Implementation Details - Revision history

Noy at 17:55, 17 October 2008

2008-10-17T17:55:57Z

Noy at 17:54, 17 October 2008

2008-10-17T17:54:44Z

Noy: /* Calls for marginal notes */

2008-10-16T00:46:46Z

Calls for marginal notes

Noy: /* Calls for marginal notes and reviews */

2008-10-16T00:40:58Z

Calls for marginal notes and reviews

Noy at 00:22, 16 October 2008

2008-10-16T00:22:04Z

Noy at 00:17, 16 October 2008

2008-10-16T00:17:00Z

Noy at 00:15, 16 October 2008

2008-10-16T00:15:14Z

Noy: /* Create a review for the ontology */

2008-10-16T00:10:29Z

Create a review for the ontology

Noy: /* Classes and properties for marginal notes and reviews */

2008-10-15T23:59:55Z

Classes and properties for marginal notes and reviews

Noy: /* Classes and properties for marginal notes and reviews */

2008-10-15T21:59:46Z

Classes and properties for marginal notes and reviews

@@ Line 16: / Line 16: @@
 === Accessing BioPortal Metadata Ontology ===
-The knowledge base variable <tt>'''bioportalMetadataOntology'''</tt> that points to the Metadata ontology (with its instances). We create all new metadata instances in this ontology.
+The knowledge base variable <tt>'''bioPortalMetadataKnowledgeBase'''</tt> that points to the Metadata ontology (with its instances). We create all new metadata instances in this ontology.
-  OWLModel bioportalMetadataOntology = new JenaOWLModel …  // however you initialize an OWL Model in BP
+  OWLModel bioPortalMetadataKnowledgeBase = new JenaOWLModel …  // however you initialize an OWL Model in BP
 === Classes to access ontology metadata ===
-  OWLClass virtualOntologyClass = bioportalMetadataOntology.getOWLNamedClass (“VirtualOntology”); // the class "Virtual Ontology"
+  OWLClass virtualOntologyClass = bioPortalMetadataKnowledgeBase.getOWLNamedClass (“VirtualOntology”); // the class "Virtual Ontology"
-  OWLClass omvOntologyClass = bioportalMetadataOntology.getOWLNamedClass (“OMV:Ontology”); // the class "OMV:Ontology"
+  OWLClass omvOntologyClass = bioPortalMetadataKnowledgeBase.getOWLNamedClass (“OMV:Ontology”); // the class "OMV:Ontology"
-  RDFProperty currentVersionProperty = bioportalMetadataOntology.getRDFProperty("currentVersion"); // the property pointing to the latest version of the ontology (attached to the individuals of the VirtualOntology class)
+  RDFProperty currentVersionProperty = bioPortalMetadataKnowledgeBase.getRDFProperty("currentVersion"); // the property pointing to the latest version of the ontology (attached to the individuals of the VirtualOntology class)
-  RDFProperty virtualURIProperty = bioportalMetadataOntology.getRDFProperty("virtualURI"); // the property "virtualURI" at the "Virtual Ontology" class
+  RDFProperty virtualURIProperty = bioPortalMetadataKnowledgeBase.getRDFProperty("virtualURI"); // the property "virtualURI" at the "Virtual Ontology" class
 We need to list the core properties somewhere and access them. This list can be represented somewhere in the ontology, but for now, we can have it initialized statically in the code:
@@ Line 51: / Line 51: @@
        for (int i = CORE_PROPERTY_NAMES.length - 1; i >= 0; i--) {
               String nextName = CORE_PROPERTY_NAMES [i];
-              RDFProperty nextProperty = bioportalMetadataOntology.getRDFProperty(nextName);
+              RDFProperty nextProperty = bioPortalMetadataKnowledgeBase.getRDFProperty(nextName);
               coreProperties.add (nextProperty);
+       }
@@ Line 59: / Line 59: @@
 The properties <tt>versionsProperty</tt> and <tt>viewsProperty</tt> provide access from the instance of a <tt>VirtualOntology</tt> class to the instances representing its versions and views, respectively:
-		versionsProperty = bioportalMetadataOntology.getRDFProperty("hasVerisons");
+		versionsProperty = bioPortalMetadataKnowledgeBase.getRDFProperty("hasVerisons");
-		viewsProperty = bioportalMetadataOntology.getRDFProperty("hasViews");
+		viewsProperty = bioPortalMetadataKnowledgeBase.getRDFProperty("hasViews");
