An annotation scheme encodes the structure of semantic annotations attached to the model or to the model entities.
Attribution is textual description to thank and appreciated e.g. certain persons or institutions.
A Change characterises how the description of a particular entity in a model differs from the description of that entity in another model or model version.
Models are changed when the encoding standard is updated. In that case, the comodi:Reason of a change is a comodi:ChangedSpecification.
Example:
The upgrade from SBML Level 2 to SBML Level 3 resulted in many changes in SBML models, which were necessary due to the comodi:ChangedSpecification.
A ComponentDefinition describes a small functional unit of the system.
https://www.cellml.org/specifications/cellml_1.1/#sec_structure_component_element
A Contributor is an annotation about a human being, who participated in the development of the model.
A Correction resolves an error in a model.
The CreationDate refers to the date and time when a model or a model entity was created.
A Creator is an annotation about a human being, who was involved in the initial development of the model or its representaiton.
A Deletion removes a component from the model.
Example:
A comodi:Change may delete a cellml:component from the network.
An Elaboration adds more detail to the model.
Example:
A new version of a model may provide a zoom into the model or certain structures therein, or it may provide more details on particular structures inside the model.
An EventDefinition describes events that occur in the system.
Example:
Events are usually triggered by "something". They may have a delay and they typically have an effect on the system's dynamics.
An Expansion adds new entities to the model in order to cover a significantly larger network, or to enlarge the domain of the model.
Example:
A model describing the Interphase of the Cell Cycle may be expanded to cover the Cell division.
A FunctionDefinition describes a model-specific function that can be used in the model's maths.
A HierarchyDefinition describes, for example, how to achieve an encapsulation or how to encode hierarchical relationships.
Example:
A modification of the component hierarchy of a CellML model comodi:affects the comodi:HierarchyDefinition.
An IdentifierEncoding specifies the structure of identifiers. That includes the encoding of links to external resources and links to entities in the model document.
Example:
SBML used different identifier schemes in the past, including identifiers.org (http://identifiers.org/obo.go/GO:0000278) and MIRIAM URNs (urn:miriam:obo.go:GO%3A0000278).
An Insertion adds a new component to the model.
Example:
For the reason of a comodi:Extension, we may insert a new sbml:parameter in the XML code.
An Intention specifies the aim of a change, particularly with respect to consequences in the future.
A KineticsDefinition describes a kinetic law.
Example:
The sbml:kineticLaw specifies the rate law of a reaction. A change in the kineticLaw comodi:affects the comodi:KineticsDefinition.
A KnowledgeGain is the process of acquiring new knowledge about the model, or the modeled system.
A MathematicalModelDefinition defines structural parts of the model that affect the dynamics of the system.
A Merge is the result of a combination, blend or unification of different models into a new model.
A MetaIdEncoding specifies the structure of meta-ids, that is global identifiers in the model that can be used to refer to model parts.
A MismatchWithPublication reflects that a discrepancy between the model and the corresponding publication was discovered.
A ModelAnnotation provides meta-data about the model and its parts.
Popular annotations include RDF blocks, dc:terms and other controlled vocabularies.
ModelCuration is the process of analysing the model itself and its correspondence to the publication. (https://www.ebi.ac.uk/biomodels-main/curationtips)
A ModelDefinition specifies a certain aspect of a model. A model typically contains a positive number of model definitions.
Example:
The sbml:kineticLaw specifies the rate law of a reaction. A change in the kineticLaw comodi:affects the comodi:ModelDefinition.
The ModelEncoding defines how the different parts of the model are to be encoded.
Example:
In SBML or CellML, the comodi:ModelEncoding reflects the structure of the XML layer.
The ModelSetup specifies necessary settings to initialise a model.
Example:
The amount of Glucose in an environment could be specified using a parameter. A change in the amount comodi:affects the comodi:ModelSetup, but does not affect the comodi:ModelDefinition.
