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EMMO use case for horizontal interoperability

Horizontal interoperability is about interoperability between different types of models and codes for a single material (i.e., one use case, multiple models).

The key here is to show how to map between EMMO (or an EMMO-based ontology) and another ontology (possible EMMO-based).

In this example we use a data-driven approach based on a C-implementation of SOFT1,2.

This is done in four steps:

  1. Generate metadata from the EMMO-based user case ontology.

    Implemented in the script step1_generate_metadata.py.

  2. Define metadata for an application developed independently of EMMO.

    In this case a metadata description of the ASE Atoms class 3 is created in atoms.json.

    Implemented in the script step2_define_metadata.py.

  3. Instantiate the metadata defined defined in step 2 with an atomistic structure interface structure.

    Implemented in the script step3_instantiate.py.

  4. Map the atomistic interface structure from the application representation to the common EMMO-based representation.

    Implemented in the script step4_map_instance.py.

Essentially, this demonstration shows how EMMO can be extended and how external data can be mapped into our extended ontology (serving as a common representational system).

Requirements for running the user case

In addition to emmo, this demo also requires:

  • DLite, a C-implementation of SOFT used for handling metadata
  • ASE, for reading atom structure from cif and visualisation