Hi all,
You can find our release policy in the chapter 2 of "Annotation
Policies" document which is available from the following URL.
http://www.wwpdb.org/docs.html
We encourage all the PDB depositors to carefully check the journal
policy for the availability of coordinates (and experimental data)
before depositing coordinate to wwPDB or submitting papers to the
journal.
For example, Nature says:
the author must authorize Protein DataBank (PDB) release on the
Wednesday of (or before) online or print publication.
From http://www.nature.com/authors/editorial_policies/availability.html
This means the PDB entry must be released BEFORE the journal
publication.
We receive publication dates and citation information from some
journals. In this case, we send email that "your entry will be
released by the journal request." to the contact person for the PDB
entry.
For other journals, we search the publication information with using
the deposited author names and deposited article title. In this
case, we send email notification to the contact person for the PDB
entry.
In each case, depositors can request to postpone the release against
the journal policy. It is not the wwPDB responsibility to force to
release data according to a journal policy. It is the depositor's
responsibility to follow the journal policies regarding release of
the coordinates. If depositors will be in any trouble with the
journal office regarding their own decision, it's on their head.
The citation information that is sent to us from the depositors or
community is also greatly appreciated.
Best regards,
Takanori
Annotators' leader, PDBj
From: Engin Ozkan <[email protected]>
Subject: Re: [ccp4bb] friction or releasing pdb's
Date: Thu, 2 Apr 2009 09:56:20 -0700
I do not mind PDB releasing only on Wednesdays at a certain time of
the day. What should happen is the authors/publishers should let PDB
know the publication date before it becomes available (supposedly
days
or weeks before the actual publication, online or in print), and PDB
can automatically release pdb/sf the week of the publication or the
Wednesday before.
With requesting pdb releases, I take two routes: ask the journal and
ask RCSB. Asking journals used to work, although my last attempt
was
unsuccessful. If the journal agrees to do anything, they may let the
authors or PDB know, so after a while, the release happens. Asking
RCSB works if they can find the reference themselves, except in the
bizarre case I cited.
But still, the reader should not have to search for data supposed to
publish simultaneously with the article, right?
Engin
On 4/2/09 8:53 AM, Phil Jeffrey wrote:
PDB seem to take about a week to release coordinates that are HPUB
(hold for publication) from when we ask them to. Sometimes they
drop
the ball, but mostly this is what we see. If I ask them to release
the coordinates early to get around this lag, I can largely
guarantee
that I'll forget to update the JRNL reference.
I believe that the lead time is unnecessarily long. Perhaps one
day
might be more reasonable.
Phil Jeffrey
Engin Ozkan wrote:
I agree that the pdb deposition process has gotten better, but I
still
regularly have issues with releasing of newly published
structures. There seem to be delays; just as you are reading this
brand new, interesting structure, you realize that the pdb and
structure factors are not released. Quite annoying. This is in
large
part the fault of the authors, but maybe PDB could do better, too.
--
MATSUURA Takanori, Ph.D.
Visiting Associate Professor
Annotators' Leader, Group of Primary Annotation,
Protein Data Bank Japan (PDBj)
Research Center for Structural and Functional Proteomics,
Institute for Protein Research, Osaka University
3-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN
Tel: +81-6-6879-8634
Fax: +81-6-6879-8636
