Retrieve Tax Id By The Match Description

Question

[Random]

I have match descriptions such as: Desulfococcus oleovorans Hxd3, complete genome Nitrobacter hamburgensis X14, complete genome

And i would like to retrieve their accession number and/or taxid.

How can i do this?

Answer 1

[Pierre Lindenbaum]

Use NCBI E-Utilies/ESearch: http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=%22Desulfococcus+oleovorans%22[ORGN]+Hxd3,%20complete%20genome&usehistory=y

it returns two gis , the first is gi:158520017

http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=158520017&retmode=xml

this record contains the accession as well as the taxonomy

(...)
<GBSeq_primary-accession>NC_009943</GBSeq_primary-accession>
(...)
<GBSeq_taxonomy>Bacteria; Proteobacteria; Deltaproteobacteria; Desulfobacterales; Desulfobacteraceae; Desulfococcus<GBSeq_taxonomy>
(...)
<GBQualifier_value>taxon:96561</GBQualifier_value>
(...)

[Random]

Thanks, that's what i was looking for. On a side note can you recommend any xslt tutorials?

[Pierre Lindenbaum]

sorry I've got nothing more than googling xslt+tutorial. Or try http://oreilly.com/catalog/9780596000530

[Random]

That will do then, thanks again!