PHES-ODM - Version 2.2.3

A patch release to address lingering bugs and issues related to the updates in the version 2.2.1 and 2.2.2 releases. This release also adds:

1. Support for the new "Supersites Template" - an updated version of the airport template used by the EU, this template is now updated and designed for use at EU "supersites" or major transit hubs (ie. harbours, ports, airports, train and bus stations, etc.). This template focuses largely on the four major priority pathogens: SARS-CoV-2, Influenza, Mpox, and Dengue.
2. Two additional data license categories (ccbyncsa40 - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, and ccbync40 - Creative Commons NonCommercial 4.0 International License) at the request of users.
3. Additional values to better align and facilitate mapping between the ODM and PHA4GE data formats (more on this in the subsequent version).

This version also corresponds to the new SQL structure, which will hopefully be shared soon.

- Python
Published by mathew-thomson over 1 year ago

PHES-ODM - Version 2.2.2

A patch release to address issue #269 and #270 - namely:

1. missingnessSets in the ERD is missingnessSet in the CSV – these should be aligned one way or another. For this issue, the ERD was incorrect. The parts list header is indeed missingnessSet. However, that should be the header, and missingnessSets should be the part type. This follows the same structure for other headers within the parts list that can also be part types, like aggregationSet (header) vs aggregationSets (part type), etc.
2. There are additional duplicate keys in one of the csv versions of the parts table (ODMparts.csv, not the ODMparts_2.2.1.csv): f456l v1104l jn17V jn1V d339h l455s flirtSLipGrp

And there are new duplicate keys in the wideNames table: sisiteID sisampleShed sipopServ smsampleID smcollType smpooled mraDateStart mraDateEnd mrfraction smsaMaterial ptrefLink mrmeasure watsahFrhMehUnhAgNRvalue mrunit mraggregation watsiNAcodmgLmeNRvalue watsiNAbod5tmgLmeNRvalue watsiNAconduSCmmeNRvalue watsiNAphunitlessmeNRvalue watsiNAtnmgLmeNRvalue watsaNAlodSewagcsinNRvalue watsaNAloqgcsinNRvalue mrreportDate coemail mr_notes

These came about from the new HPAIV H5N1 template, which has many overlapping fields with the airports template. Technically we should keep single keys from airplanes, so I've done that here.

- Python
Published by mathew-thomson over 1 year ago

PHES-ODM - Version 2.2.1

This is a patch release to correct an issue in the Zones and Parts tables of the version 2.2.0 release. See issue #267 for additional details.

- Python
Published by mathew-thomson over 1 year ago

PHES-ODM - Version 2.2.0

This is the official release for v2.2.0 of the Public Health and Environmental Surveillance Open Data Model (PHES-ODM). It includes additional provisions for AMR surveillance, as well as improved reporting for a larger diversity of pathogens, and organism reporting. We added additional mutations and variants (including the current variants of concern - FLiRT and SLip) of the SARS-CoV-2 virus, as well for emerging bird flu (H5N1) markers. Also added additional provisions to improving mapping and interoperability between the USCDC-NWSS data format and the ODM. Additional reporting metrics for protocols and standard curves were also added. Some clean up of the languages table was also done to reduce duplication and remove SQL errors. There are new parts to debug certain issues and respond to demands among the user-base. The largest change is the addition of a new look-up table: wideNames. This helps to standardize and record the wide name formatting to ensure we remain consistent in our wide-to-long and long-to-wide transformations. Additional protocol information was added, and duplication in fields in the languages table were removed.

- Python
Published by mathew-thomson over 1 year ago

PHES-ODM - Version 2.1.0

This is the official release for v2.1.0 of the Public Health and Environmental Surveillance Open Data Model (PHES-ODM). It includes the addition a few new parts as a way to debug issues, or respond to new demands among the user-base. The largest change is the addition of two new look-up tables: countries and zones. These help to standardize location information to the ISO-2 and ISO-3 and to reduce ambiguity and free-text errors when populating these fields, all while improving interoperability of location metadata. Documentation has also been updated to add more information on protocols. Protocols will be the main focus of the next release.

- Python
Published by mathew-thomson over 2 years ago

PHES-ODM - Version 2.0.0

This is the official release for v2.0.0 of the Public Health and Environmental Surveillance Open Data Model (PHES-ODM). It includes the addition of provisions for more detailed reporting of methods, measures for mutations and variants, measures for additional pathogens besides SARS-CoV-2, more detailed metadata, and improved reporting of quality measures. As this version includes a number of massive changes, additional updates with updated version numbers are likely to follow hot on the heels of this release.

- Python
Published by mathew-thomson almost 3 years ago

PHES-ODM - Initial stable release

Version 1.0.0!. The ODM development team commits to maintaining a stable version of the ODM. Future breaking changes will be made with care and after public discussion.

See changelog.md for addtions and bug fixes from previous versions.

- Python
Published by DougManuel over 4 years ago