404 error on classes page for DFO, VFB_DRIVERS ontologies

[jvendetti]

BioPortal displays a 404 error for the classes page for the DFO ontology. No errors in the production parsing log.

The underlying reason for the 404 is that the REST API is returning an empty set for the /roots endpoint and the UI can't construct a class tree without roots.

The /classes endpoint returns data appropriately, i.e.:

The /roots endpoint returns an empty set:

Opening the ontology in Protege shows two root classes:

Both of the root classes are declared using an obo prefix (DFO is an OWL, not an OBO ontology):

<Declaration>
  <Class abbreviatedIRI="obo:NCIT_C61393"/>
</Declaration>
<Declaration>
  <Class abbreviatedIRI="obo:NCIT_C79273"/>
</Declaration>

... though it's not clear if this is preventing the REST API from locating the root classes

[jvendetti]

What appears to be another instance of this issue was reported today for the VFB_DRIVERS ontology. The /roots endpoint is returning an empty set, resulting in a 404 error on the Classes page in the Rails application. Like DFO, this ontology has a total of two root classes, both of which are declared in the obo namespace:

<?xml version="1.0"?>
<rdf:RDF xmlns="http://virtualflybrain.org/data/VFB/OWL/vfb_drivers.owl#"
     xml:base="http://virtualflybrain.org/data/VFB/OWL/vfb_drivers.owl"
     xmlns:obo="http://purl.obolibrary.org/obo/"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
    <owl:Ontology rdf:about="http://virtualflybrain.org/data/VFB/OWL/vfb_drivers.owl"/>

    ...

    <!-- http://purl.obolibrary.org/obo/SO_0000110 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000110"/>

    <!-- http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010"/>

    ...

[jvendetti]

I haven't looked at this issue in a while - both of these ontologies are now displaying properly in BioPortal. I don't remember what methodology was used as a fix here.