| Lines 5-7 were replaced by line 5 |
| - It is a __DRAFT DESIGN DOCUMENT__ and does not reflect functionality |
| - as it currently exists in Kepler or SEEK. Comments and feedback are |
| - appreciated (see [Comments Page|KRSMSSemanticAnnotationComments]). |
| + It is a __DRAFT DESIGN DOCUMENT__ and does not reflect functionality as it currently exists in Kepler or SEEK. Comments and feedback are appreciated (see [Comments Page|KRSMSSemanticAnnotationComments]). |
| Lines 12-13 were replaced by line 10 |
| - This document describes an interchange syntax that can be used to express |
| - semantic types. |
| + __Semantic annotations__ leverage __ontologies__ to describe the conceptual aspects of structured __resources__, e.g., information sources such as data sets and services (workflows, actors, and web-services). Each resource is assumed to have a well defined schema that describes the structure of associated data (in the case of services, e.g., inputs and outputs). In addition to providing metadata for resources, ontology-based semantic annotations can enable improved discovery and integration of data. |
| At line 14 added 2 lines. |
| + Properly describing the semantics of a resource often requires "fine-grain" annotation, in which different parts of the resource are |
| + annotated with distinct semantic information, possibly including the assertion of semantic relations among the parts. The challenge is to provide an appropriate language for accessing, annotating, and relating portions of resources. This technical note describes basic aspects of __semantic annotation templates__, which are designed to support these fine-grain resource annotations. |
| Line 16 was replaced by line 15 |
| - !!! KR/SMS Semantic Types |
| + We use an XML-based language for representing semantic annotations, in which annotations take the form: |
| Lines 18-21 were replaced by lines 17-30 |
| - A __semantic type__ classifies and constrains the semantic, as opposed |
| - to structural interpretation of a __resource__. Datasets, actors |
| - (services), and actor input and output ports are examples of resources |
| - that may have semantic types within SEEK. |
| + {{{ |
| + <annotation id="..."> |
| + <!-- header --> |
| + <resource label="R" uri="http://resources.org/resource" type="..."/> |
| + <ontology label="ont" uri="http://ontologies.org/ont"/> |
| + ... |
| + <!-- annotation assertions --> |
| + ontology instantiation templates |
| + ... |
| + </annotation> |
| + }}} |
| + |
| + The resources being annotated and the ontologies used for annotation are assigned labels in the annotation header. For the case |
| + of ontologies, we typically refer to these labels as __prefixes__. Ontologies are assumed to be expressed using the Web Ontology Language (OWL). Annotation headers may also include information concerning who the author of the annotation is, when the annotation was created, who manages the annotation, and so on. The template information, which is the focus of this technical note, specifes fine-grain semantic annotations as mappings from resources to instances of the ontologies listed in the header. |
| Lines 23-28 were replaced by lines 32-33 |
| - A semantic type is expressed as a set of __semantic annotations__. The |
| - purpose of a semantic annotation is to assign objects of a resource a |
| - "meaning" using ontology terms. A semantic annotation serves to "link" |
| - a portion of a resource to a portion of an ontology. In this way, the |
| - semantic interpretation of a resource (its semantic type) is built |
| - from the annotation of its parts. |
| + This technical note gives an introduction to semantic annotation templates. Section 2 provides a short overview of annotation templates, and Section 3 gives a more detailed explanation. A number of the terms introduced in this technical note are defined in the Glossary at the end of the document. Following the Glossary is a list of footnotes. Some |
| + familiarity with [RDF|http://www.w3.org/TR/REC-rdf-syntax], [OWL|http://www.w3.org/TR/owl-guide/], and basic [First-Order Logic|http://en.wikipedia.org/wiki/First-order_logic] is assumed. |
| Lines 30-31 were replaced by line 35 |
| - Semantic types can be expressed using the following XML |
| - representation (see below [3] for the DTD). |
| + !!! 2 Overview of Annotation Templates |
| At line 32 added 1 line. |
| + An annotation template consists of one or more __instantiation patterns__ for constructing OWL individuals from resources. Instantiation patterns are typically based on (or driven by) resource structure and content. |
| At line 33 added 2 lines. |
| + The simplest form of an instantiation pattern is: |
| + |
| Lines 35-37 were replaced by lines 42-64 |
| - <sms:SemanticType id="..." xmlns:sms="http://seek.ecoinformatics.org/sms"> |
| - |
| - <sms:Label name="..." resource="..."/> |
| + <individual type="ont:C"/> |
| + }}} |
| + |
| + This expression creates a single, unique instance of the {{C}} class in the ontology refered to by {{ont}} (assumed to be an ontology prefix defined in the annotation header). The OWL document that results from running (executing) the pattern is: |
| + |
| + {{{ |
| + <rdf:RDF xmlns="local-ns" ...> |
| + <owl:Ontology rdf:about="">; |
| + <owl:imports rdf:resource="http://ontologies.org/ont"/> |
| + </owl:Ontology> |
| + |
| + <ont:C rdf:ID="id1"/> |
| + |
| + </rdf:RDF> |
| + }}} |
| + |
| + In this example, the pattern maps the resources given in the annotation to a single OWL individual[1]. Note that the identifier for the instance above is generated automatically as a result of executing the pattern[2]. |
| + |
| + A more common use of templates is to relate data values in a resource to class instances in the ontology. Assume we are annotating a relational table labeled {{R}} with attributes {{x}}, {{y}}, and {{z}}[3]. The following pattern, which uses a {{foreach}} attribute, creates an instance of class {{C}} for every unique value of {{x}} in the dataset. |
| + |
| + {{{ |
| + <individual type="ont:C" foreach="DISTINCT R.x"> |
| + }}} |
| Line 39 was replaced by lines 66-69 |
| - ... |
| + This pattern can be read as "For each unique x value of R create |
| + an instance of C." In this example, the term "R.x" is a __resource variable__. Executing this pattern results in the following document, assuming there are __n__ |
