Thanks for the insights... It is a pity that the dump is not consistent with
website....
One way to circumvent the problem might be utilizing division.dmp, using the
division information for taxid, using taxid: 362651 as an example
in nodes.dump, the 5th field is division (according to taxdump_readme.txt)
362651 | 540993 | no rank | | 9 |
here division is 9
In division.dump
9 | VRL | Viruses |
...
the division.dmp is tiny compare with the other nodes.dump and names.dump...
best,
-John
On Thu, Dec 9, 2010 at 4:09 AM, Miguel Pignatelli via RT <
bug-Bio-LITE-Taxonomy-NCBI@rt.cpan.org> wrote:
Show quoted text> <URL:
https://rt.cpan.org/Ticket/Display.html?id=63758 >
>
> This seems to be an inconsistency between the web based NCBI taxonomy
> browser and the Taxonomy database (nodes.dmp/names.dmp). In nodes.dmp
> the taxid for "Viruses" (10239) is classified as "no rank" instead of
> "Superkingdom":
>
> $ grep -w Viruses names.dmp | grep "scientific name"
> 10239 | Viruses | | scientific name |
> $ grep -w ^10239 nodes.dmp
> 10239 | 1 | no rank | [...]
>
> Bio::LITE::Taxonomy omits the last "no rank" level from taxonomies
> ("cellular organisms", etc...) and for consistency, the "Virus" taxon is
> also excluded for virus.
>
> This is a bug/feature of the NCBI's taxonomy databse and I don't know
> how these modules should behave (e.g. being strict with the database
> schema or add and "exception" -- only in the NCBI module, only for Virus).
>
> I will think a bit more about this. Suggestions welcome.
>
> M;
>
>
> On Wed Dec 08 18:14:59 2010, MOTIF wrote:
> > Bio::LITE::Taxonomy::NCBI doesn't return the superkingdom "Virus" for
> > a virus taxid
> >
> > my @taxonomy = $taxNCBI->get_taxonomy(362651);
> > print join("|",@taxonomy),"\n";
> > it returns:
> > Retro-transcribing
> > viruses|Retroviridae|Orthoretrovirinae|Lentivirus|Primate lentivirus
> > group|Human immunodeficiency virus 1|HIV-1 unknown group|Human
> > immunodeficiency virus
> > type 1 (isolate YU2)
> >
> >
> > There should be "Virus" as superkindom according to
> >
> NCBI..."
>
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=362651
> "
>
>
>
>
