Dear All, I have a list of NCBI taxon ids for which I would like to have both the full lineage and common name information. So I Install the package called 'genomes' (genomes_2.0.0.zip£©,then use function 'ncbiTaxonomy' as followed, > ncbiTaxonomy (1000587, "lineage") Premature end of data in tag TaxaSet line 1 I search by google to find the reason, but I conld not get any. If anyone know? Thanks very much! [[alternative HTML version deleted]]

I sent this on Friday but I'm not sure what happened to it. I apologize if this re-posts. > I have a list of NCBI taxon ids for which I would like to have both the full lineage and common name information. So I Install the package called >'genomes' (genomes_2.0.0.zip),then use function 'ncbiTaxonomy' as followed, > ncbiTaxonomy (1000587, "lineage") >Premature end of data in tag TaxaSet line 1 The new NCBI E-Utilities updates (version 2.0 of ESummary and EFetch) have broken a number of functions in my genomes package including ncbiTaxonomy, so I decided to simplify and re-write all the NCBI e-utility code and separate these from the parsers. You can find a complete description on GitHub at https://github.com/cstubben/ncbi and I will update the genomes dev package in a few weeks once I get everything worked out. It should work something like this after the next update... Run einfo to see a list of search columns einfo("taxonomy") Name FullName 1 ALL All Fields 2 ALLN All Names 3 COMN Common Name 4 EDAT Entrez Date 5 FILT Filter 6 GC GC 7 LNGE Lineage 8 MGC MGC 9 NXLV Next Level ... and then run esearch (using the lineage field) with esummary to get all taxa in the lineage (I think this usually sorts phylogenetically). esummary( esearch("Huitzilac virus[LNGE]", "taxonomy")) Id Rank Division ScientificName 1 1000587 species viruses Huitzilac virus 2 339351 viruses unclassified Hantavirus 3 11598 genus viruses Hantavirus 4 11571 family viruses Bunyaviridae 5 35301 viruses ssRNA negative-strand viruses 6 439488 viruses ssRNA viruses 7 10239 superkingdom viruses Viruses 8 1 root In addition, any search result or list of IDs can also be passed directly to esummary, efetch or elink, and I was using the xml results from EFetch to parse the Lineage tag. efetch("1000587,86782", db="taxonomy", retmode="xml") <lineage>Viruses; ssRNA viruses; ssRNA negative-strand viruses; Bunyaviridae; Hantavirus; unclassified Hantavirus</lineage>" So long story, the updated ncbiTaxonomy(1000587, "lineage") will be able to get these results again in a couple weeks. Sorry about the delay. Chris Stubben -- Los Alamos National Lab BioScience Division