GenBank & Taxonomical Nomenclature/identification

[Carol Hotton]

On Thu, 27 Jul 2000, Peter Rauch wrote:

>Can you also address the issue of retaining the history of
>identification changes which are made to a sequence ...

Yes, good question, Peter!

Changes made to names in the taxonomy database are listed explicitly
in the taxonomy browser (as synonym, or misspelling, for example).
These changes are also recorded in the sequence records
to which they are linked, so modifications to the taxonomy can be
traced in individual sequence records.

Obvious errors in species identification (e.g. bacterial or mouse
sequence submitted as human) are generally caught upon submission.
More subtle errors, as Detlef states, are difficult for us to catch.
Hence the desirability of voucher specimens.

If (for example) a species is misidentified in a sequence record after
it is deposited in GenBank, the record has to be updated manually by
the GenBank indexing staff.  We generally tell the indexer changing
the record to insert a note in the sequence record: /note="submitted
as <oldname>.  But unfortunately this has not been done consistently,
and many sequence records, especially older submissions, often lack
this information.

Hope this clarifies things a bit...

Carol Hotton
GenBank taxonomy staff
>Carol,
>Can you also address the issue of retaining the history of
>identification changes which are made to a sequence (aka a
>"specimen")?  It's important to know what name people thought
>they were dealing with when they analyzed data and drew
>conclusions about the species (i.e., about the name that was
>associated with the sequence/specimen at the time they retrieved
>the data for analysis).
>Peter
>
>On Thu, 27 Jul 2000, Carol Hotton wrote:
>...cut, cut...
>> Submitters are indeed allowed to update any data relating to their
>> sequences submssions at any time, including of course, taxonomic
>> revisions, changes in classification, voucher information, or
anything
>> else related to the deposited sequence accessions.
>
>
>> .... The five of us are responsible for maintaining
>> an up-to-date classification of the entire range of living
organisms,
>> and we need all the help we can get!
>
>Maybe we're not talking about the same objects? I thought the
>reference was to the specific epithets assigned to a _specimen_,
>and whether or not those "determinations" were able to be
>revised, and also whether or not the history of the revisions is
>kept.
>
>Peter
>