[Bioperl-l] sp. and gen. in species definition

[Jason Stajich]

Ditto - try the plasmid AE003851 - just hit this this morning.  I'm all
for lack of validation of the species name.

BTW I just wrote a simple script scripts/taxa/taxid4species.PLS which
allows retrieval of taxa id from NCBI for a genus + species name.  Would
like to integrate that into a module at some point just not sure where it
would go.

-jason
On Tue, 24 Sep 2002, Ewan Birney wrote:

>
> Has our species name checking got more strict? Is this what people were
> suggesting to remove?
>
>
> We have entries like
>
> DE   Rattus sp. mRNA for CDP-diacylglycerol synthase, complete cds.
> XX
> KW   CDP-diacylglycerol synthase.
> XX
> OS   Rattus sp.
> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
> Mammalia;
> OC   Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus.
>
>
> and
>
> DE   Rattus sp. mRNA for CDP-diacylglycerol synthase, complete cds.
> XX
> KW   CDP-diacylglycerol synthase.
> XX
> OS   Rattus sp.
> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
> Mammalia;
> OC   Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus.
>
>
>
>
>
> At the moment I am allowing sp. and gen. to
>
>
> We also have
>
>
> DE   Mouse/rat NG108-15 NBMPR-sensitive equilibrative nucleoside
> transporter
> DE   mRNA, complete cds.
> XX
> KW   .
> XX
> OS   mouse/rat NG108-15
> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
> Mammalia;
> OC   Eutheria; Rodentia; Sciurognathi; Muridae; mouse/rat hybrid cell
> lines.
>
>
>
>
> I think we should not validate the species name... though then of course
> we don't have the fecking species! Doh! Annoyance...
>
>
>
> I'll talk to the EMBL guys as to whether this is sane - ideally we want to
> work off NCBI tax_ids right for these things. Hmmm...
>
>
>
>
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu