Mouse Phenotype Ontology

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Mouse Phenotype Ontology

• George Gkoutos

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Phenotype Annotation

• Traditional phenotypic descriptions are captures
  as free text
• Information retrieval based on free text is
  extremely limited because of the inherent lack of
  accuracy and specificity.

3
Phenotype Consortium

• Part of the GO consortium
• In 2002, database curators and scientists set up
  regular meetings in order to address the issue.

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Phenotype Ontology

• Anatomy
• Ontogeny (developmental anatomy)
• GO (ready)
• Behavior
• Pathology
• Cell types
• Chemical etc

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Phenotypic Descriptor

• Provided by Michael Ashburners schema
• Cphenotype R
• Define what is a concept, a value or an attribute
  (domain expert)

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PATOphenotype trait ontology

• Michael Ashburners proposal
• concept - usedfor -attribute -has -value
  -has -qualifier
• determinedby
• assay constrainedby
• MGED (environmental genetic)- oftype -
  conditions

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Translation

• eye color brown
  light
• concept - usedfor -attribute -has -value
  -has -qualifier
• Body attribute_of
  abnormal
• position body_position
  
• determinedby
• assay constrainedby
• SHIRPA (body position)
• MGED - oftype - conditions

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• Phenotypic descriptor
• Phenotypic character Assay
• Phenotypic character Concept Attribute
• i.e. eye color
• i.e body position attribute_of _body_position
• Values such as brown, abnormal etc. are
  controlled, defined and provided by the assay

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How it will work?

• Each individual ontology will provide an
  instance(s) (phenotypic descriptor)
• One or more phenotypic descriptors will provide
  the phenotype

Phenotype
Canatomy R Ianatomy Cbehavior R Ibehavior Cetc R Ietc
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Attributes of the Organism
Individual Organism
idn T I S A D E
has
Attribute (PATO Attribute)
Concept
assayed_by
tested_for
Assay
Value (assay provided values)
returned_value
Free Text
returned_value
interpretation_of
Value (PATO values)
has_qualifier
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Attributes of the Organism
idn T I S A D E
id identifier for individual (n) identifier for individual (n)
T Species (e.g. NCBI taxonomy browser) Species (e.g. NCBI taxonomy browser)
G genotype genotype
I Strain
S genotypic sex
A alleles at named loci
E handling conditions (i.e. EUMORPHIA) handling conditions (i.e. EUMORPHIA)
D Age/stage of development (Theiler and other staging criteria e.g EMAP) Age/stage of development (Theiler and other staging criteria e.g EMAP)
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PATO structure

• 3 separate ontologies
• Attribute Ontology
• Assay Ontology
• Value Ontology
• Assay Ontology contains defined and undefined
  children

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Concept Relation Assay Value Explorer
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EUMOPRHIA protocols

• We are in the process of converting and storing
  produced phenotype protocols in an XML database.
• Link these protocols to the ASSAY ontology

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Testing the Schema

• We have employed the schema and annotated around
  600.000 mice.

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Acknowledgments

• Michael Ashburner
• Duncan Davidson
• Suzie Lewis
• Stuart Aitken
• Phenotype Consortium

• John Hancock
• Bioinformatics Group