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Known SBML annotations

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Last update to this page: 2016-10-22

This page is intended to serve as a list of the annotations known to be in use by different SBML-compatible software packages. If you are using an annotation scheme in your software that is not listed here, please contact sbml-team@googlegroups.com or else request a wiki login so that you can make updates and additions.

The kind of annotations that are meant to be described here are application-specific annotations that would be placed inside SBML's <annotation> elements, following the scheme described in Section 6 of the SBML Level 2 Version 4 specification. If a software package uses only the common annotations described in the specification (e.g., VCard for user info, bqbiol qualifiers, etc.), they will not be listed here.

CellDesigner annotations

URL: http://celldesigner.org

Annotations and purpose: CellDesigner is a versatile modeling tool for biochemical networks. CellDesigner's annotations contain graphical information such as layout (e.g., coordinates, size, structure of complex species, and etc.) and notation (e.g., type of symbol, color, state of proteins, and etc.) of each component in a model. There is unfortunately no English-language document describing the annotations, although Japanese-language documentation of the annotations is available. The CellDesigner softwrae distribution includes XML Schema files for CellDesigner's annotations. The XML Schema files are located in the directory jp/sbi/celldesigner/schema within the jar file exec/celldesigner.jar installed by the CellDesigner installer program.

JDesigner annotations

URL: http://www.cds.caltech.edu/~hsauro/JDSBMLEx.pdf

Annotations and purpose: JDesigner and JDesigner 2 are software tools with a visual interface for biochemical network simulation. The annotations used by them are mostly for embedding the visual diagram of the network; it also includes different parametrizations and time-course simulation data.

Layout and Render annotations

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

Annotations and purpose: This is an extension for storing graphical diagrams of models into the SBML of the model itself. There are two components, one for representing the spatial arrangement/layout of the diagram, and another for representing the glyphs used for entities and other rendering aspects of the diagram. At the 9th SBML Forum in Heidelberg, Oct. 2005, the proposal by Gauges et al. 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.

Manchester group (MCISB) InChI annotations

URL: http://www.comp-sys-bio.org/yeastnet

Annotations and purpose: The Manchester group attaches InChI identifiers to species in SBML models. The following example illustrates the approach:

<species metaid="metaid_M_329" id="M_329" name="H+" compartment="C_1" sboTerm="SBO:0000299"> 
  <annotation> 
    <in:inchi xmlns:in="http://biomodels.net/inchi"   
       metaid="metaid_M_329_inchi">InChI=1/p+1/fH/q+1</in:inchi> 
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"  
             xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> 
      <rdf:Description rdf:about="#metaid_M_329"> 
       <bqbiol:is> 
         <rdf:Bag> 
           <rdf:li rdf:resource="#metaid_M_329_inchi"/> 
           <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI:24636"/> 
         </rdf:Bag> 
       </bqbiol:is> 
       </rdf:Description> 
    </rdf:RDF> 
  </annotation> 
</species> 

Multiple Parameter Sets annotations

URL: http://128.208.17.26/sbwWiki/sysbio/parametersets

Annotations and purpose: This is an SBML annotation, for storing multiple parameter sets in an SBML model. A user might wish to store different parameter sets that exhibit interesting behavior of computational models. One common example would be to store parameter values for steady states, or even oscillating regimes.


Old annotations (historical reference only)

In the mid-2000's, mostly driven by the needs of the Bio-SPICE project, a number of groups developed annotations specialized to their applications. Most of those annotations are no longer in active use, but we keep the old list of annotations on a separate page for historical reference. To repeat for emphasis: the information on those pages is out of date.

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This page was last modified 22:42, 22 October 2016.



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