A ModificationDate refers to the date and time when a model or a model entity was modified.
A move rearranges parts of the model.
A NetworkDefinition specifies the biological entities, how they are related to each other, and how they interact.
An OntologyReference refers to a a term in a third-party resource, using a URI.
Example:
An example of an ontology reference is "http://identifiers.org/obo.go/GO:0000278".
The ParameterSetup describes the value and units of a parameter in a model.
Example:
Parameters can be used to define the current environment of a model, such as the temperature. If the value of a parameter changes it comodi:affects the comodi:ParameterDefinition.
A ParticipantDefinition describes the participants in the network.
Example:
A comodi:Change of an sbml:Species used in an sbml:reaction targets the comodi:ParticipantDefinition.
A comodi:Change in a comodi:ParticipantDefinition indicates that the role or definition of the biological entity have changed.
A PermutationOfEntities changes the order of model parts sharing the same parent node in the XML document (shuffling siblings).
Example:
The import/export from different software tools may change the order of the sbml:species in the sbml:listOfSpecies. This shuffling is reflected in a comodi:PermutationOfEntities.
A Person is an annotaion about a human being that, for example, contributed to the development of the model in some way.
A PortDefinition provides structure to input and output values and enables a convenient graphical representation of models. Ports are the basis for the definition of links in a network of models, representing the flow of information.
Bekey, George, and Boris Ja Kogan, eds. Modeling and Simulation: Theory and Practice: A Memorial Volume for Professor Walter J. Karplus (1927–2001). Springer Science & Business Media, 2012.
A ReactionDefinition describes a particular reaction taking place in the model.
Example:
A comodi:Change in a comodi:ReactionDefinition indicates that the biological meaning of a reaction has changed.
A ReactioNetworkDefinition describes the structure of the network underlying a model.
The reason of a change focuses on the cause of a change.
A ReversibilityDefinition describes the nature of the reaction, identifying it as reversible or irreversible.
A RuleDefinition specifies the values of the variables in a model, and the dynamic behaviors of those variables.
A Simplification decreases the level of complexity by which the model or its entities are described.
The SpeciesSetup defines a (biological) entity in the model.
Example:
Changes in the value of the initial concentration comodi:affects the corresponding comodi:SpeciesDefinition.
The Target identifies the location of a comodi:Change, and characterises its nature. It thus defines where the comodi:Change takes affect.
Example:
A comodi:Change may affect the comodi:Annotation of a cellml:component.
A comodi:Change may also affect the comodi:UnitDefinition of an sbml:Species.
The TextualDescription of a model is a human-readable explanation of the model. It can be surrounded by layout information, for example to present the textual description in a web browser.
Example:
One example for a textual description is the SBML <notes> element.
A Trial is a change resulting from playing around with the model.
Example:
Models may be examined to better understand their dynamic behaviour, or to test hypotheses. In these cases, the changes are the result of a comodi:Trial.
A Typo is a misspelling, e.g. in the description or name of a model or a model entity.
A UnitDefinition specifies a unit.
An Update replaces a part of the model with another part.
Example:
A comodi:Change may require the exchange of a species definition with an updated one.
A VariableConnectionDefinition describes how variables in a model are connected with each other.
Example:
A CellML model defines the participants of a biological system as variables. These variables can be part of different cellml:components. The comodi:VariableConnectionDefinition then defines how the variables are connected across the cellml:components. A change in these connections thus comodi:affects the comodi:VariableConnectionDefinition.
The VariableSetup defines the values of variables in a model component.
The VcardEncoding specifies how to refer to other people/institutions in a machine readable format.
An XmlAttribute contains data related to a specific XML element. (http://www.w3schools.com/xml/xml_attributes.asp)
An XML entity is part of the instance of an XML-encoded model.
An XmlNode represents a node in the XML tree.
An XmlText represents the textual content of an element or attribute.
Terms in this subtree are obsolete and shouldn't be used anymore.