NAR 2026 manuscript: sync M03_methods_construction.tex with Overleaf edits

Papers/NAR_Update_2026/latex/sections/M03_methods_construction.tex

@@ -1,6 +1,9 @@
 %% Consolidates the former methods_{collation,integration,provenance,transport,
 \subsection{Construction and Curation}\label{sec:methods-construction}
 
-We collated additional compounds and reactions from MetaCyc~\cite{caspi2020}, Rhea~\cite{bansal2022}, and ChEBI~\cite{hastings2016}. The compounds are reconciled into single ModelSEED compounds using available structures where possible and the reactions are reconciled based on the identity of the compounds. The procedure follows the 2020 release~\cite{seaver2020}. Mass and charge balance is enforced and flagged.
-
-For the 2020 release, a conflict between structures from multiple sources was either manually reviewed or dropped silently. The updated pipeline classifies each structural conflict and routes it to one of three outcomes: an automatic pick from the source variant matching the historical formula, a curator-authored override with recorded rationale, or an entry in a mass-balance exclusion registry for compounds where no source formula is defensible. Every outcome is attributed to its curator and its evidence. We retained every structure we collect, so conflict resolution can be inspected within the data in the repository. An outline of how a researcher can contribute is given in Supplementary Methods~S1 and expanded in the repository.
+We collated additional compounds and reactions from MetaCyc~\cite{caspi2020}, Rhea~\cite{bansal2022}, and ChEBI~\cite{hastings2016}, merging compounds via structures where possible and matching reactions by compound identities, similar to the 2020 release~\cite{seaver2020}.
+Mass and charge balances are enforced and flagged.
+Unlike the 2020 release, where compounds with conflicting sourced structures were either manually reviewed or silently dropped, the updated pipeline classifies structural conflicts and either 1) automatically picks from the source that matches the historical formula, 2) prioritizes curator authored and justified content, or 3) exclusion (with logged justification) for compounds without a defensible source formula.
+This enforces that every outcome is attributed to its curator and evidence.
+Every structure is retained in the repository to facilitate conflict resolution.
+Investigators can contribute to the ModelSEED Database through the procedure in Supplementary Methods~S1, which is expanded in the repository.