Tests for RO

linkml_owl/util/loader_wrapper.py

@@ -72,8 +72,6 @@ def load_structured_file(source: Union[str, dict, TextIO], target_class: Union[s
     - if the schema specified a tree_root, this is used
     - if the objects contain a type designator, this is used
 
-    TODO: add tests
-
     :param source: path or data or stream
     :param target_class: class to be instantiated, either name or the python class
     :param fmt: Any of yaml, json, csv, ttl. inferred if None and source is a file path

tests/inputs/expected_ro.ofn

@@ -19,6 +19,34 @@ Prefix( skos: = <http://www.w3.org/2004/02/skos/core#> )
 Prefix( dcterms: = <http://purl.org/dc/terms/> )
 
 Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
+    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_00000115> <http://purl.obolibrary.org/obo/BFO_0000051> "Inverse of BFO:0000050 part of" )
+    Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/BFO_0000050> ) )
+    AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/BFO_0000050> "part of" )
+    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/BFO_0000050> "a core relation that holds between a part and its whole" )
+    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/BFO_0000050> rometa:ObjectProperty )
+    SubObjectPropertyOf( <http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/RO_0002131> )
+    Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/BFO_0000051> ) )
+    AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/BFO_0000051> "has part" )
+    InverseObjectProperties( <http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000051> )
+    TransitiveObjectProperty( <http://purl.obolibrary.org/obo/BFO_0000050> )
+    SubObjectPropertyOf(     ObjectPropertyChain(
+        <http://purl.obolibrary.org/obo/BFO_0000051>
+        <http://purl.obolibrary.org/obo/BFO_0000050>
+    ) <http://purl.obolibrary.org/obo/RO_0002131> )
+    Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002131> ) )
+    AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002131> "overlaps" )
+    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002131> "a core relation that holds between a part and its whole" )
+    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0002131> rometa:DefinedObjectPropertyByChain )
+    SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0002131> <http://purl.obolibrary.org/obo/RO_0002323> )
+    SymmetricObjectProperty( <http://purl.obolibrary.org/obo/RO_0002131> )
+    SubObjectPropertyOf(     ObjectPropertyChain(
+        <http://purl.obolibrary.org/obo/RO_0000052>
+        <http://purl.obolibrary.org/obo/BFO_0000050>
+    ) <http://purl.obolibrary.org/obo/RO_0002314> )
+    Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002314> ) )
+    AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002314> "characteristic of part of" )
+    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002314> "A relationship between a characteristic and an entity where the characteristic is of either the entity itself or a part of the entity" )
+    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0002314> rometa:DefinedObjectPropertyByChain )
     AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_00000115> <http://purl.obolibrary.org/obo/RO_0002203> "Inverse of RO:0002202 develops from" )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002202> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002202> "develops from" )
@@ -31,16 +59,48 @@ Ontology( <http://purl.obolibrary.org/obo/ro/ro-metamodel.yaml>
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002203> "develops into" )
     InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002202> <http://purl.obolibrary.org/obo/RO_0002203> )
     TransitiveObjectProperty( <http://purl.obolibrary.org/obo/RO_0002202> )
+    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_00000115> <http://purl.obolibrary.org/obo/RO_9999998> "Inverse of RO:0002012 occurrent part of" )
