EuroSciVoc: REST API fails to calculate root classes for this SKOS-format ontology

[jvendetti]

We received a report from Xeni (OntoPortal Alliance member) that EcoPortal shows a "Problem retrieving classes" error when trying to view the classes for their EUROSCIVOC SKOS ontology. You can see the behavior on the EcoPortal site here:

http://ecoportal.lifewatch.eu/ontologies/EUROSCIVOC/?p=classes&conceptid=root

(EcoPortal is an instance of the OntoPortal virtual appliance)

Xeni sent me an RDF file so that we could try to reproduce this on our end. I created an entry on our staging server with the ontology here:

https://stage.bioontology.org/ontologies/EUROSCIVOCAPEU/?p=summary

... and we see the same "Problem retrieving classes" error on the classes page:

https://stage.bioontology.org/ontologies/EUROSCIVOCAPEU/?p=classes&conceptid=root

The underlying reason for this error is that the REST API is failing to calculate the set of root classes, i.e., the /roots endpoint is returning an empty set:

https://stagedata.bioontology.org/ontologies/EUROSCIVOCAPEU/classes/roots

I've looked at the content of the ontology, and it appears to meet our minimum standards for SKOS support, which are detailed on our wiki:

https://www.bioontology.org/wiki/SKOSSupport

In particular, the SKOS ontology contains the necessary ConceptScheme with a list of hasTopConcept declarations:

...
<rdf:Description rdf:about="http://data.europa.eu/8mn/euroscivoc/40c0f173-baa3-48a3-9fe6-d6e8fb366a00">
    <startDate xmlns="http://publications.europa.eu/ontology/euvoc#" rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2019-12-02</startDate>
    <created xmlns="http://purl.org/dc/terms/" rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2019-12-02</created>
    <rdf:type rdf:resource="http://www.w3.org/2004/02/skos/core#ConceptScheme"/>
    <versionInfo xmlns="http://www.w3.org/2002/07/owl#">1.3</versionInfo>
    <prefLabel xmlns="http://www.w3.org/2004/02/skos/core#" xml:lang="en">EuroSciVoc</prefLabel>
    <prefLabel xmlns="http://www.w3.org/2008/05/skos-xl#" rdf:resource="http://data.europa.eu/8mn/euroscivoc/1723cd23-0e0e-4092-9709-49f42c5fb100"/>
    <hasTopconcept xmlns="http://www.w3.org/2004/02/skos/core#" rdf:resource="http://data.europa.eu/8mn/euroscivoc/12c980a5-034f-4cd5-8ce7-fcfe109c675c"/>
    <hasTopconcept xmlns="http://www.w3.org/2004/02/skos/core#" rdf:resource="http://data.europa.eu/8mn/euroscivoc/64605fff-1946-4fd4-b021-e2e83b71dcac"/>
    <hasTopconcept xmlns="http://www.w3.org/2004/02/skos/core#" rdf:resource="http://data.europa.eu/8mn/euroscivoc/7a2dcf7b-2c20-468a-a81c-76d67c14de31"/>
    <hasTopconcept xmlns="http://www.w3.org/2004/02/skos/core#" rdf:resource="http://data.europa.eu/8mn/euroscivoc/9b9abbee-82f5-4766-bd4d-feb73cf06573"/>
    <hasTopconcept xmlns="http://www.w3.org/2004/02/skos/core#" rdf:resource="http://data.europa.eu/8mn/euroscivoc/9e8e1abb-1a14-40ef-9658-782092fa5cf6"/>
    <hasTopconcept xmlns="http://www.w3.org/2004/02/skos/core#" rdf:resource="http://data.europa.eu/8mn/euroscivoc/3d76a7f4-5a16-411e-ae44-7b712d5222ee"/>
    <identifier xmlns="http://purl.org/dc/terms/">http://data.europa.eu/8mn/euroscivoc/40c0f173-baa3-48a3-9fe6-d6e8fb366a00</identifier>
</rdf:Description>
...

Based on the snippet above, I would expect there to be 6 root classes returned by the REST API. Note that Protege correctly recognizes the ConceptScheme with associated hasTopConcepts:

[jvendetti]

From @graybeal:

I saw this once when there was a recursion in the hierarchy (A broaderThan B broaderThan A), if I recall correctly. Another possibility to consider.

[jvendetti]

Example unit test code that can be placed in test_ontology_submission.rb to debug this issue:

def test_euroscivoc_roots
  submission_parse("EUROSCIVOC_TST", "EuroSciVoc Test",
                   "./test/data/ontology_files/EuroSciVoc-skos-ap-eu.rdf", 1,
                   process_rdf: true, index_search: false, run_metrics: false)
  sub = LinkedData::Models::OntologySubmission.where(ontology: [acronym: "EUROSCIVOC_TST"], submissionId: 1)
                                              .include(:version).first
  roots = sub.roots
  refute_empty roots, 'Failed to return root classes for EuroSciVoc'
end

Example SPARQL query to retrieve root classes:

SELECT DISTINCT ?root WHERE {
GRAPH <http://data.bioontology.org/ontologies/EUROSCIVOC_TST/submissions/1> {
  ?x <http://www.w3.org/2004/02/skos/core#hasTopConcept> ?root .
}}

[syphax-bouazzouni]

Hello, If I can give you my modest help with this. I think the issue is just a miswriting of the skos hasTopConcept property.

In the resource file, it is written hasTopconcept but the correct writing is hasTopConcept

[jvendetti]

OMG, a single character in the wrong case.

😫

Thank you for pointing that out Syphax - your eyesight is clearly better than mine.

I modified the hasTopConcept declarations to use the correct case and uploaded a new version of the ontology to our staging environment. I can confirm that this fixes the issue.

[xeniacs]

Hi, thank you so much for looking into this. I made the change in EcoPortal as well - thanks Syphax! I did this on Thursday, as soon as I read abt the typo. After correcting, for some time on Thursday already I could access the Classes without being logged in, but the problem persisted when logged in as admin. I thought it might be a cache issue. Come Monday, I cannot access the classes either as admin or as unsubscribed user. I checked the SKOS file and it is the corrected version, so there was no problem with the update. Any tip on what to check in our instance? Thanks heaps

[jvendetti]

@xeniacs - was there a newer version of the ontology that was uploaded over the weekend?

Are you able to access your ontology classes and roots in a web browser via the REST API, e.g.:

http://{ip_address_of_appliance}:8080/ontologies/EUROSCIVOC/classes http://{ip_address_of_appliance}:8080/ontologies/EUROSCIVOC/classes/roots

You mentioned that you thought it might be a caching issue. Just to clarify, did you clear all of the application caches on the Admin -> Site Administration tab in your web UI?