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| - !1 Introduction |
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| - ;:''Comment: Introduction goes here. Introduce our basic vocabulary of concepts including: classes, relationships (i.e., so called owl:ObjectProperty or property definitions between concepts), attributes (owl:DatatypeProperties; property definitions between a concept and a datatype like string), objects, properties, and what we mean by package.'' |
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| - !2 The Eco-Ontology Core |
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| - This section describes the fundamental building blocks of the eco-ontology -- called the ''eco-ontology core'' (or just the ''core''). The core is represented as a single package, and all other ontologies defined within (or that extend) the eco-ontology are built from the core. The purpose of the core is to establish the set of basic semantic constructs that can be used to define more complex ecological concepts and relationships. |
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| - !''Things'' |
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| - Every concept in the eco-ontology extends the generic concept ''EcoOntThing''. The name "thing" is often informally used in ontologies to denote the set of all things. We use the term ''object'' instead of "thing", but we retain the convention of using "thing" to name generic concepts. Figure 1 defines EcoOntThing. As shown, objects can be named using the ''hasName'' attribute. Object names are optional, denoted by the '0' in the cardinality restriction '0..*'; and an object may have more than one name, denoted by the '*' in the cardinality restriction '0..*'. |
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| - [http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/docs/OntoManual/core1.png] |
| - \\__Fig. 1:__ Definition of EcoOntThing; the most general eco-ontology concept. |
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| - !''Parts and Wholes'' |
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| - Objects are often described in terms of their structural relationships. A basic structural relationship is the connection between parts and wholes in which one object serves as a ''composite'', containing zero or more other objects serving as ''parts''. Figure 2 shows how parts and wholes are defined in the core. The concepts ''Composite'' and ''Part'' are sub-concepts of EcoOntThing, and are related through the ''hasPart'' and ''partOf'' relationships. |
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| - [http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/docs/OntoManual/core2.png] |
| - \\__Fig. 2:__ Basic part-whole concepts and relationships. |
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| - We denote a hasPart relationship between a composite object c and a part object p as {{hasPart(c, p)}}, and a partOf relationship between part p and composite c as {{partOf(p, c)}}. Note that a part object can participate in zero or more composite objects -- thus, parts can be shared by composites. |
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| - The hasPart and partOf relationships are inverse and transitive. The inverse relationship states that for every composite object c and part p, {{hasPart(c, p)}} if and only if {{partOf(p, c)}}. The transitive relationship states that for every composite object c and parts p1 and p2, if {{hasPart(c, p1)}} and {{hasPart(p1, p2)}} then {{hasPart(c, p2)}}. The inverse relationship also implies that if {{partOf(p1, c)}} and {{partOf(p2, p1)}} then {{partOf(p2, c)}}. |
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| - There are four ways that part-whole relationships are specialized in the core, shown in Figures 3 - 6. The first specialization is shown in Figure 3 and defines inseparable parts, which are parts that are always contained within at least one composite -- that is, the part object does not exist separately from a collection. Inseparable parts are represented using the ''inseparablePartOf'' relationship and the concept ''InseparablePart''. As shown, the ''inseparablePartOf'' relationship is a sub-relationship (that is, specializes) the more general partOf relationship. |
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| - [http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/docs/OntoManual/core3.png] |
| - \\__Fig. 3:__ Inseparable parts. |
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| - The second specialization is shown in Figure 4 and defines essential parts, which are parts that are required by a composite. In general, composite objects can contain a variety of different part types. For example, a car contains wheels, a chassis, bumpers, and so on. For cars, wheels are essential, whereas sunroofs are optional. Essential parts are defined using the ''hasEssentialPart'' relationship and the ''EssentialPart'' concept. |
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| - [http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/docs/OntoManual/core4.png] |
| - \\__Fig. 4:__ Essential parts. |
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| - The third specialization is shown in Figure 5 and describes unique parts, which are one-of-a-kind parts of a composite. An example of a unique part is a chassis -- any one car can have at most one chassis. Unique parts are defined using the ''hasUniquePart'' relationship and the ''UniquePart'' concept. Note that a chassis is also an essential part for a car. In general, we permit part-whole specializations to be freely mixed. |
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| - [http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/docs/OntoManual/core5.png] |
| - \\__Fig. 5:__ Unique parts. |
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| - The last specialization is shown in Figure 6 and defines unshareable parts, which are parts that can be within at most one composite. All car parts are unshareable. Unshareable parts are defined using the ''isUnshareablePartOf'' relationship and the ''UnshareablePart'' concept. |
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| - [http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/docs/OntoManual/core6.png] |
| - \\__Fig. 6:__ Unshareable parts. |
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| - !''Observations and Measurements'' |
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| - Like parts and wholes, the concept of an observation, and specifically a measurement, is a fundamental building block in the eco-ontology core. Figure 7 gives a high-level definition of an observation. We introduce the ''MeasurementThing'' concept as a sub-concept of EcoOntThing to highlight the special status of observations in the core. A ''MeasurementThing'' is an abstract concept that all other measurement definitions fall under. |
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| - [http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/docs/OntoManual/core7.png] |
| - \\__Fig. 7:__ Observations and observation collections. |
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| - Observations can be grouped into collections through the ''ObservationCollection'' composite concept. Observation collections can also be grouped into other collections. We introduce the abstract concept ''ObservationCollectionPart'' to denote the types of objects that can act as parts in an observation collection object. As shown in Figure 8, we use the part-whole relationships to describe the connection between observation collections and their parts. |
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| - We define an observation, as a concept, to be more general than the concept of a measurement. Informally, observation refers to the result of recognizing or noting some fact or occurrence. In Figure 7, we define the relationship ''itemObserved'' to refer to such an object noted by an observation, which are defined as either properties of some observable entity, or to the existence of an observable entity itself. A measurement goes further by assigning a value to an observed property. |
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| - [http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/docs/OntoManual/core8a.png] |
| - \\__Fig. 8:__ Datasets. |
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| - [http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/docs/OntoManual/core9.png] |
| - \\__Fig. 9:__ Aggregate Observations. |
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| + Coming Soon ... |
