Including additional information in a model, such as details about model creation or biological information on individual model elements, is highly beneficial. This metadata becomes particularly important if you obtain a model from someone else or download it from an author’s website or a public model repository.
To standardize model annotation, the MIRIAM (Minimal Information Requested in the Annotation of biochemical Models) guidelines have been developed. These guidelines outline what information is needed to ensure a model is well-annotated and suitable for publication.
COPASI allow users to annotate models and all model elements following the MIRIAM guidelines. In COPASI’s interface, the model widget—as well as the widgets for compartments, species, reactions, and global quantities—each provide two additional tabs at the top: Annotation and RDF Browser.
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| Annotation Widget with Annotation from Model 123 from biomodels.net Database |
The Annotation tab presents the same metadata in a more user-friendly way. Different types of information can be provided for each model element. For example, you may want to record who created or added a particular element, or supply biological information describing a species’ identity.
Each annotation record is stored as a triplet: a relationship, a resource, and an identifier. The relationship is selected from a predefined list, as is the resource. For instance, to indicate that species A in your model is ATP, you might set the relationship to is and select the ChEBI (Chemical Entities of Biological Interest) database as the resource. The identifier would then be the ChEBI ID for ATP: CHEBI:A15422.
In COPASI you specify this, in the Description field, by selecting the relationship
from the dropdown, then the resource (again from the dropdown), and finally specify
the identifier. Should the resource dropdown be empty, you will have to update the
MIRIAM database.
For additional technical details on how annotations are stored in COPASI, see the COPASI MIRIAM Annotation documentation.
COPASI (and SBML) use RDF (Resource Description Framework) to store annotation information in the model file. You can view the resulting RDF structure by selecting the RDF Browser tab. Note that this view is read-only and cannot be used to edit annotations.
While COPASI installations come with an up-to-date list of MIRIAM resources, these may change over time and so it can be updated using the “Update MIRIAM” button in the toolbar. This action downloads the MIRIAM resource file from the internet, so you must have an active internet connection.