GenBank

Curators of Arctos collections should encourage researchers using their specimens for DNA sequences to submit GenBank accessions that cite the specimens by catalog number. At a meeting (report attached) in early January, the Database Working Group of the Barcode of Life and GenBank agreed to use essentially our current three-part format for specimen citations. For example:

UAM:Mamm:100000
MVZ:Herp:137370

etc. (Definition at TDWG: http://wiki.tdwg.org/twiki/bin/view/DarwinCore/GlobalUniqueIdentifier)

If the correct term is entered by the owner of the GenBank accession under “source/specimen_voucher,” then the catalog number will appear on the GenBank sequence page as a link to the specimen record. An example in GenBank: http://www.ncbi.nlm.nih.gov/nuccore/157058307?report=GenBank

If the record is not cited this way, and the owner of the GenBank accession won’t change it, then it can still be linked by including the GenBank accession number as an Other ID in the Arctos record. In these cases, the nightly-update links to Arctos from GenBank will appear in the LinkOut drop-down in GenBank accession records.

In any case, the GenBank accession numbers should be entered into Arctos and Other IDs of type GenBank, and doing so will form HTTP links to GenBank from the specimen detail page.

In an effort to lock down the abbreviations with which we are familiar, I have registered “UAM” and “MSB” with Biorepositories.org (http://www.biorepositories.org/), and Berkeley has registered “MVZ.” All three of these registrations have been confirmed. So, operations such as the Univeristy of Arkansas at Monticello will have to be more creative than we were! I also put in a few specific collections that I knew already had records in GenBank and listed the curators as contacts, so some of you have been contacted by Biorepositories as part of the confirmation process. This system may be too simplistic to survive the many potential conflicts, but humanity has come to accept internet domain names, so we can hope. In the meantime, what we’re doing works. If your collection is not registered, you can either go do it at Biorepositories, or let me know of your interest, and I will start the process.

By including an Other ID Type of “BoLD barcode ID,” Arctos records can be also linked to records in the Barcode of Life Database (BoLD), but please note that BoLD has no reciprocal capabilities and occasionally changes the format of their URLs, breaking all links. Barcode IDs in Arctos: http://arctos.database.museum/SpecimenResults.cfm?oidtype=BoLD%20barcode%20ID.

Chicago Workshop Report
Federhen et al. 2009
Federhen 2014