Mouse Phenotype Ontology George Gkoutos. Phenotype Annotation Traditional phenotypic descriptions are captures as free text Information retrieval based.

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Presentation transcript:

Mouse Phenotype Ontology George Gkoutos

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.

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

Phenotype Ontology Anatomy Ontogeny (developmental anatomy) GO (ready) Behavior Pathology Cell types Chemical etc…

Phenotypic Descriptor Provided by Michael Ashburners schema C phenotype + R Define what is a concept, a value or an attribute (domain expert)

PATO phenotype & trait ontology Michael Ashburners proposal concept - {usedfor} - attribute -{has} -value -{has} -qualifier | {determinedby} | assay – {constrainedby} | MGED (environmental & genetic)- {oftype} - conditions

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

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

How it will work? Each individual ontology will provide an instance(s) (phenotypic descriptor) One or more phenotypic descriptors will provide the phenotype C anatomy + R + I anatomy C behavior + R + I behavior C etc + R + I etc } Phenotype

Attributes of the Organism [id n & T & I & S & A & D & E] Individual Organism {has} Concept {assayed_by} Assay Undefined Defined {tested_for} Attribute (PATO Attribute) Value (assay provided values) {returned_value} Value (PATO values) {interpretation_of} {has_qualifier} {returned_value} Free Text

ididentifier for individual (n) T:Species (e.g. NCBI taxonomy browser) G:genotype I:Strain S:genotypic sex A:alleles at named loci E:handling conditions (i.e. EUMORPHIA) D:Age/stage of development (Theiler and other staging criteria e.g EMAP) Attributes of the Organism [id n & T & I & S & A & D & E]

PATO structure 3 separate ontologies – Attribute Ontology – Assay Ontology – Value Ontology Assay Ontology contains defined and undefined children

Concept Relation Assay Value Explorer

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

Testing the Schema We have employed the schema and annotated around mice.

Acknowledgments Michael Ashburner Duncan Davidson Suzie Lewis Stuart Aitken Phenotype Consortium John Hancock Bioinformatics Group