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Glossary of Concepts and Terms
Here we present concepts that are specific to our application, and terms used to refer to them. Concepts and terms established in semantic web / ontology communities and standards are taken to be known by users, and not defined here.
Concept 1: Domain Domain vs Application Ontology Content
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See the Table of Annotation and Domain Layer Files for a list of IRIs, key features and content of files that comprise the domain and application layers. |
Concept 2: Extended vs Core Domain Content (model / files / classes)
This is an artificial distinction made based on how MIREOTed content is stored and loaded into memory.
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The extended vs core distinction is important, as specific application annotations are needed to guide the software in finding axioms in the right files, as detailed in the Table of Annotation Properties and Individuals and in the Task Workflow and Scenarios below. The classification of each file in the eagle-i ontology as being extended vs core is indicated in the far right column of the Table of Annotation and Domain Layer Files .
Concept 3: Resource Resource Classes (aka Instantiated Classes)
“Resource” classes represent entities considered to be research resources for which instances are created in the eagle-i data. Subtypes of this concept include "primary" resources that are cataloged and shared, "embedded" resources that are directly related (1:1) with a single primary resource instance, and "stubbed" resources that can be related to more than one primary or embedded resource instance (and also not cataloged or shared in eagle-i).
| Class Type | Description | Examples |
|---|---|---|
| Primary Resource Classes | Represents the main resources types cataloged and shared as instances in the eagle-i data. | Examples include: 'antibody reagent', 'software', 'service offering', 'instrument', ‘cell line’, etc. |
| Embedded Resource Classes | Represents non-primary resources for which instances are created and that are linked 1:1 with a single resource instance. Embedded resources are not cataloged and shared by eagle-i. | Examples include: 'construct inserts' as embedded resource types for 'DNA constructs', 'phenotype annotations' as embedded resource types for 'organisms'. |
| Stubbed Resource Classes | Represents non-primary resources for which instances are created that can be linked to more than one resource instance. Stubbed resources are also not cataloged and shared by eagle-i. | Examples include: 'genetic alteration’ instances, which can be associated with both primary resources or other stubbed resources (such as a ‘cell line’ instance and a ‘human subject’), and 'human subject' instances, which can be linked to more than one 'primary cell line' instance. |
Concept 4: Referenced Taxonomy
Referenced Taxonomies are ontology hierarchies that hold non-resource classes used as values to describe resource attributes. In the data, the IRIs of referenced taxonomy classes are used directly as the objects of RDF triples about a resource instance. Instances of referenced taxonomy classes are not created in the eagle-i data.
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Overview
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