Releases: cidgoh/pathogen-genomics-package
Releases · cidgoh/pathogen-genomics-package
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.
Pathogen Genomics Package 4.1.0
Includes DataHarmonizer 1.6.1 with improved validation speed.
| Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) |
|---|---|---|---|
| CanCOGeN (SC2) | 2.2.3 | added "Newfoundland and Labrador - Newfoundland and Labrador Health Services" as new "sample collected by" and "sequence submitted by" value. "Newfoundland and Labrador - Newfoundland and Labrador Health Services" is the new name replacing "Newfoundland and Labrador - Newfoundland and Labrador Eastern Health" | |
| DEXA (One Health) | 1.0.0 | ||
| GISAID (SC2) | 1.0.0 | ||
| GRDI | 8.8.7 | Change to field label | New IDs, removal of picklist values |
| Mpox | 4.3.3 | updated schema names to Mpox from Monkeypox | |
| Mpox-international | 4.3.3 | updated schema names to Mpox from Monkeypox | |
| PHA4GE (SC2) | 1.0.1 | ||
| AMBR | 2.3.0 | ||
| Pathogen_Agnostic | 1.0.0 | ||
| Influenza | 1.0.0 |
Pathogen Genomics Package 4.0.0
This includes a new Influenza template.
| Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) |
|---|---|---|---|---|
| CanCOGeN (SC2) | 2.1.3 | |||
| DEXA (One Health) | 1.0.0 | |||
| GISAID (SC2) | 1.0.0 | |||
| GRDI | 7.7.5 | |||
| Monkeypox | 3.3.3 | |||
| Monkeypox-international | 3.3.3 | |||
| PHA4GE (SC2) | 1.0.1 | |||
| AMBR | 2.3.0 | |||
| Pathogen_Agnostic | 1.0.0 | |||
| Influenza | 1.0.0 | New template |
PGP3.3.0 + DHv1.5.0
This release adds DataHarmonizer 1.5 to PGP 3.3.0, enabling development and testing of stand-alone templates.
Pathogen Genomics Package 3.3.0
Includes DataHarmonizer v1.4.10; and Updated GRDI v7.7.5
| Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) |
|---|---|---|---|---|
| CanCOGeN (SC2) | 2.1.3 | |||
| DEXA (One Health) | 1.0.0 | |||
| GISAID (SC2) | 1.0.0 | |||
| GRDI | 7.7.5 | New values and IDs | New definitions, etc. | |
| Monkeypox | 3.3.3 | |||
| Monkeypox-international | 3.3.3 | |||
| PHA4GE (SC2) | 1.0.1 | |||
| AMBR | 2.3.0 | |||
| Pathogen_Agnostic | 1.0.0 |