+    Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002012> ) )
+    AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002012> "occurrent part of" )
+    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0002012> rometa:DefinedObjectPropertyByDomainAndRange )
+    SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/BFO_0000050> )
+    ObjectPropertyDomain( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/BFO_0000003> )
+    ObjectPropertyRange( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/BFO_0000003> )
+    Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_9999998> ) )
+    AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_9999998> "has occurrent part" )
+    InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002012> <http://purl.obolibrary.org/obo/RO_9999998> )
     SubObjectPropertyOf(     ObjectPropertyChain(
         <http://purl.obolibrary.org/obo/RO_0002215>
         <http://purl.obolibrary.org/obo/RO_0002481>
         <http://purl.obolibrary.org/obo/RO_0002400>
     ) <http://purl.obolibrary.org/obo/RO_0002447> )
+    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_00000115> <http://purl.obolibrary.org/obo/RO_9999999> "Inverse of RO:0002447 phosphorylates" )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002447> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002447> "phosphorylates" )
+    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002447> "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a kinase activity that takes the object as input" )
     AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0002447> rometa:ObjectPropertyDefinedByInteractionProcess )
     SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0002447> <http://purl.obolibrary.org/obo/RO_0002436> )
+    Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_9999999> ) )
+    AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_9999999> "phosphorylated by" )
+    InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0002447> <http://purl.obolibrary.org/obo/RO_9999999> )
     SubClassOf( <http://purl.obolibrary.org/obo/GO_0016301>     ObjectHasSelf( <http://purl.obolibrary.org/obo/RO_0002481> ) )
     Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0002481> ) )
     AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0002481> "is kinase activity" )
+    SubObjectPropertyOf(     ObjectPropertyChain(
+        <http://purl.obolibrary.org/obo/RO_0002215>
+        <http://purl.obolibrary.org/obo/RO_0018001>
+        <http://purl.obolibrary.org/obo/RO_0002400>
+    ) <http://purl.obolibrary.org/obo/RO_0018002> )
+    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_00000115> <http://purl.obolibrary.org/obo/RO_0018003> "Inverse of RO:0018002 myristoylates" )
+    Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0018002> ) )
+    AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0018002> "myristoylates" )
+    AnnotationAssertion( <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0018002> "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" )
+    AnnotationAssertion( dcterms:conformsTo <http://purl.obolibrary.org/obo/RO_0018002> rometa:ObjectPropertyDefinedByInteractionProcess )
+    SubObjectPropertyOf( <http://purl.obolibrary.org/obo/RO_0018002> <http://purl.obolibrary.org/obo/RO_0002436> )
+    Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0018003> ) )
+    AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0018003> "myristoylated by" )
+    InverseObjectProperties( <http://purl.obolibrary.org/obo/RO_0018002> <http://purl.obolibrary.org/obo/RO_0018003> )
+    SubClassOf( <http://purl.obolibrary.org/obo/GO_0019107>     ObjectHasSelf( <http://purl.obolibrary.org/obo/RO_0018001> ) )
+    Declaration( ObjectProperty( <http://purl.obolibrary.org/obo/RO_0018001> ) )
+    AnnotationAssertion( rdfs:label <http://purl.obolibrary.org/obo/RO_0018001> "is myristoyltransferase activity" )
 )

