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[ccp4bb]: [SUMMARY]: Problems with PDB entry 1muo
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Dear colleagues,
Two weeks after my message to these lists I want to make a summary of
what it followed, and of some of the messages I got.
First, I'm glad to tell you that the coordinates of the 1muo entry were
released last week. Unfortunately, the structure factors are not yet
deposited. Therefore, one may think that, at least partially, pressure
can work.
I want to acknowledge the support and help that I have received from
Christine A. Zardecki, from the PDB. She wrote me back when they finally
heard from the authors of this entry and announced me that the
coordinates would be released. She also helped me to clarify some issues
concerning the journal policies about structural data.
I got replies from about fifteen people, some of them giving me examples
of what they would consider similar problems. I have compiled a short
list with these cases, that you'll find at the end of this
message. It's, of course, not a comprehensive list. I have checked the
PDB status of these cases and the current policies of the involved
journals (when appropriate), but I don't know their full details. The
list is not to be considered a "shame list" or whatsoever, because I
can't know all the reasons (if any) behind these problems. It rather was
for me, and hopefully will be now for others, a sort of taste of the
problems we can find when looking for structural data that we think
should be publicly available. Other problems are not in the list. I
wasn't aware, for instance, of cases where people has deposited
structures at low resolution, and then, exploit structures of higher
resolution (never deposited) for their research/publications.
I consider that for this matter, at least this two principles should be
respected by people doing scientific research:
1. Published results should be backed by publicly available
data. Neither ourselves, scientists, nor the peer-review system are
perfect. Anyone can make mistakes, but these can hardly been tackled
without the relevant data.
2. In order to keep the publishing system as fair as possible, one must
follow the policies of the journal where one is publishing.
I know there have been long and sometimes bitter discussions concerning
the first point. And many will follow, probably... The immediate reason
to defend the opposite view comes from the wish of keeping some kind of
advantage over the results one gets first. Different motives can lead to
hold this:
On one hand, science has become such a competitive activity (in my
opinion, far too much of what would be desirable/required) that, in
consequence, many people may think it's fair to keep this advantage. I
disagree with this point of view, but I know that it will be difficult
to "convert" the people that shares it as long as science continues to
be so competitive.
However, other reasons to try to "keep the advantage" have nothing to do
with science but with bussiness... and in the way things are evolving,
these may get worse. I think that we should say loud and clear that this
is against science's ethics, and we should provide us with mechanisms to
prevent such behaviour.
Back to the journals policies, one interesting suggestion I have
received is that the journals that require immediate release of the data
should check that the data has the "HPUB" ("hold until publication")
tag. Christine Zardecki, from the PDB, has told me that apparently some
journals (e.g. Nature Structural Biology and PNAS) do so. The problem
comes when either the authors prefer to deposit the data after the paper
being accepted, or they deposit first but putting a hold on
them. However, this could easily be negotiated after the paper is
accepted.
As for the time on "hold", I think we should find ways to make sure that
as long as this somehow controversial procedure is accepted, its maximum
term (currently one year) is respected.
I think the scientific community should discuss in depth these and
similar questions. I would like that this message would encourage such
discussions.
Thanks to all the people that showed their interest and provided help
and advice, and thanks to all you for your attention.
Hoping that these and other issues will be discussed again and again in
the never-ending process of getting a fairer and more ethical
environment for scientific research.
Cheers,
Miguel
#####
A list with some problems concerning structural data.
Breaks
PDB journal
Protein entry rules? Problem
---------------------------------------------------------------------------
MutS 1E3M No Change in title prevented automatic release
2F5-fab' 2F5A No Pending on publication since April-99
2F5B No Pending on publication since April-99
Methem-albumin 1N5U No Published in Mar-02
Deposited in Nov-02, on hold till Nov-03
They will not be available one year after
the publication
EGF 1MOX No Published in Sep02, on hold till Sep-03
(Journal NOW requires immediate release of
coordinates and SFs -Cell-, but at the
time of publication it didn't)
spectrin (NMR) --- Yes Published in Oct-95, not deposited
(Journal required deposition and tolerated
6 months hold -EMBO-)
However,authors have shared them upon request
Chk1 1NVQ Yes |Published in Nov-02
1NVS Yes |Deposited and released in Feb-03
1NVR Yes |(Journal requires immediate release of
coordinates and SFs -JBC-)
Aurora-2 1MUO Yes Published in Nov-02, coordinates released
in Apr-03. No structure factors deposited.
