Extract & persist IAO:0000700 as hasOntologyRootTerm

[matthewhorridge]

Extract & persist IAO:0000700 as hasOntologyRootTerm

Part of ncbo/bioportal-project#218 (full design and decisions there).

Read an ontology's declared root terms (IAO:0000700, "has ontology root term") at submission-processing time and store them as a submission attribute, so the UI can start the class hierarchy at the declared roots instead of owl:Thing. This issue only exposes the metadata — it does not change /roots.

Changes

1. Declare the attribute — config/schemes/ontology_submission.yml:

hasOntologyRootTerm:
  display: "relations"
  label: "Ontology root term(s)"
  helpText: "Class(es) the ontology declares as display roots (IAO:0000700)."
  example: 'http://purl.obolibrary.org/obo/CL_0000000'
  extractedMetadata: true
  metadataMappings: [ "obo_purl:IAO_0000700" ]

2. Declare it on the model — models/ontology_submission.rb:

attribute :hasOntologyRootTerm, type: [:list, :uri]

(Mirrors obsoleteParent, but a list.)

Notes / verification

• obo_purl (http://purl.obolibrary.org/obo/) is already registered in Goo.namespaces, so obo_purl:IAO_0000700 resolves with no new namespace.
• The existing submission_extract_metadata operation queries with the ontology IRI as subject (SELECT … FROM <submission-graph> WHERE { <ontology_uri> obo_purl:IAO_0000700 ?o }) and handles :list URI attributes, so no new extraction code is expected.
• The attribute must be kept out of the content_metadata_attributes reject list so it appears in the API catalog and the submission edit form (which is generated from that catalog). The user_provided_value guard preserves a manually set value across re-processing.

Acceptance

• Re-process an ontology that declares IAO:0000700 (CL / Cell Ontology is the reference case); latest_submission?display=hasOntologyRootTerm returns the declared root(s).
• An ontology without the annotation returns an empty value, not an error.
• A submission where the value was set manually is not overwritten by re-processing.

Out of scope

• Changing /roots to prefer declared roots (deferred — P4 in CSV Format Change: prefLabel Field Now Contains List Instead of String Value #218).
• Any UI (see the bioportal_web_ui issue).
• Backfill of existing submissions (optional follow-up; same extract_metadata step with process_rdf: false etc.).