| + unique values of {{x}} in {{R}}[4]. As above, identifiers are generated as a result of |
| + executing the pattern over {{R}}. |
| Line 41 was replaced by lines 71-111 |
| - <sms:Annotation object="..." meaning="..."/> |
| + {{{ |
| + <rdf:RDF xmlns="local-ns" ...> |
| + <owl:Ontology rdf:about=""> |
| + <owl:imports rdf:resource="http://ontologies.org/ont"/> |
| + </owl:Ontology> |
| + |
| + <ont:C rdf:ID="id-val1"/> |
| + <ont:C rdf:ID="id-val2"/> |
| + ... |
| + <ont:C rdf:ID="id-valn"/> |
| + |
| + </rdf:RDF> |
| + }}} |
| + |
| + Note that this document has a different namespace than the |
| + corresponding ontology(ies), but imports the ontologies referenced in |
| + the annotation header. Thus, the individuals listed in this document |
| + are treated as distinct from the ontology itself, but OWL-based tools |
| + (such as Protege or a description-logic reasoner) can display and |
| + reason over the individuals as though they were part of the original |
| + ontology. |
| + |
| + We use rules expressed in first-order logic to formalize how |
| + instantiation patterns should be interpreted[5]. For |
| + example, the first-order logic rule for the above pattern is: |
| + |
| + {{{ |
| + (Axyz) R(x, y, z), u=id_p1(x) -> triple(u, rdfs:type, ont:C). |
| + }}} |
| + |
| + Here, the predicate {{triple}} asserts an RDF triple |
| + (with subject, property, value), and {{id_p1}} is a (Skolem) |
| + function mapping values into identifiers. The function |
| + {{id_p1}} is meant to apply only within this rule, where p1 |
| + stands for "pattern 1." We say in this case that each {{x}} |
| + value of {{R}} constitues a particular {{C}}. |
| + |
| + There are a number of additional features of instantiation |
| + patterns for describing fine-grain semantic annotations. These |
| + features are discussed in more detail in the next section. |
| + |
| Line 43 was replaced by lines 113-114 |
| - ... |
| + <a name="section3"></a> |
| + <h2>3. Template Instantiation Patterns</h2> |
| Line 45 was replaced by line 116 |
| - <sms:OntologyDefinitions> ... </sms:OntologyDefinitions> |
| + !!3.1 Individuals |
| Line 47 was replaced by lines 118-125 |
| - </sms:SemanticType> |
| + __Iteration.__ More than one variable can be given in a |
| + {{foreach}} expression. For example, the following pattern |
| + creates an instance of {{C}} for every unique pair of |
| + {{x}} and {{y}} values occurring together in tuples |
| + of {{R}}. |
| + |
| + {{{ |
| + <individual type="ont:C" foreach="DISTINCT R.x, R.y"/> |
| Lines 50-57 were replaced by lines 128-130 |
| - To be used within the SEEK architecture, semantic types must 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 an 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). |
| + This pattern can be read as "For each unique x, y (tuple) value |
| + pair of R, create an instance of C." The corresponding first-order |
| + rule for this pattern is: |
| Lines 59-61 were replaced by lines 132-134 |
| - As shown above, a semantic type consists of a set of labels, a set of |
| - annotations, and an optional ontology definition section. The rest of |
| - this page describes these components. |
| + {{{ |
| + (Axyz) R(x, y, z), u=id_p2(x, y) -> triple(u, rdfs:type, ont:C). |
| + }}} |
| At line 62 added 2 lines. |
| + In this example, we say that each {{x,y}} value |
| + constitutes a particular {{C}}. |
| At line 63 added 7 lines. |
| + Resource labels (such as {{R}}) in annotations are used |
| + in a similar way as tuple variables (i.e., "range variables") in |
| + SQL. In particular, a different label can be applied to the same |
| + resource in an annotation header. For example, if {{R1}} and |
| + {{R2}} are both labels for the {{Employee}} |
| + relation, the iteration expression "{{R1.x, R2.x}}" is |
| + equivalent to the SQL cross-product projection: |
| Line 65 was replaced by lines 147-150 |
| - !!! Semantic-Type Labels |
| + {{{ |
| + SELECT DISTINCT R1.x, R2.x |
| + FROM Employee R1, Employee R2 |
| + }}} |
| Lines 67-76 were replaced by lines 152-154 |
| - Labels within a semantic-type description provide a mechanism to |
| - identify and name the resources and ontology terms used in the |
| - corresponding annotations. In a {{Label}} element, the the {{name}} |
| - attribute is assigned to the resource identified by the {{resource}} |
| - attribute. Each {{Label}} element is required to have exactly one |
| - {{name}} and {{resource}} attribute. A {{SemanticType}} element must |
| - contain at least two {{Label}} elements: one identifying the resource |
| - to be annotated and the other identifying an ontology |
| - concept. Further, no two {{Label}} elements within a semantic type may |
| - have the same {{name}} attribute. |
| + In a similar way, one can view {{foreach}} expressions as |
| + group constructors, similar to the {{GROUP BY}} clause in |
| + SQL. |
| Lines 78-80 were replaced by lines 156-159 |
| - The first label shown below associates a dataset to the name {{crops}} |
| - and the second label associates an ontology concept to the name |
| - {{Biomass}}. |
| + __Conditions.__ Conditions can be added to restrict the |
| + application of a pattern. For example, the following pattern restricts |
| + the creation of {{C}} instances based on positive values of |
| + {{x}}. |
| Line 83 was replaced by lines 162-167 |
| - <sms:Label name="crops" resource="KBS019-003"/> |
| + <individual type="ont:C" foreach="DISTINCT R.x, R.y" if="R.x>0"/> |
| + }}} |
| + |
| + This pattern can be read as "For each unique x, y (tuple) value |
| + pair of R in which x is greater than 0, create an instance of C." The |
| + corresponding first-order rule for this pattern is: |
| Line 85 was replaced by lines 169-170 |
| - <sms:Label name="Biomass" resource="http://seek.ecoinformatics.org/seek/ontos/DefaultOnto#Biomass"/> |
| + {{{ |
| + (Axyz) R(x, y, z), x>0, u=id_p3(x, y) -> triple(u, rdfs:type, ont:C). |
| At line 87 added 19 lines. |
| + In general, conditions are Boolean expressions of the form |
| + {{term op term}}, where a {{term}} is a constant or |
| + variable (such as {{R.x}} or the value {{5}}), and |
| + {{op}} is a Boolean operator such as {{<}}, |
