Open alexskr opened 1 year ago
All these ontologies indeed have errors in their structure, resulting in malformed queries downstream. Examples:
SELECT DISTINCT ?id ?prefLabel ?definition ?synonym ?obsolete
FROM <http://data.bioontology.org/ontologies/AUTISM/submissions/1>
WHERE { ?id a <http://www.w3.org/2002/07/owl#Class> .
OPTIONAL { ?id ?rewrite0 ?prefLabel .
FILTER(?rewrite0 = <http://data.bioontology.org/metadata/def/prefLabel> ||
?rewrite0 = <http://www.w3.org/2004/02/skos/core#prefLabel>) }
OPTIONAL { ?id ?rewrite1 ?definition .
FILTER(?rewrite1 = <http://purl.obolibrary.org/obo/IAO_0000115> ||
?rewrite1 = <http://www.w3.org/2000/01/rdf-schema#comment> ||
?rewrite1 = <http://purl.obolibrary.org/obo/def> ||
?rewrite1 = <http://www.w3.org/2004/02/skos/core#definition>) }
OPTIONAL { ?id ?rewrite2 ?synonym .
FILTER(?rewrite2 = <http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> ||
?rewrite2 = <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> ||
?rewrite2 = <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> ||
?rewrite2 = <http://purl.obolibrary.org/obo/synonym> ||
?rewrite2 = <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> ||
?rewrite2 = <http://www.w3.org/2004/02/skos/core#altLabel>) }
OPTIONAL { ?id <http://www.w3.org/2002/07/owl#deprecated> ?obsolete . }
FILTER(?id = <C:/Users/maryk_000/2020/7/untitled-AutismOn#[OWL]_a109c71b_678e_4d1a_9a69_0d61f66b2a52Defintion> ||
?id = <C:/Users/maryk_000/2020/7/untitled-AutismOn#[OWL]_2aaf4433_1364_442f_b187_2caa2463b0d3Defintion> ||
?id = <C:/Users/maryk_000/2020/7/untitled-AutismOn#[OWL]_6626a718_0552_45ea_bc3d_d8239d7b92b7Defintion> ||
?id = <C:/Users/maryk_000/2020/7/untitled-AutismOn#[OWL]_c3456d7b_ee8b_4c5f_abbd_bdcb365c7e94Defintion> ||
?id = <C:/Users/maryk_000/2020/7/untitled-AutismOn#[OWL]_283ae24f_3b85_44fc_b31b_9dec20ee4398Defintion> ||
?id = <C:/Users/maryk_000/2020/7/untitled-AutismOn#[OWL]_ae391391_9b4e_4a57_8dcb_7662fd433803Defintion> ||
?id = <C:/Users/maryk_000/2020/7/untitled-AutismOn#[OWL]_c009618f_346f_46c7_8bc1_9a32653854feDefintion> ||
?id = <C:/Users/maryk_000/2020/7/untitled-AutismOn#[OWL]_3c9e4ec4_04f7_4633_abe2_3b0020b7e892Defintion>) })
SELECT DISTINCT ?id
FROM <http://data.bioontology.org/ontologies/ANC/submissions/1>
WHERE { ?id a <http://www.w3.org/2004/02/skos/core#Concept> .
FILTER(?id = <http://vocab.vodana.org/gdmt/Dateofvisit (DD/MM/YY)>) })
SELECT DISTINCT ?id FROM <http://data.bioontology.org/ontologies/ETH_ANC/submissions/2>
WHERE { ?id a <http://www.w3.org/2004/02/skos/core#Concept> .
FILTER(?id = <http://vocab.vodana.org/ETH-ANC/KnownHIVpositives (transferredfromART)>) })
ncbo_ontology_report_rebuild
errors out when running for ANC, AUTISM,CMECS2, ELD, ETH_ANC (and other) ontologies with the following error: