Some flanking markers require additional validation & post-processing

[arnikz]

For example, QTL:3464107_4_15 is associated with two (flanking) markers:

• TG194-J1 tagged as
  • TG194
    • http://localhost:8890/genome/Solanum_lycopersicum/variation/gene72_0-i22; chromosome 11:2947789-2948311
    • http://localhost:8890/genome/Solanum_lycopersicum/variation/gene73_0-i22; chromosome 11:2947789-2948309
  • J1
    • http://localhost:8890/genome/Solanum_pennellii/variation/cLES-5-J1; chromosome 1:95577802-95577596 (which is orthologous to http://localhost:8890/genome/Solanum_lycopersicum/variation/gene358_0-i2; chromosome 1:85319942-85322549)

[gurnoor1990]

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

[arnikz]

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))
	} ;

[arnikz]

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