--- a/ontology/ProvenanceFormalModel.html Wed Oct 12 15:44:16 2011 +0100
+++ b/ontology/ProvenanceFormalModel.html Wed Oct 12 16:03:09 2011 +0100
@@ -209,7 +209,7 @@
<code>prov:Role</code> might appear in the rdfs:range of
<code>prov:assuming</code>
</div>
- <section>
+ <section id="entity">
<h4>Entity</h4>
<div><b>Class Description</b></div>
<p>Entity is defined to be "An Entity represents an identifiable characterized thing." [[PROV-DM]]</p>
@@ -248,7 +248,7 @@
<div class='issue'>Definition of Entity in PROV-DM is confusing, maybe over-complex <a href="http://www.w3.org/2011/prov/track/issues/85">ISSUE-85</a>.</div>
</section> <!-- Classes -->
- <section>
+ <section id = "processexecution">
<h4>ProcessExecution</h4>
<div><b>Class Description</b></div>
<p>ProcessExecution is defined to be "an identifiable activity, which performs a piece of work." [[PROV-DM]]</p>
@@ -269,7 +269,7 @@
- <section>
+ <section id ="agent">
<h4>Agent</h4>
<div><b>Class Description</b></div>
<p>Agent is defined to be a "characterized entity capable of activity" [[PROV-DM]]</p>
@@ -290,7 +290,7 @@
- <section>
+ <section id="recipe">
<h4>Recipe</h4>
<div><b>Class Description</b></div>
<p>Recipe represents a process specification. The definition of process specifications is outside the scope of PROV:DM. Therefore, this class acts as a place holder in the ontology that can be extended and specialized by users.</p>
@@ -302,7 +302,7 @@
- <section>
+ <section id="time">
<h4>Time</h4>
<div><b>Class Description</b></div>
<p>Time represents temporal information about entities in the Provenance model.</p>
@@ -321,7 +321,7 @@
- <section>
+ <section id="revision">
<h4>Revision</h4>
<div><b>Class Description</b></div>
<p>Revision is defined as a modified version of a Entity.</p>
@@ -332,7 +332,7 @@
- <section>
+ <section id="provenancecontainer">
<h4>ProvenanceContainer</h4>
<div><b>Class Description</b></div>
<p>ProvenanceContainer is defined to be an aggregation of provenance assertions. A provenance container should have an URI associated with it. The ProvenanceContainer class can also be used to model the PROV-DM concept of <a href="http://dvcs.w3.org/hg/prov/raw-file/default/model/ProvenanceModel.html#expression-Account">Account</a>.</p>
@@ -347,7 +347,7 @@
- <section>
+ <section id="location">
<h4>Location</h4>
<div><b>Class Description</b></div>
<p>Location is defined to be "is an identifiable geographic place (ISO 19112)." [[PROV-DM]]</p>
@@ -369,7 +369,7 @@
- <section>
+ <section id="entityinrole">
<h4>EntityInRole</h4>
<div><b>Class Description</b></div>
<p>EntityInRole is defined to be a "realizable entity" (cite?) "assumed by a Entity or an agent." [[PROV-DM]]</p>
@@ -399,14 +399,14 @@
</section>
- <section>
+ <section id="object-properties">
<h3>Object Properties</h3>
<p>The Provenance Model consists of the following object properties. </p>
<p><i>Note: Names of properties starts with a verb in lower case followed by verb(s) starting with upper case </i></p>
- <section>
+ <section id="wasgeneratedby">
<h4>wasGeneratedBy</h4>
<p>wasGeneratedBy links Entity with ProcessExecution representing that Entity was generated as a result of ProcessExecution</p>
<p><i>Note: No arity constraints are assumed between Entity and ProcessExecution</i></p>
@@ -431,7 +431,7 @@
- <section>
+ <section id="wasderivedfrom">
<h4>wasDerivedFrom</h4>
<p>wasDerivedFrom links two distinct characterized entities, where "some characterized entity is transformed from, created from, or affected by another characterized entity."</p>
<img src="http://www.w3.org/2011/prov/wiki/images/3/34/WasDerivedFrom.png" alt="wasDerivedFrom links Entity to Entity"/>
@@ -450,7 +450,7 @@
- <section>
+ <section id="used">
<h4>Used</h4>
<p>Used links ProcessExecution to Entity, where Entity is consumed by ProcessExecution.</p>
<p><i>Note: No arity constraints are assumed between Entity and ProcessExecution</i></p>
@@ -470,7 +470,7 @@
- <section>
+ <section id="hadparticipant">
<h4>hadParticipant</h4>
<p>hadPariticipant links Entity to ProcessExecution, where Entity used or wasGeneratedBy ProcessExecution.