tests/inputs/ro-data.yaml

@@ -1,3 +1,41 @@
+## basic example
+
+- id: BFO:0000050
+  conforms_to: ObjectProperty
+  label: part of
+  inverse_of:
+    id: BFO:0000051
+    label: has part
+  subproperty_of: RO:0002131 ## overlaps
+  definition: a core relation that holds between a part and its whole
+  transitive: true
+  locally_reflexive: true
+
+## chains
+
+- id: RO:0002131
+  conforms_to: DefinedObjectPropertyByChain
+  label: overlaps
+  subproperty_of: RO:0002323
+  definition: a core relation that holds between a part and its whole
+  symmetric: true
+  subproperty_of_pairwise_chain:
+    - first_member: BFO:0000051
+      last_member: BFO:0000050
+
+## chains to reflexive, see https://oborel.github.io/obo-relations/reflexivity/
+
+- id: RO:0002314
+  conforms_to: DefinedObjectPropertyByChain
+  #conforms_to: DefinedObjectPropertyByChainToReflexive ### TODO
+  label: characteristic of part of
+  definition: A relationship between a characteristic and an entity where the characteristic is of either the entity itself or a part of the entity
+  subproperty_of_pairwise_chain:
+    - first_member: RO:0000052
+      last_member: BFO:0000050
+
+## test for transitive form, e.g. develops-from is transitive form of directly-develops-from
+
 - id: RO:0002202
   conforms_to: TransitiveForm
   label: develops from
@@ -12,17 +50,55 @@
   domain: BFO:0000004
   range: BFO:0000004
   transitive: true
+
+## See https://github.com/oborel/obo-relations/pull/522
+
+- id: RO:0002012
+  conforms_to: DefinedObjectPropertyByDomainAndRange
+  label: occurrent part of
+  subproperty_of: BFO:0000050
+  inverse_of:
+    id: RO:9999998
+    label: has occurrent part
+  domain: BFO:0000003
+  range: BFO:0000003
+
+
+## https://github.com/oborel/obo-relations/pull/522
+
+# this one exists in RO
 - id: RO:0002447
   conforms_to: ObjectPropertyDefinedByInteractionProcess
   label: phosphorylates
-  subproperty_of: RO:0002436
-  #inverse_of:
-  #  id: TODO
-  #  label: phosphorylated by
+  definition: >-
+    A molecularly-interacts-with relationship between two entities,
+    where the subject catalyzes a kinase activity that takes the object as input
+  subproperty_of: RO:0002436  ## molecularly interacts with
+  inverse_of:
+    id: RO:9999999
+    label: phosphorylated by
   subject_to_process_property: RO:0002215  ## capable of
   uses_rolified_property:
     id: RO:0002481
     label: is kinase activity
     rolification_of: GO:0016301
-  object_to_process_property: RO:0002400   ## has direct input
+  process_to_object_property: RO:0002400   ## has direct input
+
+# new one proposed in https://github.com/oborel/obo-relations/pull/522
+- id: RO:0018002
+  conforms_to: ObjectPropertyDefinedByInteractionProcess
+  label: myristoylates
+  definition: >-
+    A molecularly-interacts-with relationship between two entities,
+    where the subject catalyzes a myristoylation activity that takes the object as input
+  subproperty_of: RO:0002436  ## molecularly interacts with
+  inverse_of:
+    id: RO:0018003
+    label: myristoylated by
+  subject_to_process_property: RO:0002215  ## capable of
+  uses_rolified_property:
+    id: RO:0018001
+    label: is myristoyltransferase activity
+    rolification_of: GO:0019107
+  process_to_object_property: RO:0002400   ## has direct input
 

tests/inputs/ro-metamodel.yaml

@@ -24,14 +24,6 @@ default_prefix: rometa
 default_curi_maps:
   - semweb_context
 
-enums:
-  ActivationStateEnum:
-    permissible_values:
-      ACTIVATED:
-        meaning: PATO:0002354
-      INACTIVATED:
-        meaning: PATO:0002355
-
 types:
   label type:
     typeof: string
@@ -121,6 +113,9 @@ slots:
     slot_uri: rdfs:range
     multivalued: false
     range: Class
+  subproperty_of_pairwise_chain:
+    multivalued: true
+    range: PairwisePropertyChain
   operands:
     range: NamedThing
     multivalued: true
@@ -209,6 +204,24 @@ slots:
 
 classes:
 