 === Classes and properties for marginal notes and reviews ===
 The properties that link the annotations and the objects that they annotate:
-  annotatesByVirtualIdProperty = bioportalMetadataOntology.getRDFProperty(Names.ANNOTATES_BY_VIRTUAL_ID_PROPERTY); // property that links an annotations to the virtual id of an ontology ora conccept that it annotates
+  annotatesByVirtualIdProperty = bioPortalMetadataKnowledgeBase.getRDFProperty(Names.ANNOTATES_BY_VIRTUAL_ID_PROPERTY); // property that links an annotations to the virtual id of an ontology ora conccept that it annotates
-  annotatesProperty = bioportalMetadataOntology.getRDFProperty(Names.ANNOTATES_PROPERTY); // property that links an annotations to the object that it annotates
+  annotatesProperty = bioPortalMetadataKnowledgeBase.getRDFProperty(Names.ANNOTATES_PROPERTY); // property that links an annotations to the object that it annotates
-  associatedAnnotationsProperty = bioportalMetadataOntology.getRDFProperty(Names.ASSOCIATED_ANNOTATIONS_PROPERTY); // property that links from an ontology or a concept object to the list of corresponding annotations
+  associatedAnnotationsProperty = bioPortalMetadataKnowledgeBase.getRDFProperty(Names.ASSOCIATED_ANNOTATIONS_PROPERTY); // property that links from an ontology or a concept object to the list of corresponding annotations
 Classes for the review and the values for the review:
-  reviewClass = bioportalMetadataOntology.getOWLNamedClass(Names.REVIEW_CLASS); // instances of this class represent reviews on ontologies
+  reviewClass = bioPortalMetadataKnowledgeBase.getOWLNamedClass(Names.REVIEW_CLASS); // instances of this class represent reviews on ontologies
-  evaluationDimensionClass = bioportalMetadataOntology.getOWLNamedClass(Names.EVALUATION_DIMENSION_CLASS); // instances of this auxiliary class represent
+  evaluationDimensionClass = bioPortalMetadataKnowledgeBase.getOWLNamedClass(Names.EVALUATION_DIMENSION_CLASS); // instances of this auxiliary class represent
-  numericRatingProperty = bioportalMetadataOntology.getRDFProperty(Names.NUMERIC_RATING_PROPERTY); // property in Evaluation Dimension class that contains the numeric rating
+  numericRatingProperty = bioPortalMetadataKnowledgeBase.getRDFProperty(Names.NUMERIC_RATING_PROPERTY); // property in Evaluation Dimension class that contains the numeric rating
-  textualReviewProperty = bioportalMetadataOntology.getRDFProperty(Names.TEXTUAL_REVIEW_PROPERTY); // property in Evaluation Dimension class that contains the numeric rating
+  textualReviewProperty = bioPortalMetadataKnowledgeBase.getRDFProperty(Names.TEXTUAL_REVIEW_PROPERTY); // property in Evaluation Dimension class that contains the numeric rating
 We need to list the dimensions to specify the order in which review dimensions appear. This list can be represented somewhere in the ontology, but for now, we can have it initialized statically in the code:
@@ Line 211: / Line 211: @@
     */
   public static Collection<OWLIndividual> getReviewsForAnOntology (String virtualOntologyURI) {
-         Collection<OWLIndividual> relevantAnnotations = Constants.bioportalMetadataOntology.getFramesWithValue(Constants.annotatesByVirtualIdProperty, null, false, virtualOntologyURI);
+         Collection<OWLIndividual> relevantAnnotations = Constants.bioPortalMetadataKnowledgeBase.getFramesWithValue(Constants.annotatesByVirtualIdProperty, null, false, virtualOntologyURI);
          return relevantAnnotations;
+  }

← Older revision		Revision as of 17:54, 17 October 2008
Line 1:		Line 1:
		+	This document is part of [[BioPortal_Metadata\|a series of documents describing the representation of metadata in BioPortal]]
		+	----
		+
	Note: These notes are for BioPortal developers only and are not critical in understanding the BioPortal approach to metadata representation.		Note: These notes are for BioPortal developers only and are not critical in understanding the BioPortal approach to metadata representation.

