Example inputs needed for APE to run and compose workflows

in this repository we have examples for :

1. Bioinformatics Domain from the Bio.Tools dataset in the 'proteomics' folder.
2. 3 Examples from the Comp. Materials Science domain
3. Pizza baking domain (including domain model as a logic program)

In General, the 4 inputs as described in Default input are needed for APE to work. APE does the translation from the inputs into the domain model by itself. An example of a possible domain model be in ASP folder. Here the domain model for baking a pizza is shown. This only to showcase into what kind of rules APE might translate the input.

Default input

• .OWL file containing the Ontology.
• tool_annotations.json contains like a database all possible tools used in that domain.
• config.json contains the workflow specification: starting data, goal and other settings for APE i.e. maximum and minimum workflow length
• constraints.json contains additional constraints that are used to reduce the search space. written in mathematical notation.

for the ASP / clingo route

To use an Answer Set Programming based approach the solver needs a workable translation of the domain model. Here we have one example stored as a logic programm containing facts.

• domain_model.lp