PROconsortium / PRoteinOntology

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SPARQL service currently unavailable #312

Closed allenbaron closed 1 year ago

allenbaron commented 1 year ago

Describe the issue PROs SPARQL service is not usable in federated queries (returns "Service unavailable") or at https://lod.proconsortium.org/yasgui.html (returns response time but without any results displayed).

To Reproduce Steps to reproduce the behavior:

  1. Go to https://lod.proconsortium.org/yasgui.html
  2. Click on any query (I've tried PQ1, PQ4 & GQ1).
  3. See error

For federated query:

  1. Go to https://disease-ontology.org/do-kb/sparql
  2. Paste in this query (it's a modified version of PQ4 that usually works):
    
    ########### 
    # PQ4 (from https://lod.proconsortium.org/yasgui.html) modified.
    # Retrieve proteoforms associated with CANCER disease progression.
    ########### 

PREFIX rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema# PREFIX owl: http://www.w3.org/2002/07/owl# PREFIX xsd: http://www.w3.org/2001/XMLSchema# PREFIX dc: http://purl.org/dc/elements/1.1/ PREFIX dcterms: http://purl.org/dc/terms/ PREFIX obo: http://purl.obolibrary.org/obo/ PREFIX oboInOwl: http://www.geneontology.org/formats/oboInOwl# PREFIX paf: http://pir.georgetown.edu/pro/paf#

SELECT distinct ?DO_term ?disease ?PRO_term ?PRO_name WHERE { SERVICE https://sparql.proconsortium.org/virtuoso/sparql { ?x a rdf:Statement ; rdf:subject ?PRO_term ; rdf:predicate [ paf:relation "associated_with_disease_progression" ] ; rdf:object ?xo .

        ?xo paf:ontologyID ?doid .

        ?PRO_term paf:objectTerm ?PRO_name .
}

?DO_term a owl:Class ;
    oboInOwl:id ?doid ;
    rdfs:label ?disease ;
    rdfs:subClassOf* obo:DOID_162 .

}


3. See error

**Browser**
Occurs with Chrome (117.0.5938.132) and Firefox (118.0.1).
nataled commented 1 year ago

Dear @allenbaron,

Thank you for alerting us to the issue. It is now working properly again.

Best regards, Darren Natale