<p><i>Note: No arity constraints are assumed between Entity and ProcessExecution</i></p>
@@ -479,14 +479,14 @@
- <section>
+ <section id="wascomplementof">
<h4>wasComplementOf</h4>
<p>wasComplementOf links two instances of Entity, where "it is relationship between two characterized entities asserted to have compatible characterization over some continuous time interval." <i>(from the Provenance Conceptual Model)</i></p>
</section>
- <section>
+ <section id="wascontrolledby">
<h4>wasControlledBy</h4>
<p>wasControlledBy links ProcessExecution to Agent, where "Control represents the involvement of an agent or a Entity in a process execution"<i>(from the Provenance Conceptual Model)</i></p>
<img src="http://www.w3.org/2011/prov/wiki/images/2/2f/WasControlledBy.png" alt="wasControlledBy links ProcessExecution to Agent"/>
@@ -511,7 +511,7 @@
- <section>
+ <section id="hadrecipe">
<h4>hadRecipe</h4>
<p>The ProcessExecution activity performed can be described as
having the given recipe resource. It is out of the scope for PROV to
@@ -524,7 +524,7 @@
- <section>
+ <section id="wasinformedby">
<h4>wasInformedBy</h4>
<p> This object property links two process executions. It is used to express the fact that a given process execution used an entity that was generated by another process execution.
</p>
@@ -533,7 +533,7 @@
- <section>
+ <section id="wascheduledafter">
<h4>wasScheduledAfter</h4>
<p>
This object property links two instances of ProcessExecution to specify the order in which they took place. Specifically, it is used to specify that a given process execution starts after the end of another process execution.
@@ -543,7 +543,7 @@
</section>
- <section>
+ <section id="characteristics-of-object-properties">
<h3>Characteristics of Object Properties </h3>
<p>The table below summarizes the characteristics of the object properties that are defined in the OWL schema.
</p>
@@ -635,7 +635,7 @@
</div>
</section>
- <section>
+ <section id="annotation-properties">
<h3>Annotation Properties</h3>
<p>The PROV ontology uses the OWL2 annotation properties to describe additional information about the PROV ontology classes, properties, individuals, and axioms. OWL2 defines nine annotation properties that are part of the OWL2 structural specification (see OWL2 Syntax document for additional details [[!OWL2-SYNTAX]]):</p>
<ul>
@@ -655,7 +655,7 @@
</div>
</section>
- <section>
+ <section id="overview-of-the-ontology">
<h3>Overview of the ontology</h3>
<p>The following diagram illustrates the complete PROV ontology schema along with the cardinality restrictions imposed on the properties. </p>
<img src="http://www.w3.org/2011/prov/wiki/images/9/9a/Object_Properties_overall_diagram.png" alt="Object properties among all classes in the PROV OWL ontology"/>
@@ -665,7 +665,7 @@
- <section>
+ <section id="specializing-provenance-ontology-for-domain-specific-provenance-applications">
<h2>Specializing Provenance Ontology for Domain-specific Provenance Applications</h2>
<p>The PROV Ontology is conceived as a reference ontology that can be extended by various domain-specific applications to model the required set of provenance terms. The PROv Ontology classes and properties can be specialized using the following two RDFS properties:</p>
<ul>
@@ -676,7 +676,7 @@
- <section>
+ <section id="moeling-the-crime-file-scenario">
<h3>Modeling the Crime File Scenario</h3>
