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MGED Ontology [--usage]

MGED Ontology [--usage]. MGED Ontology Working Group Dec, 2003. 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. Ontologies in general.

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MGED Ontology [--usage]

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  1. MGED Ontology [--usage] MGED Ontology Working Group Dec, 2003

  2. 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

  3. 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

  4. 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

  5. MAGE and MO

  6. MAGE and MO

  7. BioMaterial OntologyEntry Main focus of MGED Ontology • Structured and rich description of BioMaterials +characteristics +associations

  8. A graph representation

  9. 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 • Lot’s 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 ontology’s term (e.g. “Organism”)

  10. Referencing MO Terms <MAGE-ML> … <Database name="The MGED Ontology" identifier="MO" URI="http://mged.sourceforge.net/ontologies/MGEDontology.php" /> … <OntologyEntry category="SomeMOClass" value= "some_MO_instance"> <OntologyReference_assn> <DatabaseEntry accession="#some_MO_instance" URI="http://mged.sourceforge.net/ontologies/MGEDontology.php#some_MO_instance"> <Database_assnref> <Database_ref identifier="MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> </OntologyEntry> … </MAGE-ML>

  11. Graph representation of previous slide’s XML

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

  13. 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

  14. Measurement Example

  15. Enumeration of instances Base type Class/Instance

  16. Enumerated instances example

  17. Base type example

  18. Class/Property example

  19. This is BAD! An example of node skipping or tree collapsing

  20. 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

  21. Here we have included the parent term “Action” to the instance term “add” and have included the full term tree.

  22. “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”

  23. 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

  24. Without extra DatabaseEntry

  25. With DatabaseEntry

  26. Thanks • MGED Ontology Working Group

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