| + {{>}}, {{<=}}, {{>=}}, or |
| + {{=}}. |
| + |
| + As with {{foreach}} expressions, {{if}} |
| + expressions can be given as a conjunction of comma-separated |
| + conditions. Further, condition expressions may contain resource |
| + variables that are outside the condition's __<a |
| + href="#context">iteration context</a>__, i.e., the set of variables |
| + (or particular bindings of the variables) used in the condition's |
| + corresponding {{foreach}} expression. Note that any given |
| + binding of {{foreach}} variables may have many associated |
| + values for an "out-of-context" variable. For these cases, the |
| + {{if}} expression is satisfied whenever the condition is true |
| + for any one of these values (i.e., similar to the {{ANY}} |
| + keyword in SQL). |
| At line 89 added 1 line. |
| + !!3.2 Object Properties |
| Line 91 was replaced by lines 196-205 |
| - !!! Semantic Annotations |
| + A {{property}} expression assigns OWL properties to |
| + corresponding individuals within an instantiation pattern. For |
| + example, the following pattern creates instances of {{C}} |
| + containing properties {{P}}: |
| + |
| + {{{ |
| + <individual type="ont:C" foreach="DISTINCT R.x"> |
| + <property type="ont:P" valuetype="ont:D"/> |
| + </individual> |
| + }}} |
| Lines 93-98 were replaced by lines 207-210 |
| - An annotation asserts that an object of a resource has a particular |
| - meaning according to definitions within an ontology. The {{object}} |
| - and {{meaning}} attributes of an {{Annotation}} element relate the |
| - object and ontology expressions, respectively. We provide a uniform |
| - __annotation language__ for identifying resource objects and |
| - specifying ontology expressions. |
| + This pattern can be read as "For each unique x value of R, create |
| + an instance of C that has a property P to an instance of D." Executing |
| + this pattern results in the following document, assuming there are |
| + __n__ unique values of {{x}} in {{R}}[6]. |
| Lines 100-108 were replaced by lines 212-216 |
| - 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. |
| + {{{ |
| + <rdf:RDF xmlns="local-ns" ...> |
| + <owl:Ontology rdf:about=""> |
| + <owl:imports rdf:resource="htt://ontologies.org/ont"/> |
| + </owl:Ontology> |
| Lines 110-111 were replaced by lines 218-228 |
| - The annotation language has two forms: an abbreviated syntax, and a |
| - more complex, full syntax. |
| + <ont:C rdf:ID="id-val1"> |
| + <ont:P> |
| + <ont:D/> |
| + </ont:P> |
| + </ont:C> |
| + ... |
| + <ont:C rdf:ID="id-valn"> |
| + <ont:P> |
| + <ont:D/> |
| + </ont:P> |
| + </ont:C> |
| Line 113 was replaced by lines 230-231 |
| - !! The Abbreviated Annotation-Language Syntax |
| + </rdf:RDF> |
| + }}} |
| Lines 115-117 were replaced by line 233 |
| - For expressing annotation objects, the abbreviated syntax permits the |
| - following atoms given a resource label {{T}} and attributes {{A1}} to |
| - {{An}}. |
| + The first-order rule for this pattern is: |
| Line 120 was replaced by lines 236-239 |
| - T |
| + (Axyz) R(x, y, z), u=id_p4(x) -> (Ev) triple(u, rdf:type, ont:C'), |
| + triple(u, ont:P, v), |
| + triple(v, rdf:type, ont:D'). |
| + }}} |
| Line 122 was replaced by lines 241-245 |
| - T.A1 |
| + Note that in this rule, {{v}} is existentially |
| + quantified, which we assume is interpreted as an RDF anonymous |
| + identifier. Alternatively, we could have introduced a new Skolem |
| + function over {{x}} values (similar to {{id_p4}}) |
| + for generating the appropriate {{D}} identifiers. |
| Line 124 was replaced by lines 247-257 |
| - T.A1.A2. ... .An |
| + __Nested Properties.__ Property expressions corresponding to |
| + OWL object properties can be arbitrarily nested within instantiation |
| + patterns. For example, the following pattern further elaborates the |
| + {{D}} instances above with {{Q}} properties: |
| + |
| + {{{ |
| + <individual type="ont:C" foreach="DISTINCT R.x"> |
| + <property type="ont:P" valuetype="ont:D"> |
| + <property type="ont:Q" valuetype="ont:E"/> |
| + </property> |
| + </individual> |
| At line 126 added 4 lines. |
| + This pattern can be read as "For each unique x value of R, create |
| + an instance of C that has a property P to an instance of D such that |
| + the D instance has a property Q to an instance of E." The first-order |
| + rule for this pattern is: |
| Lines 128-140 were replaced by lines 265-271 |
| - The first 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 second atom {{T.A1}} selects |
| - {{A1}} objects contained within {{T}} objects. 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[1], |
| - {{T.A1.A2}} selects the {{A2}} objects nested within {{A1}} objects |
| - contained in {{T}} objects. Atoms can be combined to form expressions. In particular, an |
| - expression is either: (a) a single atom or (b) a comma-separated |
| - list of atoms of the form {{T.A1}} or {{T.A1.A2. ... An}}. |
| + {{{ |
| + (Axyz) R(x, y, z), u=id_p5(x) -> (Evw) triple(u, rdf:type, ont:C), |
| + triple(u, ont:P, v), |
| + triple(v, rdf:type, ont:D) |
| + triple(v, ont:Q, w), |
| + triple(w, rdf:type, ont:E). |
| + }}} |
| Lines 142-143 were replaced by lines 273-275 |
| - In the abbreviated syntax, ontology expressions only consist of a |
| - single concept label {{C}}. |
| + __Multiple Properties.__ Individuals can be assigned more than |
| + one property. The following pattern assigns two properties |
| + {{P1}} and {{P2}}. |
| Lines 145-146 were replaced by lines 277-282 |
| - To illustrate, consider the following semantic-type description for |
| - the {{crops}} data-set resource. |
| + {{{ |
| + <individual type="ont:C" foreach="DISTINCT R.x"> |
| + <property type="ont:P1" valuetype="ont:D1"/> |
| + <property type="ont:P2" valuetype="ont:D2"/> |
| + </individual> |
| + }}} |
| At line 148 added 3 lines. |
| + This pattern can be read as "For each unique x value of R, create |
| + an instance of C that has two properties, P1 to an instance of D1, and |
| + P2 to an instance of D2." The first-order rule for this pattern is: |
| Line 150 was replaced by lines 289-294 |
| - <sms:SemanticType id="mySemType" xmlns:sms="http://seek.ecoinformatics.org/sms" xmlns:ont="http://seek.ecoinformatics.org/seek/ontos/DefaultOnto#"> |
