Fig. 2

WINGS workflow components ontology for our clinical omics use-case. WINGS components are used to encapsulate individual steps of an analysis pipeline and are classified within an ontology in a workflow template. Individual components can be classified as their own component-class or as a subclass of a component-type. Component-types are used to group components sharing a common base set of input and output datasets such as those encapsulating code for different versions of the same tool or different tools performing similar functions. Component-types can also be used to effectively organize and enhance the flexibility of individual components within a workflow template. Each step of our clinical omics analysis pipeline was encapsulated within a component-type, even if only one component is currently defined (a). Individual component-types are shown in grey while individual components are depicted in yellow. Each component is defined with the following: 1) input datasets, 2) computational code, and 3) output datasets. For example, each PredictProteinConsequence component was defined with the following two input datasets: 1) Patient_Called_DNA_Variant_File and 2) Transcript_File and the following output dataset: 1) Predicted_Protein_Consequence (b). The R code needed for the analysis of this step was included to complete the creation of the component