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Remove all xrefs to self #752

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matentzn opened this issue Apr 6, 2020 · 1 comment · May be fixed by #1665
Open

Remove all xrefs to self #752

matentzn opened this issue Apr 6, 2020 · 1 comment · May be fixed by #1665
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@matentzn
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matentzn commented Apr 6, 2020

Currently there are a few hasdbxref annotations to self. We should get rid of them.
@matentzn
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These are the 265 cases we have in EFO:

?term_curie	?xref_curie
"RO:0002159"	"RO:0002159"
"FBbt:00004784"	"FBbt:00004784"
"RO:0002285"	"RO:0002285"
"PO:0003023"	"PO:0003023"
"FMA:3906"	"FMA:3906"
"FBbt:00000127"	"FBbt:00000127"
"RO:0002180"	"RO:0002180"
"GO:0009314"	"GO:0009314"
"PO:0002000"	"PO:0002000"
"FBbt:00005523"	"FBbt:00005523"
"FBbt:00017019"	"FBbt:00017019"
"ZFA:0001269"	"ZFA:0001269"
"EFO:0005128"	"EFO:0005128"
"PO:0025022"	"PO:0025022"
"FBbt:00005067"	"FBbt:00005067"
"PATO:0000047"	"PATO:0000047"
"FBbt:00005528"	"FBbt:00005528"
"ZFA:0000141"	"ZFA:0000141"
"FBbt:00005422"	"FBbt:00005422"
"RO:0002131"	"RO:0002131"
"FBbt:00004914"	"FBbt:00004914"
"GO:0008150"	"GO:0008150"
"FBbt:00005424"	"FBbt:00005424"
"RO:0002082"	"RO:0002082"
"FBbt:00005550"	"FBbt:00005550"
"FMA:3884"	"FMA:3884"
"FBbt:00005834"	"FBbt:00005834"
"FBbt:00005551"	"FBbt:00005551"
"DOID:7551"	"DOID:7551"
"FBbt:00001724"	"FBbt:00001724"
"ZFA:0000963"	"ZFA:0000963"
"FBbt:00005552"	"FBbt:00005552"
"FBbt:00005554"	"FBbt:00005554"
"RO:0002087"	"RO:0002087"
"FMA:3832"	"FMA:3832"
"FBbt:00005606"	"FBbt:00005606"
"FBbt:00000461"	"FBbt:00000461"
"BFO:0000020"	"BFO:0000020"
"RO:0003000"	"RO:0003000"
"ZFA:0001244"	"ZFA:0001244"
"FBbt:00005556"	"FBbt:00005556"
"UBPROP:0000100"	"UBPROP:0000100"
"RO:0003001"	"RO:0003001"
"ZFA:0001370"	"ZFA:0001370"
"FMA:24984"	"FMA:24984"
"FBbt:00005608"	"FBbt:00005608"
"UBPROP:0000101"	"UBPROP:0000101"
"FBbt:00005501"	"FBbt:00005501"
"FBbt:00005609"	"FBbt:00005609"
"FBbt:00004891"	"FBbt:00004891"
"RO:0002160"	"RO:0002160"
"RO:0002161"	"RO:0002161"
"FBbt:00005504"	"FBbt:00005504"
"FBbt:00000109"	"FBbt:00000109"
"RO:0002162"	"RO:0002162"
"FBbt:00005630"	"FBbt:00005630"
"FBbt:00005505"	"FBbt:00005505"
"BSPO:0001113"	"BSPO:0001113"
"FBbt:00005506"	"FBbt:00005506"
"PATO:0000383"	"PATO:0000383"
"ZFA:0000226"	"ZFA:0000226"
"RO:0002215"	"RO:0002215"
"EFO:0003503"	"EFO:0003503"
"BSPO:0001114"	"BSPO:0001114"
"RO:0002573"	"RO:0002573"
"RO:0001015"	"RO:0001015"
"UBREL:0000001"	"UBREL:0000001"
"PATO:0000384"	"PATO:0000384"
"RO:0002216"	"RO:0002216"
"FBbt:00017020"	"FBbt:00017020"
"BSPO:0001115"	"BSPO:0001115"
"BSPO:0000096"	"BSPO:0000096"
"UBREL:0000002"	"UBREL:0000002"
"FBbt:00005508"	"FBbt:00005508"
"UBPROP:0000001"	"UBPROP:0000001"
"BSPO:0000097"	"BSPO:0000097"