| + (Axyz) R(x, y, z), u=id_p6(x) -> (Evw) triple(u, rdf:type, ont:C), |
| + triple(u, ont:P1, v), |
| + triple(v, rdf:type, ont:D1) |
| + triple(u, ont:P2, w), |
| + triple(w, rdf:type, ont:D2). |
| + }}} |
| Removed lines 152-157 |
| - <sms:Label name="crops" resource="KBS019-003"/> |
| - <sms:Label name="Measurement" resource="ont:Measurement"/> |
| - <sms:Label name="Biomass" resource="ont:Biomass"/> |
| - <sms:Label name="Species" resource="ont:Species"/> |
| - <sms:Label name="Year" resource="ont:Year"/> |
| - <sms:Label name="Location" resource="ont:Location"/> |
| Lines 159-163 were replaced by lines 297-299 |
| - <sms:Annotation object="crops" meaning="Measurement"/> |
| - <sms:Annotation object="crops.bm" meaning="Biomass"/> |
| - <sms:Annotation object="crops.spp" meaning="Species"/> |
| - <sms:Annotation object="crops.yr" meaning="Year"/> |
| - <sms:Annotation object="crops.station" meaning="Location"/> |
| + The general form of a pattern consists of an |
| + {{individual}} expression, followed by any number of |
| + (possibly nested) {{property}} expressions: |
| Line 165 was replaced by lines 301-307 |
| - </sms:SemanticType> |
| + {{{ |
| + <individual type="..." foreach="..." if="..." ...> |
| + <property type="..." ...> |
| + ... nested property expressions ... |
| + </property> |
| + ... additional property expressions ... |
| + </individual> |
| At line 167 added 3 lines. |
| + The additional attributes of {{individual}} and |
| + {{property}} statements are described further below (as well |
| + as in the footnotes). |
| Lines 169-176 were replaced by line 314 |
| - In this simple example, we (1) associate the label {{crops}} to the |
| - data-set resource identifed as {{KBS019-003}}, (2) associate the |
| - remaining labels to corresponding ontology concepts (simplifying their |
| - identifiers using XML namespaces), (3) state with the first annotation |
| - that each {{crops}} tuple is a {{Measurement}} instance, (4) state |
| - with the second annotation that each {{bm}} attribute value is a |
| - {{Biomass}} instance, (5) state with the thrid annotation that each |
| - {{spp}} attribute value is a {{Species}} instance, and so on. |
| + !!3.3 Datatype Properties |
| At line 177 added 5 lines. |
| + The examples so far assume the use of OWL object properties, whose |
| + ranges (i.e., what the properties "point" to) are individuals. Here we |
| + describe support for annotating to datatype properties, in which |
| + ranges are assumed to be atomic data values (e.g., strings, integers, |
| + or doubles). |
| At line 178 added 23 lines. |
| + Datatype {{property}} statements use the attribute |
| + {{value}} instead of {{valuetype}}. In general, a |
| + {{value}} attribute is used to assign a specific data value |
| + or individual identifier to a property, whereas a |
| + {{valuetype}} attribute is used to give the type of the |
| + individual linked to the property. Thus, {{valuetype}} |
| + attributes are used exclusively for object properties, and |
| + {{value}} attributes can be used for assigning both object |
| + and datatype properties. {{Property}} statements that use a |
| + {{value}} attribute (for either an object or datatype |
| + property) cannot be further nested. |
| + |
| + __Constants.__ One use of a datatype property annotation is for |
| + assigning constant values to each corresponding individual generated |
| + by a pattern. For example, the following pattern assigns a |
| + property {{P}} with the value {{5}} to each |
| + generated {{C}} instance. |
| + |
| + {{{ |
| + <individual type="ont:C" foreach="DISTINCT R.x"> |
| + <property type="ont:P" value="5"/> |
| + </individual> |
| + }}} |
| At line 179 added 3 lines. |
| + This pattern can be read as "For each unique x value of R, create |
| + an instance of C that has a property P with the value 5." The |
| + corresponding first-order rule for this pattern is: |
| Line 181 was replaced by lines 350-353 |
| - !! Semantic-Type Ontology Definitions |
| + {{{ |
| + (Axyz) R(x, y, z), u=id_p7(x) -> triple(u, rdf:type, ont:C), |
| + triple(u, ont:P, 5). |
| + }}} |
| Lines 183-188 were replaced by lines 355-358 |
| - For convenience, we permit ontology concept definitions to be directly |
| - included within a semantic type using the {{OntologyDefinitions}} |
| - element. The purpose of this features is to allow specialized concept |
| - definitions 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[2]. |
| + __Resource Values.__ Another common use of datatype property |
| + annotations is for capturing associated resource values. For example, |
| + the following pattern assigns each instance a property {{P}} |
| + whose value is taken from the resource variable {{x}}. |
| Lines 190-194 were replaced by lines 360-364 |
| - To illustrate, part of the previous semantic type is shown below with an |
| - embedded concept. (Note that to simplify the definition below we take |
| - liberty with the use of namespaces in OWL). This embedded concept |
| - definition states that {{MyMeasurement}} is both a {{Measurement}} and |
| - a {{SubjectiveObservation}}. |
| + {{{ |
| + <individual type="ont:C" foreach="DISTINCT R.x"> |
| + <property type="ont:P" value="$R.x"/> |
| + </individual> |
| + }}} |
| At line 195 added 5 lines. |
| + This pattern can be read as "For each unique x value of R, create |
| + an instance of C that has a property P with the value x." Note that |
| + the symbol '$' is used to distinguish references to resource values |
| + from constants. The corresponding first-order rule for this pattern |
| + is: |
| Lines 198-202 were replaced by lines 373-385 |
| - <sms:SemanticType id="mySemType" xmlns:sms="http://seek.ecoinformatics.org/sms" |
| - xmlns:ont="http://seek.ecoinformatics.org/seek/ontos/DefaultOnto#" |
| - xmlns:owl="http://www.w3.org/2002/07/owl#" |
| - xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" |
| - xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> |
| + (Axyz) R(x, y, z), u=id_p8(x) -> triple(u, rdf:type, ont:C), |
| + triple(u, ont:P, x). |
| + }}} |
| + |
| + Resource variables can be used outside of the current iteration |
| + context (i.e., the enclosing {{foreach}} expression). In this |
| + case, the current iteration context is used to determine the |
