[NHCOLL-L:2028] genbank
Robert Hanner
rhanner at coriell.umdnj.edu
Mon Aug 11 11:39:07 EDT 2003
Greetings NHColl,
As a former Curatorial Associate at the AMNH and designer of their
Ambrose Monell Cryo Collection (AM-CC), I have a few words to offer
on the voucher specimen/Genbank accession thread:
Linking sequence data to voucher specimens is of critical importance
and there are pubs in the literature calling for more widespread
inclusion of museum catalog numbers of voucher specimens associated
with GenBank submissions (see attached pdf from terry yates lab, for
example).
The microbial sequences always reference a strain number while most
botanical sequences reference an herbarium sheet number. It is the
animal folks who have yet to get their act together. Una is correct
in that there is no formal policy requiring a catalog number but that
it can be included. Ultimately, it would be nice if NCBI could offer
greater atomization of this provenance data into distinct fields, but
the point is - there is a way to include this data and responsible
users do so. Our tissue collections should include in their loan
policies the requirement that 1) all sequence data from their
materials be deposited in the public domain 2) that sequence
submissions must include reference to the catalog number of the
museum voucher specimen and 3) genbank accession numbers be reported
back to the museum for inclusion in their catalogs.
There are lots of sequences from museum specimens which cannot be
attributed to the voucher because this information was not recorded
and even when it was, mining this data is not straightforward
(although see link below for the Berkeley initiative).
As President of the International Society for Biological and
Environmental Repositories (ISBER) I advocate linking electronic
catalogs of tissue collections with Genbank as a best practice. This
can be done via the linkout feature (for information on Linkout see:
http://www.ncbi.nlm.nih.gov/entrez/linkout/ )
We managed to get it implemented while I was at AMNH (see the online
catalog at http://research.amnh.org/amcc/) If there has been a
genbank submission for a particular specimen and this data has been
recorded in the catalog, it will show up as a hotlink and clicking on
it will take you directly to the sequence from that specimen. Also,
if the catalog number of the specimen has been submitted with the
sequence data to genbank, you can go from the sequence in GenBank to
the online catalog entry for the voucher specimen in the museum by
using the Linkout hotlink in Genbank. We are also implementing it
here at Coriell for the nonhuman primate tissue bank
(http://www.ipbir.org/). Gordon Jarrell has also done this at UAM
(see: http://arctos.museum.uaf.edu:8080/) and now Berkeley is
following suit as well, in an attempt to link data already submitted
from their collections (see:
http://bnhmdev.berkeley.edu/genbank/index.php).
Next year, there will be a joint meeting of SPNHC and ISBER at the
AMNH in mid-May. If there is sufficient interest, perhaps we could
ask NCBI to host a workshop for data managers on how to link online
catalogs as part of the proceedings. We had a similar presentation at
the ISBER meeting last May in Philadelphia. NCBI understands the
importance of voucher specimens and they are willing to work with us.
It is the user community which must be educated on the need for
depositing vouchers as well as journal editors who must not let
people publish papers without reference to voucher specimens!!!
Robert Hanner, Ph.D.
Scientific Program Director
Coriell Institute for Medical Research
403 Haddon Avenue
Camden, NJ 08103
Voice: (856) 757-9727
Fax: (856) 757-9737
http://cimr.umdnj.edu
President
International Society for Biological and Environmental Repositories
http://www.ISBER.org
>
>>Hi all
>>
>>Here at the KU Natural History Museum we have a large fish tissue
>>collection that is extensively used. Recently I came across an
>>interesting question with regard to sequences submitted to Genbank
>>using material from our collection. I would like to link Genbank
>>accession numbers to voucher material in our collection database
>>for future reference. However it appears that it is not common
>>practice for researchers to lodge voucher information with Genbank
>>or the facility to do so does not exist in Genbank.
>>
>>I have asked a number of our users if there is any prerequisite for
>>them to submit museum voucher numbers along with sequences to
>>Genbank and none of them could answer my question (most didn't
>>think so) - and none of them had lodged voucher numbers with their
>>sequences. I also contacted Genbank with the same query and got a
>>similar answer. Is there anyone out there who can answer this
>>question? I would think that having a field in Genbank to enter
>>this information would be very useful and would be advantageous not
>>only to the collection concerned but also to Genbank in terms of
>>the validity of the material used to generate the sequences.
>>
>>If anyone who has had dealings with this issue or with Genbank
>>concerning this issue I would be interested to hear from you off
>>list.
>>
>>Thanks
>>
>>Andy
>>
>> A : A : A :
>>}<(((_°>.,.,.,.}<(((_°>.,.,.,.}<)))_°>
>> V V V
>>Andy Bentley
>>Ichthyology Collection Manager
>University of Kansas
>
>>Yes. Your users are correct, GenBank requires no voucher or other
>>provenance data, nor does it have a specific field for such data.
>>However, GenBank does have a mechanism for passing such data on to
>>users. That mechanism is the notes field. The HIV/AIDS research
>>community uses the notes field extensively to submit data in GenBank
>>accession records...for explicit use by the HIV Sequence Database
>>here at Los Alamos. Examine some HIV records in GenBank, and you
>>will see that many include data about where, when, and from whom
>>the source sample was collected; also the subtype (taxonomic group)
>>to which the sequence belongs. GenBank is just a conduit for this
>>data, and has no role in defining policy or procedure wrt vouchers.
>>I think this role properly lies in the research community, not with
>>GenBank, and one way to perform this role is to offer your users
>>helpful guidance re how best to prepare GenBank accession records
>>so that you and all other users can identify data derived from the
>>specimens you curate.
>>
>> Una Smith
>> Postdoc
>> HIV Sequence Database
>>
>>Los Alamos National Laboratory, MS K-710, Los Alamos, NM 87545
--
Robert Hanner, Ph.D.
Scientific Program Director
Coriell Institute for Medical Research
403 Haddon Avenue
Camden, NJ 08103
Voice: (856) 757-9727
Fax: (856) 757-9737
http://cimr.umdnj.edu
President
International Society for Biological and Environmental Repositories
http://www.ISBER.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.yale.edu/mailman/private/nhcoll-l/attachments/20030811/bc15aa5e/attachment.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ruedas_et_al.pdf
Type: application/pdf
Size: 40634 bytes
Desc: not available
Url : http://mailman.yale.edu/mailman/private/nhcoll-l/attachments/20030811/bc15aa5e/attachment.pdf
More information about the Nhcoll-l
mailing list