← Older revision		Revision as of 00:46, 16 October 2008
Line 263:		Line 263:

	== Calls for marginal notes ==		== Calls for marginal notes ==
		+
		+	=== Given a concept, get all top-level marginal notes associated with a concept ===
		+	''Use cases'': Present marginal notes for a concept. Note that we need only the notes that are at the top level of the discussion threads.
		+
		+	''Input'': concept id
		+
		+	''Output'': A collection of OWL individuals with marginal notes.
		+
		+	''Implementation'':

@@ Line 193: / Line 193: @@
 * …
-== Calls for marginal notes and reviews ==
+== Calls for ontology reviews ==
 === Get the list of reviews for an ontology ===
@@ Line 261: / Line 261: @@
         return review;
+}

@@ Line 1: / Line 1: @@
 Note: These notes are for BioPortal developers only and are not critical in understanding the BioPortal approach to metadata representation.
-This page provides sample code for using the Protege API to access and edit the metadata instances. You can also [[http://www.bioontology.org/wiki/index.php/Image:Source.zip | download the code]].
+This page provides sample code for using the Protege API to access and edit the metadata instances. You can also [http://www.bioontology.org/wiki/images/3/3c/Source.zip download the code].
 = Dealing with instance data =

← Older revision		Revision as of 00:10, 16 October 2008
Line 239:		Line 239:

	''Implementation'':		''Implementation'':
		+
		+	/**
		+	* @param: currentOntologyIndividual an OWL individual representing a virtual ontology
		+	* @param: project is an optional reference to the project if the review is performed in the context of a project
		+	* @param: reviewElements is a collection of the review rating and textual values
		+	*/
		+	public static OWLIndividual createReview (OWLIndividual currentOntologyIndividual, OWLIndividual project, Collection<EvaluationDimensionData> reviewElements) {
		+	OWLIndividual review = (OWLIndividual)Constants.reviewClass.createInstance(null);
		+	review.setPropertyValue(Constants.annotatesProperty, currentOntologyIndividual);
		+	String virtualID = (String) currentOntologyIndividual.getPropertyValue(Constants.virtualURIProperty);
		+	review.setPropertyValue(Constants.annotatesByVirtualIdProperty, virtualID);
		+	for (Iterator i = reviewElements.iterator(); i.hasNext(); ) {
		+	EvaluationDimensionData next = (EvaluationDimensionData)i.next();
		+	OWLIndividual nextElement = (OWLIndividual)Constants.evaluationDimensionClass.createInstance(null);
		+	if (next.rating != null)
		+	nextElement.setPropertyValue(Constants.numericRatingProperty, next.rating.intValue());
		+	if (next.text != null)
		+	nextElement.setPropertyValue(Constants.textualReviewProperty, next.text);
		+	review.setPropertyValue(next.dimension, nextElement);
		+	}
		+	return review;
		+	}

← Older revision		Revision as of 21:59, 15 October 2008
Line 63:		Line 63:
	annotatesByVirtualIdProperty = bioportalMetadataOntology.getRDFProperty(Names.ANNOTATES_BY_VIRTUAL_ID_PROPERTY); // property that links an annotations to the virtual id of an ontology ora conccept that it annotates		annotatesByVirtualIdProperty = bioportalMetadataOntology.getRDFProperty(Names.ANNOTATES_BY_VIRTUAL_ID_PROPERTY); // property that links an annotations to the virtual id of an ontology ora conccept that it annotates

		+	We need to list the dimensions to specify the order in which review dimensions appear. This list can be represented somewhere in the ontology, but for now, we can have it initialized statically in the code:

	= Specifications for the API calls =		= Specifications for the API calls =