Development

This page outlines the features of the current version of the converter.

PD2AF version 1.0

The implemented logic takes into account on the work by Vogt and coauthors (Vogt et al., 2013, doi: 10.1186/1752-0509-7-115) and further develops the logic to minimise the number of complexes in AF version and to introduce pattern recognition functionalities. In particular, the PD2AF tool inlcudes pattern recognition functionality for removing “intermediate” complexes that can be omitted in the AF representation and the corresponding Boolean models. There is also an advnanced functuionality for identifying so-called “hidden” inhibition when inhibition mechanisms are represented without using the inhibition arc.

For convenient implementation and testing, we have developed the following infrastructure.

Figure 2

The infrustructure modules:

The PD-to-AF conversion includes the following steps.

Figure 2

The red arrows show the transformations implemented.

  1. An SBGN Process Description diagram is produced in SBGN editors such as VANTED/SBGN-ED and Newt.
  2. The PD2AF tool builds an internal represenattion of the diagram by transforming SBGN-ML PD XML to sexp expression.
  3. Next, it cleans and normalises the sexp expression, making it ready for pattern matching.
  4. Then, we have the main stage of the conversion from PD to AF. The converter matches patterns and replaces these PD patterns with the prescripted AF forms.
  5. Then, these forms are cleaned again to provide a more compact and sensible AF output.
  6. Finally, sexp expression is transforrmed back to XML, this time SBGN-ML AF format. This XML file can be viewed and edited in SBGN editors such as VANTED/SBGN-ED and Newt.