[NHCOLL-L:2031] Fwd: Genbank

[Tim White]

This just in, courtesy of Bob Hanner.

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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.

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