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Application-Driven Ontology Framework Overview
Many functionalities of the eagle-i SWEET curation tool are driven by directly consuming the eagle-i ontologies. For example, axioms in the ontology define the primary research resources for which the application collects data, control what fields of metadata are presented for a given resource type, define the order in which these fields are presented, and restrict what values are allowable. There are two primary types of axioms that are used to direct application behavior.
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Concept 1: Domain vs Application Ontology Content
"Domain" content in the eagle-i ontologies includes all axioms representing general knowledge pertinent to the domain of research resources. This content is partitioned into a set of files referred to as the "domain layer" of the ontology, which comprise the publicly released ERO ontology module that is shared for community re-use.
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"Application" content includes axioms meant to drive application functionality. This is not shareable domain knowledge, and not part of publicly released ERO ontologies. This content is partitioned into a set of files that is referred to as the "application layer" of the ontology.
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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. |
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Concept 3: 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 |
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| 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. |
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