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Kirsty A LeeICCS
Developing and assessing a compositional terminology to describe mutant phenotypes
Background
Biology background: ENU mouse mutagenesis screens provide vast amount of phenotypic data
Need for mechanism to describe data which is
1: amenable to computation and
2: allows researchers to maintain precision of phenotype descriptions
Growing use of ontologies in the sharing of biological data
Research Interests
Traditional vs. CompositionalTraditional: atomic, free text description
Compositional: Concept
(eye)
Value(small)
Assay(visual inspection)
Attribute(size)
QualifierComment
Environmental conditions
Preliminary ResearchDiGeorge syndrome – phenotypically variable and
well characterized pathway
Codified traditional descriptions into compositional framework and combined with existing PaTO phenotype description
Raised many issues such as how to encode phenotypes where fusion processes result in a new concept being formed
Classified dependancies within ontological framework eg. Preyer reflex
Kidney disease– similar characterization of kidney organogenesis
Testing terminologyDeveloping developmental and clinical
PaTO-style ontology based on DiGeorge and kidney descriptions
Assess ability of ontology to cluster genes with similar function, by clustering phenotypes
Test clustering of pathway X using three sets of genes
1: Genes known to be involved in pathway X2: Genes in an unrelated pathway Y3: Genes independent from but weakly
related to genes in pathway X
Future Questions
– consider intermediates between traditional and compositional; utilize NLP tools to structure traditional description from research papers?
– Look at how phenotypes are described at the point of data capture
– Consider current and future techniques for formal reasoning which may be applied to content structured by ontology
Kirsty A Lee ICCS
Developing and assessing a compositional terminology for
describing mutant phenotypes