Pathogen Genomics Package 5.5.0

Schema updates to Mpox, Mpox International GRDI and CanCOGeN templates. Minor bug fixes in dates for GRDI and syntax errors for GRDI, AMBR, CanCOGeN and Influenza.

Issues resolved as part of this release PGP #19 (syntax errors), #17 (AGRO duplicate ID) as well as issues #3, #2 and #1 from the CanCOGeN specification.

Template Name	Template Versionx.y.z	x changes (field)	y changes (values/IDs)	z changes (defs/formats/examples)
CanCOGeN (SC2)	2.5.2		Add picklist term to 'sample collected by' and 'sequence submitted by'	Fix syntax error
DEXA (One Health)	1.2.0		Added STypeMenu, changed export field targets
GISAID (SC2)	1.0.2
GRDI	13.4.4		Update ID for 'pig manure'	Fix date formatting issue
Mpox	7.5.5	Add 'depth of coverage', 'depth of coverage threshold' and 'breadth of coverage' back into schema
MpoxInternational	8.5.5	Add 'breadth of coverage', update ID for 'assay target name' to GENEPIO:0102052
PHA4GE (SC2)	1.0.2
AMBR	2.3.2			Fix syntax error
PathogenAgnostic	1.0.1
Influenza	1.0.2			Fix syntax error
WWSC2	4.1.1	New fields for 'target taxonomic name'(1,2,3 etc).
WWAMR	4.1.1	New fields for 'target taxonomic name'(1,2,3 etc).
WWPathogenAgnostic (formerly WWSinglePathogen)	4.1.1	New fields for 'target taxonomic name'(1,2,3 etc).
HPAI	1.0.0
HPAIFood	1.0.0
HPAIWW	1.0.0
HPAIEnviro	1.0.0
HPAIHost	1.0.0

Pathogen Genomics Package 5.4.2

Bug fix to two CanCOGeN menus.

Template Name	Template Versionx.y.z	x changes (field)	y changes (values/IDs)	z changes (defs/formats/examples)
CanCOGeN (SC2)	2.4.0		Bug fix to "border testing test day type menu" and "host disease menu"
DEXA (One Health)	1.1.0
GISAID (SC2)	1.0.2
GRDI	13.3.3
Mpox	6.5.5
MpoxInternational	7.5.5
PHA4GE (SC2)	1.0.2
AMBR	2.3.1
PathogenAgnostic	1.0.1
Influenza	1.0.1
WWSC2	3.1.1
WWAMR	3.1.1
WWPathogenAgnostic (formerly WWSinglePathogen)	3.1.1
HPAI	1.0.0
HPAIFood	1.0.0
HPAIWW	1.0.0
HPAIEnviro	1.0.0
HPAIHost	1.0.0

Pathogen Genomics Package 5.4.1

Introduction of HPAI suite of specifications.
LinkML slot/field coding name addition to most templates, with revision of corresponding export scripts and some validation scripts. Scripts still present "title" field containing plain language oriented names of fields.
Also some addition of date entry field validation to check <= {today}.

