1. Omics Modeling 9/27/2011

2. Experimental Study and Experiment

3. Definitions ExperimentStudy- – Current Definition: A detailed examination or analysis designed to discover facts about a system under investigation. Systems may include intact organisms, biologic specimens, natural or synthetic materials, diseases, and pathways. – The definition is application for research, clinical studies and clinical diagnosis that involves molecular testing.

4. Definitions Experiment- – Current Definition: A coordinated set of actions and observations designed to generate data, with the ultimate goal of discovery or hypothesis testing. – Proposed Definition: A coordinated set of actions and observations designed to generate data, with the ultimate goal of either discovery/hypothesis or diagnostic testing.

5. ExperimentalStudy Attributes name: A non-unique identifier by which the experimental study is know or referred. activeDateRange: The timeframe within which the experiment is ongoing. typeCode: Identifies the type of experimental study. EXAMPLES: microarray experiment, model organism experiment designType: A term allowing the classification of the study based on the overall experimental study design. EXAMPLES: time-course design, cross-over design, parallel group design, titration study. Description: A textual explanation of the study, with components, such as objectives or goals. (source: ISA-TAB)

6. Experiment Attribute name: The designation by which an experiment is referenced. activeDateRange: The timeframe within which the experiment is ongoing. typeCode: Identifies the type of experiment. EXAMPLES: microarray experiment, model organism experiment designType: A term allowing the classification of the experiment based on the overall experimental design. EXAMPLES: factorial designs, covariance designs, blocking designs. – Comment (Michael Miller): Do we need the designType in class experiment? It seems duplicate of ExperimentalStudy. Are there examples that show a ExperimentalStudyDesign deciding the design of the Experiment (ExperimentDesign)? – TCGA project is nested at top design type is multi-omics, within that multiple omics experiments-within which multiple centers producing data through runs Description: A textual explanation of the experiment, with components, such as objectives or goals. (source: ISA-TAB)

7. Other Topics Discussed today Activity and subclasses (defined, Planned, Performed Activity) and relationship to ExperimentalStudy and Experiment. ExperimentalFactor – Question (9/29/2011) Michael in Omics call- The Experimenatalfactor has an attribute value as DSET but in the current model we can not associate an experiment to an individual time (we will have all the time associated to the experiment). – Suggestion to LSDAM- Create a separate class called "ExperimentFactorValue". Attributes- 1) value 2) unit. The class will exist between Experimental Factor and Experiment. (Business rule: An experiment has one and only 1 value for each experimental factor). – Would need to delete "Value" attribute from ExperimentalFactor. – Change Request sent to Lisa (9/27/2011) – Need to make change in our model here. Material and related class

8. Next Topic ExperimentalItem Material and related class