Version 3.0.0

Version 3.0.0 of the PHES-ODM represents a major structural expansion compared to version 2.2.3, increasing the model to 19 report tables and 7 look-up tables. The primary differences involve the introduction of new tables for public health actions and data processing, significant refinements to existing attributes, and a massive expansion of genomic and environmental descriptors.

1. New Table Structures

Version 3.0.0 introduces several dedicated tables that were not present in version 2.2.3:

• Public Health Actions (phActions): This table was created to record specific interventions and designations, such as travel bans, mask mandates, and stay-at-home orders. Consequently, the "outbreak" marker was moved from a measure attribute to this dedicated table, and the original outbreak class was depreciated.
• Calculations (calculations): This new table tracks the nature of data treatments, recording the specific equations and standards (e.g., normalization to PMMoV or wastewater flow) applied to raw data.
• Accessions (accessions): Introduced to track external data IDs, specifically for linking genetic sequences to large external repositories like the European Nucleotide Archive (ENA) or GenBank.
• Polygon Relationships (polygonRelationships): This table allows users to define logical connections between geographic areas, such as whether two polygons are neighboring or overlapping.

2. Attribute Refinements and Relational Changes

Version 3.0.0 modified several existing parts to improve clarity and reduce technical conflicts in databases:

• Part ID Changes: The attribute derived was renamed to derivedSamp to better specify its relationship to samples. Similarly, the time part type was renamed to timeClass to avoid collisions with standard "time" data type names.
• Foreign Key Removal: To streamline the model, datasetID was removed as a foreign key from the organizations and instruments tables.

3. Expanded Dictionary Content

Version 3.0.0 significantly increased the number of "building block" parts in the dictionary:

• Bioinformatics Library: v3.0.0 added dozens of parts for specific sequencing and quality control software, such as DADA2, Minimap2, Kraken2, and AdapterRemoval, allowing for more detailed provenance of genomic data.
• Site Aggregation Metadata: New attributes like siteLevel were added to define the scale of a sampling location, allowing users to categorize sites by whether they represent a single building, a neighborhood, or an entire municipality.
• New Environmental Measures: Support was added for new physical and chemical properties, including dissolved oxygen (dissOxy) and oxidation-reduction potential (orp), alongside new units like the practical salinity unit (psu).
• Population Data Intervals: To handle sensitive or approximate data, version 3.0.0 introduced categorical ranges for population counts, such as <10 people or 100,000 - 1,000,000 people.

For additional information on additions and how to use them, please read up on the documentation website, and stay tuned for additional written and video content.