Question: dbFetch from EBI with bogus accession number returns valid record
2
gravatar for Jeroen Van Goey
22 months ago by
Jeroen Van Goey2.0k
Ghent, Belgium
Jeroen Van Goey2.0k wrote:

I'm using dbFetch from EBI in a project. I construct URLs from the format

https://www.ebi.ac.uk/Tools/dbfetch/emblfetch?id=[ACCESSION_NUMBER]

to retrieve sequences, e.g.: 

https://www.ebi.ac.uk/Tools/dbfetch/emblfetch?id=CO069431

Accession numbers need to be of the format 1 letter + 5 numerals OR 2 letters + 6 numerals

so I added a test with the clearly bogus accession code `XX`.

To my surprise, the URL 

https://www.ebi.ac.uk/Tools/dbfetch/emblfetch?id=XX

returned a valid response, namely the sequence for "Avocado sunblotch viroid, complete genome" with accession number `J02020`.

My questions:

  1. Why does the accession number `XX` fetches the record with accession number `J02020`?
  2. Is this a bug in the dbFetch software or incorrectly submitted data?
  3. If so, should this be reported somewhere?
dbfetch ebi • 663 views
ADD COMMENTlink modified 21 months ago by Biostar ♦♦ 10 • written 22 months ago by Jeroen Van Goey2.0k
1

Interestingly, I couldn't find any other invalid code that returns something when it shouldn't - only 'XX'. Also, https://www.ebi.ac.uk/Tools/dbfetch/emblfetch?id=J02020 also returns the correct entry, so there are (at least) two pointers to this entry. Definitely looks like an error, but I'm not sure who the best person to report it to is. 

ADD REPLYlink written 22 months ago by shelly.deforte170
1

It's a rather old entry, which could mean that perhaps once XX really was its accession. Check for example this. Keep us updated..

..
CC   See also Symons R.H. Nucl. Acids Res. 9:6527-6537(1981) for
CC   sequence of an Australian isolate of ASBV (identical to
CC   unchanged sequence reported here). Accession number J02020; XX.
..
ADD REPLYlink modified 22 months ago • written 22 months ago by 5heikki6.1k
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