"UBPROP:0000002"	"UBPROP:0000002"
"BSPO:0000098"	"BSPO:0000098"
"FBbt:00004202"	"FBbt:00004202"
"RO:0002219"	"RO:0002219"
"UBPROP:0000003"	"UBPROP:0000003"
"GO:0007610"	"GO:0007610"
"BSPO:0000099"	"BSPO:0000099"
"RO:0001019"	"RO:0001019"
"ZFA:0001273"	"ZFA:0001273"
"BFO:0000050"	"BFO:0000050"
"CHEBI:5931"	"CHEBI:5931"
"FBbt:00004204"	"FBbt:00004204"
"BFO:0000051"	"BFO:0000051"
"HP:0010865"	"HP:0010865"
"FBbt:00005072"	"FBbt:00005072"
"FBbt:00001069"	"FBbt:00001069"
"BFO:0000053"	"BFO:0000053"
"UBPROP:0000007"	"UBPROP:0000007"
"PO:0004518"	"PO:0004518"
"UBPROP:0000008"	"UBPROP:0000008"
"FBbt:00005534"	"FBbt:00005534"
"BFO:0000056"	"BFO:0000056"
"http://semanticscience.org/resource/SIO_000008"	"http://semanticscience.org/resource/SIO_000008"
"PO:0009033"	"PO:0009033"
"ZFA:0001047"	"ZFA:0001047"
"FBbt:00005535"	"FBbt:00005535"
"FBbt:00000441"	"FBbt:00000441"
"ZFA:0000023"	"ZFA:0000023"
"FBbt:00005536"	"FBbt:00005536"
"FBbt:00000442"	"FBbt:00000442"
"GO:0072718"	"GO:0072718"
"FBbt:00000210"	"FBbt:00000210"
"FBbt:00015256"	"FBbt:00015256"
"ZFA:0000841"	"ZFA:0000841"
"FBbt:00005662"	"FBbt:00005662"
"RO:0002371"	"RO:0002371"
"ZFA:0000257"	"ZFA:0000257"
"BSPO:0000120"	"BSPO:0000120"
"DOID:10718"	"DOID:10718"
"FBbt:00005663"	"FBbt:00005663"
"FBbt:00000444"	"FBbt:00000444"
"RO:0002372"	"RO:0002372"
"BSPO:0000121"	"BSPO:0000121"
"PO:0004542"	"PO:0004542"
"FBbt:00005431"	"FBbt:00005431"
"FBbt:00005664"	"FBbt:00005664"
"PO:0000256"	"PO:0000256"
"RO:0002373"	"RO:0002373"
"BSPO:0000122"	"BSPO:0000122"
"FBbt:00005665"	"FBbt:00005665"
"RO:0002374"	"RO:0002374"
"BSPO:0000123"	"BSPO:0000123"
"FBbt:00000447"	"FBbt:00000447"
"BSPO:0000124"	"BSPO:0000124"
"FBbt:00005610"	"FBbt:00005610"
"FBbt:00005667"	"FBbt:00005667"
"ZFA:0000563"	"ZFA:0000563"
"BSPO:0000125"	"BSPO:0000125"
"FBbt:00005611"	"FBbt:00005611"
"ZFA:0000972"	"ZFA:0000972"
"FBbt:00005668"	"FBbt:00005668"
"BSPO:0000126"	"BSPO:0000126"
"FBbt:00005612"	"FBbt:00005612"
"GO:0008152"	"GO:0008152"
"ZFA:0000281"	"ZFA:0000281"
"ZFA:0000973"	"ZFA:0000973"
"FBbt:00017000"	"FBbt:00017000"
"FBbt:00005669"	"FBbt:00005669"
"FMA:85972"	"FMA:85972"
"RO:0002322"	"RO:0002322"
"FBbt:00005614"	"FBbt:00005614"
"ZFA:0001484"	"ZFA:0001484"
"GO:0050896"	"GO:0050896"
"FBbt:00017003"	"FBbt:00017003"
"FBbt:00005565"	"FBbt:00005565"
"FBbt:00005616"	"FBbt:00005616"
"ZFA:0009150"	"ZFA:0009150"
"GO:0042747"	"GO:0042747"
"ZFA:0005040"	"ZFA:0005040"
"FBbt:00005566"	"FBbt:00005566"
"GO:0042748"	"GO:0042748"
"FBbt:00005510"	"FBbt:00005510"
"FBbt:00005618"	"FBbt:00005618"
"GO:0008283"	"GO:0008283"
"RO:0002503"	"RO:0002503"
"UBPROP:0000111"	"UBPROP:0000111"
"FBbt:00005511"	"FBbt:00005511"
"RO:0002220"	"RO:0002220"
"FBbt:00005744"	"FBbt:00005744"
"FBbt:00005568"	"FBbt:00005568"
"FBbt:00005619"	"FBbt:00005619"
"FBbt:00005512"	"FBbt:00005512"
"RO:0000052"	"RO:0000052"
"RO:0002221"	"RO:0002221"
"FBbt:00005745"	"FBbt:00005745"
"BSPO:1000000"	"BSPO:1000000"
"FBbt:00017008"	"FBbt:00017008"