| + particular resource values that are accessed. Note that it is possible |
| + for multiple properties to be created when the resource variables are |
| + outside of the iteration context. For example, the following pattern |
| + assigns to each instance associated with {{x}}, a property |
| + {{P}} for each of {{x}}'s corresponding |
| + {{y}} values. |
| Line 204 was replaced by lines 387-391 |
| - <sms:Label name="crops" resource="KBS019-003"/> |
| + {{{ |
| + <individual type="ont:C" foreach="DISTINCT R.x"> |
| + <property type="ont:P" value="$R.y"/> |
| + </individual> |
| + }}} |
| Line 206 was replaced by lines 393-395 |
| - <sms:Label name="Measurement" resource="MyMeasurement"/> |
| + This pattern can be read as "For each unique x value of R, create |
| + an instance of C that has a property P with value y, for each unique y |
| + value of x"[7]. The corresponding first-order rule for this pattern is: |
| Line 208 was replaced by lines 397-400 |
| - <sms:Annotation object="crops" meaning="MyMeasurement"/> |
| + {{{ |
| + (Axyz) R(x, y, z), u=id_p9(x) -> triple(u, rdf:type, ont:C), |
| + triple(u, ont:P, y). |
| + }}} |
| Line 210 was replaced by lines 402-409 |
| - <sms:OntologyDefinitions> |
| + In this case, if a particular {{x}} value has multiple |
| + {{y}} values, each such {{y}} value will result in a |
| + {{P}} property. Note that if {{x}} and |
| + {{y}} were not related, (e.g., if the expressions were |
| + {{R1.x}} and {{R2.y}}, respectively), the result |
| + would be a cross-product in which every {{x}} value would be |
| + {{P}}-related to every {{y}} value. For example, the |
| + following pattern: |
| Lines 212-219 were replaced by lines 411-415 |
| - <owl:Class rdf:ID="MyMeasurement"> |
| - <owl:equivalentClass> |
| - <owl:intersectionOf rdf:parseType="Collection"> |
| - <owl:Class rdf:resource="ont:Measurement"/> |
| - <owl:Class rdf:resource="ont:SubjectiveObservation"/> |
| - </owl:intersectionOf> |
| - </owl:equivalentClass> |
| - </sms:Resource> |
| + {{{ |
| + <individual type="ont:C" foreach="DISTINCT R1.x"> |
| + <property type="ont:P" value="$R2.y"/> |
| + </individual> |
| + }}} |
| Line 221 was replaced by lines 417-419 |
| - </sms:OntologyDefinitions> |
| + corresponds to the following first-order rule, assuming |
| + {{R1}} and {{R2}} both represent relation |
| + {{R}}: |
| Line 223 was replaced by lines 421-423 |
| - </sms:SemanticType> |
| + {{{ |
| + (Axvzwyt) R(x, v, z), R(w, y, t), u=id_p10(x) -> triple(u, rdf:type, ont:C), |
| + triple(u, ont:P, y). |
| At line 225 added 4 lines. |
| + In an instantiation pattern, {{value}} expressions must |
| + evaluate to a single value. Although not considered here, it may be |
| + useful to define functions for use in {{value}} expressions, |
| + such as concatenation, addition, and so on. |
| Line 227 was replaced by lines 431-437 |
| - !! The Full Annotation-Language Syntax |
| + __Conditional Properties.__ A {{property}} statement |
| + can be conditionally applied using an {{if}} expression. In |
| + particular, the conditions of the {{if}} expression must hold |
| + for the {{property}} to be added to the corresponding |
| + individual. For example, the following pattern only adds |
| + {{P}} to the individual if {{x}} is a positive |
| + value. |
| Lines 229-236 were replaced by lines 439-443 |
| - The full annotation-language syntax provides more access to various |
| - parts of a complex structure and the ability to assign those parts to |
| - more complex ontology expressions. To support a wide variety of |
| - structural models -- the primary ones including relational, XML, and |
| - the Ptolemy type system -- we consider a generic model consisting |
| - of nested-relational-style constructs. In addition, we permit |
| - multi-valued attributes in which an attribute can have an associated |
| - collection of values. |
| + {{{ |
| + <individual type="ont:C" foreach="DISTINCT R.x"> |
| + <property type="ont:P" value="$R.x" if="R.x>0"/> |
| + </individual> |
| + }}} |
| Lines 238-241 were replaced by line 445 |
| - The abbreviated annotation-language syntax is shorthand for a subset |
| - of the full syntax (we give more details of the relationship below). |
| - In the full syntax, resource expressions consist of lists |
| - of atoms (separated by commas) taking one of the following forms. |
| + This patterns must be represented using two first-order rules: |
| Line 244 was replaced by line 448 |
| - x:T |
| + (Axyz) R(x, y, z), u=id_p11(x) -> triple(u, rdf:type, ont:C). |
| Line 246 was replaced by line 450 |
| - x[A1=y] |
| + (Axyz) R(x, y, z), x>0, u=id_p11(x) -> triple(u, ont:P, x). |
| Lines 249-253 were replaced by lines 453-458 |
| - Here, symbols {{x}} and {{y}} denote either constants, variables, or |
| - skolem terms. Variables are prefixed with a '$' sign. Constants that |
| - contain spaces must be delimited using single quotes. A skolem term |
| - takes the form {{f(z1, ..., zn)}} for symbols {{z1}} to {{zn}} and {{n |
| - > 0}}. |
| + Thus, the condition on the property does not affect whether the |
| + individual is created, only whether the individual has a |
| + {{P}} property. Using property conditions, it is possible to |
| + define simple mappings from resource values to standard property |
| + values, e.g., for converting coded values in a dataset to their |
| + corresponding "full" names. |
| Lines 255-257 were replaced by lines 460-467 |
| - For {{x}} and {{y}} constants, the atom {{x:T}} is true if {{x}} is a |
| - {{T}} object, and the atom {{x[[A1=y]}} is true if {{x}} is an object |
| - that has {{y}} as one of its {{A1}} attribute values. |
| + Like with conditions on {{individual}} statements, no |
| + restrictions are placed on the variables that can be used in |
| + {{property}} statement conditions. Variables used in |
| + property conditions that are outside the iteration context of the |
| + property, with the exception of variables within {{value}} |
| + expressions[8], require only one associated value to |
| + satisfy the condition for the property to be applied (again, similar |
| + to the {{ANY}} keyword in SQL). |
| Removed lines 259-264 |
| - Complex expressions are constructed as follows: each atom is an |
| - expression; expressions {{x:T}} and {{x[[A1=y]}} can be composed to |