(Journal requires immediate release of
coordinates and SFs -JBC-)
ErbB2 --- Yes Published in Feb-03, not deposited
(Journal requires immediate release of
coordinates and SFs -Molecular Cell-)
Hsp90 1HK7 Yes Published in Mar-03, on hold till Mar-04
But the authors would share the coordinates
(Journal requires immediate release of
coordinates and SFs -Molecular Cell-)
APH3'-IIa 1ND4 Yes Published in Mar-03, coordinates on 'HPUB'
but not released yet.
No structure factors deposited.
(Journal requires deposition of coordinates
and SFs and tolerates "on hold" if the
release date is stated in the paper -JMB-)
#####
Miguel Ortiz Lombardía <mol@ysbl.york.ac.uk>, 07/04/2003:
> Date: Mon, 7 Apr 2003 17:31:28 +0100
> From: Miguel Ortiz Lombardía <mol@ysbl.york.ac.uk>
> To: PDB list <pdb-l@sdsc.edu>, CCP4bb <ccp4bb@dl.ac.uk>,
> O-info list <o-info@origo.imsb.au.dk>
> Subject: Problems with PDB entry 1muo
> User-Agent: Mutt/1.4i
>
> Dear colleagues,
>
> This is not actually a question but a petition that concerns
> crystallography, or more accurately, the public availability of
> crystallographic data.
>
> Background:
>
> On March 28 I tried to fetch from the PDB the coordinates of a kinase
> whose structure was published in the Journal of Biological Chemistry the
> last November. It has ID, 1muo.
>
> "Crystal structure of aurora-2, an oncogenic serine/threonine kinase"
> Cheetham GM, Knegtel RM, Coll JT, Renwick SB, Swenson L, Weber P, Lippke
> JA, Austen DA.
> J Biol Chem. 2002 Nov 8;277(45):42419-22.
>
> In this paper you can read:
>
> "The atomic coordinates and structure factors (code 1MUO) have been
> deposited in the Protein Data Bank, Research Collaboratory for
> Structural Bioinformatics, Rutgers University, New Brunswick, NJ
> (http://www.rcsb.org/)."
>
> The "Instruction to Authors" from the Journal of Biological Chemistry
> (http://www.jbc.org/misc/ifora.shtml) states:
>
> "Crystallographic Studies
>
> Authors of papers describing new structure determinations must submit to
> the Protein Data Bank at Research Collaboratory for Structural
> Bioinformatics http://www.rcsb.org/pdb all structural data required to
> validate the conclusions, including both x-ray amplitudes and phases and
> the derived atomic coordinates. JOURNAL policy requires that such data
> be available upon request IMMEDIATELY after publication (...)"
>
> Facts:
>
> 1. There is a 1muo entry in the PDB with the right title and authors,
> but:
>
> 1.1. This entry doesn't include the structure factors, only coordinates.
>
> 1.2. This entry ins "ON HOLD" until 24 September 2003.
>
> 2. When I contacted the PDB asking them to release the coordinates,
> according to the journal policies, they told me that they were in
> contact with the author to do so, and they encouraged me to write the
> author as well.
>
> 3. I wrote to Dr. Cheetham on March 31. No answer yet.
>
> 4. I wrote to the Journal of Biological Chemistry on April 2. They wrote
> as well to Dr. Cheetham.
>
> 5. The coordinates are still "on hold" and no structure factors have
> been deposited (April 7).
>
> Discussion:
>
> I've been adviced that the PDB has no authority to release data without
> the authors' consent. The journal, of course, has not this authority
> either.
>
> I don't know yet what happened in this particular case. There may be a
> reasonable explanation for the author not remembering to instruct the
> PDB to release the coordinates, and not answering now our emails.
>
> But, what can we do to avoid this happening? It is not honest or
> responsible to publish an article in a journal with the clear
> requirement of releasing coordinates and data, and then not to do
> so. Otherwise, anybody following the rules will be at big disadvantage
> with respect of people failing to do so.
>
> Petition:
>
> Please email me with details of any other abuses of journal policies of
> which you are aware. I feel that only through publicity and public
> complaints will the avowed policy of immediate release after publication
> of coordinates and the deposition of the corresponding structure factors
> be achieved.
>
> Thank you for your attention.
>
> Cheers,
>
> Miguel
>
> PS: Please, excuse me if you receive this email more than once.
> --
> Miguel Ortiz Lombardía
> email: mol@ysbl.york.ac.uk
> http://www.ysbl.york.ac.uk/~mol
> -----------------------------------------------------------------------
> Quand la verité n'est pas libre, la liberté n'est pas vraie.
> Jacques Prévert
~~~~~~~~~
--
Miguel Ortiz Lombardía
email: mol@ysbl.york.ac.uk
http://www.ysbl.york.ac.uk/~mol
-----------------------------------------------------------------------
Quand la verité n'est pas libre, la liberté n'est pas vraie.
Jacques Prévert