Adding new annotation from ModelSeed

Current behavior:

Considering that MEMOTE includes reaction and metabolite annotations from ModelSEED as part of its scoring, I have generated a list of matching reactions and metabolites between Human-GEM and ModelSEED based on the SMILES information of the metabolites.

A total of 4,391 metabolites and 2,680 reactions were successfully matched. The addition of these annotation details will enhance the score of Human-GEM in MEMOTE.

You can find more details in this All_Seed_mapping_mets.xlsx and All_Seed_mapping_rxns.xlsx.

I believe the annotation should end up in the corresponding TSV files.

@JHL-452b

Thanks Mihail! Totally agree! Please proceed @JHL-452b by expanding the corresponding tsv files

chore: annotation overhaul plan and structure/formula/charge audit

feat: add ModelSEED cross-references (metSeedID column) (#968)

chore: annotation overhaul plan and structure/formula/charge audit

feat: add ModelSEED cross-references (metSeedID column) (#968)

feat: structure-verified annotation overhaul (metabolite + reaction c…

#1105 corrects some of the ModelSEED ids that #1086 added. A check of each id against its ModelSEED equation or compound found that about 1-2 % point to a different reaction or compound. These ids are now corrected or removed. The other ids are unchanged.

Reactions: id of a different reaction removed

Reaction	Removed id	Why
MAR03964	rxn09694 (kept rxn00062)	proton-pumping variant on a plain ATP hydrolysis
MAR03975, MAR03977, MAR03979, MAR06912, MAR07794	rxn42569 (kept rxn00001)	same, on plain diphosphate hydrolysis
MAR04207	rxn42210 (kept rxn00439)	same
MAR02530	rxn45259	18:2 elongation; the model reaction is 18:3 (the id stays on MAR02423)
MAR00267, MAR02961	rxn33912	degenerate ATP + CoA reaction; it was matched through elaidoyl-CoA, which carried the ModelSEED id of elaidate
MAR02031	rxn06311	plant reaction, reversed and unbalanced
MAR08573	rxn41233 (kept rxn08936)	celloheptaose reaction
MAR08773	rxn19443	D-ribulose 1-phosphate aldolase; the model reaction uses D-xylulose 1-phosphate

Reactions: proton coupling. #1086 keeps H+ when it crosses a membrane, so that proton-coupled and plain transporters stay apart. 11 transport ids did not follow that rule. 5 are replaced by the proton-coupled ModelSEED reaction: MAR05099 rxn09339 -> rxn05301, MAR05101 rxn08625 -> rxn09678, MAR05102 rxn08625 -> rxn13301, MAR05107 rxn08747 -> rxn05244, MAR05118 rxn05245 -> rxn05669. The other 6 are removed because ModelSEED has no reaction with the right coupling: MAR04964, MAR06327, MAR06381, MAR06382, MAR06604, and MAR06921 (complex I without proton pumping).

Compounds

Metabolite	Before -> after	Why
MAM00188c cob(II)alamin (enzyme-bound)	cpd12872 -> cpd27507	cpd12872 is the cob(I)alamin form
MAM01224c 9,13-di-cis-retinoate	cpd11177 -> removed	cpd11177 is 9-cis-retinoate
MAM02454c mannose-1-phosphate	cpd00736 -> cpd00485	cpd00736 is a generic hexose 1-phosphate
MAM02683c, MAM02330g paragloboside	cpd02989 -> cpd03740	cpd02989 is Lc4Cer

Related changes in other open PRs:

fix: curate metabolite structure, formula and identity inconsistencies (#1085) #1104: MAM03652e cpd16300 -> cpd40310, MAM03714 (Leu-Gly) cpd01391 -> cpd32743, and removal of cpd04763 (oxypurinol) from alloxan MAM01315, cpd03813 from D-galactosamine MAM03585 and cpd02184 from MAM00303.
fix: pre-existing metabolite identity, structure and cross-reference errors #1107:
- L-carnitine MAM02348 goes from D-carnitine cpd10719 to cpd00266, and the carnitine reactions move to the (R)-carnitine ModelSEED reactions (MAR02591, MAR02593, MAR02780, MAR03030 rxn15328 -> rxn01726; MAR06982 rxn15330 -> rxn01727).
- cpd01398 (linoleoyl-CoA) is removed from (6Z,9Z)-octadecadienoyl-CoA MAM00106, and cpd26827 (D-ribulose 1-P) from D-xylulose 1-P MAM01760.
- Details are in Metabolite identity and cross-reference corrections #1115.

MAR01444 and MAR08892 carry rxn08762 (bacterial Kdp). The id matched the model equation, but the model's H+/K+-ATPase left out H+ efflux. #1106 corrects the stoichiometry of MAR08892 and merges MAR01444 into it (see #1111); rxn08762 no longer matches and should be revisited there.

Fixed in Human 2.1.0.

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Adding new annotation from ModelSeed #968

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Adding new annotation from ModelSeed #968

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mihai-sysbio commented on Mar 20, 2025

feiranl commented on Mar 21, 2025

edkerk commented on Sep 27, 2026

edkerk commented on Oct 5, 2026

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