| - form the expression {{x:T[[A1=y]}}; expressions {{x[[A1=y]}} and |
| - {{x[[A2=z}} can be composed to form the expression {{x[[A1=y, A2=z]}}; |
| - expressions {{y:T1[[A2=z]}} and {{x:T[[A1=y]}} can be composed to form |
| - the expression {{x:T[[A1=y:T1[[A2=z]]}}; and so on. |
| Lines 266-271 were replaced by line 470 |
| - This same syntax is used to describe ontology expressions, where {{T}} |
| - can be replaced with a concept label {{C}} and {{A1}} represents a |
| - property label. For {{x}} and {{y}} constants, the atom {{x:C}} is |
| - true if {{x}} is an instance of concept {{C}}, and the atom |
| - {{x:[[A1=y]}} is true if {{x}} has {{y}} as one of its {{A1}} property |
| - values. |
| + !!3.3 Complex Instantiation Patterns |
| Lines 273-284 were replaced by lines 472-479 |
| - The meaning of an annotation using the full syntax can be interpreted |
| - as follows. Assume we have an annotation {{A}} such that {{R}} is the |
| - expression selecting resource objects (the expression in the |
| - {{object}} attribute) and {{O}} is the expression selecting ontology |
| - objects (the expression in the {{meaning}} attribute). The annotation |
| - is a constraint that says whenever the {{object}} attribute is true, |
| - the {{meaning}} attribute is true. Let {{Vo}} be the set of variables |
| - in the {{object}} expression and {{Vm}} be the set of variables in the |
| - {{meaning}} expression not in {{Vm}}. We interpret {{A}} as: |
| - {{(forall Vo) R => (exists Vm) O}}. That is, the annotation asserts |
| - that for each variable assignment making {{R}} true there are variable |
| - assignments for {{Vm}} that make {{O}} true. |
| + We have described two mechanisms to link individuals to object |
| + properties: through {{valuetype}} expressions that generate |
| + new, anonymous individuals "in place"; and through {{value}} |
| + expressions containing pre-defined individual identifiers. Here, we |
| + introduce the use of __pattern labels__ and |
| + __pattern references__ to additionally |
| + allow object properties to link to individuals created in other |
| + instantiation patterns. |
| Lines 286-291 were replaced by lines 481-483 |
| - For instance, consider the semantic type below, which is a more |
| - detailed version of the previous semantic type. |
| - |
| - {{{ |
| - <sms:SemanticType id="mySemType" xmlns:sms="http://seek.ecoinformatics.org/sms" |
| - xmlns:ont="http://seek.ecoinformatics.org/seek/ontos/DefaultOnto#"> |
| + __Pattern Labels.__ Each individual instantiation pattern can |
| + be assigned a unique label. For example, the following pattern is |
| + assigned the label 'o1'. |
| Lines 293-301 were replaced by lines 485-487 |
| - <sms:Label name="crops" resource="KBS019-003"/> |
| - <sms:Label name="Measurement" resource="ont:Measurement"/> |
| - <sms:Label name="Biomass" resource="ont:Biomass"/> |
| - <sms:Label name="Species" resource="ont:Species"/> |
| - <sms:Label name="Year" resource="ont:Year"/> |
| - <sms:Label name="Location" resource="ont:Location"/> |
| - <sms:Label name="measProp" resource="ont:measurementProperty"/> |
| - <sms:Label name="measItem" resource="ont:measurementItem"/> |
| - <sms:Label name="measContext" resource="ont:measurementContext"/> |
| + {{{ |
| + <individual label="o1" type="ont:C" foreach="DISTINCT R.x"/> |
| + }}} |
| Lines 303-307 were replaced by line 489 |
| - <sms:Annotation object="$x:crops" meaning="$x:Measurement"/> |
| - <sms:Annotation object="$x:crops[bm=$y]" meaning="$x[measProp=$y:Biomass]"/> |
| - <sms:Annotation object="$x:crops[spp=$y]" meaning="$x[measItem=$y:Species]"/> |
| - <sms:Annotation object="$x:crops[yr=$y]" meaning="$x[measContext=$y:Year]"/> |
| - <sms:Annotation object="$x:crops[station=$y]" meaning="$x[measContext=$y:Location]"/> |
| + The first-order rule for this pattern is: |
| Line 309 was replaced by lines 491-492 |
| - </sms:SemanticType> |
| + {{{ |
| + (Axyz) R(x, y, z) u=o1(x) -> triple(u, rdf:type, ont:C). |
| Lines 312-314 were replaced by lines 495-498 |
| - The advantage of using full syntax here is that we can properly |
| - connect the attributes of a given tuple to its proper semantic |
| - components. |
| + The use of labels in this way does not change the interpretation |
| + of the pattern, thus, the first-order rule associated with this |
| + pattern is the same as above (p1). However, for convenience, we use |
| + the label name as the Skolem function here. |
| Lines 316-320 were replaced by lines 500-504 |
| - Another advantage of using the full syntax is that it can provide |
| - support for data sets that have "promoted" data to schema. Consider |
| - the following semantic-type description for a data set with attributes |
| - {{station}}, {{MEDSA}}, and {{GLYMX}}, where {{MEDSA}} and {{GLYMX}} |
| - are species codes whose values are biomass measurements. |
| + __Referencing Patterns.__ Properties can reference patterns |
| + using pattern labels in {{value}} expressions[9]. To distinguish pattern references from constants |
| + and resource variables, pattern references are prefixed with an '@' |
| + sign. For example, the following pattern contains a reference to the |
| + pattern labeled 'o1' above. |
| At line 321 added 5 lines. |
| + {{{ |
| + <individual label="o2" type="ont:D" foreach="DISTINCT R.x, R.y"> |
| + <property type="ont:P" value="@o1"/> |
| + </individual> |
| + }}} |
| At line 322 added 5 lines. |
| + This pattern can be read as "For each unique x, y (tuple) value |
| + pair in R, create an instance of D that has a property P to the |
| + corresponding instance of C." The first-order rule for this pattern |
| + is: |
| + |
| Line 324 was replaced by lines 518-520 |
| - <sms:SemanticType id="mySemType" xmlns:sms="http://seek.ecoinformatics.org/sms" xmlns:ont="http://seek.ecoinformatics.org/seek/ontos/DefaultOnto#"> |
| + (Axyz) R(x, y, z) u=o1(x), v=o2(x, y) -> triple(v, rdf:type, ont:D), |
| + triple(v, ont:P, u). |
| + }}} |
| Lines 326-333 were replaced by lines 522-529 |
| - <sms:Label name="ds" resource="..."/> |
| - <sms:Label name="Measurement" resource="ont:Measurement"/> |
| - <sms:Label name="Biomass" resource="ont:Biomass"/> |
| - <sms:Label name="Species" resource="ont:Species"/> |
| - <sms:Label name="Location" resource="ont:Location"/> |
