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

[Ewan Birney]

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...