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arnikz avatar arnikz commented on August 26, 2024

Hmm, the query returned this error:

Virtuoso 42000 Error The estimated execution time 323359 (sec) exceeds the limit of 400 (sec).

I have seen this before but not for this query. We don''t want to wait that long, right?

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gurnoor1990 avatar gurnoor1990 commented on August 26, 2024

Runs after
make restart-srv

Similar to Issue #31

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matthijsbrouwer avatar matthijsbrouwer commented on August 26, 2024

It does seem to work (at least circumventing the timeout warning) with

PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX uniprot: <http://purl.uniprot.org/core/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX so: <http://purl.obolibrary.org/obo/so#>
PREFIX go: <http://www.geneontology.org/formats/oboInOwl#>

SELECT
   DISTINCT
   str(?gene_name) AS ?gene_name
   concat('[', ?sgn_gene_id, '](https://solgenomics.net/locus/Solyc00g005000.2/view)') AS ?sgn_gene_id
   concat('[', ?uniprot_acc, '](', ?prot, ')') AS ?uniprot_acc
   concat('[', ?uniprot_id, '](', ?prot, ')') AS ?uniprot_id
   str(?uniprot_des) AS ?uniprot_des
   str(?go_term) AS ?go_term
   concat('[', ?go_id, '](', ?go, ')') AS ?go_id
   str(?go_cat) AS ?go_cat
FROM NAMED <http://www.uniprot.org/proteomes/Solanum_lycopersicum>
FROM NAMED <http://plants.ensembl.org/Solanum_lycopersicum>
FROM NAMED <http://purl.obolibrary.org/obo/go.owl>
WHERE {
   GRAPH ?g1 {
      ?prot uniprot:classifiedWith ?go ;
          uniprot:encodedBy/skos:prefLabel ?gene_name
   }
   GRAPH ?g2 {
      ?prot dc:identifier ?uniprot_acc ;
          rdfs:label ?uniprot_id ;
          dc:description ?uniprot_des ;
          ^<http://rdf.ebi.ac.uk/terms/ensembl/CHECKSUM> ?ensembl_prot_id .
       ?ensembl_transcript_id so:translates_to ?ensembl_prot_id ;
          so:transcribed_from/dc:identifier ?sgn_gene_id .
   }
   GRAPH ?g3 {
      ?go ?p ?o ;
         rdfs:label ?go_term ;
         go:id ?go_id ;
         go:hasOBONamespace ?go_cat .
      ?o bif:contains '( fruit AND ripening )' .
      FILTER regex(?go, obo:GO_)
   }
}
ORDER BY ?gene_name

resulting in

gene_name sgn_gene_id uniprot_acc uniprot_id uniprot_des go_term go_id go_cat
ACO1 Solyc07g049530.2 P05116 ACCO1_SOLLC 1-aminocyclopropane-1-carboxylate oxidase 1 fruit ripening GO:0009835 biological_process
ACO3 Solyc09g089580.2 P10967 ACCH3_SOLLC 1-aminocyclopropane-1-carboxylate oxidase homolog fruit ripening GO:0009835 biological_process
ACO4 Solyc07g049550.2 P24157 ACCO4_SOLLC 1-aminocyclopropane-1-carboxylate oxidase 4 fruit ripening GO:0009835 biological_process
ACS2 Solyc01g095080.2 P18485 1A12_SOLLC 1-aminocyclopropane-1-carboxylate synthase 2 fruit ripening GO:0009835 biological_process
ACS3 Solyc02g091990.2 Q42881 1A13_SOLLC 1-aminocyclopropane-1-carboxylate synthase 3 fruit ripening GO:0009835 biological_process
ARF2A Solyc03g118290.2 Q2LAJ3 Q2LAJ3_SOLLC Auxin response factor fruit ripening, climacteric GO:0009836 biological_process
ARF2A Solyc03g118290.2 Q2LAJ3 Q2LAJ3_SOLLC Auxin response factor fruit ripening GO:0009835 biological_process
ARF2B Solyc12g042070.1 K4DF01 K4DF01_SOLLC Auxin response factor fruit ripening GO:0009835 biological_process
GP1 Solyc05g005560.2 Q40161 GP1_SOLLC Polygalacturonase-1 non-catalytic subunit beta fruit ripening GO:0009835 biological_process
PG2 Solyc10g080210.1 P05117 PGLR_SOLLC Polygalacturonase-2 fruit ripening GO:0009835 biological_process
PME1.9 Solyc07g064170.2 P14280 PME1_SOLLC Pectinesterase 1 fruit ripening GO:0009835 biological_process
PME2.1 Solyc07g064180.2 P09607 PME21_SOLLC Pectinesterase 2.1 fruit ripening GO:0009835 biological_process

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