<p>The example scenario can be encoded as a <a href = "http://www.w3.org/TR/rdf-primer/"> Resource Description Framework (RDF) </a> graph in <a href = "">Figure X</a>:</p>
<div class='issue'>insert figure X</div>
@@ -726,10 +726,10 @@
</rdf:RDF>
</pre>
</div>
- <section>
+ <section id="specialization-of-prov-ontology-classes">
<h4>Specialization of PROV Ontology Classes</h4>
<p> The following new classes were created in the CrimeFile Ontology by extending the PROV ontology classes:</p>
- <section>
+ <section id="cf-journalist">
<h5>cf:Journalist</h5>
<p>The cf:Journalist is a specialization of the PROV ontology <a href="#agent">Agent</a> class and models all individuals that participate in creating, editing, and sharing the crime file.The following RDF/XML code illustrates how cf:Journalist is asserted to be a specialization of <a href="#agent">PROV:Agent.</a></p>
<div class="exampleOuter">
@@ -740,7 +740,7 @@
</pre>
</div>
</section>
- <section>
+ <section id="cf-crimefile">
<h5>cf:CrimeFile</h5>
<p> The cf:CrimeFile is a specialization of the PROV ontology <a href="#entity">Entity</a> class and it models the the file describing the crime statistics in the <a href="http://dvcs.w3.org/hg/prov/raw-file/default/model/ProvenanceModel.html#a-file-scenario">provenance scenario</a>, including the multiple versions of the file. The following RDF/XML code illustrates how cf:Journalist is asserted to be a specialization of <a href="#entity">PROV:Entity</a>.
</p>
@@ -752,7 +752,7 @@
</pre>
</div>
</section>
- <section>
+ <section id="cf-filecreation">
<h5>cf:FileCreation, cf:FileEditing, cf:FileAppending, cf:EmailProcessExecution, cf:SpellChecking</h5>
<p>The classes cf:FileCreation, cf:FileEditing,
cf:FileAppending, cf:EmailProcessExecution, cf:SpellChecking are
@@ -776,10 +776,10 @@
<em>Example extension of PROV ontology in order to describe the crime file scenario</em>
</section>
</section>
- <section>
+ <section id="specialization-of-prov-ontology-properties">
<h4>Specialization of PROV Ontology Properties</h4>
<p> The following new object property was created in the CrimeFile Ontology by extending the PROV ontology object property:</p>
- <section>
+ <section id="cf-hadfilepath">
<h5>cf:hadFilePath</h5>
<p>The property cf:hadFilePath is a specialization of the PROV ontology hadLocation object property and links the class CrimeFile to the FileDirectory class. The following RDF/XML code illustrates the use of rdfs:subPropertyOf to create hadFilePath property.</p>
<div class="exampleOuter">
@@ -799,7 +799,7 @@
<em>Example extension of PROV ontology in order to describe the crime file scenario</em>
</section>
</section>
- <section>
+ <section id="modeling-an-example-scientific-workflow-scenario">
<h3>Modeling an Example Scientific Workflow Scenario</h3>
<p>This section describes an example of extending the PROV
ontology to create a provenance ontology for scientific
@@ -838,7 +838,7 @@
<em>Example extension of PROV ontology in order to describe
workflow provenance</em>
</p>
- <section>
+ <section id="workflow-extensions-to-prov-classes">
<h4>Workflow extensions to PROV classes</h4>
<p>
In order to describe workflow executions following the
@@ -893,7 +893,7 @@
</dd>
</dl>
</section>
- <section>
+ <section id="workflow-extensions-to-prov-properties">
<h4>Workflow extensions to PROV properties</h4>
<p>
While for most cases subclassing will provide the
@@ -991,7 +991,7 @@
</dd>
</dl>
</section>
- <section>
+ <section id="workflow-structure">
<h4>Workflow structure</h4>
<p>
