KRSMS Semantic Annotation Language

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SMS Semantic-Annotation XML Interchange Format

An annotation is composed of three parts:

1. Resources. These are the objects being annotated (referred to). Typically there will only be one resource. We currently provide support for resources that are datasets, actors as a whole, or actor input and output ports.
2. Semantic Types. These are ontology-based (i.e., concept) descriptions of the classifications of the resources. Typically there will be only one semantic type for a resource(s).
3. Encodings. These are optional sets of expressions that link portions of resources to portions of the semantic types. An encoding links the two items, thus describing how the semantic types are "realized" within the resources.

An annotation takes the following form, expressed in XML:

<sms:Annotation ID="...">

   <sms:Resources>

      ...

   </sms:Resources>

   <sms:SemanticTypes>

      ...

   </sms:SemanticTypes>

   <sms:Encodings>

      ...

   </sms:Encodings>

</sms:Annotation>

Note that every annotation should have a unique identifier, preferably an LSID. We describe each of the annotation subelements in turn below.

Resources

A resource can take one of the following three forms, depending its resource type (i.e., dataset, actor, or actor input/output port):

<sms:Dataset resource="..."/>

<sms:Actor resource="..."/>

<sms:ActorPort portName="..." resource="..."/>

The Dataset tag designates a dataset resource, whose resource identifier is given via the resource attribute. A dataset identifier is a unique identifier (e.g., an LSID) for the dataset, and we assume that the dataset identifier can be used (via additional tools) to retrieve the actual dataset. The Actor tag designates an actor resource and the resource attribute the unique identifier for the actor being reference. The ActorPort tag denotes a port of an actor. The portName attribute specifies the port for an actor identified via the resource attribute. A Resources element in an annotation must specify at least one resource subelement (either Dataset, Actor, or ActorPort). More than one resource subelement is permitted. For each subelement, the resource is attribute is required. In addition, for ActorPort elements, the portName attribute is required.

Semantic Types

The SemanticTypes element contains one or more class references or anonymous class expressions:

<owl:Class rdf:about="..."/>

<owl:Class>

   ...

</owl:Class>

Each of these expressions are defined solely in terms of concepts and roles from existing ontologies. Every class definition defines a semantic type for the resource(s). That is, the resources are said to "contribute" the semantic types. Every annotation is required to contain a SemanticTypes tag that contains at least one semantic type.

Encodings

Encodings define the "glue" or "links" between the resource(s) and the semantic type(s) and are optional. An encoding takes the form:

<sms:Link> ... </sms:Link>

The content of the Link element uses a specific textual language that we define briefly here.

Examples