Ontology Metrics - Revision history

Whetzel: /* REST service access */

2012-09-06T09:13:00Z

REST service access

Fergerson at 22:05, 2 September 2011

2011-09-02T22:05:44Z

Palexand: /* REST service access */

2010-01-25T23:25:20Z

REST service access

Palexand: /* Quality-Control and Quality-Assurance Metrics */

2009-12-10T02:13:18Z

Quality-Control and Quality-Assurance Metrics

Palexand: /* Quality-Control and Quality-Assurance Metrics */

2009-12-10T02:06:17Z

Quality-Control and Quality-Assurance Metrics

Noy: /* Storing metrics in BioPortal */

2009-10-16T00:56:09Z

Storing metrics in BioPortal

Noy: OntologyMetrics moved to Ontology Metrics: Easier linking.

2009-10-16T00:54:37Z

OntologyMetrics moved to Ontology Metrics: Easier linking.

Noy: /* Generating metrics */

2009-10-16T00:49:45Z

Generating metrics

Noy: /* Generating metrics */

2009-10-16T00:48:54Z

Generating metrics

Noy: /* REST service access */

2009-10-16T00:48:27Z

REST service access

@@ Line 74: / Line 74: @@
 ''Note: there is no version of this service that uses virtual ontology id yet.''
-* '''Signature''': ./ontologies/metrics/{ontologyVersionId}?email={email_address}
+* '''Signature''': ./ontologies/metrics/{ontologyVersionId}?apikey={YourAPIKey}
-* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40616?email=example@example.org
+* '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40133?apikey=YourAPIKey
 The service returns a <tt>ontologyMetricsBean</tt> that contains the version id for the ontology and the values for the metrics that have values computed for them:

@@ Line 1: / Line 1: @@
 = Ontology Metrics in BioPortal =
-This page describes the metrics that BioPortal calculates for the ontologies in its repository. In general, BioPortal will calculate the metrics when the ontology is uploaded and will store it as part of  the [http://www.bioontology.org/wiki/index.php/BioPortal_Metadata Ontology Metadata]. There are two groups of metrics:
+This page describes the metrics that BioPortal calculates for the ontologies in its repository. BioPortal calculates metrics when the ontology is uploaded and will store them as part of  the [http://www.bioontology.org/wiki/index.php/BioPortal_Metadata Ontology Metadata]. There are two groups of metrics:
 * '''Statistical''' metrics
 * '''Quality-control''' and '''quality-assurance''' metrics
-Each ontology may have all, some, or no values filled in for its metrics. Some metrics are meaningful only for ontologies in a specific representation language (e.g., number of axioms matters only for OWL ontologies; there are no individuals to count in the ontologies in OBO format).
+Some metrics are meaningful only for ontologies in a specific representation language (e.g., there are no individuals to count in the ontologies in OBO format).
 == Statistical Metrics ==
 We calculate the following statistics on each ontology in BioPortal:
-* '''number of classes''': the number of classes in the ontology. For OWL ontologies
+* '''number of classes''': the number of named (not anonymous) classes in the ontology.
 * '''number of properties:''' the number of properties or slots in the ontology.
-* '''number of individuals:''' the number of individuals in the ontology. Note:
+* '''number of individuals:''' the number of individuals in the ontology.
 * '''maximum depth:''' the maximum depth of the hierarchy tree.
 ** For OWL, RDFS, Protege, and RRF ontologies, we consider only the ''is-a'' relationship as a hierarchical relationship
@@ Line 28: / Line 23: @@
 * '''classes with only one subclass''': a list of classes that have only one subclass in the ''is-a'' hierarchy. While technically there is no problem in having only one subclass, this situation often indicates that either the hierarchy is under-specified, or the distinction between the class and the subclass is not appropriate.
-* '''classes with too many subclasses''': a list of classes that have more direct subclasses than a certain threshold. The specific threshold is an internal parameter in BioPortal (currently set to 25). This situation may be an indication that additional distinctions and categorization are needed.
+* '''classes with more than 25 subclasses''': a list of classes that have more than direct subclasses. A class that has more than 25 subclasses is a candidate for additional distinctions and categorization are needed.
-* '''classes with no definition''': a list of classes that have no value for the definition property. For ontologies in OBO and RRF formats, the property for definition is part of the language. For OWL ontologies, the authors specify this property as part of the ontology metadata (the default is <tt>skos:definition</tt>). If the ontology author has not specified any property as a definition property, we do not fill out this value.
+* '''classes with no definition''': a list of classes that have no value for the definition property. For ontologies in OBO and RRF formats, the property for definition is part of the language. For OWL ontologies, the authors specify this property as part of the ontology metadata (the default is <tt>skos:definition</tt>).
 Please, contact us at [mailto:support@bioontology.org support@bioontology.org], if there are additional metrics of any kind that you would like to see.
@@ Line 41: / Line 31: @@
 = Generating metrics =
-At the moment, we ''do not'' generate metrics as part of the ontology load process, but we will shortly. The process will be as follows: When BioPortal loads and parses a version of an ontology, it then starts a process that calculates the metrics and stores the values as part of the metadata about that ontology version.
+When BioPortal loads and parses a version of an ontology, it then starts a process that calculates the metrics and stores the values as part of the metadata about that ontology version.
 == Metrics computation and ontology metadata ==

