This repository contains the metabolic maps of Yeast-GEM that Metabolic Atlas serves, in three formats, and the files from which the first maps were made.
The maps match Yeast-GEM 9.1.1.
subsystem/: 102 maps, one per subsystem of the model, 27 of them for the transport subsystems (Transport [a, b], astransport_<a>_<b>); exchange reactions have no map.compartment/: 19 maps, one per compartment. The cytoplasm, the endoplasmic reticulum membrane and the mitochondrion are each divided over several maps, each holding whole subsystems.
Each folder holds the same maps in each format:
| Folder | Format | Content |
|---|---|---|
svg/ |
SVG | The map as Metabolic Atlas shows it. |
sbgn/ |
SBGN-ML 0.3, process description | Metabolites as simple chemicals, reactions as processes, genes as macromolecules catalysing them, at the positions of the SVG. Validated against the libsbgn schema. |
escher/ |
Escher map (JSON, schema 1-0-0) | Metabolites and reactions where the SVG draws them, edges as Bézier curves through the SVG's bends, with stoichiometry, reversibility and gene rules from Yeast-GEM 9.1.1; the title and compartment headings as text labels (Escher has no compartment boxes or gene boxes). Open it in Escher with Load map JSON; loading the model as well (COBRA JSON) shows names and lets you overlay data. Checked against Escher's schema and its own consistency checks. |
Gene boxes show the gene name over its systematic (ORF) name.
The first maps were drawn for Yeast8 (Yeast-GEM 8.3) in CellDesigner. Those drawings (SBMLfiles/, with the whole map in SBMLfiles/Yeast8.xml) and the files used to split them by subsystem (scripts/) are in the repository history up to commit 93b787c. Since Yeast-GEM 9.1.1 the maps are fitted to each model release by script, keeping the drawing: identifiers follow the model, removed reactions and metabolites are taken off, reactions of a map's subsystem or compartment that were not drawn are added, maps for new subsystems and for the compartments are drawn, and parts that share a metabolite are connected. The script and its rules are in MetabolicAtlas/data-generation (maps, rules in maps/RULES.md). The SVG maps that Metabolic Atlas serves are kept in MetabolicAtlas/data-files (svg/Yeast-GEM), and the SBGN and Escher files are written from them with maps/publish_maps.py. After each model update in data-files, a workflow there opens a pull request here with the new maps.
The custom map (chloroalkane and chloroalkene degradation) is only in data-files.