Linking Models & Data within the ISA structure Stuart Owen (based upon notes by Olga Krebs).

2 Approaches Defining modeling at the : – STUDY level – ASSAY level – Neither approach is right – we need YOUR help!

Defining at the STUDY level when creating a new STUDY – offer the possibility to choose between 2 types: “experimental” or “modelling” add field to define the Biological Problem addressed within that STUDY, from a controlled vocabulary E.g. Metabolism, Signaling, Expression, Gene Networks, Structure, Evolution, Cell cycle, plus your suggestions Means a STUDY can’t contain a mixture of Modeling & Experimental ASSAYS.

Create ASSAY for modeling STUDY Instead of the usual Assay and Technology types, we have: – Modeling approach – Analysis methods – Model types – Software tools – Model format

Attaching the Model to the ASSAY Only ASSAYS linked to a Modeling STUDY may have models linked to it. There may be more that one model, or versions of the same model. Also attach Data that was used within the testing and validation of that Model Can also link to existing Experimental data

A Picture Modeling STUDY Biological problem Modeling STUDY Biological problem Modeling ASSAY Approach Analysis Method Model types Model formats Software tools Modeling ASSAY Approach Analysis Method Model types Model formats Software tools Model Data 1..n 0..n

Modeling defined at ASSAY level. No changes to the STUDY entity, it remains the same for Modeling or Experimental work. A Study can contain both Experimental and Modeling based ASSAYS Means that STUDIES can contain a mix of Experimental and Modeling ASSAYS.

ASSAY for Modeling If an ASSAY is defined to represent Modeling then it becomes possible to link Models to that ASSAY (along with SOPs and DATA). Should be linked to a SOP which describes – Modeling approach – Could have a Modeling SOP template. Extend and reuse the Assay types to describe modeling. Extend and reuse the Technology types to describe software tools for modeling.

Model describes its format and type Models currently describe their format and type. This can be enhanced. The format and type is directly related to the Model. An ASSAY can aggregate the associated Model format and types, and present an overview.

Data attached to ASSAY Once again, can also link to existing Experimental data generated by Experimentalists. When data is linked to an ASSAY, allow this link to be annotated as a named association: – E.g. Test data, Validation data.

A Picture STUDY ASSAY Software tools ASSAY Software tools SOP Approach Analysis Method SOP Approach Analysis Method Model Model types Model format Model Model types Model format Data Test data, Validation data, … 1..n 0..n 1..n 0..n