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gurnoor1990 avatar gurnoor1990 commented on August 26, 2024

Error vanishes after
make restart-srv

from pbg-ld.

matthijsbrouwer avatar matthijsbrouwer commented on August 26, 2024

They do seem to run (even all together in one query) with

PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT
   str(?g1) AS ?g1
   str(?feature_name) AS ?feature_name
   ?feature_id
   COUNT(*) AS ?n
FROM NAMED <http://solgenomics.net/genome/Solanum_lycopersicum>
FROM NAMED <http://solgenomics.net/genome/Solanum_pennellii>
FROM NAMED <http://solgenomics.net/genome/Solanum_tuberosum>
FROM NAMED <http://plants.ensembl.org/Solanum_lycopersicum>
FROM NAMED <http://plants.ensembl.org/Solanum_tuberosum>
FROM NAMED <http://purl.obolibrary.org/obo/so.owl>
WHERE {
   GRAPH ?g1 {                             
      ?ft a ?feature_type .
      FILTER regex(?feature_type, obo:SO_) .
      BIND(concat('[', replace(replace(str(?feature_type), '.+\\/', ''), '_', ':'), '](', ?feature_type, ')') AS ?feature_id)
   }
   GRAPH ?g2 {
      ?feature_type rdfs:label ?feature_name
   }
}
GROUP BY ?g1 ?g2 ?feature_name ?feature_id
ORDER BY ASC(?g1) DESC(?n)

