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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