@@ Line 87: / Line 87: @@
 * '''Example''': http://rest.bioontology.org/bioportal/ontologies/metrics/40616?email=example@example.org
-The service returns a <tt>ontologyMetricsBean</tt> that contains the version id for the ontology and the values for the metrics that have some values computed for them:
+The service returns a <tt>ontologyMetricsBean</tt> that contains the version id for the ontology and the values for the metrics that have values computed for them:
 <pre>
 <success>
-   <accessedResource>/bioportal/ontologies/metrics/40616</accessedResource>
+   <accessedResource>/bioportal/ontologies/metrics/42031</accessedResource>
-   <accessDate>2009-10-15 17:43:25.978 PDT</accessDate>
+   <accessDate>2010-01-25 15:15:36.742 PST</accessDate>
    <data>
      <ontologyMetricsBean>
-       <id>40616</id>
+       <id>42031</id>
-       <numberOfClasses>1577</numberOfClasses>
+      <numberOfAxioms>0</numberOfAxioms>
-       <numberOfIndividuals>74</numberOfIndividuals>
-       <numberOfProperties>72</numberOfProperties>
+       <numberOfClasses>293</numberOfClasses>
      </ontologyMetricsBean>
    </data>
 </success>
 </pre>

@@ Line 25: / Line 25: @@
 == Quality-Control and Quality-Assurance Metrics ==
-We calculate the following metrics that may give some indication of the quality of the ontology and help ontology authors improve the quality. To improve their usefulness, we limit the size of lists for any one of these metrics to 200. Ontologies that more than 200 classes in a category will still have the total number of classes in that category counted, but no list will be available.
+We calculate the following metrics that may give some indication of the quality of the ontology and help ontology authors improve the quality. To improve their usefulness, we limit the size of lists for any one of these metrics to 200. Ontologies with more than 200 classes in a category will still have the total number of classes in that category counted, but no list will be available.
 * '''classes with only one subclass''': a list of classes that have only one subclass in the ''is-a'' hierarchy. While technically there is no problem in having only one subclass, this situation often indicates that either the hierarchy is under-specified, or the distinction between the class and the subclass is not appropriate.

@@ Line 25: / Line 25: @@
 == Quality-Control and Quality-Assurance Metrics ==
-We calculate the following metrics that may give some indication of the quality of the ontology and help ontology authors improve the quality.
+We calculate the following metrics that may give some indication of the quality of the ontology and help ontology authors improve the quality. To improve their usefulness, we limit the size of lists for any one of these metrics to 200. Ontologies that more than 200 classes in a category will still have the total number of classes in that category counted, but no list will be available.
 * '''classes with only one subclass''': a list of classes that have only one subclass in the ''is-a'' hierarchy. While technically there is no problem in having only one subclass, this situation often indicates that either the hierarchy is under-specified, or the distinction between the class and the subclass is not appropriate.
 * '''classes with too many subclasses''': a list of classes that have more direct subclasses than a certain threshold. The specific threshold is an internal parameter in BioPortal (currently set to 25). This situation may be an indication that additional distinctions and categorization are needed.
 * '''classes with no definition''': a list of classes that have no value for the definition property. For ontologies in OBO and RRF formats, the property for definition is part of the language. For OWL ontologies, the authors specify this property as part of the ontology metadata (the default is <tt>skos:definition</tt>). If the ontology author has not specified any property as a definition property, we do not fill out this value.
-* '''univocality''': the consistency of expression of concepts in an ontology (developed by Karin Verspoor∗, Daniel Dvorkin, K. Bretonnel Cohen, and Lawrence E. Hunter, University of Colorado)
+* '''univocality''' (future implementation): the consistency of expression of concepts in an ontology (developed by Karin Verspoor∗, Daniel Dvorkin, K. Bretonnel Cohen, and Lawrence E. Hunter, University of Colorado)
 == Auditing and other information ==

@@ Line 56: / Line 56: @@
 * property used to specify the author of a class (default <tt>dc:creator</tt>)
-= Storing metrics in BioPortal =
+= Representing metrics in BioPortal =
 The metrics in BioPortal are stored as part of the ontology metadata. Specifically, each instance of the <tt>OMV:Ontology</tt> class, which describes the metadata about a single ontology version, has a number of properties that store the metrics. Some of these properties are imported from the Ontology Metadata Vocabulary, OMV (the <tt>omv:</tt> prefix) and the rest are defined locally in the BioPortal Metadata Ontology (the <tt>metrics:</tt> prefix). These properties include:

← Older revision		Revision as of 00:48, 16 October 2009
Line 42:		Line 42:

	At the moment, we do not generate metrics as part of the ontology load process, but we will shortly. The process will be as follows: When BioPortal loads and parses a version of an ontology, it then starts a process that calculates the metrics and stores the values as part of the metadata about that ontology version.		At the moment, we do not generate metrics as part of the ontology load process, but we will shortly. The process will be as follows: When BioPortal loads and parses a version of an ontology, it then starts a process that calculates the metrics and stores the values as part of the metadata about that ontology version.
		+
		+	== Metrics computation and ontology metadata ==

	Metric generation relies on the following information being specified in the ontology metadata:		Metric generation relies on the following information being specified in the ontology metadata: