OntologyDBWiki/MAGEOMDiscussion

Discussion of the MAGE object model (MAGE-OM) ontology classes

Introduction

In the section "overview" I introduce the classes as they were defined by Michi in O2DBI. I also highlight differences to the "official" documentation at the EBI: [1]. In the next section, "use case", I create a simple use case to show why it is not such a good idea to try to store a complex ontology like the MGED in this object model.

Overview

The MAGE-OM has three classes that are dedicated to referencing text entries from a controlled vocabulary or ontology. These classes are (O2DBI version):

• Class OntologyEntry EBI Documentation
  • Attributes:
    • category: String
    • value: String
    • description: String
    • association: References to OntologyEntry
    • ontologyReference: Reference to DBEntry
    • owner: String [?]
    • creator: String [?]
• Class DBEntry EBI Documentation
  • Attributes:
    • accession: String
    • accessionVersion: String
    • URI: String
    • database: Reference to Database
• Class Database EBI Documentation
  • Attributes:
    • version: String
    • URI: String
    • description: String [?]
    • name: String [from Identifiable?]
    • db_ref: External BRIDGE reference [?]
    • alt_URI: List of Strings [?]
    • type: OntologyEntry [?]
    • maintainer_email: String [?]

Comments/Questions

• all the attributes marked with [?] were not found in the array express object model documentation. Where do these come from?