Template Name	Template Versionx.y.z	x changes (field)	y changes (values/IDs)	z changes (defs/formats/examples)
CanCOGeN (SC2)	2.4.0		French translation update	Underscored rename of {sample collection date}
DEXA (One Health)	1.1.0		Adding LinkML name field to slots and enums
GISAID (SC2)	1.0.2			Coding name normalization
GRDI	13.3.3	New time/date fields for longitudinal sample collection	New picklist values and IDs environmental_site and presampling_Activity	Minor bug fix in multiselect excel template
Mpox	6.5.5	New fields: assay target name, genome sequence file name, genome sequence file path, experimental specimen role type, INSDC sequence read accession (replaces SRA accession), INSDC assembly accession (replaces GenBank accession).	new values for experimental specimen role type and gene symbol	Formatting (sequencing info);Underscored rename of {sample collection date}
MpoxInternational	7.5.5	New fields: assay target name, genome sequence file name, genome sequence file path, experimental specimen role type, INSDC sequence read accession (replaces SRA accession), INSDC assembly accession (replaces GenBank accession).	new values for experimental specimen role type and gene symbol	Formatting (sequencing info);Underscored rename of {sample collection date}
PHA4GE (SC2)	1.0.2			Coding name normalization
AMBR	2.3.1			Underscored rename of {sample collection date}
PathogenAgnostic	1.0.1			Underscored rename of {sample collection date}
Influenza	1.0.1			Underscored rename of {sample collection date}
WWSC2	3.1.1	New fields: INSDC sequence read accession, INSDC assembly accession, genome sequence file name, genome sequence file path, proximal environmental site	new picklist IDs: environmental site, presampling activity	updated picklist defintions;Underscored rename of {sample collection date}
WWAMR	3.1.1	New fields: INSDC sequence read accession, INSDC assembly accession, genome sequence file name, genome sequence file path, proximal environmental site	new picklist IDs/defs: environmental site, presampling activity	updated picklist defintions;Underscored rename of {sample collection date}
WWPathogenAgnostic (formerly WWSinglePathogen)	3.1.1	New fields: INSDC sequence read accession, INSDC assembly accession, genome sequence file name, genome sequence file path, proximal environmental site	new picklist IDs/defs: environmental site, presampling activity	updated picklist defintions;Underscored rename of {sample collection date}
HPAI	1.0.0	Master specification (contains all fields/terms)		Underscored rename of {sample collection date}
HPAIFood	1.0.0	Food-specific template for HPAI surveillance		Underscored rename of {sample collection date}
HPAIWW	1.0.0	Wastewater-specific template for HPAI surveillance		Underscored rename of {sample collection date}
HPAIEnviro	1.0.0	Environment-specific template for HPAI surveillance (wastewater template contains more specific fields)		Underscored rename of {sample collection date}
HPAIHost	1.0.0	Host-specific template for HPAI surveillance		Underscored rename of {sample collection date}

Pathogen Genomics Package 5.3.0

A GRDI update to 12.2.2

Template Name	Template Versionx.y.z	x changes (field)	y changes (values/IDs)	z changes (defs/formats/examples)
CanCOGeN (SC2)	2.3.4
DEXA (One Health)	1.0.0
GISAID (SC2)	1.0.0
GRDI	12.2.2	Added new fields label_claim and environmental_material_constituent	New terms for food_product, animal_source_of_food, organism, specimen_processing	Resolved missing FOODON IDs with some minor definition changes.
Mpox	4.3.3
Mpox-international	5.3.3
PHA4GE (SC2)	1.0.1
AMBR	2.3.0
Pathogen_Agnostic	1.0.0
Influenza	1.0.0
WWSC2	2.0.0
WWAMR	2.0.0
WWPathogenAgnostic (formerly WWSinglePathogen)	2.0.0

Pathogen Genomics Package 5.2.0

New updates to CanCoGen, Wastewater, and GRDI templates. Note that for updated templates, a slight change to the LinkML schema occurs in the exact_mappings enumeration value, which is now URL escaped, to allow for spaces and other URL incompatible elements.

Template Name	Template Versionx.y.z	x changes (field)	y changes (values/IDs)	z changes (defs/formats/examples)
CanCOGeN (SC2)	2.3.4
DEXA (One Health)	1.0.0
GISAID (SC2)	1.0.0
GRDI	11.1.1	Additional Bioinformatics and QC metrics Taxonomic identification modules, plus new specimen processing fields	New picklist values and IDs; added "isolated_by" menu	Reformat (pull existing fields into new modules)
Mpox	4.3.3
Mpox-international	5.3.3	removed duplicate "host subject ID" field; removed Canadian picklist so only data type is "string"
PHA4GE (SC2)	1.0.1
AMBR	2.3.0
Pathogen_Agnostic	1.0.0
Influenza	1.0.0
WWSC2	2.0.0	corrected "instantaneous flow rate measurement unit menu"	changes "Waste water" to "Wastewater" in enums; changed "cycle threshold (Ct) / quantification cycle (Cq)" to "cycle threshold (Ct)"
WWAMR	2.0.0	corrected "instantaneous flow rate measurement unit menu"; added organism, breadth of coverage value, depth of coverage value, depth of coverage threshold, number of base pairs sequenced, number of total reads, number of unique reads, minimum post-trimming read length	changes "Waste water" to "Wastewater" in enums; changed "cycle threshold (Ct) / quantification cycle (Cq)" to "cycle threshold (Ct)"
WWPathogenAgnostic (formerly WWSinglePathogen)	2.0.0	corrected "instantaneous flow rate measurement unit menu"	changes "Waste water" to "Wastewater" in enums; changed "cycle threshold (Ct) / quantification cycle (Cq)" to "cycle threshold (Ct)"