This ontology includes a simple definition language for
@@ -1058,7 +1058,7 @@
</dd>
</dl>
</section>
- <section>
+ <section id="example-workflow">
<h4>Example workflow</h4>
<img src="http://www.w3.org/2011/prov/wiki/images/5/56/Concatsha1.png"
alt="An example workflow with input, three processes, and two outputs." />
@@ -1129,7 +1129,7 @@
</rdf:RDF>
</pre></div>
</section>
- <section>
+ <section id="example-workflow-run">
<h4>Example workflow run</h4>
<p>
This example shows how using the workflow extensions
@@ -1297,7 +1297,7 @@
</section>
</section>
</section>
- <section>
+ <section id="formal-semantics-of-the-prov-ontology">
<h2>Formal Semantics of the PROV Ontology</h2>
<p>The PROV ontology uses OWL2 as the ontology language, hence it supports a set of entailments based on the standard RDF semantics [[!RDF-MT]] and OWL2 semantics ([[!OWL2-DIRECT-SEMANTICS]], [[!OWL2-RDF-BASED-SEMANTICS]]). In this section, we describe these set of semantics as applied to the PROV ontology along with a set of constraints introduced in the PROV-DM [[PROV-DM]] that are provenance-specific. It is intended that provenance applications can leverage this normative description of the formal semantics of PROV ontology to support:</p>
<ul>
@@ -1307,7 +1307,7 @@
- <section>
+ <section id="rdf-semantics-for-prov-ontology">
<h3>RDF Semantics for PROV Ontology</h3>
<p> We briefly summarize the essential features of the RDF Semantics and refer to the RDF semantics [[!RDF-MT]] for the normative specification. The RDF Semantics uses model theory, with a notion of interpretation I defined over RDF (rdf-interpretation) or RDFS (rdfs-interpretation) vocabulary, for specifying the formal semantics of a RDF or RDFS graph [[!RDF-MT]]. The rdf-interpretation is an interpretation that satisfies a set of constraints called "<i>RDF semantic conditions</i>" and a set of "<i>RDF axiomatic triples</i>" (see Section 3.1 of RDF Semantics [[!RDF-MT]]). The rdfs-interpretation is defined over the additional terms in the RDFS vocabulary, including <i>rdfs:domain</i>, <i>rdfs:range</i>, <i>rdfs:Class</i>, <i>rdfs:subClassOf</i>, and <i>rdfs:subPropertyOf</i>. An rdfs-interpretation satisfies a set of constraints called "<i>RDFS semantic conditions</i>" and "<i>RDFS axiomatic triples</i>" (see Section 4.1 of RDFS Semantics [[!RDF-MT]]).
</p>
@@ -1360,7 +1360,7 @@
- <section>
+ <section id="owl2-semantics-for-prov-ontology">
<h3>OWL2 Semantics for PROV Ontology</h3>
<p>In addition to RDF Semantics, the OWL2 semantics as described in [[!OWL2-DIRECT-SEMANTICS]], [[!OWL2-RDF-BASED-SEMANTICS]] are also applicable to PROV ontology. We consider the OWL2 RDF-Based Semantics (since it is a semantics superset of OWL2 Direct Semantics) and specifically the extension of the D-interpretation, which satisfies the constraints for rdf-interpretation, rdfs-interpretation (as defined in previous section), graphs with blank nodes, and interpretation defined for RDF datatypes (see Section 5.1 in RDF Semantics [[!RDF-MT]]). The OWL2 RDF-based semantics introduces the notion of "facets" to constrain datatypes, both the rdf:XMLLiteral defined in the RDF Semantics [[!RDF-MT]] and datatypes defined in the OWL2 Structural Specifications [[!OWL2-SYNTAX]]. The OWL2 RDF-based interpretation, also called <b>D-interpretation with facets</b> is a D-interpretation that also satisfies the OWL2 RDF-based semantics called "semantic constraints" (see Section 5 in OWL2 RDF-Based Semantics [[!OWL2-RDF-BASED-SEMANTICS]]).
