Collections Ontology Specification

Abstract

SWAN (Semantic Web Applications in Neuromedicine) is an interdisciplinary project to develop a practical, common, semantically-structured, framework for biomedical discourse initially applied, but not limited, to significant problems in Alzheimer Disease (AD) research. The SWAN ontology of scientific discourse has been developed in the context of building a series of applications for biomedical researchers, as well as extensive discussions and collaborations with the larger bio-ontologies community.

Collections and sequences are a natural part of the world we need to model: sequence of authors, protein sequences etc.

The Collections ontology defines unordered collections (or Set) and ordered collections (or List).

Status of this document

This specification is currently an evolving document and it is not yet complete.

Table of contents

• 1. Introduction
• 1.1. Terminology and notation
• 2. Collections ontology at a glance
• 3. Collections ontology overview
• 4. Collections ontology description
• 5. Cross-reference for Collections classes and properties
• 6. Pellet reasoner validation results

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1. Introduction

The Collections ontology defines unordered collections (Set and Bag) and ordered collections (or List). This ontology has been inspired by the work "Putting OWL in Order: Patterns for Sequences in OWL" by Drummond et al. (OWL-ED 2006).

1.1. Terminology and notation

The keywords "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be interpreted as described in RFC 2119.

Namespace URIs of the general form "http://www.example.com/" represent some application-dependent or context-dependent URI as defined in RFC 2396.

The XML Namespace URIs that MUST be used by implementations of this specification is: http://swan.mindinformatics.org/ontologies/1.2/collections/

2. Collections ontology at a glance

An alphabetical index of Collections ontology terms, by class (concepts) and by property (relationships, attributes), are given below. All the terms are hyperlinked to their detailed description for quick reference.

3. Collections ontology overview

A Set is a collection that cannot contain duplicate elements. A Set is expressed by linking to it directly all the elements multiple identical values of element will be eliminated because by default they are treated as a set.

Figure 1 - How the Set is implemented

The Bag is characterized by a collection that can have multiple copies of each object. This is performed through the Item entity. The Item is linking exaclty one resource through the relationship itemResource.

Figure 2 - How the Bag is implemented

Note: The Bag and Set classes usage is discuraged if the collection is not an entity per se. In this case it is recommanded to make multiple use of the relationship with the different objects.

Figure 3 - How the List is implemented

4. The Collections ontology description

The Collections ontology defines unordered collections (or Set) and ordered collections (or List). This ontology has been inspired by:

•   » "Putting OWL in Order: Patterns for Sequences in OWL" by Drummond et al. (OWL-ED 2006).
•   » "Exporting Knowledge Bases into OWL" by Chaudhri, et al. (OWL-ED 2006).

5. Cross-reference for Collections classes and properties

» Class collections:Bag

Bag - Collection that can have a number of copies of each object

Note: the usage of the Bag class is discuraged if the set is not a collection per se. In this case it is recommanded to duplicate the relationship with the different objects.

sub-class-of: collections:Collection

» Class collections:Collection

Collection - A generic collection

Note: the usage of the Collection class is discuraged if the set is not a collection per se. In this case it is recommanded to duplicate the relationship with the different objects.

» Class collections:Item

Item - Element belonging to a bag

» Class collections:List

List - An ordered array of items or ordered collection

sub-class-of: collections:Bag

» Class collections:ListItem

ListItem - Element belonging to a list

sub-class-of: collections:Item

» Class collections:Set

Set - A collection that cannot contain duplicate elements

Note: the usage of the Set class is discuraged if the set is not an entity per se. In this case it is recommanded to duplicate the relationship with the different objects.

sub-class-of: collections:Collection

» Property collections:element

element - The link to on of the element of a Collection

Domain: collections:Collection

» Property collections:firstitem

firstitem - The link to the first item of the list

sub-property-of: collections:item
Domain: collections:List
Range: collections:ListItem

» Property collections:followedBy

followedBy - The link to the first item of the list

OWL Type: http://www.w3.org/2002/07/owl#TransitiveProperty
Domain: collections:ListItem
Range: collections:ListItem

» Property collections:item

item - The link to every item of the set

sub-property-of: collections:element
Domain: collections:Bag
Range: collections:Item

» Property collections:itemContent

itemContent - The link to the actual resource to which the item refers.

Domain: collections:Item
Range: http://www.w3.org/2002/07/owl#Thing

» Property collections:lastItem

lastItem - The link to the first item of the list

sub-property-of: collections:item
Domain: collections:List
Range: collections:ListItem

» Property collections:nextItem

nextItem - The link to the next item in a list (ordered collection)

sub-property-of: collections:followedBy
OWL Inverse: collections:previousItem
Domain: collections:ListItem
Range: collections:ListItem

» Property collections:preceededBy

preceededBy - The link to the previous item in a list (ordered collection)

OWL Type: http://www.w3.org/2002/07/owl#TransitiveProperty
Domain: collections:ListItem
Range: collections:ListItem

» Property collections:previousItem

previousItem - The link to the previous item in a list (ordered collection)

sub-property-of: collections:preceededBy
OWL Inverse: collections:nextItem
Domain: collections:ListItem
Range: collections:ListItem

» Property collections:size

size - The number of item belonging to a collection

Domain: collections:Collection
Range: http://www.w3.org/2001/XMLSchema#int

6. Pellet reasoner validation results

OWL Species: DL
DL Expressivity: SHIF(D)
Consistent: Yes
Time: 1314 ms (Loading: 1161 Species Validation: 107 Consistency: 13 Classification: 33 )

Classification:

owl:Thing
    collections:Collection
        collections:Set
        collections:Bag
            collections:List
    collections:Item
        collections:ListItem

Non OWL-Lite features used:
Complement Class: owl:complementOf construct is used complementOf(collections:Item)
Disjoint Classes: owl:disjointWith construct is used DisjointClasses(collections:Item collections:Collection)
Disjoint Classes: owl:disjointWith construct is used DisjointClasses(collections:Bag collections:Set)