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SBMLTable

Extracts SBML attributes into a CSV file, or imports attributes from a CSV file. SBML model building blocks (such as species and reactions) have attributes like id, name and compartment (for species). This components extracts some of them into CSV files that can be further manipulated by other components. Not all attributes are extracted. Using the optional input ports, attributes can also be imported into an existing SBML model. A common workflow is to extract attributes, manipulate them, and import them back. Note that a model is always needed as input, even when attributes are imported; this component does not attempt to cover the complete set of SBML elements and attributes.

Version 1.3
Bundle tools
Categories Pathway
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
Issue tracker View/Report issues
Requires colt.jar (jar) ; csbl-javatools.jar (jar) ; jung-algorithms-2.0.jar (jar) ; jung-api-2.0.jar (jar) ; jung-graph-impl-2.0.jar (jar) ; libsbmlj.jar (jar)
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
model SBML Mandatory The SBML model.
species CSV Optional Species attributes to be imported. The id column must always be present; other columns are optional. The format is similar to the corresponding output CSV file.
reactions CSV Optional Reaction attributes to be imported. The id column must always be present; other columns are optional. The format is similar to the corresponding output CSV file.
parameters CSV Optional Parameter attributes to be imported. The id column must always be present; other columns are optional. The format is similar to the corresponding output CSV file.
compartments CSV Optional Compartment attributes to be imported. The id column must always be present; other columns are optional. The format is similar to the corresponding output CSV file.
rules CSV Optional Rule attributes to be imported. All columns must be present. The format is similar to the corresponding output CSV file.
events CSV Optional Event attributes to be imported. The trigger columns must always be present. The format is similar to the corresponding output CSV file.
annotations CSV Optional RDF (Resource Description Framework) attributes of model components to be imported. All columns must be present. The format is similar to the corresponding output CSV file.

Outputs

Name Type Description
model SBML If input table are present, this is the modified SBML model. Otherwise, this is the same model as the input.
species CSV Extracted species attributes. The columns include id, name, compartment, initialAmount, initialConcentration, substanceUnits, boundaryCondition, notes. They mirror the corresponding SBML attributes.
reactions CSV Extracted reaction attributes. The columns include id, name, reversible, fast, reactants, products, modifiers, kineticLaw. The columns reactants, products and modifiers contain comma-separated lists of species IDs. Other columns mirror the corresponding SBML attributes.
parameters CSV Extracted parameter attributes. The columns include id, name, reaction, value, units, constant. They mirror the corresponding SBML attributes. The reaction column contains a reaction ID if the parameter is local to the reaction; otherwise, the column notains NA.
compartments CSV Extracted parameter attributes. The columns include id, name, size, outside. They mirror the corresponding SBML attributes.
rules CSV Extracted rule attributes. The columns include type (one of algebraic, assignment, rate); variable (only for assignment and rate rules); formula.
events CSV Extracted event attributes. The columns include trigger (a Boolean math formula); delay (delay formula, if any); variableN (name of N'th assignment variable); formulaN (new value of N'th assignment). There may be any number of variableN/formulaN column pairs.
annotations_out CSV Extracted RDF (Resource Description Framework) annotations for model components. See SBML specification for details on the annotation system. In contrast to other output tables, this contains data for many types of model components, including species, reactions and parameters. The columns include id (e.g. species/reaction id), namespace (RDF resource namespace URI); qualifier (defined by SBML: e.g, isDescribedBy, isPartOf, ...); resourceHead, resourceTail. The last two columns form a resource URL or URN that describes the model component.

Test cases

Test case Parameters IN
model
IN
species
IN
reactions
IN
parameters
IN
compartments
IN
rules
IN
events
IN
annotations
OUT
model
OUT
species
OUT
reactions
OUT
parameters
OUT
compartments
OUT
rules
OUT
events
OUT
annotations_out
case1 (missing) model (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing)

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