CellDesigner Help

There are two ways to annotate a Component (Compartment, Species, or Reaction); by adding MIRIAM information or by adding free text Notes.

Notes

The Notes allows you to type in additional text information for your Component and save it in the xml file.

Each Protein, Gene, RNAs or asRNA has the Protein/Gene/RNA/asRNA Notes as well as the Species Notes. You should be careful which Notes you want to change when editing.

The Notes should be written in XHTML format. For details on XHTML tags and attributes, please check the XHTML 1.0 specification provided at http://www.w3.org/TR/xhtml1/

You can enter PubMed ID in the Notes, and directly link to the relevant reference.

Connect to Databases

MIRIAM

MIRIAM (the Minimal Information Requested In the Annotation of Models) is a standard to annotate and curate computational models in biology. http://www.ebi.ac.uk/miriam/. SBML Level 2 Version 4 recommends using MIRIAM as an annotation scheme. CellDesigner 4.1 now supports MIRIAM annotation.

MAPK41.xml is a sample file installed with CellDesigner. The file already contains MIRIAM information to give you a picture of how MIRIAM information is added on a model.