Creating templates

The Template Builder (the Templates workspace) creates, edits, reviews, imports and exports model-independent templates. No GEM is needed: you draw a pathway and define what each node is. Applying the template to a model comes later, through the same matcher and review dialog as the built-ins.

Template Design Mode

Open a template from the library (Open), make your own copy of a built-in (Duplicate), or start from scratch (New template). The canvas is the Map Builder's, with the same gestures; the blue banner reminds you that nodes are template entities, not model metabolites.

The built-in TCA cycle in Template Design Mode. Green checks mark confirmed identities. Built-ins are read-only; Save as my version keeps the original unchanged.

Action	How
New metabolite	Double-click empty canvas, or the Metabolite tool (M); the identity search opens at once
Define or change an identity	Double-click the node, type a name or an identifier (C00031, CHEBI:17634, MNXM…, cpd00027), choose
New reaction	Drag from a node's outer ring to another node; drop on empty canvas to extend the chain
Reaction identity	Double-click the arrow: built-in reactions with the same participants, and MNXref / BiGG reactions (with the backend)
Cofactors	Inspector → Stoichiometry → + side compound (part of the equation, not drawn)
Same metabolite twice	Inspector → + Instance, or copy and paste the node: one biology, several drawings
Other compartment	Inspector → Make independent, then change its compartment
Link to another pathway	Select a metabolite → + Pathway link (a port, never matched to model reactions)
Group, compartment box, labels	Add section of the left panel
How a node or arrow looks	Inspector → Appearance: label position, circle or text only, radius and fill colour for a metabolite; routing, curvature, Reverse, Flip label and Auto label position for a reaction. Saved in the template, so the map drawn from it looks the same
Fold the panels	Click a section title in either side panel to fold it; Expand all / Collapse all at the top

Defining identities

The identity search merges the GEMs MAP library, the BiGG tables, and KEGG and ChEBI resolved through MetaNetX. Free-text searches also return loosely related compounds, which is why a person confirms the identity.

The search looks in the GEMs MAP library (offline), the BiGG tables (offline, if installed) and KEGG and ChEBI resolved through MetaNetX (online, through the backend; answers cached for 90 days). Each candidate shows its identifiers, formula, sources and why it matched. Without the backend the search uses the library only and says so.

Identity statuses belong to the template, not to any model:

Status	Badge	Meaning
confirmed	✓	Chosen or reviewed by a person (curated by hand for the built-ins)
suggested	?	Proposed by a search, Auto Identify or AI; not reviewed
ambiguous	!	Several plausible candidates stored; a person must choose
unresolved	○	Not defined

A partial name hit (a substring) is never an identity; a suggestion needs an exact name, synonym or identifier.

• Auto Identify searches every entity that is not confirmed, by name and synonyms. A confirmed identity is never changed by Auto Identify or by any later suggestion. If a suggestion disagrees, the node keeps its identity and gets a red !, a potential identity conflict, with Keep mine / Use the suggestion.
• Add BiGG IDs adds bigg.metabolite / bigg.reaction identifiers, plus BiGG's cross-references, where exactly one BiGG entry fits and nothing contradicts the template. This lets templates match models downloaded from BiGG. Ties (for example MDHf / MDHm) are listed for you to choose; identifiers are added, never removed.
• The Review queue lists every element with its identity, status and source; click to select, review to open the search.

Validating

Validate template lists issues; click one to select the element.

Severity	Examples
Error	Invalid identifier syntax or EC number; a reaction without participants; an edge to a missing metabolite
Warning	Missing or ambiguous identity; the same entity twice in one compartment (draw instances instead); two entities sharing an identifier; an identifier that looks like a model ID (g6p_c, C00031[c]); an unbalanced reaction (heavy atoms, when all formulas are known); duplicate or contradictory reactions; an unconnected node; a potential identity conflict
Note	Suggested identities not yet reviewed; direction not stated; balance not checkable; an AI-generated template

Completeness is two plain ratios and their mean: metabolites identified and reactions identified. "Identified" means at least one database identifier (or an EC number for a reaction) and a confirmed or suggested identity. Preferred compartments are optional and not part of the score: the person applying the template chooses compartments when several fit.

Saving, exporting, applying

• Save (Ctrl+S): your templates live in the browser (IndexedDB). A built-in is saved as my version; the original never changes. An unsaved template survives a workspace switch, and a browser reload offers to resume it.
• Export (Ctrl+E) writes one self-contained .gemsmap-template.json: identities, annotations, topology, layout, compartments and metadata (version, scope, authors, license, citations). Export figure of the template… exports a picture.
• Apply to GEM… saves, switches to the Map Builder and opens the mapping review against the model loaded there.

The file format (schema 1.1) and all fields are documented in the Template Builder technical notes.

Next: Sharing and reuse.