Example Query 4 not working

[gurnoor1990]

This Query is not working, I think Uniprot data has been revised. No GO term associated to Ripening now

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
WHERE {
   GRAPH <http://www.uniprot.org/proteomes/Solanum_lycopersicum> {
      ?prot uniprot:classifiedWith ?go ;
          uniprot:encodedBy/skos:prefLabel ?gene_name
   }
   GRAPH <http://plants.ensembl.org/Solanum_lycopersicum> {
      ?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 <http://purl.obolibrary.org/obo/go.owl> {
      ?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

[arnikz]

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?

[gurnoor1990]

Runs after make restart-srv

Similar to Issue #31

[matthijsbrouwer]

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