"FBbt:00005746"	"FBbt:00005746"
"PO:0020019"	"PO:0020019"
"FMA:86003"	"FMA:86003"
"FBbt:00017009"	"FBbt:00017009"
"ZFA:0001384"	"ZFA:0001384"
"PO:0009013"	"PO:0009013"
"RO:0002224"	"RO:0002224"
"BSPO:0005001"	"BSPO:0005001"
"ZFA:0001385"	"ZFA:0001385"
"FBbt:00007049"	"FBbt:00007049"
"ZFA:0000003"	"ZFA:0000003"
"FBbt:00005748"	"FBbt:00005748"
"FBbt:00005516"	"FBbt:00005516"
"RO:0002225"	"RO:0002225"
"FBbt:00005749"	"FBbt:00005749"
"PO:0020147"	"PO:0020147"
"ZFA:0000821"	"ZFA:0000821"
"RO:0001025"	"RO:0001025"
"PO:0009015"	"PO:0009015"
"FBbt:00005466"	"FBbt:00005466"
"RO:0002226"	"RO:0002226"
"BSPO:0000100"	"BSPO:0000100"
"HP:0000708"	"HP:0000708"
"PO:0020148"	"PO:0020148"
"FBbt:00005643"	"FBbt:00005643"
"MA:0002714"	"MA:0002714"
"FBbt:00005518"	"FBbt:00005518"
"FBbt:00000197"	"FBbt:00000197"
"FBbt:00005519"	"FBbt:00005519"
"BSPO:0000102"	"BSPO:0000102"
"ZFA:0001389"	"ZFA:0001389"
"http://www.w3.org/2000/01/rdf-schema#seeAlso"	"http://www.w3.org/2000/01/rdf-schema#seeAlso"
"ZFA:0000541"	"ZFA:0000541"
"RO:0002229"	"RO:0002229"
"GO:0042493"	"GO:0042493"
"GO:0010960"	"GO:0010960"
"FBbt:00005822"	"FBbt:00005822"
"FBbt:00005646"	"FBbt:00005646"
"FBbt:00005824"	"FBbt:00005824"
"BFO:0000062"	"BFO:0000062"
"ZFA:0001104"	"ZFA:0001104"
"ZFA:0000085"	"ZFA:0000085"
"BSPO:0000107"	"BSPO:0000107"
"FBbt:00005542"	"FBbt:00005542"
"ZFA:0000778"	"ZFA:0000778"
"PO:0020048"	"PO:0020048"
"BSPO:0000108"	"BSPO:0000108"
"http://semanticscience.org/resource/SIO_000657"	"http://semanticscience.org/resource/SIO_000657"
"FBbt:00001433"	"FBbt:00001433"
"ZFA:0000672"	"ZFA:0000672"
"http://semanticscience.org/resource/SIO_000658"	"http://semanticscience.org/resource/SIO_000658"
"FBbt:00005544"	"FBbt:00005544"
"RO:0004029"	"RO:0004029"
"FBbt:00016000"	"FBbt:00016000"
"FBbt:00005670"	"FBbt:00005670"
"FBbt:00005545"	"FBbt:00005545"
"ZFA:0000265"	"ZFA:0000265"
"RO:0002254"	"RO:0002254"
"FBbt:00016001"	"FBbt:00016001"
"FBbt:00005546"	"FBbt:00005546"
"RO:0002255"	"RO:0002255"
"BFO:0000068"	"BFO:0000068"
"RO:0002256"	"RO:0002256"
"BFO:0000069"	"BFO:0000069"
"PO:0009046"	"PO:0009046"
"FBbt:00005673"	"FBbt:00005673"
"FBbt:00005548"	"FBbt:00005548"
"DOID:13406"	"DOID:13406"
"FBbt:00005498"	"FBbt:00005498"
"BSPO:0001100"	"BSPO:0001100"
"FBbt:00005442"	"FBbt:00005442"
"RO:0002202"	"RO:0002202"
"ZFA:0000678"	"ZFA:0000678"
"FBbt:00005675"	"FBbt:00005675"
"BSPO:0001101"	"BSPO:0001101"
"DOID:1947"	"DOID:1947"
"RO:0002203"	"RO:0002203"
"PATO:0001340"	"PATO:0001340"
"FBbt:00004011"	"FBbt:00004011"
"FBbt:00005571"	"FBbt:00005571"
"MA:0000191"	"MA:0000191"
"http://purl.org/dc/elements/1.1/creator"	"http://purl.org/dc/elements/1.1/creator"
"RO:0002207"	"RO:0002207"
"FBbt:00017011"	"FBbt:00017011"
"BSPO:0001106"	"BSPO:0001106"
"ZFA:0001369"	"ZFA:0001369"
"DOID:10113"	"DOID:10113"
"BSPO:0001107"	"BSPO:0001107"
"RO:0002158"	"RO:0002158"
"GO:0007600"	"GO:0007600"
"BSPO:0001108"	"BSPO:0001108"
"PO:0009073"	"PO:0009073"

