PHA4GE-Wastewater specification package 4.4.4

Contents:

Field and Term Reference Guides 4.4.4
Curation Standard Operating Procedure (SOP) 4.4
DataHarmonizer Template Standard Operating Procedure (SOP) 4.4
New Term Request Standard Operating Procedure (SOP) 1.2

Updates:

New exports have been added to the DH implementation of the specification. In addition the following fields have undergone changes.

Schema	Field	Change
All templates	diagnostic target presence 2	Empty slot_uri updated to GENEPIO:0100962.
WastewaterPathogenAgnostic	isolate id	Corrected ID from GENEPIO:0100456 to GENEPIO:0001644.
All templates	fecal coliform count unit	Picklist IDs added to existing terms; colony forming units per 100 milliliter (CFU/100 mL) [GENEPIO:0102203], colony forming units per grams total solids (CFU/gTS) [GENEPIO:0102204], most probable number per milliliter (MPN/mL) [GENEPIO:0102205], most probable number per 100 milliliter (MPN/100 mL) [GENEPIO:0102206]
All templates	sequenced by contact email	Corrected ID from GENEPIO:0100471 to GENEPIO:0100422.
All templates	diagnostic measurement unit	Picklist IDs added to existing terms; cycle threshold (Ct) [UO:0010077], colony forming units per 100 milliliter (CFU/100 mL)[GENEPIO:0102203], colony forming units per grams total solids (CFU/gTS [GENEPIO:0102204], most probable number per milliliter (MPN/mL) [GENEPIO:0102205], most probable number per 100 milliliter (MPN/100 mL) [GENEPIO:0102206]
All templates	diagnostic measurement method	Picklist IDs added to existing terms; Digital real time polymerase chain reaction (dPCR) [GENEPIO:0102209], Cell culture [OBI:0001876]
All templates	sequencing instrument	New picklist term added SOLiD 5500xl-W Genetic Analyzer [GENEPIO:0100970]; removed MGISEQ-2000RS [GENEPIO:0100971] from picklist as this is a duplicate (model rebranded to "DNBSEQ-G400")
All templates	experimental protocol url	Updated definition and guidance

Updated curation guidance for version compatibility.

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Details can be found under release notes issue #17

PHA4GE-Wastewater specification package 4.2.2

Contents:

Field and Term Reference Guides 4.2.2
Curation Standard Operating Procedure (SOP) 4.2
DataHarmonizer Template Standard Operating Procedure (SOP) 4.2
New Term Request Standard Operating Procedure (SOP) 1.0

Updates:

Field	Change
dissolved oxygen measurement value	Updated ID
oxygen reduction potential (ORP) measurement value	Updated ID
environmental site	New picklist IDs
experimental protocol url	New field
amplicon pcr primer scheme URL	New field
AMR analysis date	GENEPIO:0102069
lineage/clade analysis date	GENEPIO:0102070
target taxonomic name 1	New field
target taxonomic name 2	New field
target taxonomic name 3	New field
assay target name 1	Updated ID
assay target details 1	Updated ID
assay target name 2	Updated ID
assay target details 2	Updated ID
gene symbol 2	Updated ID
assay target name 3	Updated ID
assay target details 3	Updated ID
gene symbol 3	Updated ID

Updated curation guidance for version compatibility.

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Details can be found under release notes issue #12

PHA4GE-Wastewater specification package 3.1.1

Contents:

DataHarmonizer template 3.1.1
Field and Term Reference Guides 3.1.1
Curation Standard Operating Procedure (SOP) 3.1.1
DataHarmonizer GRDI Template Standard Operating Procedure (SOP) 3.1.1
New Term Request Standard Operating Procedure (SOP) 1.0

Updates:

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

Updated curation guidance for version compatibility.

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Details can be found under release notes issue #7

PHA4GE-Wastewater specification package 1.0.0

Release v1.0 - Contextual Data Specification for Wastewater Pathogen Genomics

Initial release of the Wastewater Contextual Data Specification, developed as part of the Public Health Alliance for Genomic Epidemiology (PHA4GE), in collaboration with the CIDGOH and supported by the Gates Foundation. This specification aims to harmonize wastewater pathogen genomics contextual data across a variety of use cases, ensuring consistency and interoperability of data.

Key features

• Standardized fields - ontology based fields, which have been grouped into concise modules aid interoperability.
• Defined picklist terms - ontology based terms make up the picklists for a number of terms, to facilitate consistency in data.
• Comprehensive reference guides - detailed field and reference guides to assist users in accurately classifying and entering data.
• SOPs - standard operating procedures for curation and requests for new terms, ensuring the specification remains up-to-date and inclusive.

Contents

• Wastewater_Master-Reference-Guide-Fields_v1-0-0.pdf
• Wastewater_Master-Reference-Guide-Terms_v1-0-0.pdf
• Wastewater_Master-Reference-Guide_v1-0-0.xlsx
• Wastewater_Contextual-Data-Curation-SOP_1.0.pdf
• Wastewater_Data-Specification-Metadata-NTR-SOP_1.0.pdf
• Wastewater_DataHarmonizer-Curation-SOP_1-0.pdf
• DataHarmonizer Templates - WWAMR-enums.tsv
• DataHarmonizer Templates - WWAMR-slots.tsv
• DataHarmonizer Templates - WWSC2-enums.tsv
• DataHarmonizer Templates - WWSC2-slots.tsv
• DataHarmonizer Templates - WWSinglePathogen-enums.tsv
• DataHarmonizer Templates - WWSinglePathogen-slots.tsv