ETL steps are represented with ontologies.

<p>Components and processes involved in the extraction, transformation and loading of data are represented with ontologies. The mappings (1) and (2) illustrate “simple” and “complex” mappings, respectively.</p

Cascading of mapping nodes.

<p>Cascaded mapping nodes allow the definition of arbitrary data transformations. The illustration has to be read from the right to the left, hasOperand1 before hasOperand2. Paraphrased, it means: If no data for Gleason 3 (left side) exist, add the Gleason 1 and Gleason 2 data and export these as Gleason 3 (right side) records. Details about the NOTEXISTS, ADD and IF nodes’ semantics and why NOTEXISTS requires a second operand are given in Tables F and G in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116656#pone.0116656.s001" target="_blank">S1 File</a>.</p

Command type definitions describe how to process mapping nodes from the mapping ontology.

<p>All intermediate nodes in the mapping ontology are connected to a command type definition. They contain SQL code fragments, which describe how to filter and transform the facts data derived from operands 1 and 2 (OP1 and OP2).</p

Overloading internal data model properties.

<p>This real-world example illustrates how semantic relationships between source data elements are stored explicitly in the ontologies and how they can be processed: Stating that <i>Gleason1 hasDateStartValueColumn DateBiops</i> e.g. tells the export software to use the data entry in the Value column of DateBiops as DateStartValue in Gleason1. Gleason2 is processed the same way.</p

Overview of the approach.

<p>The illustration shows an overview of our approach by combining several of the previous figures in a simplified fashion. The upper part (blue box) represents a mapping, which is visible to the user. The parts in the middle are internal ontology concepts that are hidden for the user. The SQL code in the lower part has been automatically compiled from the above ontologies.</p

Types and numbers of intermediate nodes that were used in complex mappings in the urology project.

<p>Types and numbers of intermediate nodes that were used in complex mappings in the urology project.</p