1 month ago

New picklist IDs

`presampling activity`	ID
Wastewater sludge removal	GENEPIO:0101201
Wastewater sludge dewatering	GENEPIO:0101202
Wastewater sludge drying	GENEPIO:0101718
Wastewater aerobic digestion	GENEPIO:0101199
Wastewater anaerobic digestion	GENEPIO:0101200
Wastewater screening process	GENEPIO:0101198
wastewater comminution process	GENEPIO:0101719

cbarcl01 commented 1 month ago

Additional fields added to DataHarmonizer template only to allow for diagnostic testing of multiple targets (this will eventually be replaced by one to many functionality in the DH).

gene symbol 2
diagnostic target presence 2
diagnostic measurement value 2
diagnostic measurement unit 2
diagnostic measurement method 2
gene symbol 3
diagnostic target presence 3
diagnostic measurement value 3
diagnostic measurement unit 3
diagnostic measurement method 3

cbarcl01 commented 4 weeks ago

New fields

field	ID
sequenced by laboratory name	GENEPIO:0100470
sample collected by laboratory name	GENEPIO:0100428
sample collector contact name	GENEPIO:0100432

cbarcl01 commented 3 weeks ago

Updated to 3-1-1 to harmonise with DH release version.