| - <sms:Label name="measProp" resource="ont:measurementProperty"/> |
| - <sms:Label name="measItem" resource="ont:measurementItem"/> |
| - <sms:Label name="measContext" resource="ont:measurementContext"/> |
| + As with resource variables, pattern references are interpreted |
| + with respect to the current iteration context. In this example, |
| + because {{P}}'s iteration context is "R.x, R.y" and |
| + {{o1}}'s iteration context is "R.x" (i.e., {{o1}}'s |
| + {{foreach}} expression is contained in {{P}}'s |
| + enclosing {{foreach}} expression), the added {{P}} |
| + property is assigned the individual corresponding to the current |
| + {{x}} value of the iteration context. |
| Lines 335-338 were replaced by lines 531-533 |
| - <sms:Annotation object="$x:ds[site=$y, MEDSA=$z]" |
| - meaning="f1($x):Measurement[measContext=$y:Location, measProp=$z:Biomass, measItem=MEDSA]"/> |
| - <sms:Annotation object="$x:ds[site=$y, GLYMX=$z]" |
| - meaning="f2($x):Measurement[measContext=$y:Location, measProp=$z:Biomass, measItem=GLYMX]"/> |
| + The iteration context of a property is not required to be a |
| + superset of its referenced pattern. For example, in the following |
| + pattern: |
| Line 340 was replaced by lines 535-538 |
| - </sms:SemanticType> |
| + {{{ |
| + <individual label="o3" type="ont:D" foreach="DISTINCT R.y, R.z"> |
| + <property type="ont:P" value="@o1"/> |
| + </individual> |
| Lines 343-347 were replaced by lines 541-558 |
| - Here, each tuple of the dataset represents two distinct measurements |
| - of biomass: one for the MEDSA species and the other for the GLYMX |
| - species. The skolem terms {{f1($x)}} and {{f2($x)}} distinguish these |
| - two observations given a tuple {{$x}}, that is, the skolem terms can be |
| - seen as an creating new objects from the original object {{$x}}. |
| + each unique {{y}}, {{z}} pair for {{R}} |
| + will be assigned a property {{P}} for every corresponding |
| + {{x}} value of the pair. Note that in this example, any given |
| + {{y}}, {{z}} pair may have multiple associated |
| + {{x}} values. |
| + |
| + Also, the iteration context of a property only applies to the |
| + referenced pattern, and does __not__ apply to additionally nested |
| + pattern references. For example, consider the following two patterns. |
| + |
| + {{{ |
| + <individual label="o5" type="ont:E" foreach="DISTINCT R.x, R.z"> |
| + <property type="ont:Q" value="@o4"/> |
| + </individual> |
| + |
| + <individual label="o4" type="ont:D" foreach="DISTINCT R.y"> |
| + <property type="ont:P" value="@o1"/> |
| + </individual> |
| At line 348 added 1 line. |
| + }}} |
| Line 350 was replaced by line 562 |
| - The abbreviated syntax has a natural "translation" to the full syntax. In particular, the following two annotations are equivalent. |
| + The corresponding first-order rules for these patterns are: |
| Line 353 was replaced by lines 565-566 |
| - <sms:Annotation object="T" meaning="C"/> |
| + (Axyz) R(x, y, z) u=o1(x), v=o4(y) -> triple(v, rdf:type, ont:D), |
| + triple(v, ont:P, u). |
| Line 355 was replaced by lines 568-569 |
| - <sms:Annotation object="$x:T" meaning="$x:C"/> |
| + (Axyz) R(x, y, z) v=o4(y), w=o5(x, z) -> triple(w, rdf:type, ont:E), |
| + triple(w, ont:Q, v). |
| Line 358 was replaced by lines 572-576 |
| - For atoms {{T.A1}}, the following two annotations are equivalent. |
| + Thus, although property values containing pattern references are |
| + assigned values from within the context of the enclosing |
| + {{foreach}} expression, each distinct pattern is still |
| + executed within its own context. To illustrate, let {{R}} be |
| + defined as follows. |
| Line 361 was replaced by lines 579-585 |
| - <sms:Annotation object="T.A1" meaning="C"/> |
| + x y z |
| + --- --- --- |
| + 1 4 8 |
| + 2 4 9 |
| + }}} |
| + |
| + The triples created from pattern {{o1}} are: |
| Line 363 was replaced by lines 587-589 |
| - <sms:Annotation object="$x:T[A1=$y]" meaning="$y:C"/> |
| + {{{ |
| + triple(o1(1), rdf:type, ont:C) |
| + triple(o1(2), rdf:type, ont:C) |
| Line 366 was replaced by line 592 |
| - For atoms {{T.A1.A2. ... .An}}, the following two annotations are equivalent. |
| + The triples created from pattern {{o4}} are: |
| Line 369 was replaced by lines 595-598 |
| - <sms:Annotation object="T.A1.A2. ... .An" meaning="C"/> |
| + triple(o4(4), rdf:type, ont:D) |
| + triple(o4(4), ont:P, o1(1)) |
| + triple(o4(4), ont:P, o1(2)) |
| + }}} |
| Line 371 was replaced by lines 600-606 |
| - <sms:Annotation object="$x:T[A1=$y1], $y2:[A2=$y3] ... $yn-1:[An=$yn]" meaning="$yn:C"/> |
| + And the triples created from pattern {{o5}} are: |
| + |
| + {{{ |
| + triple(o5(1, 8), rdf:type, ont:E) |
| + triple(o5(1, 8), ont:Q, o4(4)) |
| + triple(o5(2, 9), rdf:type, ont:E) |
| + triple(o5(2, 9), ont:Q, o4(4)) |
| Lines 374-376 were replaced by lines 609-615 |
| - And finally, atoms of the form {{T.A1, T.A2, ..., T.Am}}, the |
| - following two annotations are equivalent, where {{f}} is a unique |
| - skolem symbol. |
| + Notice that both individuals of pattern {{o5}} are |
| + {{Q}}-related to the same {{o4}} |
| + individual. Similarly, this {{o4}} individual is |
| + {{P}}-related to both individuals of {{o1}}, |
| + corresponding to __both__ {{x}} values of |
| + {{R}}, and thus going "out of context" for pattern |
| + {{o5}}. |
| At line 377 added 5 lines. |
| + To use the iteration context of {{o5}} for |
| + {{o1}} while still generating intermediate instances of |
| + {{D}}, we can use the following pattern, combining |
| + {{o5}} and {{o4}}: |
| + |
| Line 379 was replaced by lines 623-628 |
| - <sms:Annotation object="T.A1, T.A2, ..., T.Am" meaning="C"/> |
| + <individual label="o6" type="ont:E" foreach="DISTINCT R.x, R.z"> |
| + <property type="ont:Q" valuetype="ont:D"> |
| + <property type="ont:P" value="@o1"/> |
| + </property> |
| + </individual> |
| + }}} |
| Line 381 was replaced by lines 630-636 |
| - <sms:Annotation object="$x:T, $x[A1=$y1], $x[A2=$y2], ..., $x[Am=$ym]" meaning="f($x, $y1, $y2, ..., $ym):C"/> |
| + The corresponding first-order rule for this pattern is: |
| + |
| + {{{ |
| + (Axyz) R(x, y, z) u=o1(x), w=o6(x, z) -> (Ev) triple(w, rdf:type, ont:E), |
| + triple(w, ont:Q, v), |
| + triple(v, rdf:type, ont:D), |
