Skip to content

Templates

A GEMs MAP template is a reusable pathway layout that knows what each molecule is, not what it is called in one particular model. The same template draws glycolysis on a BiGG model (g6p_c), a ModelSEED model (cpd00079_c0) or a KEGG-based model (C00092[c]), always with the same recognisable shape. A matcher finds the model's names for each molecule and asks you to review the uncertain cases.

A template describes biological identity and pathway topology; a GEM provides model-specific identifiers.

Why templates?

Drawing a clear pathway figure takes time, and most groups redraw the same pathways for every new model. Simply copying a map from one model to another rarely works, because each model uses its own identifiers, compartments and level of detail. A drawing that stores g6p_c breaks on a model that says cpd00079_c0.

Templates separate the parts that can be shared from the parts that cannot:

Layer What it is Stored in
Visual layout Coordinates, arrows and their routing, labels, groups, repeated drawings of cofactors The template
Biological identity Which chemical each node stands for (names, synonyms, formula, database identifiers), in which conceptual compartment, and the stoichiometry of each reaction The template
Model-specific mapping Which metabolite and reaction of this GEM corresponds to each template node and arrow The application: per-model mapping profiles, never the template file

The layout is part of a pathway's identity: readers recognise a circular TCA cycle or a vertical glycolysis at a glance. That is why mapping never moves template nodes.

Diagram: on the figure a node is labelled G6P (a display label). In the template it stands for D-glucose 6-phosphate in the cytosol, with KEGG C00092, BiGG g6p and ModelSEED cpd00079. The matcher finds it as g6p_c in a BiGG-style model, cpd00079_c0 in a ModelSEED model and C00092[c] in a KEGG-based model. A legend explains the four layers: display label, model ID, cross-database identifier, compartment-qualified identity.

From a template to a pathway on your model

flowchart LR
    T["Template<br/>identity + layout"] --> M["Matcher<br/>(in the browser)"]
    G["GEM<br/>IDs · names · formulas ·<br/>annotations · compartments · reactions"] --> M
    M --> R{"Review<br/>uncertain slots"}
    R -->|"confirm · choose · mark absent"| P["Mapping profile<br/>(per model)"]
    R --> D["Pathway on the map<br/>template layout,<br/>bound to model IDs"]
    P -.->|"reused next time"| M
  1. The matcher scores every model metabolite against every template node, using identifiers, names, formula, compartment and the reactions that connect neighbouring nodes.
  2. High-confidence matches are applied; medium ones are applied provisionally and marked; ambiguous or missing ones stay open.
  3. You review only what needs a person; your decisions go into the model's mapping profile.
  4. The pathway is drawn with the template's layout and bound to the model's IDs, so results from COBRAGUI colour it immediately.

See Identity and matching for the details, and Linking a map to a model for the workflow on screen.

What exists today, and what is planned

Capability Status
Built-in templates: global central carbon, glycolysis, TCA cycle, oxidative PPP Implemented
KEGG-derived templates (map00010, map00020, map00030, map00250) and an amino acid overview AI-generated, awaiting review
Template Builder: create, edit, duplicate, validate, import and export templates without a model Implemented
Identity search (GEMs MAP library offline; KEGG, ChEBI, MetaNetX online; local BiGG tables), Auto Identify, Add BiGG IDs Implemented
Deterministic matching with evidence, review dialog, mapping profiles, reproducibility report Implemented
Sharing templates as files (.gemsmap-template.json) Implemented
A searchable community template hub with versions, provenance and review Future direction
Generate with AI inside the application Future direction
Escher maps from BiGG as templates; more pathways (glyoxylate shunt, β-oxidation, oxidative phosphorylation…) Planned

In this section