Kirsty A LeeICCS

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

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

k.a.lee@sms.ed.ac.uk

Developing and assessing a compositional terminology for

describing mutant phenotypes