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Standardize CLI output, logging, and progress indication across all scripts

Status: Open.

#319 In berkeleybop/metpo;

· turbomam opened on Nov 25, 2025

Sync ChromaDB with Repository Ontology Changes

Status: Open.

#313 In berkeleybop/metpo;

· turbomam opened on Nov 18, 2025

Review Python codebase for usefulness and best practices

Status: Open.

#309 In berkeleybop/metpo;

· turbomam opened on Nov 18, 2025

Do not use obsolete ontology classes as definition sources

Status: Open.

#307 In berkeleybop/metpo;

· turbomam opened on Nov 17, 2025

Reconcile facultatively aerobic vs facultatively anaerobic terms

Status: Open.

#306 In berkeleybop/metpo;

· turbomam opened on Nov 17, 2025

are BSL level definitions constant across different authorities? should we explicitly align with any particular authority?

Status: Open.

#304 In berkeleybop/metpo;

· turbomam opened on Nov 14, 2025

Add CLI command reference section to main README

Status: Open.

#299 In berkeleybop/metpo;

· turbomam opened on Nov 11, 2025

Register count_extraction_results.py as CLI command or document as internal-only

Status: Open.

#298 In berkeleybop/metpo;

· turbomam opened on Nov 11, 2025

Add unit tests for literature mining CLI commands

Status: Open.

#297 In berkeleybop/metpo;

· turbomam opened on Nov 11, 2025

do something like pagerank on ontology classes to see which are most imported into other ontologies, and give them more weigh as definition sources

Status: Open.

#296 In berkeleybop/metpo;

· turbomam opened on Nov 11, 2025

write python tests

Status: Open.

#295 In berkeleybop/metpo;

· turbomam opened on Nov 11, 2025

split synonym column into data path and synonym values columns, or similar as needed

Status: Open.

#292 In berkeleybop/metpo;

· realmarcin opened on Nov 10, 2025