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The SEPIO Information Model

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Matthew Brush edited this page Jul 31, 2018 · 4 revisions

To Do: Content below is minimal text copied from the 'SEPIO Framework' page - expand here with additional info:

  • updated text and more diagrams (e.g. hierarchical model and associative model)
  • description of shortcut relations and how they 'expand.
  • sub-properties of starred attributes.
  • description of Qualified Contribution alternative approach (along with modified Info Model Diagram.

The SEPIO Information Model provides an informal description for how the terms and design patterns defined in the ontology can be applied as a model for structuring data. This is an abstract model that is independent of any schema language. At present it is encoded as a UML diagram that provides a 'maximal' specification of what is possible to express using SEPIO (Figure 1). Each type in the information model maps to a SEPIO ontology class, and attributes of each type map to ontology properties. Cardinality constraints in this model are minimally restrictive and consistent with the logic defined in the ontology. More information can be found here (LINK).

In practice, the SEPIO Information Model is a useful guide for implementers to understand the overall model, and help them identify which elements and patterns they should included in defining a ‘SEPIO Profile’ for their particular application (see below). In this way it helps to bridge the gap between the conceptual model implemented in the ontology, and formal schema specifications that will enable data representation and validation.

Figure 1: UML diagram of the maximal SEPIO Information model. Presents data modeling patterns that are possible using the SEPIO Framework. Boxes represent data model types, which contain their attributes possible to model using SEPIO. Attributes in orange are ‘shortcut’ relations that can be used to directly link data that are connected by more than one relationship in a fully normalized model. Attributes with asterisks (*) are those that have sub-properties in the underlying SEPIO ontology, which can be used to refine the parent attribute in the diagram when a more precise relationship is desired. Edges in the diagram represent attributes connecting to other core data types in the model.

Updated Pages

Introduction

  1. Home
  2. Overview
  3. Use Cases
  4. The SEPIO Framework

Framework Components

  1. SEPIO Core Ontology
  2. SEPIO Information Model
  3. SEPIO Profiles
  4. SEPIO Value Sets

Core Concept Pages

  1. Core Concept Home
  2. Evidence Lines

Data Examples

  1. Gene Ontology Annotation
  2. CIViC Variant Interpretation
  3. ClinGen-ACMG Variant Interpretation

Profile Implementations

  1. ClinGen-ACMG Profile
  2. GO Annotation Profile

Obsolete Pages

Core Concepts (obsolete)

  1. Information Content Entities
  2. Assertion
  3. Evidence Item
  4. Evidence Line
  5. Activity
  6. Agent
  7. Contribution
  8. Statements
  9. Proposition 10: Concept-Attribute Tables

Data Examples (obsolete)

  1. ZFIN G2P Association
  2. IMPC G2P Association
  3. CIViC Variant Interpretation
  4. ClinVar Variant Interpretation
  5. ClinGen Variant Interpretation
  6. Panepinto et al. Publication

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