Errors in curie_id property of nodes in KG

[finnagin]

Some of the curie_id properties of the nodes in the KG on the rtxsteve container on rtxdev.saramsey.org seem to have errors in them. I found the following nodes with the cypher command match (n) where n.curie_id =~ '(?i).*[a-z]' return n.curie_id, n.description limit 50:

n.curie_id	n.description
"UBERON:0001029PHENOTYPE"	"obsolete neuromuscular junction phenotype"
"CL:0000573PHENOTYPE"	"retinal cone cell phenotype"
"CL:0001035PHENOTYPE"	"bone cell phenotype"
"UBERON:0001467PHENOTYPE"	"shoulder phenotype"
"GO:0007610PHENOTYPE"	"behavior phenotype"
"UBERON:0001799PHENOTYPE"	"vitreous chamber of eyeball phenotype"
"UBERON:0002107PHENOTYPE"	"liver phenotype"
"GO:0050890PHENOTYPE"	"cognition phenotype"
"GO:0060004PHENOTYPE"	"reflex phenotype"
"NBO:0000607PHENOTYPE"	"cognitive behavior phenotype"
"UBERON:0003657PHENOTYPE"	"limb joint phenotype"
"NBO:0000056PHENOTYPE"	"walking behavior phenotype"
"UBERON:0001090PHENOTYPE"	"synovial fluid phenotype"
"UniProt:EBI"	"MGAT5B"
"UniProt:TNF"	"ENSG00000204490"
"UniProt:CYorf15B"	"CY15B"
"UniProt:NFKBIA"	"ENSG00000100906"
"UniProt:HLA"	"ENSG00000204287"
"UniProt:MAFG"	"Q9BRP3"
"UniProt:EP400NL"	"H9KV84"
"UniProt:null"	"ANON1"

Might be caused by an error in the KG construction?

[dkoslicki]

@saramsey Pinging Steve as he'll know how to address this.

[saramsey]

Working on it

[saramsey]

Testing a fix now, on rtxsteve

…

----------------------------------------------------- Stephen Ramsey Assistant Professor, Oregon State University * School of Electrical Engineering and Computer Science * Department of Biomedical Sciences 208A Dryden Hall stephen.ramsey@oregonstate.edu<mailto:stephen.ramsey@oregonstate.edu> http://lab.saramsey.org On Apr 18, 2018, at 12:32 PM, Finn Womack <notifications@github.com<mailto:notifications@github.com>> wrote: Some of the curie_id properties of the nodes in the KG on the rtxsteve container on rtxdev.saramsey.org<http://rtxdev.saramsey.org> seem to have errors in them. I found the following nodes with the cypher command match (n) where n.curie_id =~ '(?i).*[a-z]' return n.curie_id, n.description limit 50: n.curie_id n.description "UBERON:0001029PHENOTYPE" "obsolete neuromuscular junction phenotype" "CL:0000573PHENOTYPE" "retinal cone cell phenotype" "CL:0001035PHENOTYPE" "bone cell phenotype" "UBERON:0001467PHENOTYPE" "shoulder phenotype" "GO:0007610PHENOTYPE" "behavior phenotype" "UBERON:0001799PHENOTYPE" "vitreous chamber of eyeball phenotype" "UBERON:0002107PHENOTYPE" "liver phenotype" "GO:0050890PHENOTYPE" "cognition phenotype" "GO:0060004PHENOTYPE" "reflex phenotype" "NBO:0000607PHENOTYPE" "cognitive behavior phenotype" "UBERON:0003657PHENOTYPE" "limb joint phenotype" "NBO:0000056PHENOTYPE" "walking behavior phenotype" "UBERON:0001090PHENOTYPE" "synovial fluid phenotype" "UniProt:EBI" "MGAT5B" "UniProt:TNF" "ENSG00000204490" "UniProt:CYorf15B" "CY15B" "UniProt:NFKBIA" "ENSG00000100906" "UniProt:HLA" "ENSG00000204287" "UniProt:MAFG" "Q9BRP3" "UniProt:EP400NL" "H9KV84" "UniProt:null" "ANON1" Might be caused by an error in the KG construction? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#74>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AFTe-1fAEBC_dcY-uvluphbaBT5eS9qOks5tp5TNgaJpZM4TapTr>.

[saramsey]

When we query with: Q16665; we get a node with alias: Q9BRP3

[saramsey]

I'm testing the fix now... but it will take another two hours before I know if it worked.

[saramsey]

restarted test, in order to fold in fixes for #80 and #79

[saramsey]

@finnagin , +1 for putting the cypher query in the issue report; super helpful!

[saramsey]

Current status: I believe this issue is fixed in the code, except for the node "UniProt:null"; I have embedded debugging code to track down where that one is coming from. Once this issue has been fixed in the rtxdev.saramsey.org:7474 KG, then I will close out this issue.

[saramsey]

testing a fix for the "UniProt:null" now (that was due to an unexpected returned response from DisGeNET).

[saramsey]

fixed in KG:
http://rtxdev.saramsey.org:7674