MGED Ontology [--usage]
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MGED Ontology [--usage]
MGED Ontology Working GroupDec, 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
BioMaterial
OntologyEntry
+characteristics
+associations
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A graph representation
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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– 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”)
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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>
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Graph representation of previous slide’s XML
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Individuals
• Instance term goes into value and is the referenced term.
• Parent term goes into category
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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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Enumerated instances example
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Base type example
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Class/Property example
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This is BAD! An example of node skipping or tree collapsing
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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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Here we have included the parent term “Action” to the instance term “add” and have included the full term tree.
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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