1. Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypes The Case of Autism Samson W. Tu, MS, Lakshika Tennakoon, RMP, MSC, MPhil, Amar Das, MD, PhD Stanford Center for Biomedical Informatics Research Stanford University, Stanford, CA, USA http://bmir.stanford.edu/publications/view.php/using_an_integrated_ontology_ and_information_model_for_querying_and_reasoning_about_phenotypes_th e_case_of_autism

2. Research questions How can the structure of clinical and research data be reflected in the ontology so that the formulation of analytical questions are informed by available data? How can abstractions defined in terms of clinical and research data be incorporated into the ontology and related to concepts in the literature? How can concepts and definitions used in studies of autism be formulated as extensions of the BIRNLex ontology and, when appropriate, as PATO phenotypes?

3. Information model Extended the BIRNLex ontology’s information-content entity with an Assessment result class that represents results of study assessments Define super-property and sub-properties to classify the items of assessment instruments into domains.

4. Phenotype values Phenotype Status of age of word - an OWL class defined by being the disjoint union of Delayed word, No word, and Not delayed word Phenotype Status of age of word annotated with citation (Hus) Phenotype values annotated with SWRL definitions

5. SWRL rule If the acqorlossoflang_aword value (represented by the variable ?wordage) of an ADI 2003 assessment (represented by the variable ?assessment) is greater than 24 (months), then the human (represented by the variable ?subject) whose subject id is that of the assessment is the bearer-of Delayed_word.

6. Analytical query Use encoding rules to transform phenotype values into variable values in data set Use SQWL to construct data set for analysis

7. Representation in terms of PATO The status of Delayed word can be formally decomposed in OWL as Delay in the onset of the capability to use words Delay (PATO quality) capability to use words: a kind of developmental capabilities onset: a property relating a developmental capability to the time of its occurrence