fix: ChEBI-based metabolite-name curation, first batch

[edkerk]

Main improvements in this PR:

First batch for #1037 (ChEBI-based curation of metabolite names).

• Regenerated the diff. Compared every metabolite name to its ChEBI id's preferred name and all synonyms, against the current model/metabolites.tsv and the ChEBI flat files, and added it as data/modelCuration/metaboliteNameChEBIdiff.tsv (547 rows, categorized: close-typo / moderate / far-check-id / pool / unresolved-chebi-id / stylistic). Of 1490 metabolites with a ChEBI id and a name, 943 (63%) already match a ChEBI preferred name or synonym.
• Fixed 6 clearly garbled names (and kept the reaction names that embed them in sync): betaine_aldehyde -> betaine aldehyde, Docosanedioicacid -> docosanedioic acid, W-Hydroxydecanoicacid -> 10-hydroxydecanoic acid, W-Hydroxydocosanoicacid -> 22-hydroxydocosanoic acid, Phenylacetylglycine_phacgly -> phenylacetylglycine, Sebacicacid -> sebacic acid. Names only; model structure and balance are unchanged.

The reaction names were updated surgically (only the lines embedding these strings), not by re-running the name generator, so existing reaction-name curation is untouched.

Left for follow-up (per the issue's staged approach): the Title-Case Recon3D name cluster (a larger normalization with a ~315-reaction-name cascade, to be done as separate commits), the ~64 pool metabolites, the wrong-ChEBI-id cases (e.g. MAM00075), and the 35 metabolites whose ChEBI id is absent from the current ChEBI dump.

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[github-actions]

Model quality report

✅ Model QC checks fine, no changes compared to develop.

Model QC checks

Check	Result	Δ vs develop
Growth (biomass producible)	125	0	✅
Metabolites missing formula	7	0	✅
Metabolites missing charge	0	0	✅
Reaction bound / GPR issues	0	0	✅
Malformed cross-references	59	0	✅
Cross-refs inconsistent across compartments	59	0	✅
MEMOTE score (%)	pending		⏳

MACAW and mass/charge balance

MACAW: dead-end and duplicate tests

Mass and charge balance

(balance report unavailable)

Gene essentiality (Hart 2015)

cellLine	TP	TN	FP	FN	accuracy	sensitivity	specificity	F1	MCC
DLD1	38	2158	60	280	0.8659	0.1195	0.9729	0.1827	0.1588
GBM	34	2137	64	300	0.8564	0.1018	0.9709	0.1574	0.1276
HCT116	47	2181	55	308	0.8599	0.1324	0.9754	0.2057	0.1906
HELA	32	2241	70	250	0.8766	0.1135	0.9697	0.1667	0.1332
RPE1	15	2179	83	258	0.8655	0.05495	0.9633	0.08086	0.02935
all	7	2379	95	112	0.9202	0.05882	0.9616	0.06335	0.02199

Per-finding detail is committed to data/testResults/ (qc_metabolite_completeness.csv, qc_reaction_sanity.csv, qc_annotation_issues.csv, macaw_results.csv, balance_results.csv, gene-essential.csv); the full MEMOTE result is uploaded as a build artifact.

Results for commit 909f22a.

Full workflow run · this comment is edited on subsequent runs

[edkerk]

No structural model changes