GenBank & Taxonomical Nomenclature/identification

[Scott Federhen]

Stuart Poss wrote:

>Nonetheless, it would be extremely helpful for GenBank to recommend
>(require?) that a collection voucher number is attached to the archive
>entry,

We do encourage submitters to send us specimen vouchers -
we added a fielded slot specifically for this purpose last year.
We have just recently added some text in our instructions
to submittors in our sequence submission tool (Sequin) -

  If you are submitting a sequence from a cultured microorganism,
  please include a strain name, isolate name and/or a culture collection
  accession number in the source feature block of your entries.
  (This is important information whether or not you have identified
  your organism with formal binomial species name.)

  If you are submitting a sequence from an uncultured molecular isolate
  (an environmental sample sequence) please include a clone name
  (or DDGE band number) with each of your entries.

  If you are submitting a sequence from a museum or herbarium specimen,
  or from a field isolate, please submit a /specimen_voucher
  for each entry, if one is available.

  This will ensure that each of your sequence entries can be
  reliably linked with published (and unpublished) reports
  about these organisms.

We can't really require that submitters provice these data, though.
In practice, if we did require submitters to give us a voucher with
every entry I think that we would get a lot of incorrect information
information from submitters who don't understand what voucher
specimens are.

Scott Federhen,
for the GenBank taxonomy database staff

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>From: "Stuart G. Poss" <Stuart.Poss at USM.EDU>
>Subject: Re: GenBank & Taxonomical Nomenclature/identification
>Comments: To: Carol Hotton <hotton at DAISY.NLM.NIH.GOV>
>To: TAXACOM at USOBI.ORG
>
>I know for a fact that GenBank does change names, as I caught a
>misspelling of a lancelet species a few years ago and they were very
>quick to correct it.
>
>Nonetheless, it would be extremely helpful for GenBank to recommend
>(require?) that a collection voucher number is attached to the archive
>entry, either from the same specimen (best) or from another specimen
>known (believed) to be the same species.  That way, regardless of what
>identification is given, there is at least a reasonable chance that an
>expert can examine the voucher and determine what the species is
>regardless of the name used.   Otherwise, one can only hope that the
>molecular biologist submitting the sequence has had a good course in
>taxonomy or has sent the material to a specialist.  This probably does
>not present too much of a problem for birds and mammals, but can be more
>of a problem for fishes and invertebrates, where many species appear
>"similar" to better known forms or may later prove to be more than one
>species.
>
>This number would be extremely useful in the event that the nomenclature
>in GenBank does not exactly track that in current useage.  As molecular
>biology becomes more uibquitous and extends to encompass greater
>diversity, the productive interaction of taxonomists and molecular
>biologists becomes increasingly important.
>
>
>Carol Hotton wrote:
>
>> On Thu, 27 Jul 2000, Doug Yanega wrote:
>>
>> > Apparently, after depositing a sequence in GenBank's archives, you
>> > CANNOT change its species designation, even if it is later
>> > discovered (by reference to voucher material, taxonomic revision,
>> > etc.) to be erroneous.
>>
>> Speaking for the five individuals who maintain the taxonomy database
>> associated with the GenBank sequence databases, I just want to correct
>> an erroneous statement from Doug Yanega that it is not possible to
>> correct species designations after an associated sequence has been
>> deposited in GenBank.  It would certainly be most distressing,
>> especially to us, if this were true, but fortunately it is not true.
>>
>> 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.  Updates
>> originating from submitters of sequences may be sent to:
>> update at ncbi.nlm.nih.gov, or through the submission
>> tool Sequin (for further details see
>> http://www.ncbi.nlm.nih.gov/Sequin/index.html).
>>
>> Furthermore, we strongly urge the community of people who use the
>> GenBank taxonomy database to let us know about errors that they find
>> there, whether they are misspellings, orthgraphic variants, misnomers
>> or incorrect or outdated classifications, by sending their comments to
>> info at ncbi.nlm.nih.gov. 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!
>>
>> By the way, Doug, I would be interested in knowing the details of your
>> colleague's experience with GenBank.
>>
>> Carol Hotton,
>> for the GenBank taxonomy database staff
>> (Scott Federhen, Mimi Harrington, Ian Harrison, Carol Hotton, Detlef
>> Leipe)
>>
>> >
>> >On Thu, 27 Jul 2000, Doug Yanega wrote:
>> >
>> >> Apparently, after depositing a sequence in GenBank's archives, you
>> >CANNOT
>> >> change its species designation, even if it is later discovered (by
>> >> reference to voucher material, taxonomic revision, etc.) to be
>> >erroneous.
>> >
>> >then on Thu, 27 Jul 2000, Peter Rauch wrote:
>> >
>> >>How about "add a new designation to the record", with
>> >>date/authority/etc, so that the history of designations is
>> >>retained with the record (with the sequence)?
>> >
>> >Peter is right, the best procedure is to build a permanent record of
>> all
>> >names and identifications that were used or are being used for a
>> sequence,
>> >etc. In taxonomy we call these synonymies, etc. and the procedure
>> dates back
>> >to Linnaeus and before.
>> >
>> >BUT DOES ANYONE KNOW exactly what the GenBank policy is?  Is Doug
>> really
>> >correct in his statement?
>> >
>> >
>> >
>> >F. Christian Thompson
>> >Systematic Entomology Lab., ARS, USDA
>> >Smithsonian Institution
>> >Washington, D. C. 20560-0169
>> >(202) 382-1800 voice
>> >(202) 786-9422 FAX
>> >cthompso at sel.barc.usda.gov
>> >visit our Diptera site at www.diptera.org