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Kirsty A Lee ICCS k.a.lee@sms.ed.ac.uk

Kirsty A Lee ICCS k.a.lee@sms.ed.ac.uk. 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

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Kirsty A Lee ICCS k.a.lee@sms.ed.ac.uk

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  1. Kirsty A LeeICCS k.a.lee@sms.ed.ac.uk Developing and assessing a compositional terminology to describe mutant phenotypes

  2. 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

  3. Research Interests • Traditional vs. Compositional • Traditional: atomic, free text description • Compositional: Concept (eye) Attribute (size) Environmental conditions Assay (visual inspection) Value (small) Comment Qualifier

  4. Preliminary Research • DiGeorge 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

  5. Testing terminology • Developing 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 X • 2: Genes in an unrelated pathway Y • 3: Genes independent from but weakly related to genes in pathway X

  6. 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

  7. Kirsty A Lee ICCSk.a.lee@sms.ed.ac.uk Developing and assessing a compositional terminology for describing mutant phenotypes

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