8000 AG: ontology report errors out with `SPARQL::Client::MalformedQuery: MALFORMED QUERY: Line 1, Found '<'.` · Issue #147 · ncbo/goo · GitHub
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AG: ontology report errors out with SPARQL::Client::MalformedQuery: MALFORMED QUERY: Line 1, Found '<'. #147

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alexskr opened this issue Aug 29, 2023 · 1 comment
Open

AG: ontology report errors out with SPARQL::Client::MalformedQuery: MALFORMED QUERY: Line 1, Found '<'. #147

alexskr opened this issue Aug 29, 2023 · 1 comment
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@alexskr
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alexskr commented Aug 29, 2023

ncbo_ontology_report_rebuild errors out when running for ANC, AUTISM,CMECS2, ELD, ETH_ANC (and other) ontologies with the following error:

E, [2023-08-28T16:59:56.515128 #10922] ERROR -- : Error during ontologies report paging - SPARQL::Client::MalformedQuery: MALFORMED QUERY: Line 1, Found '<'. Was expecting one of: ABS, AVG, BNODE, BOUND, CEIL, COALESCE, CONCAT, CONTAINS, COUNT, DATATYPE, DAY, DECIMAL, DOUBLE, ENCODE_FOR_URI, EXISTS, FALSE, FLOOR, GROUP_CONCAT, HOURS, IF, INTEGER, IRI, ISBLANK, ISIRI, ISLITERAL, ISNUMERIC, ISTRIPLE, ISURI, LANG, LANGMATCHES, LCASE, MAX, MD5, MIN, MINUTES, MONTH, NOT, NOW, NUMERIC-PLUS, Q_IRI_REF, QNAME, QNAME_NS, RAND, REGEX, REPLACE, ROUND, SAMETERM, SAMPLE, SECONDS, SHA1, SHA256, SHA384, SHA512, STR, STRAFTER, STRBEFORE, STRDT, STRENDS, STRING_LITERAL1, STRING_LITERAL2, STRING_LITERAL_LONG1, STRING_LITERAL_LONG2, STRLANG, STRLEN, STRSTARTS, STRUUID, SUBSTR, SUM, TIMEZONE, TRUE, TZ, UCASE, URI, UUID, VARNAME, YEAR or punctuation '!', '(', '+', '-', '<<'.
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mdorf commented Aug 29, 2023

All these ontologies indeed have errors in their structure, resulting in malformed queries downstream. Examples:

AUTISM:

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>) })

ANC:

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)>) })

ETH_ANC:

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)>) })

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