Pathogen Genomics Package 5.1.0

Update GRDI to 10.0.0 and Wastewater templates to 2.0.0

Template Name	Template Versionx.y.z	x changes (field)	y changes (values/IDs)	z changes (defs/formats/examples)
CanCOGeN (SC2)	2.3.4
DEXA (One Health)	1.0.0
GISAID (SC2)	1.0.0
GRDI	10.0.0	new 'sequencing_assay_type' field	new picklist IDs under food_product. anatomical_part, environmental_site, environmental_material, host (common name), host (scientific name), organism, collection_method
Mpox	4.3.3
Mpox-international	4.3.3
PHA4GE (SC2)	1.0.1
AMBR	2.3.0
Pathogen_Agnostic	1.0.0
Influenza	1.0.0
WWSC2	2.0.0	lineage/clade information section added	environmental site tems added; "sample collection time" removed and "sample collection start time" and "sample collection end time" fields added instead; "sample collection end date" added; 16S sequencing assay type added
WWAMR	2.0.0	AMR information section added	environmental site tems added; 16S sequencing assay type added
WWSinglePathogen	2.0.0	metagenomics fields added; strain and isolate information section added	environmental site tems added; 16S sequencing assay type added

Pathogen Genomics Package 5.0.1

A fix to PGP5.0.0 involving restore of accidental missing CanCOGeN enumeration lists.

DataHarmonizer version 1.6.5 and CanCoGeN 2.3.4 and GRDI v9.0.0 and Wastewater 1.0.0 templates

Template Name	Template Versionx.y.z	x changes (field)	y changes (values/IDs)	z changes (defs/formats/examples)
CanCOGeN (SC2)	2.3.4		new picklist IDs
DEXA (One Health)	1.0.0
GISAID (SC2)	1.0.0
GRDI	9.0.0	new unit fields	added IDs under food_products and food_product_properties	minor edits (typos etc) to defs and guidance
Mpox	4.3.3
Mpox-international	4.3.3
PHA4GE (SC2)	1.0.1
AMBR	2.3.0
Pathogen_Agnostic	1.0.0
Influenza	1.0.0
WWSC2	1.0.0
WWAMR	1.0.0
WWSinglePathogen	1.0.0

Pathogen Genomics Package 5.0.0

DataHarmonizer version 1.6.5 and CanCoGeN 2.3.4 and GRDI v9.0.0 and Wastewater 1.0.0 templates

Template Name	Template Versionx.y.z	x changes (field)	y changes (values/IDs)	z changes (defs/formats/examples)
CanCOGeN (SC2)	2.3.4		new picklist IDs
DEXA (One Health)	1.0.0
GISAID (SC2)	1.0.0
GRDI	9.0.0	new unit fields	added IDs under food_products and food_product_properties	minor edits (typos etc) to defs and guidance
Mpox	4.3.3
Mpox-international	4.3.3
PHA4GE (SC2)	1.0.1
AMBR	2.3.0
Pathogen_Agnostic	1.0.0
Influenza	1.0.0
WWSC2	1.0.0
WWAMR	1.0.0
WWSinglePathogen	1.0.0

Pathogen Genomics Package 4.1.2

DataHarmonizer v1.6.4 which fixes a minor menu bug, along with:

Template Name	Template Versionx.y.z	x changes (field)	y changes (values/IDs)	z changes (defs/formats/examples)
CanCOGeN (SC2)	2.2.3
DEXA (One Health)	1.0.0
GISAID (SC2)	1.0.0
GRDI	8.9.8		New picklist values and IDs	New definitions for new picklist values
Mpox	4.3.3
Mpox-international	4.3.3
PHA4GE (SC2)	1.0.1
AMBR	2.3.0
Pathogen_Agnostic	1.0.0
Influenza	1.0.0

Pathogen Genomics Package 4.1.1

Includes DataHarmonizer 1.6.2 which fixes a bug in multiselect picklists where a < p > tag was included around selections.