</p>
@@ -1368,33 +1368,33 @@
<section id = "entailments-supported-by-the-provenance-model">
<h3>Provenance-specific Entailments Supported by PROV Ontology</h3>
<p>The PROV-DM [[PROV-DM]] introduces a set of specific constraints applicable to PROV ontology. The following is a list of constraints that will be supported by the PROV ontology and any provenance application that uses the PROV ontology.</p>
- <section>
+ <section id="provenance-constraint-on-processexecution">
<h4>Provenance constraint on ProcessExecution</h4>
<p>The PROV-DM describes a constraint on ordering of time (or event) associated with a <a href="#processexecution">ProcessExecution.</a> </p>
<div class='issue'>"From a process execution expression, one can infer that the start event precedes the end event of the represented activity." This is <a href="http://www.w3.org/2011/prov/track/issues/121">ISSUE-121</a></div>
</section>
- <section>
+ <section id="provenance-constraint-on-wasgeneratedby-generation-affects-attributes">
<h4>Provenance constraint on wasGeneratedBy (generation-affects-attributes)</h4>
<p>The PROV-DM describes a constraint on wasGeneratedBy that associates the values of attributes of an Entity with the ProcessExecution that generated the Entity.</p>
<div class='issue'>"Given a process execution pe, entity e, role r, and optional time t, if the assertion wasGeneratedBy(e,pe,r) or wasGeneratedBy(e,pe,r,t) holds, the values of some of e's attributes are determined by the activity denoted by pe and the entities used by pe. Only some (possibly none) of the attributes values may be determined since, in an open world, not all used entities may have been asserted." This is <a href="http://www.w3.org/2011/prov/track/issues/122">ISSUE-122 </a> and <a href="http://www.w3.org/2011/prov/track/issues/105">ISSUE-105</a></div>
</section>
- <section>
+ <section id="provenance-constraint-on-wasgeneratedby-generation-pe-ordering">
<h4>Provenance constraint on wasGeneratedBy (generation-pe-ordering)</h4>
<p>The second constraint on wasGeneratedBy associates an ordering of events associated with the generation of an Entity instance and the start, end time or event of the PE instance.</p>
<div class='issue'>"Given an assertion wasGeneratedBy(x,pe,r) or wasGeneratedBy(x,pe,r,t), one can infer that the generation of the thing denoted by x precedes the end of pe and follows the beginning of pe." This is <a href="http://www.w3.org/2011/prov/track/issues/122">ISSUE-122</a> and <a href="http://www.w3.org/2011/prov/track/issues/105">ISSUE-105</a></div>
</section>
- <section>
+ <section id="provenance-constraint-on-wasgeneratedby-generation-unicity">
<h4>Provenance constraint on wasGeneratedBy (generation-unicity)</h4>
<p>The PROV-DM describes a constraint on wasGeneratedBy that asserts that given an account, only one PE instance can be associated to an Entity instance by the property wasGeneratedBy.</p>
<div class='issue'>"Given an entity expression denoted by e, two process execution expressions denoted by pe1 and pe2, and two qualifiers q1 and q2, if the expressions wasGeneratedBy(e,pe1,q1) and wasGeneratedBy(e,pe2,q2) exist in the scope of a given account, then pe1=pe2 and q1=q2." This is <a href="http://www.w3.org/2011/prov/track/issues/105">ISSUE-105</a></div>
</section>
- <section>
+ <section id ="provenance-constraint-on-used-use-attributes">
<h4>Provenance constraint on Used (use-attributes)</h4>
<p>A constraint is defined for the Used relation in PROV-DM, that makes it necessary for an attribute-value to be true for an Entity instance linked to a ProcessExecution instance by relation Used.
</p>
<div class='issue'>"Given a process execution expression identified by pe, an entity expression identified by e, a qualifier q, and optional time t, if assertion used(pe,e,q) or used(pe,e,q,t) holds, then the existence of an attribute-value pair in the entity expression identified by e is a pre-condition for the termination of the activity represented by the process execution expression identified by pe." This is <a href="http://www.w3.org/2011/prov/track/issues/124">ISSUE-124</a></div>
</section>
- <section>
+ <section id ="provenance-constraint-on-used-pe-ordering">
<h4>Provenance constraint on Used (use-pe-ordering)</h4>
<p>The PROV-DM describes a constraint for Used relation, which makes it necessary for an Entity instance e (linked to a ProcessExecution instance pe by Used relation) to be "used" before pe terminates and also the "generation" of e precedes "use" of e.
</p>