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Extract & persist IAO:0000700 as hasOntologyRootTerm #316

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Extract & persist IAO:0000700 as hasOntologyRootTerm #316

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11 changes: 11 additions & 0 deletions config/schemes/ontology_submission.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -1410,6 +1410,17 @@ translationOfWork:
extractedMetadata: true
metadataMappings: [ "adms:translation", "schema:translationOfWork" ]

#Ontology root term(s)
hasOntologyRootTerm:
display: "relations"

@jvendetti jvendetti Aug 19, 2026

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Should this be display: "content"? "relations" is otherwise ontology→ontology (hasPriorVersion, ontologyRelatedTo, isAlignedTo), while the other class-valued attributes — obsoleteParent, keyClasses — are under content, as is the root-resources entry at line 1523. Affects grouping in the
metadata catalog and the submission edit form, so easier to change now than once something is rendering it.

label: "Ontology root term(s)"
helpText: "Class(es) the ontology declares as its display roots, used to start the class hierarchy below owl:Thing and upper-ontology terms."
example: 'http://purl.obolibrary.org/obo/CL_0000000'
description: [
"IAO: Relates an ontology to a term that is a designated root term of the ontology; display tools can use these as the starting point when rendering the class hierarchy. There can be more than one." ]
extractedMetadata: true
metadataMappings: [ "obo_purl:IAO_0000700" ]

### Content

#Identifier pattern
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6 changes: 6 additions & 0 deletions lib/ontologies_linked_data/models/ontology_submission.rb
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Expand Up @@ -147,6 +147,12 @@ class OntologySubmission < LinkedData::Models::Base
attribute :usedBy, namespace: :voaf, type: %i[uri list]
attribute :workTranslation, namespace: :schema, type: %i[uri list]
attribute :translationOfWork, namespace: :schema, type: %i[uri list]
# Class(es) the ontology declares as display roots via IAO:0000700. No
# namespace: the source property has a numeric local name (IAO_0000700), so
# it is stored under the default :metadata namespace and read from the source
# IRI via metadataMappings in config/schemes/ontology_submission.yml (same
# pattern as obsoleteParent).
attribute :hasOntologyRootTerm, type: %i[list uri]

# Content metadata
attribute :uriRegexPattern, namespace: :void
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48 changes: 48 additions & 0 deletions test/data/ontology_files/custom_root_terms.owl
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@@ -0,0 +1,48 @@
<?xml version="1.0"?>


<!DOCTYPE rdf:RDF [
<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
<!ENTITY obo "http://purl.obolibrary.org/obo/" >
<!ENTITY msotes "http://bioportal.bioontology.org/ontologies/msotes#" >
]>


<rdf:RDF xmlns="http://bioportal.bioontology.org/ontologies/msotes#"
xml:base="http://bioportal.bioontology.org/ontologies/msotes"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:msotes="http://bioportal.bioontology.org/ontologies/msotes#">

<!-- The ontology declares two display roots via IAO:0000700 (has ontology
root term): class1 and class2. class1 is a true top; class2 is nested
under class1, so this also exercises "declared root that is not a
structural owl:Thing child". -->
<owl:Ontology rdf:about="http://bioportal.bioontology.org/ontologies/msotes">
<obo:IAO_0000700 rdf:resource="&msotes;class1"/>
<obo:IAO_0000700 rdf:resource="&msotes;class2"/>
</owl:Ontology>

<!-- IAO:0000700 as an annotation property (so the source is well-formed). -->
<owl:AnnotationProperty rdf:about="&obo;IAO_0000700"/>

<owl:Class rdf:about="&msotes;class1">
<rdfs:label>class 1</rdfs:label>
</owl:Class>

<owl:Class rdf:about="&msotes;class2">
<rdfs:subClassOf rdf:resource="&msotes;class1"/>
<rdfs:label>class 2</rdfs:label>
</owl:Class>

<owl:Class rdf:about="&msotes;class3">
<rdfs:subClassOf rdf:resource="&msotes;class1"/>
<rdfs:label>class 3</rdfs:label>
</owl:Class>
</rdf:RDF>
31 changes: 31 additions & 0 deletions test/models/test_ontology_submission.rb
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Expand Up @@ -308,6 +308,37 @@ def test_submission_parse
assert_equal ['La première ontologie déddiée aux concepts de la médecine associée'], sub.notes
end

# IAO:0000700 ("has ontology root term") declared on the ontology is extracted
# into the submission's hasOntologyRootTerm attribute (a list of class URIs).
def test_extract_ontology_root_terms
submission_parse("ROOTTERMS", "Root terms TEST",
"./test/data/ontology_files/custom_root_terms.owl", 1,
process_rdf: true, extract_metadata: true)

sub = LinkedData::Models::OntologySubmission
.where(ontology: [acronym: "ROOTTERMS"], submissionId: 1)
.include(:hasOntologyRootTerm).first
refute_nil sub

roots = Array(sub.hasOntologyRootTerm).map(&:to_s).sort
assert_equal ["http://bioportal.bioontology.org/ontologies/msotes#class1",
"http://bioportal.bioontology.org/ontologies/msotes#class2"],
roots
end

# An ontology without IAO:0000700 leaves hasOntologyRootTerm empty (not an error).
def test_extract_ontology_root_terms_absent
submission_parse("NOROOTTERMS", "No root terms TEST",
"./test/data/ontology_files/custom_properties.owl", 1,
process_rdf: true, extract_metadata: true)

sub = LinkedData::Models::OntologySubmission
.where(ontology: [acronym: "NOROOTTERMS"], submissionId: 1)
.include(:hasOntologyRootTerm).first
refute_nil sub
assert_empty Array(sub.hasOntologyRootTerm)
end

def test_generate_language_preflabels
submission_parse("D3OTEST", "DSMZ Digital Diversity Ontology Test",
"./test/data/ontology_files/d3o.owl", 1,
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