This is the query that can be used to fix it:

prefix owl: <http://www.w3.org/2002/07/owl#>
prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>

#SELECT ?term_curie ?xref_curie
DELETE {
  ?term oboInOwl:hasDbXref ?xref .
}
WHERE 
{ 
    ?term oboInOwl:hasDbXref ?xref .
  	FILTER (isIRI(?term))
	BIND(
		IF(	
			regex(str(?xref), "http[:][/][/]www[.]ebi[.]ac[.]uk[/]efo[/]EFO[_]")
				|| regex(str(?xref), "http[:][/][/]purl[.]obolibrary[.]org[/]obo[/]")
				|| regex(str(?xref), "http[:][/][/]www[.]orpha.net[/]ORDO[/]"),
			REPLACE(
				REPLACE(STR(?xref), "http[:][/][/]purl[.]obolibrary[.]org[/]obo[/]|http[:][/][/]www[.]ebi[.]ac[.]uk[/]efo[/]|http[:][/][/]www[.]orpha.net[/]ORDO[/]", "", "i"),
			"[_]", ":", "i")
      ,str(?xref)) as ?xref_curie)
    BIND(
		IF(	
			regex(str(?term), "http[:][/][/]www[.]ebi[.]ac[.]uk[/]efo[/]EFO[_]")
				|| regex(str(?term), "http[:][/][/]purl[.]obolibrary[.]org[/]obo[/]")
				|| regex(str(?term), "http[:][/][/]www[.]orpha.net[/]ORDO[/]"),
			REPLACE(
				REPLACE(STR(?term), "http[:][/][/]purl[.]obolibrary[.]org[/]obo[/]|http[:][/][/]www[.]ebi[.]ac[.]uk[/]efo[/]|http[:][/][/]www[.]orpha.net[/]ORDO[/]", "", "i"),
			"[_]", ":", "i")
      , str(?term))  as ?term_curie)
  FILTER(str(?term_curie)=str(?xref_curie))
}

Unfortunately, the diff is just so enormous when running this query, that I don't feel confident to do this right now. Moving to

@dhimmel dhimmel mentioned this issue Jun 30, 2022
Closed
@matentzn matentzn linked a pull request Jul 8, 2022 that will close this issue
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Removing self-xrefs from release EBISPOT/efo
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@matentzn @zoependlington