[Genbank-bb] PROJECT linetype to be replaced by DBLINK

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Sep 26 15:41:11 EST 2008


Greetings GenBank Users,

The PROJECT linetype allows a sequence record to be linked to
information
about the sequencing project that generated the data which ultimately
resulted in the record's submission to the International Nucleotide
Sequence
Database ( INSD : http://www.insdc.org ).

This complete bacterial GenBank record illustrates the use of PROJECT:

LOCUS       CP000964             5641239 bp    DNA     circular BCT
24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
PROJECT     GenomeProject:28471

When viewed on the web in NCBI's Entrez:Nucleotide, the record's project
identifier (28471) links to an entry in the Genome Project Database
(GPDB) :

 
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=
Overview&uid=28471

where information about the sequencing center, the bacterium, and other
GenBank records (eg, plasmids) associated with the sequencing project
can
be obtained.

Since the introduction of PROJECT, the scope of the "Genome" Project
Database
has expanded, to include projects that are not necessarily targeted to
the sequencing of a complete genome.

In addition, there can be other resources which underlie an INSD
sequence
record, such as the Trace Assembly Archive at the NCBI:

 
http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi?cmd=show&f=t
ree&m=main&s=tree

Because of the expanded scope of the GPDB, and because we anticipate a
need
to link to more resources than just the GPDB, the PROJECT linetype is
going
to be replaced by a new linetype:

   DBLINK

Further details about this change, and its timetable, follow.

Mark Cavanaugh
GenBank
NCBI/NLM/NIH/HHS

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Modifications to linetypes can be disruptive, so the switch to DBLINK
will
occur in several stages.

Starting in October 2008, links to the NCBI Trace Assembly Archive will
be
supported via a line of text in the COMMENT section of sequence records.

Here is a mock-up, based on CP000964, which illustrates this change:

LOCUS       CP000964             5641239 bp    DNA     circular BCT
24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
PROJECT     GenomeProject:28471
....
COMMENT     Trace Assembly Archive:123456
            The source for the DNA and/or cells is:  Professor Eric W.
            Triplett, Chair, Department of Microbiology and Cell
Science,
            Institute of Food and Agricultural Sciences, University of
Florida,
            P.O. Box 110700, Gainesville, FL 32611-0700, ewt from ufl.edu.

Note: Use of the Trace Assembly Archive is still in its early stages, so
only a few records are expected to have these links in the short term.

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The new DBLINK linetype will be introduced as of GenBank Release 170.0
(February 15, 2009) .

The Genome Project ID and the Trace Assembly Archive ID will be
presented
via DBLINK, and the existing PROJECT line will continue to be displayed:


LOCUS       CP000964             5641239 bp    DNA     circular BCT
24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
PROJECT     GenomeProject:28471
DBLINK      Project:28471
            Trace Assembly Archive:123456
....
COMMENT     The source for the DNA and/or cells is:  Professor Eric W.
            Triplett, Chair, Department of Microbiology and Cell
Science,
            Institute of Food and Agricultural Sciences, University of
Florida,
            P.O. Box 110700, Gainesville, FL 32611-0700, ewt from ufl.edu.

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PROJECT and DBLINK will co-exist for one GenBank release, until Release
171.0
(April 15, 2009), at which point the PROJECT line will be removed.

In its final state, our mock-up for CP000964 becomes:

LOCUS       CP000964             5641239 bp    DNA     circular BCT
24-SEP-2008
DEFINITION  Klebsiella pneumoniae 342, complete genome.
ACCESSION   CP000964
VERSION     CP000964.1  GI:206564770
DBLINK      Project:28471
            Trace Assembly Archive:123456
....
COMMENT     The source for the DNA and/or cells is:  Professor Eric W.
            Triplett, Chair, Department of Microbiology and Cell
Science,
            Institute of Food and Agricultural Sciences, University of
Florida,
            P.O. Box 110700, Gainesville, FL 32611-0700, ewt from ufl.edu.

In summary:

   PROJECT -> DBLINK

   'GenomeProject' -> 'Project'

   Additional linkages, such as Trace Assembly, will be added to
   DBLINK as-needed

   The PROJECT line will be removed as of April 15 2009.

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For those who process sequence data in NCBI's ASN.1 format:

The underlying representation for (Genome) Project IDs will remain
unchanged; there will be no changes to the ASN.1 User-object that 
is used to store them:

    user {
      type
        str "GenomeProjectsDB" ,
      data {
        {
          label
            str "ProjectID" ,
          data
            int 28471 } ,
        {
          label
            str "ParentID" ,
          data
            int 0 } } } ,

However, to support linkages to other resources, like the Trace
Assembly Archive, a new "DBLink" User-object will be introduced:

    user {
      type
        str "DBLink" ,
      data {
        {
          label
            str "Trace Assembly Archive" ,
          data
            ints { 123456 } } } }

As new types of linkages are established, they will be added to
the DBLink User-object, and displayed via the DBLINK linetype in
the GenBank flatfile format. 

There is a possibility that the GenomeProjectsDB User-object
might someday be incorporated into the new DBLink User-object.
But at the moment, there are no firm plans to do so.

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