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[Genbank-bb] BioProject Accession Numbers to replace numeric Genome Project IDs : DBLINK linetype

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Wed Nov 16 18:04:13 EST 2011


Greetings GenBank Users,

The Genome Project Database resource at the NCBI was redesigned in recent months,
culminating in the implementation of a new BioProject resource:

	http://www.ncbi.nlm.nih.gov/bioproject

An article that describes the goals of BioProject is available:

	http://www.ncbi.nlm.nih.gov/books/NBK54015/

BioProject is a collaborative effort of the International Nucleotide Sequence
Database Collaboration (INSDC), and project data are exchanged with NCBI's
partner INSDC institutions, EBI and DDBJ. A BioProject website is also available
at DDBJ:

	http://trace.ddbj.nig.ac.jp/bioproject/index_e.shtml

BioProjects are uniquely identified by BioProject Accession Numbers, which
utilize this format:

	"PRJ"
	"E" or "N" or "D"
	one letter
	one or more digits

Examples of valid BioProject accessions are PRJNA12521 and PRJEB1 .

With BioProject now in operation, we are preparing to implement links from
sequence records to the new resource. Previously, links to the Genome Project
Database were provided by numeric 'Project' DBLINKs . Here's an example for a
bacterial complete-genome record:

LOCUS       CP002497             1110245 bp    DNA     linear   PLN 14-NOV-2011
DEFINITION  Eremothecium cymbalariae DBVPG#7215 chromosome 1, complete
            sequence.
ACCESSION   CP002497
VERSION     CP002497.1  GI:356887709
DBLINK      Project: 60715

When this link is switched to a BioProject accession, the DBLINK line will
change slightly:

LOCUS       CP002497             1110245 bp    DNA     linear   PLN 14-NOV-2011
DEFINITION  Eremothecium cymbalariae DBVPG#7215 chromosome 1, complete
            sequence.
ACCESSION   CP002497
VERSION     CP002497.1  GI:356887709
DBLINK      BioProject: PRJNA60715

In the coming weeks, many millions of sequence records will gradually be
modified, to make use of the new BioProject DBLINK. They will not be
distributed via daily GenBank and RefSeq incremetal update products. However,
these new BioProject links *will* start to be seen in GenBank and RefSeq
release products as of December 2011. In addition, the new BioProject
links will become visible via NCBI's Entrez:Nucleotide resource, as soon
as the modification process begins. 

Please contact the NCBI Service Desk (info from ncbi.nlm.nih.gov) if you have
any questions or concerns about this change.

Mark Cavanaugh
GenBank
NCBI/NLM/NIH/HHS




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