nmdp-bioinformatics / gfe-db

Graph database representing IPD-IMGT/HLA sequence data as GFE
https://gfe-db.readthedocs.io
GNU General Public License v3.0
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missing feature in database running at https://dev-gfedb.b12x.org:7473/browser/ #70

Closed mmaiers-nmdp closed 7 months ago

mmaiers-nmdp commented 1 year ago

This query should return two features but it only returns one: MATCH (f:Feature)-[]-(n:GFE)-[]-(a:IPD_Allele) where a.name="HLA-DPB1*100:01" RETURN n,a,f

returns:

n
{
  "identity": 36458,
  "labels": [
    "GFE"
  ],
  "properties": {
"name": "HLA-DPB1w0-0-0-483-0-331-0-0-0-0-0",
"locus": "HLA-DPB1"
  }
}

a
{
  "identity": 158050,
  "labels": [
    "IPD_Allele"
  ],
  "properties": {
"gene": "HLA-DPB1",
"name": "HLA-DPB1*100:01",
"lg": "HLA-DPB1*100:01g"
  }
}

f
{
  "identity": 95676,
  "labels": [
    "Feature"
  ],
  "properties": {
"rank": "3",
"term": "EXON",
"accession": "331",
"locus": "HLA-DPB1"
  }
}
mmaiers-nmdp commented 1 year ago

This is fixed in the latest dev server

mmaiers-nmdp commented 1 year ago

Latest output:

{
  "identity": 104450,
  "labels": [
    "Feature"
  ],
  "properties": {
"sequence": "AGAATTACCTTTTCCAGGGACGGCAGGAATGCTACGCGTTTAATGGGACACAGCGCTTCCTGGAGAGATACATCTACAACCGGGAGGAGCTCGTGCGCTTCGACAGCGACGTGGGGGAGTTCCGGGCGGTGACGGAGCTGGGGCGGCCTGAGGCGGAGTACTGGAACAGCCAGAAGGACATCCTGGAGGAGAAGCGGGCAGTGCCGGACAGGATGTGCAGACACAACTACGAGCTGGGCGGGCCCATGACCCTGCAGCGCCGAG",
"rank": "2",
"term": "EXON",
"accession": "99",
"locus": "HLA-DPB1"
  }
}
mmaiers-nmdp commented 7 months ago

I think this is right now.

DPB1*100:01:01 is an interesting case:

image