[ensembl-dev] EnsemblGenomes search error

陈岗 danielchen06 at gmail.com
Fri Jan 4 02:32:41 GMT 2013


Hi All

Our EnsemblGenomes mirror suffers a search error. For instance, search dnaA
in species Escherichia coli K12, the mirror returns 12 entries.

Gene: EBESCG00000003429 [Region in detail]
Gene: EBESCG00000007452 [Region in detail]
Gene: EBESCG00000013460 [Region in detail]
Gene: EBESCG00000018762 [Region in detail]
Gene: EBESCG00000023601 [Region in detail]
Gene: EBESCG00000031974 [Region in detail]
Gene: EBESCG00000037518 [Region in detail]
Gene: EBESCG00000048558 [Region in detail]
Gene: EBESCG00000052321 [Region in detail]
Gene: EBESCG00000057553 [Region in detail]
Gene: EBESCG00000003435 [Region in detail]
Gene: EBESCG00000002586 [Region in detail]

However, some linkages of these entries are unavailable, report a internal
page error, including
EBESCG00000007452
EBESCG00000013460
EBESCG00000018762
EBESCG00000023601 and so on.

I checked above IDs from tables ensembl_compara_bacteria_16_69.member
and ensembl_compara_bacteria_16_69.genome_db, they are not belong to
species Escherichia coli K12,
but e_coli_atcc_8739, e_coli_atcc_27325, e_coli_o139_h28, e_coli_edl933
respectively.

If change the URLs which return the internal error with above names, they
work correctly. For example, change
http://172.16.10.16:8899/e_coli_k12/Gene/Summary?g=EBESCG00000007452;db=core
to
http://172.16.10.16:8899/e_coli_atcc_8739/Gene/Summary?db=core;g=EBESCG00000007452

Therefore, the search error is caused by wrong species name which is
applied as a part of URL. Could you fix the error?

Best regards

-- 
Gang Chen
TILSI
Taicang Institute For Life Science Information
Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province,
P.R.China
Phone:(+86)512-82782588
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