Templates and Fstrings

The previous method of annotating slots with OWL interpretations works well for cases where there is a relatively straightforward mapping between slots and axioms.

For full grained control you can use either

• formatted strings, e.g. SubClassOf({id} {sublass_of}), for cases with no or minimal logic
• Jinja templates, for cases where control logic or advanced mappings are required

Either of these methods can be used to make either annotations or logical axioms

Here is an example of a more advanced schema involving nesting where we might want to model parts with counts - examples include reaction participants with stoichiometry, or protein complexes where members may be present with different counts or activation states:

PartWithCounts:
    is_a: Anonymous
    attributes:
      unit:
        range: NamedThing
        multivalued: false
        annotations:
          owl: SomeValuesFrom
      count:
        range: integer
        minimum_value: 1
        annotations:
          owl: HasValue
      state:
        range: ActivationStateEnum
        annotations:
          owl: SomeValuesFrom

  CollectionOfPartsWithCounts:
    is_a: NamedThing
    slots:
      - has_part
    slot_usage:
      has_part:
        range: PartWithCounts
        inlined: true
    annotations:
      owl.template: |-
        {% for p in has_part %}
        SubClassOf(
          {{id}}
          ObjectSomeValuesFrom(
             BFO:0000051
             ObjectIntersectionOf( {{p.unit }}
                                   ObjectSomeValuesFrom(RO:0000053 {{p.state.meaning}})
                                   {% if p.count %}
                                   DataHasValue(PATO:0001555 {{p.count}})
                                   {% endif %}
                                 )
                              )
                  )
        {% endfor %}

Given an input file:

id: x:collection
has_part:
  - unit: x:p1
    count: 2
    state: ACTIVATED
  - unit: x:p2
    count: 3
    state: ACTIVATED

(note that we use using nesting / a normalized representation here, this is harder to represent in a spreadsheet/TSV).

This will generate the following OWL:

SubClassOf( x:collection
            ObjectSomeValuesFrom( BFO:0000051
                                  ObjectIntersectionOf(
                                                       x:p1
                                                       ObjectSomeValuesFrom( RO:0000053 <http://purl.obolibrary.org/obo/PATO_0002354> )
                                                       DataHasValue( PATO:0001555 "2"^^xsd:integer ))))
SubClassOf( x:collection
            ObjectSomeValuesFrom( BFO:0000051
                                  ObjectIntersectionOf(
                                                       x:p2
                                                       ObjectSomeValuesFrom( RO:0000053 <http://purl.obolibrary.org/obo/PATO_0002354> )
                                                       DataHasValue( PATO:0001555 "3"^^xsd:integer ))))