Ncbi Eutils : Retrieving Taxonomic Id From Organism Name Doesn'T Work Anymore

Question

[magvazaryarvtre]

Hi, some time ago I wrote a script that retrieves complete taxonomic lineage from organism name, using ncbi eutilities. It makes two queries ;

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=ORGANISM

to get the taxonomic id of the organism, then

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=TAXONOMY_ID&retmode=xml

to get the lineage. This script was working fine until today. Now the first query returns the following error message :

"Search Backend failed: Database is not supported: taxonomy"

(The second query still works fine for now (2013-05-15))

Does someone know whether this is permanent or not? In that case, is there an alternative?

thanks

[aravind ramesh]

It may not be permanent, wait for couple of hours(or days). Alternatively you can download whole taxonomy database from NCBI ftp site.

[magvazaryarvtre]

You were right, it works again (2013-05-15, ~6 hours later), I got worried for no reason -_-

Answer 1

[Hamish]

In the first instance the E-utilities help-desk ([e-mail]) should be able to help you out with details of the service status.

However if you still have problems, or want to enable your processing to fail-over to an alternative source of taxonomy data, then the following may help...

The NCBI Taxonomy is used by all of the INSDC member databases and is available in their services:

• NCBI:
  • E-utilities
  • FTP site
• EMBL-EBI:
  • ENA Browser, for scripting information see http://www.ebi.ac.uk/ena/about/browser
  • FTP site
  • EBI Search (for scripting see the EB-eye web service) and dbfetch/WSDbfetch
• DDBJ:
  • TXSearch

UniProt align their taxonomy with the NCBI Taxonomy, the main difference being a few species where an different authority has been chosen for the scientific name, the name used by INSDC is kept as an alias. So you could use it to perform the look-ups. For details of how to script against UniProt.org see http://www.uniprot.org/faq/28

Answer 2

[Istvan Albert]

Just to mark this as answered: the problem was a temporary outage.