resulting in

g1 feature_name feature_id n
http://plants.ensembl.org/Solanum_lycopersicum exon SO:0000147 162535
http://plants.ensembl.org/Solanum_lycopersicum protein_coding_primary_transcript SO:0000120 34725
http://plants.ensembl.org/Solanum_lycopersicum protein_coding_gene SO:0001217 33785
http://plants.ensembl.org/Solanum_lycopersicum miRNA_gene SO:0001265 3153
http://plants.ensembl.org/Solanum_lycopersicum miRNA SO:0000276 3153
http://plants.ensembl.org/Solanum_lycopersicum tRNA_gene SO:0001272 908
http://plants.ensembl.org/Solanum_lycopersicum snoRNA SO:0000275 390
http://plants.ensembl.org/Solanum_lycopersicum snoRNA_gene SO:0001267 390
http://plants.ensembl.org/Solanum_lycopersicum snRNA_gene SO:0001268 255
http://plants.ensembl.org/Solanum_lycopersicum snRNA SO:0000274 255
http://plants.ensembl.org/Solanum_lycopersicum rRNA SO:0000252 94
http://plants.ensembl.org/Solanum_lycopersicum rRNA_gene SO:0001637 94
http://plants.ensembl.org/Solanum_lycopersicum pseudogenic_tRNA SO:0000778 76
http://plants.ensembl.org/Solanum_lycopersicum RNA SO:0000356 2
http://plants.ensembl.org/Solanum_tuberosum exon SO:0000147 177518
http://plants.ensembl.org/Solanum_tuberosum protein_coding_primary_transcript SO:0000120 56215
http://plants.ensembl.org/Solanum_tuberosum protein_coding_gene SO:0001217 39021
http://plants.ensembl.org/Solanum_tuberosum miRNA SO:0000276 1203
http://plants.ensembl.org/Solanum_tuberosum miRNA_gene SO:0001265 1203
http://plants.ensembl.org/Solanum_tuberosum snoRNA SO:0000275 938
http://plants.ensembl.org/Solanum_tuberosum tRNA_gene SO:0001272 938
http://plants.ensembl.org/Solanum_tuberosum snoRNA_gene SO:0001267 938
http://plants.ensembl.org/Solanum_tuberosum snRNA SO:0000274 392
http://plants.ensembl.org/Solanum_tuberosum snRNA_gene SO:0001268 392
http://plants.ensembl.org/Solanum_tuberosum pseudogenic_tRNA SO:0000778 332
http://plants.ensembl.org/Solanum_tuberosum rRNA SO:0000252 107
http://plants.ensembl.org/Solanum_tuberosum rRNA_gene SO:0001637 107
http://plants.ensembl.org/Solanum_tuberosum RNA SO:0000356 1
http://solgenomics.net/genome/Solanum_lycopersicum exon SO:0000147 160001
http://solgenomics.net/genome/Solanum_lycopersicum CDS SO:0000316 157233
http://solgenomics.net/genome/Solanum_lycopersicum intron SO:0000188 125276
http://solgenomics.net/genome/Solanum_lycopersicum protein_coding_gene SO:0001217 34725
http://solgenomics.net/genome/Solanum_lycopersicum protein_coding_primary_transcript SO:0000120 34725
http://solgenomics.net/genome/Solanum_lycopersicum genetic_marker SO:0001645 30718
http://solgenomics.net/genome/Solanum_lycopersicum three_prime_UTR SO:0000205 15343
http://solgenomics.net/genome/Solanum_lycopersicum five_prime_UTR SO:0000204 13548
http://solgenomics.net/genome/Solanum_lycopersicum chromosome SO:0000340 13
http://solgenomics.net/genome/Solanum_lycopersicum genome SO:0001026 1
http://solgenomics.net/genome/Solanum_pennellii exon SO:0000147 278874
http://solgenomics.net/genome/Solanum_pennellii CDS SO:0000316 252950
http://solgenomics.net/genome/Solanum_pennellii intron SO:0000188 204027
http://solgenomics.net/genome/Solanum_pennellii protein_coding_primary_transcript SO:0000120 48923
http://solgenomics.net/genome/Solanum_pennellii protein_coding_gene SO:0001217 44965
http://solgenomics.net/genome/Solanum_pennellii genetic_marker SO:0001645 2225
http://solgenomics.net/genome/Solanum_pennellii chromosome SO:0000340 13
http://solgenomics.net/genome/Solanum_pennellii genome SO:0001026 1
http://solgenomics.net/genome/Solanum_tuberosum CDS SO:0000316 202449
http://solgenomics.net/genome/Solanum_tuberosum exon SO:0000147 165573
http://solgenomics.net/genome/Solanum_tuberosum intron SO:0000188 109913
http://solgenomics.net/genome/Solanum_tuberosum reagent SO:0000695 70326
http://solgenomics.net/genome/Solanum_tuberosum protein_coding_primary_transcript SO:0000120 56215
http://solgenomics.net/genome/Solanum_tuberosum protein_coding_gene SO:0001217 39028
http://solgenomics.net/genome/Solanum_tuberosum genetic_marker SO:0001645 5692
http://solgenomics.net/genome/Solanum_tuberosum chromosome SO:0000340 13
http://solgenomics.net/genome/Solanum_tuberosum genome SO:0001026 1

from pbg-ld.

matthijsbrouwer avatar matthijsbrouwer commented on August 26, 2024

And to improve performance, it can be simplified to

PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT
   STR(?g1) AS ?g1
   STR(?feature_name) AS ?feature_name
   CONCAT('[', replace(replace(str(?feature_type), '.+\\/', ''), '_', ':'), '](', ?feature_type, ')') AS ?feature_id
   COUNT(*) AS ?n
FROM NAMED <http://solgenomics.net/genome/Solanum_lycopersicum>
FROM NAMED <http://solgenomics.net/genome/Solanum_pennellii>
FROM NAMED <http://solgenomics.net/genome/Solanum_tuberosum>
FROM NAMED <http://plants.ensembl.org/Solanum_lycopersicum>
FROM NAMED <http://plants.ensembl.org/Solanum_tuberosum>
FROM NAMED <http://purl.obolibrary.org/obo/so.owl>
WHERE {
   GRAPH ?g1 {                             
      ?ft a ?feature_type .
   }
   GRAPH ?g2 {
      ?feature_type rdfs:label ?feature_name
   }
}
GROUP BY ?g1 ?g2 ?feature_name ?feature_type
ORDER BY ASC(?g1) DESC(?n)

from pbg-ld.

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