+  Expression:
+    abstract: true
+
+  PropertyChain:
+    abstract: true
+    todos:
+      - implement for more than pairwise
+
+  PairwisePropertyChain:
+    description: a property chain of length 2
+    attributes:
+      first_member:
+        range: ObjectProperty
+        #required: true
+      last_member:
+        range: ObjectProperty
+        #required: true
+
   NamedThing:
     slots:
       - id
@@ -254,6 +267,7 @@ classes:
       - reflexive
       - locally_reflexive
       - has_transitive_form
+      - subproperty_of_pairwise_chain
     slot_usage:
       genus:
         range: ObjectProperty
@@ -277,6 +291,13 @@ classes:
         {% if inverse_of and not inverse_of.definition %}
         AnnotationAssertion( IAO:00000115 {{inverse_of.id}} "Inverse of {{id}} {{label}}")
         {% endif %}
+        {% for chain in subproperty_of_pairwise_chain %}
+            SubObjectPropertyOf(
+               ObjectPropertyChain({{chain.first_member}}
+                                   {{chain.last_member}})
+               {{id}})
+        {% endfor %}
+
   GroupingObjectProperty:
     is_a: ObjectProperty
     description: An ObjectProperty that has is used for grouping purposes and should not be instantiated
@@ -305,36 +326,78 @@ classes:
   DefinedObjectPropertyByDomain:
     is_a: DefinedObjectProperty
     description: An ObjectProperty that is defined by a parent property and a domain
+    slot_usage:
+      definition:
+        string_serialization: "A {genus} that holds between a {domain} and something"
     comments:
       - hidden GCI analogs not supported (i.e. adding a more specific domain that is used for classification)
     todos:
       - rolification
+    see_also:
+      - https://oborel.github.io/obo-relations/domain-or-range-specific-relation/
     annotations:
       swrl: |-
         {{genus}}(?s, ?o), {{domain}}(?s) -> {{id}}(?s, ?o)
   DefinedObjectPropertyByRange:
     is_a: DefinedObjectProperty
     description: An ObjectProperty that is defined by a parent property and a range
+    slot_usage:
+      definition:
+        string_serialization: "A {genus} that holds between something and a {range}"
     comments:
       - hidden GCI analogs not supported (i.e. adding a more specific domain that is used for classification)
     todos:
       - rolification
+    see_also:
+      - https://oborel.github.io/obo-relations/domain-or-range-specific-relation/
     annotations:
       swrl: |-
         {{genus}}(?s, ?o), {{range}}(?o) -> {{id}}(?s, ?o)
   DefinedObjectPropertyByDomainAndRange:
     is_a: DefinedObjectProperty
     description: An ObjectProperty that is defined by a parent property and a domain and a range
+    slot_usage:
+      definition:
+        string_serialization: "A {genus} that holds between a {domain} and a {range}"
     comments:
       - hidden GCI analogs not supported (i.e. adding a more specific domain that is used for classification)
     todos:
       - SWRL rule
       - rolification
+    see_also:
+      - https://oborel.github.io/obo-relations/domain-or-range-specific-relation/
+    annotations:
+      swrl: |-
+        {{genus}}(?s, ?o), {{range}}(?o), {{domain}}(?s) -> {{id}}(?s, ?o)
   DefinedObjectPropertyByChain:
     is_a: DefinedObjectProperty
-    description: An ObjectProperty that is defined by a chain of relations
+    description: An ObjectProperty that is defined by a chain of two properties
+    slot_usage:
+      subproperty_of_pairwise_chain:
+        required: true
+    examples:
+      - value: overlaps
+        description: overlaps is defined as the chain of has-part followed by part-of
+    todos:
+      - this currently assumes chains of length 2
+      - swrl
+  DefinedObjectPropertyByChainToReflexive:
+    is_a: DefinedObjectPropertyByChain
+    description: |-
+      An ObjectProperty that is defined by a chain of two properties where the second/final member
+      is used in a reflexive sense (regardless of whether it is actually reflexive). This has
+      the effect of making the chain relation a subproperty of the first member of the chain
+    slot_usage:
+      subproperty_of_pairwise_chain:
+        required: true
     examples:
       - value: characteristic of part of
+    todos:
+      - this currently assumes chains of length 2
+      - swrl
+    #annotations:
+    #  owl.template: |-
+    #     SubObjectPropertyOf( {{subproperty_of_pairwise_chain.last_member}} {{id}} )
   TransitiveForm:
     is_a: DefinedObjectProperty
     description: An ObjectProperty that is defined as the transitive form of another relation
@@ -363,21 +426,28 @@ classes:
     attributes:
       subject_to_process_property:
         range: ObjectProperty
-      object_to_process_property:
+      process_to_object_property:
         range: ObjectProperty
       uses_rolified_property:
         range: RolifiedObjectProperty
         inlined: true
     see_also:
       - https://oborel.github.io/obo-relations/interaction-relations/
       - http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29
+      - https://github.com/oborel/obo-relations/pull/522
+      - https://github.com/oborel/obo-relations/issues/521
     annotations:
       owl.template: |-
         SubObjectPropertyOf(
            ObjectPropertyChain({{subject_to_process_property}}
                                {{uses_rolified_property.id}}
-                               {{object_to_process_property}})
+                               {{process_to_object_property}})
            {{id}})
+      swrl: |-
+        {{subject_to_process_property}}(?s, ?proc),
+        {{uses_rolified_property.rolification_of}}(?proc),
+        {{process_to_object_property}}(?o, ?proc)
+        -> {{id}}(?s, ?o)