[Fwd: subspecies information in submitted DNA sequences (tuli) (SUB#117690)]

[Susan McCouch]

Pankaj,

This is an excellent suggestion and I am glad to see that EMBL, 
GenBank, DDBJ and NCBI have agreed to help promote the concept of 
indicating whether a rice submission belongs to the indica or 
japonica sub-species group.

Susan


>datasubs at ebi.ac.uk wrote:
>>
>>  >Date: Thu, 14 Feb 2002 14:40:26 -0500
>>  >From: pj37 at cornell.edu
>>  >Reply-to:
>>  >To: Robin Buell <rbuell at tigr.org>, tsasaki at nias.affrc.go.jp,
>>  gb-admin at ncbi.nlm.nih.gov, DATASUBS at ebi.ac.uk, ddbjsub at ddbj.nig.ac.jp
>>  >Subject: subspecies information in submitted DNA sequences
>>
>>  >
>>  > Dear All,
>>  >
>>  > I have two suggestions and probably they are addressed to the 
>>Databases EBI,
>>  > GenBank and DDBJ and also to IRGSP members. This is in relation to the
>>  > subspecies for rice Oryza.
>>  >
>>  > The two groups doing rice genome sequencing are
>>  >
>>  > The IRGSP is doing for Japonica subspecies (Cultivar: 
>>Nipponbare) of O.sativa
>>  > and Chinese are doing it for Indica Subspecies (Cultivar: 93-11) 
>>of O.sativa.
>>  >
>>  > However there are several others who are not part of the above 
>>two but does it
>>  > in some small way for either the same cultivars or for the 
>>cultivars coming
>>  from
>>  > same sub species.
>>  >
>>  > Take a look at the GenBank Statistics
>>  > 210302 nucleotide sequences from O.sativa
>>  > 398 from indica
>>  > 287 from japonica
>>  >
>>  > We at Gramene are trying to populate the database with Rice 
>>sequences and its
>>  > really hard to classify according to the subspecies information in the
>>  database.
>>  > This way we may loose some important information. Is it possible for these
>>  > databases to make sure when a person submits the sequence he/she 
>>mentions the
>>  > subspecies info (preferred as mandatory) and wherever possible 
>>the cultivar
>>  > also. At least the rice community can get together and make sure that they
>>  > always report this information.
>>  >
>>  > With best wishes
>>  >
>>  > Pankaj
>>  >
>>  >
>>  Dear Pankaj,
>>  Thank you for your message. I apologise for the delay in my reply.
>>
>>  I discussed your question with the both GenBank and DDBJ aswell as the
>>  taxonomists at the NCBI (whose taxonomy the three database of the 
>>collaboration
>>  use).
>>
>>  We have agreed to encourage submitters of either japonica or 
>>indica to use the
>>  unique taxonomic node which reflects these "cultivar-groups".
>>  So we have either:
>>  Oryza sativa (japonica cultivar-group)
>>
>>  Oryza sativa (indica cultivar-group)
>>
>>  If submitters select either of these when submitting using Webin (our WWW
>>  submission tool) they will have to enter something other than 
>>japonica or indica
>>  (accordingly) in the cultivar field.
>>
>>  We are working on creating a list of most common cultivated plants 
>>so that it
>>  becomes mandatory for submitters to include a cultivar where we feel there
>>  should be one.
>>
>>  The curator who communicates with submitters of long term 
>>sequencing projects
>>  will be contacting them to inform them of the changes.
>>
>>  I hope this improves the situation.
>>
>>  Please do not hesitate to contact me should you have further questions.
>>
>>  Yours sincerely
>>
>>  Mary Ann Tuli
>>
>> 
>>--------------------------------------------------------------------------------
>>  Mary Ann Tuli
>>  WEBIN Administrator and
>>  Nucleotide Sequence Database Curator Co-ordinator
>>
>>  EMBL Outstation Hinxton, The European Bioinformatics Institute,
>>  Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K.
>>  Tel: +44 1223 494444. Fax: +44 1223 494468
>>
>>  Internet electronic addresses:
>>  datasubs at ebi.ac.uk (data submissions), update at ebi.ac.uk (updates)
>>  datalib at ebi.ac.uk (general enquiries)
>>  http://www.ebi.ac.uk/ (world wide web submissions, updates, services, info)
>
>--
>
>******************************************
>Pankaj Jaiswal, Ph.D.                                  
>Postdoctoral Associate
>Dept. of Plant Breeding                            
>Cornell University                                  
>Ithaca, NY-14853, USA  
>
>Tel:+1-607-255-3103 / Fax:+1-607-255-6683
>E mail: pj37 at cornell.edu
>http://www.gramene.org  
>******************************************


-- 
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Susan McCouch
Dept of Plant Breeding
418 Bradfield Hall
Cornell University
Ithaca, NY  14853-1901
Phone: 607-255-0420
Fax: 607-255-6683
E-Mail: srm4 at cornell.edu

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