Old known SBML annotations list

Last updated: 13 October 2005 — this content is out of date

This page is intended to serve as a list of the annotations known to be in use by different groups. If you are using an annotation scheme in your software that is not listed here, please contact the site administrators to get a wiki login so that you can make updates and additions.

Name: JigCell

URL: http://jigcell.biol.vt.edu/

Supporting group: Bio-SPICE

Annotations and purpose:

blankline: An indication that the line is blank.

ratelaw: Give a biological name to a specific rate law. Has a name parameter.

species: Make something that looks like a species because the modeler wants to have an intermediate value. Makes a fake species and assigns it. Has two parameters: 1. equation is the appearance of the species. If species is fake, gives the name, if intermediate value, gives equation of that value. 2. constmods defines all constants used in the equation.

conservationlaw: Identifies algebraic rules used for the conservation relationships. Has a dependent parameter which is the variable eliminated by the conservation element. Example:

Status : Actively used.

Name: JDesigner

URL: http://www.sys-bio.org/software/jdesigner.htm

Supporting group: Sauro group

Annotations and purpose: JDesigner is a Win32 application which allows one to draw a biochemical network and export the network in the form of SBML. The Designer has an SBW interface that allows it to be called from other SBW compliant modules, for example Python. In addition, JDesigner has the ability to use Jarnac as a simulation server (via SBW) thus allowing models to be run from within JDesigner. This annotation also includes provision for named rate laws (see UPenn annotation).

Status: Actively Used

Name: UPenn BioCharon

URL: http://www.cis.upenn.edu/group/biocomp/Hybrid%20Use%20Case/AnnotationScheme.doc

Supporting group: Bio-SPICE

Annotations and purpose: We are using a list of rate laws that were part of the SBML Level 1 specification, but we add reaction types that appear useful as we try to annotate various models. The primary purpose is to facilitate the automated construction of hybrid approximations to biochemical network models described in SBML files. However, the issue of easily recognizing common reaction law types is also faced by other software that uses SBML.

ConstantLaw
MassActionLaw
MichaelisMentenLaw
HillLaw
MichaelisMentenReversibleLaw

Status:

Name: Karyote

URL: http://biodynamics.indiana.edu/cyber_cell/

Supporting group: Bio-SPICE

Annotations and purpose: The dynamics of a living cell are modeled using a comprehensive reaction, transport, genomic approach. The calibration of the model and the difficulty arising from the incompleteness of our (and any) model of such a complex system are addressed via an information theory approach. Species annotations contain internal ids of the species in the Karyote database.

Status: Actively Used

Name: TJU Modules

URL: http://www.dbi.tju.edu/tools/biospice/usecase/#moduledocs

Supporting group: Bio-SPICE

Annotations and purpose:

unigene
dbi

Status: Actively Used

Name: SBML Layout Extension

URL: http://projects.eml.org/bcb/sbml/

Supporting group: EML Research.

Annotations and purpose: This is an extension for storing graphical diagrams of models into the SBML of the model itself.

Status: At the 9th SBML Forum in Heidelberg, Oct. 2005, this was voted as the recommended approach for storing diagrams in SBML. The recommendation is to use annotations to store the information in SBML Level 2. In SBML Level 3, it will become a standard package; when this happens, the tags will no longer have to be placed inside annotations but instead will be graduated to top-level SBML status.

Name: BioUML Workbench/Diagram Markup Language

URL: http://www.biouml.org/index.shtml

Supporting group: biouml.org

Annotations and purpose: BioUML is Java framework for systems biology. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization and simulations. Developed a diagram layout extension for use with the BioUML Workbench.

Status: Active

Name: Biomodels database

URL: http://www.ebi.ac.uk/compneur-srv/biomodels

Supporting group: EBI

Annotations and purpose: Biomodels is a database of quantitative models in biology. The current format to feed the database and to export the results is SBML Level 2 Version 1. Annotations used are "submitter" (dc:contributor plus vCard), "creator" (dc:creator plus vCard) and links to other resources (dc:relation, cf. proposal of Andrew Finney and Nicolas Le Novère 2004)

Status: Actively used

Name: Metabolic flux model annotations

URL: http://arep.med.harvard.edu/fluxns

Supporting group: Harvard Medical School Church Lab

Annotations and purpose: Metabolic flux analysis requires the ability to constrain reaction fluxes so that a feasible space can be obtained. The current SBML specification does not have a natural place for this information, so we add it to annotation. In the future, we expect this will be replaced by a general-purpose constraints specification.

As an annotation of Model:

 <annotation xmlns:flux="http://arep.med.harvard.edu/fluxns">
> <flux:listOfAnalysisTypes>
    <flux:analysisType id="fba" name="Flux Balance Analysis"/>
    <flux:analysisType id="moma" name="Minimization of Metabolic Adjustment"/>
    <flux:analysisType id="room" name="Regulatory On/Off mechanism"/>
 </flux:listOfAnalysisTypes>
 <flux:listOfAnalyses>
    <flux:analysis id="wild_type" name="Wild-Type FBA" analysisType="fba"/>
    <flux:analysis id="mutant_fba" name="Mutant FBA" analysisType="fba"/>
    <flux:analysis id="mutant_moma" name="Mutant MOMA" analysisType="moma"/>
 </flux:listOfAnalyses>
 </annotation>

Note that this annotation includes information about what kinds of analysis will be performed with the model which is strictly outside the scope of SBML.

As an annotation of Reaction:

<annotation xmlns:flux="http://arep.med.harvard.edu/fluxns">
   <flux:limit analysis="wild_type" upper="INF" lower="-INF" objective="0" prediction="10"/>
   <flux:limit analysis="mutant_fba" upper="INF" lower="-INF" objective="0" prediction="0"/>
   <flux:limit analysis="mutant_moma" upper="INF" lower="-INF" objective="10" prediction="6.7"/>
 </annotation>

Note that this information includes objective and prediction, which are simulation parameters and simulation results, which are strictly outside the scope of SBML.