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 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

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

MAGE and MO

MAGE and MO

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

A graph representation

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”)

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>

Graph representation of previous slide’s XML

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

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

Measurement Example

Enumeration of instances Base type Class/Instance

Enumerated instances example

Base type example

Class/Property example

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

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

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

“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”

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

Without extra DatabaseEntry

With DatabaseEntry

Thanks MGED Ontology Working Group