MGED Ontology usage

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MGED Ontology --usage

• MGED Ontology Working Group
• Dec, 2003

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Outline

• Brief overview of MGED Ontology (MO)
• Structure of MO
• What is in MO
• Uses of MO
• MAGE and MO
• MGED Ontology use policies
• Simple examples
• Nested term examples
• Referencing outside terms with MO

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Ontologies in general

• Explicit specification of a conceptualization
• Defines a vocabulary with which queries and
  assertions are made
• Classes - base type
• Animal, Cat, Dog
• BioMaterial, Age, TechnologyType
• IS-A relationships Cat IS-A Animal
• Properties - attributes of classes
• number_of_legs, natural_enemy
• HAS-A relationships Cat HAS 4 legs
• Individuals - instantiations of classes
• calico, hound, Stinky Pete
• Axioms - logic statements
• Cat ! Dog

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MGED Ontology (MO)

• Core ontology limited to MAGE-OM v.1.1
• Extended Ontology augments the Core with terms
  currently outside the scope of MAGE v.1.1

OilEd editor http//oiled.man.ac.uk/ Protogé
do google search for it
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MAGE and MO
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MAGE and MO
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Main focus of MGED Ontology

• Structured and rich description of BioMaterials

characteristics
associations
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MGED Ontology Announcements

• http//www.mged.sf.net/ontologies
• About to release first stable release of the Core
  ontology (version 1.1.7)
• Provide usage of the ontology and examples
• Lots of links to ontology resources on the web
• Policies
• Any term not referenced via DatabaseEntry is by
  default user-defined and not part of MO
• accession and URI are not both needed
• Refers to OntologyEntry.value
• MO terms may be used in category for other
  ontologys term (e.g. Organism)

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Referencing MO Terms

• ltMAGE-MLgt
• ltDatabase name"The MGED Ontology"
  identifier"MO"
• URI"http//mged.sourceforge.net/ontologies/MGEDo
  ntology.php" /gt
• ltOntologyEntry category"SomeMOClass" value
  "some_MO_instance"gt
• ltOntologyReference_assngt
• ltDatabaseEntry accession"some_MO_instance"
• URI"http//mged.sourceforge.net/ontologies/MGEDon
  tology.phpsome_MO_instance"gt
• ltDatabase_assnrefgt
• ltDatabase_ref identifier"MO"/gt
• lt/Database_assnrefgt
• lt/DatabaseEntrygt
• lt/OntologyReference_assngt
• lt/OntologyEntrygt
• lt/MAGE-MLgt

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Individuals

• Instance term goes into value and is the
  referenced term.
• Parent term goes into category

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Including parent classes

• You may include parent classes for ease of
  queries, but you must reproduce all of the
  structure from the parent to the term of interest

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Classes with Properties

• Nested structure via OntologyEntry.Association
• Fillers
• base types (boolean, string, etc.)
• Classes/Instances
• Enumeration of Instances
• OntologyEntry category value Property
• Filler is given as OntologyEntry Association
• follow the rules
• When a base type, OntologyEntry.category
  Property

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Measurement Example
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Enumeration of instances
Base type
Class/Instance
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Abstract classes

• These are classes without individuals
• Usually have user-defined instance terms
• Term goes in OntologyEntry category and value
  attributes and referenced via DatabaseEntry
• User-defined term is Association (or child
  OntologyEntry term) with abstract class in
  category and new term in value, unreferenced
• Example Your BioMaterial source had a Disease
  foobar

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Referencing terms in other ontologies

• Special case of last slide, were new term
  optionally references some other ontology via its
  DatabaseEntry
• In addition, specify from within the MGED
  Ontology where the term hailed from
• Is-a OntologyEntry term has properties
• has_database source for the term
• accesion accession for the term in
• value the term from the source

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Without extra DatabaseEntry
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With DatabaseEntry
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Thanks

• MGED Ontology Working Group