New Version Release: Version 3.0.1 + Version 2.3.0

New features
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The version 3.0.1 release is finally live!

This includes:

With this release, we are also pushing a one-time jump to the version 2 family of releases to the PHES-ODM: version 2.3.0. The rationale for this other addition, and his break with our stance on not supporting old version families, is that we want to have our tool suite continue to work for version 2 users, which means including some structural fixes (specifically the fix of the column partLabel to correctly be label).

There has also been an update to the project workflow, which can be found here. Before, we had a selectively-shared excel file that served as the staging ground for model development prior to release. Moving forward, to streamline the process, any edits, proposed changes, etc. will be managed through GitHub. Simply make an issue request or new part request, or make the changes yourself in a cloned repo and create a pull request. Larger questions and bugs can still be managed here.

Thank you for your continued support of the project, and please let us know if you have any questions :slight_smile:

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For remaining items and to finish updating the sync with the dictionary update:

Next steps

  1. Review and merge the 3 open PRs (MapGenerator #1, Mapper #26, Validation #271).
  2. Fix the PHA4GE mapping workbook — missing odm>=3.0 selector tag on accession-related rows, in MapGenerator’s mapping_config_files/. Root cause of the accessions leak that Mapper #26 works around.
  3. Run real sample data end-to-end through Mapper’s new/refreshed pipeline modules — only config loading and schema resolution were verified, not an actual transform.
  4. PHES-ODM-Validation-Web needs a real update pass once Validation #271 merges: requirements.txt pins odm_validation to a stale commit (ac12fde) on the pre-transfer Big-Life-Lab URL, and src/odm/odm_defs.py’s Version enum hardcodes only v1.0.0/v1.1.0/v2.0.0 — missing even v2.1.0/v2.2.3, let alone v2.3.0/v3.0.1.
  5. PHES-ODM-sharing — a quick audit found no ODM-version pinning or odm_validation dependency; likely doesn’t need action, but wasn’t deeply audited.
  6. ontology-mapping — has static ODM-term-to-ontology reference/evaluation data (e.g. data/reference/pha4ge-odm-translator.csv) built against an older dictionary. v3.0.1’s new partIDs and four new tables (accessions, polygonRelationships, calculations, phActions) mean this likely needs re-running the mapping evaluation, not a file swap — real rework, as flagged. Past evaluation results showed perfect ontology mapping is hard for most concepts: even concept-level matches often sit in ontologies that shouldn’t be used that way, and many ontology concepts reflect a higher level than the ODM’s (e.g. “watercraft” vs. the ODM’s cruise ship/shipping vessel/boat). Every PHA4GE-mapped item should have a valid ontology reference pairing; most of the rest of the dictionary does not. NCBI organism ontology linking is still possible for many ODM groups, but time-intensive for what’s seen as limited practical value.