feat: structure-verified annotation overhaul (metabolite + reaction cross-references, pH-7.3 structures)#1058

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edkerk merged 16 commits into

annotation-overhaul

Jul 14, 2026

Commits on Jul 14, 2026

chore: annotation overhaul plan and structure/formula/charge audit
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feat: store SMILES/InChI in metabolites.tsv with a consistency QC test
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fix: regenerate protonation-mismatched structures to the pH-7.3 microspecies
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feat: structure-based cross-reference verifier (MetaNetX hub)
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fix: update 2792 deprecated MetaNetX metabolite IDs to current
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feat: add 7673 structure-verified metabolite cross-references
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feat: add ModelSEED cross-references (metSeedID column) (#968)
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chore: tooling to classify model formula/charge errors (deferred)
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fix: correct 12 invalid metabolite charges, improving balance 277->271
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fix: update 1217 deprecated MetaNetX reaction IDs to current (#967)
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feat: add structure-verified reaction cross-references (#967)
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fix: correct 61 metabolite cross-references to the right compound
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fix: harmonize cross-references across compartments, drop malformed MetaNetX ids
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chore: reconcile with #1057 after rebasing on develop
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refactor: replace one-off overhaul scripts with a reusable annotation verifier
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chore: update model QC results [skip ci]

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