| + triple(v, ont:P, u). |
| Line 384 was replaced by lines 639-643 |
| - ---- |
| + Note that in this case, however, we generate only one |
| + {{D}} instance per {{x}}, {{z}} |
| + pair,(instead of one for every value of {{y}}. Also, with |
| + pattern {{o6}}, we can no longer reference the {{D}} |
| + instances in other patterns. |
| Lines 386-392 were replaced by lines 645-649 |
| - [#1] 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''. |
| + __Property Iteration and Labels__. It is also possible to apply |
| + {{foreach}} expressions to {{property}} statements, |
| + e.g., allowing one to additionally specify how intermediate |
| + individuals, for cases like {{o6}} above, should be |
| + constructed. For example, the following pattern: |
| Line 394 was replaced by lines 651-657 |
| - [#2] Perhaps originally converted from a Sparrow expression. |
| + {{{ |
| + <individual label="o7" type="ont:E" foreach="DISTINCT R.x, R.z"> |
| + <property type="ont:Q" valuetype="ont:D" foreach="DISTINCT R.y" label="o8"> |
| + <property type="ont:P" value="@o1"/> |
| + </property> |
| + </individual> |
| + }}} |
| Line 396 was replaced by lines 659-660 |
| - [#3] The semantic type interchange syntax DTD is: |
| + results in the first-order rule: |
| + |
| Line 398 was replaced by lines 662-666 |
| - ... |
| + (Axyz) R(x, y, z) u=o1(x), w=o7(x, z), v=o8(x, y, z) -> |
| + triple(w, rdf:type, ont:E), |
| + triple(w, ont:Q, v), |
| + triple(v, rdf:type, ont:D), |
| + triple(v, ont:P, u). |
| At line 400 added 61 lines. |
| + As shown, labels may also be applied to intermediate individuals |
| + (via their corresponding {{property}} statements), allowing |
| + these individuals to be referenced from within other patterns. In this |
| + case, the iteration context of the nested pattern is the union of its |
| + {{foreach}} expression with each of its ancestor's |
| + {{foreach}} expressions. |
| + |
| + |
| + !!!Glossary |
| + |
| + ;Semantic Annotation: A mapping from a resource to an instance(s) of an ontology(ies). Semantic annotations in our framework have identifiers as well as associated metadata (who created the annotation, and so on). |
| + |
| + ;Resource: A structured information source with a defined schema. Can be a dataset or a service, such as a workflow, actor, or web-service. |
| + |
| + ;Ontology: Here, by ontology we mean an OWL-based representation of a set of concepts, properties, and constraints (axioms). |
| + |
| + ;Semantic Annotation Template: A set of instantiation patterns within a particular semantic annotation. |
| + |
| + ;Instantiation Pattern: An XML-based specification of a mapping from portions of a resource to instances of an ontology. |
| + |
| + ;Prefix Label: A label used to represent an ontology location. |
| + |
| + ;Resource Variable: An attribute of a resource, which in an annotation template takes the form 'R.x' (or more generally a path expression 'R.x1.x2...xn' for nested relations). |
| + |
| + ;Iteration Context: The set of resource variables, or current variable bindings (as the pattern is being executed), for a property or condition in an instantiation pattern. The iteration context is determined by the enclosing {{foreach}} expression of the item in question. |
| + |
| + ;Pattern Label: A label assigned to a template instantiation pattern. |
| + |
| + ;Pattern Reference: A reference to a template instantiation pattern (using a pattern label) from within an object property in another (or possibly the same) pattern. |
| + |
| + |
| + !!!Footnotes |
| + |
| + [#1] In OWL, instances of classes are called 'individuals.' |
| + |
| + [#2] Alternatively, we could use anonymous identifiers for generated OWL individuals. However, using explicit as opposed to anonymous identifiers has a number of advantages, e.g., identifiers can be used for "provenance" (that is, using conventions for identifier names one could go from the created OWL individuals back to the resource item used to generte the resource), and also make it easier to formalize the interpretation of patterns in first-order logic. |
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| + [#3] The examples of resources in this document are assumed to be relational data sets. However, the approach described here can be used with a variety of resource structures, including nested relational data (e.g., like in XML). |
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| + [#4] By default, variables in {{foreach}} expressions that are null in the resource do not generate corresponding ontology class instances. |
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| + [#5] We use the notation {{(Axy)}} for universal quantification over variables {{x}} and {{y}}; {{(Exy)}} for existential quantification over variables {{x}} and {{y}}; and {{->}} for implication. |
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| + [#6] Note that the use of {{property}} expressions in this way is useful for cases in which the property is either (i) not defined (or optional) in the ontology for the associated class, or (ii) is a required property, but the {{valuetype}} expression gives a subclass of the property's defined range. |
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| + [#7] Implicitly, this pattern is equivalent to the pattern: |
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| + {{{ |
| + <individual type="ont:C" foreach="R.x"> |
| + <property type="ont:P" value="$R.y" foreach="R.y"> |
| + </individual> |
| + }}} |
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| + That is, for each unique {{x}}, {{y}} pair, assign a {{P}} property with value {{y}} to the corresponding {{C}} instance. Additional uses of {{foreach}} attributes on properties are discussed later. |
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| + [#8] Because the variable used within a {{value}} attribute is implicitly carried over to the {{property}} statement's {{foreach}} expression (see [7]), these resource variables are considered to be part of the {{property}} statement's iteration context. |
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| + [#9] Pattern references can be cyclic, i.e., a property within a pattern p can contain a property that refers to p. |
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