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gurnoor1990 avatar gurnoor1990 commented on July 3, 2024

Solved in the new data! which will be updated while solving issue #21

3464107 4 15 TG194-J1
http://solgenomics.net/genome/Solanum_lycopersicum/variation/gene358_0-i2;
http://solgenomics.net/genome/Solanum_lycopersicum/variation/gene72_0-i22;
http://solgenomics.net/genome/Solanum_lycopersicum/variation/gene73_0-i22;
http://solgenomics.net/genome/Solanum_pennellii/variation/cLES-5-J1

from pbg-ld.

arnikz avatar arnikz commented on July 3, 2024

Requires revision of this code:

pbg-ld/src/update_rdf.sql

Lines 497 to 589 in 673ed9e

SPARQL
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dcmitype: <http://purl.org/dc/dcmitype/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX sly: <http://purl.obolibrary.org/obo/NCBITaxon_4081>
PREFIX so: <http://purl.obolibrary.org/obo/so#>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>
INSERT INTO <$u{EPMC_G_URI}> {
?qtl so:overlaps ?gene
}
WHERE {
GRAPH <$u{EPMC_G_URI}> {
?dts a dcmitype:Dataset ;
so:genome_of sly: ;
dcterms:hasPart ?qtl .
?qtl a obo:SO_0000771 ;
faldo:location ?loc ;
obo:RO_0003308 ?trait .
?loc faldo:begin ?begin ;
faldo:end ?end
}
GRAPH <$u{SGN-SL_G_URI}> {
?begin faldo:position ?begin_pos ;
faldo:reference ?chr .
?end faldo:position ?end_pos
}
GRAPH <$u{SGN-SL_G_URI}> {
?loc2 faldo:begin ?begin2 ;
faldo:end ?end2 ;
^faldo:location ?gene .
?gene a obo:SO_0001217 .
?begin2 faldo:position ?begin_pos2 ;
faldo:reference ?chr2 .
?end2 faldo:position ?end_pos2
}
FILTER(?chr = ?chr2)
FILTER((xsd:integer(?begin_pos) > xsd:integer(?begin_pos2) &&
xsd:integer(?begin_pos) < xsd:integer(?end_pos2)) ||
(xsd:integer(?end_pos) > xsd:integer(?begin_pos2) &&
xsd:integer(?end_pos) < xsd:integer(?end_pos2)) ||
(xsd:integer(?begin_pos) < xsd:integer(?begin_pos2) &&
xsd:integer(?end_pos) > xsd:integer(?end_pos2)) ||
xsd:integer(?begin_pos) > xsd:integer(?begin_pos2) &&
xsd:integer(?end_pos) < xsd:integer(?end_pos2))
} ;
SPARQL
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dcmitype: <http://purl.org/dc/dcmitype/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX stu: <http://purl.obolibrary.org/obo/NCBITaxon_4113>
PREFIX so: <http://purl.obolibrary.org/obo/so#>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>
INSERT INTO <$u{EPMC_G_URI}> {
?qtl so:overlaps ?gene
}
WHERE {
GRAPH <$u{EPMC_G_URI}> {
?dts a dcmitype:Dataset ;
so:genome_of stu: ;
dcterms:hasPart ?qtl .
?qtl a obo:SO_0000771 ;
faldo:location ?loc ;
obo:RO_0003308 ?trait .
?loc faldo:begin ?begin ;
faldo:end ?end
}
GRAPH <$u{SGN-ST_G_URI}> {
?begin faldo:position ?begin_pos ;
faldo:reference ?chr .
?end faldo:position ?end_pos
}
GRAPH <$u{SGN-ST_G_URI}> {
?loc2 faldo:begin ?begin2 ;
faldo:end ?end2 ;
^faldo:location ?gene .
?gene a obo:SO_0001217 .
?begin2 faldo:position ?begin_pos2 ;
faldo:reference ?chr2 .
?end2 faldo:position ?end_pos2
}
FILTER(?chr = ?chr2)
FILTER((xsd:integer(?begin_pos) > xsd:integer(?begin_pos2) &&
xsd:integer(?begin_pos) < xsd:integer(?end_pos2)) ||
(xsd:integer(?end_pos) > xsd:integer(?begin_pos2) &&
xsd:integer(?end_pos) < xsd:integer(?end_pos2)) ||
(xsd:integer(?begin_pos) < xsd:integer(?begin_pos2) &&
xsd:integer(?end_pos) > xsd:integer(?end_pos2)) ||
xsd:integer(?begin_pos) > xsd:integer(?begin_pos2) &&
xsd:integer(?end_pos) < xsd:integer(?end_pos2))
} ;

from pbg-ld.

arnikz avatar arnikz commented on July 3, 2024

The code is correct, however, the marker J1 (as indicated in the article) could be different from cLES-5-J1.

from pbg-ld.

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