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| - Semantic types should be uniquely identified. The unique identifier of a semantic type can be stated using the {{id}} attribute of the {{SemanticType}} element. An identifier is (preferably) expressed as a Life-Science Identifer (LSID) in which the semantic type is managed as an LSID data object. Alternatively, if a semantic type is embedded within a document, the semantic-type id can be expressed as a fragment identifier (for example, when used within EML). As shown above, a semantic type consists of a set of labels and annotations. The rest of this page describes these two components, starting with labels and then describing annotations. |
| + Semantic types can be uniquely identified. The unique identifier of a semantic type can be stated using the {{id}} attribute of the {{SemanticType}} element. An identifier is (preferably) expressed as a Life-Science Identifer (LSID) in which the semantic type is managed as an LSID data object. Alternatively, if a semantic type is embedded within a document, the semantic-type id can be expressed as a fragment identifier (for example, when used within EML). |
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| + As shown above, a semantic type consists of a set of labels and annotations as well as an optional set of definitions. The rest of this page describes these components. |
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| - Some resources (in particular, data sets and actors with input/output ports) can have complex data structures. For example, a data set typically is structured according to a schema, which specifies among other things a relation name (that is, the name of the table) and names for each attribute of the relation. Actor ports can also have complex structure, including arbitrarily nested relations. The annotation language facilitates the selection of the various (sub-) objects of structured resources. |
| + Some resources (in particular, data sets and actors with input/output ports) can have complex data structures. For example, a data set typically is structured according to a schema, which specifies among other things a relation name (that is, the name of the table) and names for each attribute of the relation and their data types. Actor ports can also have complex structure, including arbitrarily nested relations. The annotation language facilitates the selection of the various (sub-) objects of structured resources. The entire resource itself can also be selected using the annotation language. |
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| - The atom {{T}} selects corresponding objects of the resource. For example, if the resource is a data set, {{T}} selects the tuple objects of the resource. If the resource is an actor, {{T}} selects instances of the actor. The expression {{T.A1}} selects the nested {{A1}} objects for objects of {{T}}. For {{T}} representing a data set, this expression would select the values of attribute {{A1}} for tuples of {{T}}. The last expression selects nested attributes for complex structures occuring, for example, in actor input/output ports. For instance, if {{T}} represents an input port to some actor, the expression {{T.A1.A2}} selects the {{A2}} objects nested within {{A1}} objects for {{T}} objects. |
| + The atom {{T}} selects corresponding objects of the resource. For example, if the resource is a data set, {{T}} selects the tuple objects of the resource. If the resource is an actor, {{T}} selects instances of the actor. The expression {{T.A1}} selects the nested {{A1}} objects for objects of {{T}}. For {{T}} representing a data set, {{T.A1}} selects the values of attribute {{A1}} for tuples of {{T}}. The last atom selects nested attributes for complex structures occuring, for example, in actor input/output ports. For instance, if {{T}} represents an input port to some actor[2], {{T.A1.A2}} selects the {{A2}} objects nested within {{A1}} objects for {{T}} objects. |
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| - Atoms can be combined to form expressions. In particular, an expression is either one of the three style of atoms above, or a comma-separated list of the last two style of atoms. |
| + Atoms can be combined to form expressions. In particular, an expression is composed of: (a) a single atom or (b) a comma-separated list atoms of the form {{T.A1}} or {{T.A1.A2. ... An}}. |
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| - Using the abbreviated syntax, ontology expressions only consist of single concept labels {{C}}. |
| + In the abbreviated syntax, ontology expressions can only consist of a single concept label {{C}}. |
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| - For convenience, we also permit ontology concept expressions to be "embedded" within labels. The purpose of this features is to allow one to specialize certain concepts to more accurately annotate objects, without having to go through the process of creating a new ontology, or editing an existing one. These concept definitions are expressed using OWL[1]. |
| + ! Semantic-Type Definitions |
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| + For convenience, we permit ontology concept expressions to be included in a sematnic type. The purpose of this features is to allow one to specialize certain concepts to more accurately annotate objects, without having to go through the process of creating a new ontology, or editing an existing one. These concept definitions are expressed using OWL[1]. |
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| + [#2] We note that actor ports may not always be represented as an identifiable resource, and instead may be modeled as components of an actor. For example, consider an actor ''A'' having two ports ''P1'' and ''P2''. For the case where ''P1'' and ''P2'' are not separate resources, we can define the structural type of ''A'' as having two attributes {{P1}} and {{P2}} where {{A.P1}} denotes port ''P1'' and {{A.P2}} denotes port ''P2''. |
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