Up: Component summary
Up: Component summary
Component
SBMLTableExtracts 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) |