Network model¶

cy3sbml converts every SBML object into a node, and the relations between the objects into edges. This page describes the networks, node types, edge types and table columns that an import creates.

Networks¶

For every model, the import creates one network collection (root network) <name> with three networks, and one more network per layout of the model. <name> is the model id, or the file name if the model has no id. After the import, the base network of the main model is the current network.

The comp package can define several models in one file, and refer to models in other files. Every model gets its own network collection: the main model, every model definition and every external model. The flattened model of a model with submodels gets the collection Flat__<name>, with the networks Flat__<name>, Flat__<name>__kinetic and Flat__<name>__all.

Node types¶

The type of a node is in the column sbml type.

In a layout network, the node of a glyph of an element has the columns of the node of the element, including sbml type.

The column sbml type ext refines the type for the visual style: reactions are reaction reversible or reaction irreversible.

Edge types¶

The type of an edge is in the column interaction type. All edges are directed.

In a layout network, the edges between a reaction and its species are copies of the edges of the model with their type and columns. An edge of a species reference glyph without edge in the model gets the type of its role, for example reaction-product or reaction-inhibitor. See Layouts.

The column shared interaction refines the type for the visual style: a modifier edge whose SBO term is an inhibitor term (for example SBO:0000020) is reaction-inhibitor, one with an activator or catalyst term (for example SBO:0000459 or SBO:0000013) is reaction-activator.

Table columns¶

These columns are set on nodes, when the SBML object has the value:

Package columns:

• qual: qual_initialLevel, qual_maxLevel, qual_sign, qual_tresholdLevel, qual_transitionEffect, qual_qualitativeSpecies, qual_outputLevel, qual_resultLevels.
• fbc: fbc_strict (network table), fbc_charge and fbc_chemicalFormula (species), fbc_lowerFluxBound and fbc_upperFluxBound (reactions), one column fbc_objective-<objective id> per objective with the objective coefficient of the reactions and, for fbc version 3, fbc_objective-<objective id>_variableType with the variable type; fbc_lowerBound and fbc_upperBound (user defined constraints), fbc_coefficient and fbc_variableType (edges of the constraint components).
• comp: comp_portRef, comp_idRef, comp_unitRef, comp_metaIdRef, comp_sBaseRef, comp_submodelRef, comp_conversionFactor, comp_deletion, comp_modelRef, comp_timeConversionFactor, comp_extentConversionFactor, and the resolved target comp_targetModel, comp_targetId, comp_targetType, comp_targetMetaId with comp_resolution.
• distrib: distrib_uncertainty and distrib_uncertaintyCount on the node of every element with uncertainties, and on the edges of species references. See distrib.

Annotations become columns too. Every resource of an RDF annotation is stored in a column named after its identifiers.org collection, with the identifier as value. For models with the fbc package, the KEY: value paragraphs in the notes of species, reactions and gene products (the COBRA notes format, for example GENE_ASSOCIATION) are stored as columns named KEY.

The model is stored in the network table, in the row of the __all network: the columns sbmlNetwork (sbml), sbmlVersion (for example L3 V1), the id, name, metaid, SBO term and annotations of the model, and the model attributes substanceUnits, timeUnits, volumeUnits, areaUnits, lengthUnits, extentUnits and conversionFactor. The base and the kinetic network have only their name. The layout networks have sbmlNetwork sbmlLayout. Every network has the column sbmlSubnetwork with its kind: base, kinetic, all or layout. Unlike the name, it does not change when Cytoscape renames a network of a model imported twice; the automation commands return it as the network type. The root network of a model imported from a COMBINE archive has the column archive with the name of the archive.

The layout networks have their own columns (not in the other networks):

Mapping to the SBML document¶

cy3sbml keeps the SBML document of every imported network, and maps every node to its SBML object with the cyId column. The info panel uses this mapping. Networks created from an SBML network with Cytoscape functions, for example File → New Network → From Selected Nodes, All Edges, keep the mapping, because they belong to the same network collection.

The documents and mappings are saved in Cytoscape session files (.cys) and restored when the session is opened.