I must "say" that there were some emails exchanged between me and Gerard
later, in which I pointed out that I wasn't against deposition of images
(data frames). In fact, if SR sources kept user's data there would be
one more structure from here in the PDB: HDD failure here, the data on a
mirror HDD but the company in charge of maintenance erased the data
frames and data processing statistics by accident. For a trypanosomal
enzyme there is no chance that I can ever get funding now to replicate
the work (protein production and purification, crystallisation, data
collection) so that "Table 1" could be produced for a manuscript.
However, my email to the bb was provocative - I admit I was doing this
willingly - to write that in such harsh funding times someone could
start a career, get some small grant, enough to clone produce purify
crystallize and collect a first data set. And then find him or herself
without funding for X years (success rate = less than 10% these days).
If this person then gets scooped by whoever, end of a promising career.
Unfortunately, such a prospect doesn't seem to be science fiction any
more nowadays. I hope this clears things. I wanted to be provocative and
point out the difficulties we are all facing wrt funding so that we
shouldn't set up a system that may result in killing careers. Our
politicians do not need any help from us on that I think.
Fred.
Gerard Bricogne wrote:
Dear Remy,
You are right, and I was about to send a message confessing that I had
been rash in my response to Fred's. Another person e-mailed me off-list to
point out that sometimes a structure can be quickly solved, but that doing
all the rest of the work involved in wrapping that structure into a good
biological story for publication can take a very long time, and that it
would be wrong for a SR source's forced disclosure policy to start imposing
deadlines on that process. I entirely agree with both of you and admit that
I reacted too quickly and with insufficient thought to Fred's message.
However, as you point out yourself, this issue is related to a
different question (SR sources' disclosure policy towards all data collected
on their beamlines) from the original one that started this thread
(deposition of raw images with the pdb entries they led to). The two topics
became entangled through the idea of prototyping an approach to the latter
by tweaking the storage and access features involved in the former.
Many thanks to you and to the other correspondent for picking up and
correcting my error. This however leaves the main topic of this thread
untouched.
With best wishes,
Gerard.
--
On Fri, Oct 28, 2011 at 01:38:29PM +0200, Remy Loris wrote:
Dear Gerard,
I cannot agree. Last year my group published a paper in Cell which
contained a structure for which the native data were collected at a
synchrotron around 1997. Various reasons contributed to the long lag period
for solving this structure, but basically it all came down to money needed
to do the work. Equally I am sure there are other cases for which a first
good native data set is a breakthrough you wish to protect rather than hand
it out to anyone who might potentially scoop you after you have put lots of
money and effort into the project.
Therefore: Images corresponding to structures I deposit in the PDB: No
problem. That is what we do with processed data as well. But images of
unsolved structures, I don't see why that should be enforced or done
automatically by synchrotrons. Nobody deposits processed data without an
accompanying structure either.
I do agree that one could be given the option to deposit interesting data
with which he/se will not continue for whatever reason. But this should be
optional, and a clear consensus should emerge within the community as how
the original producers of the data have to be acknowledged if these data
are used and the results published by another team, especially if the use
of that particular dataset is crucial for the publication.
Remy Loris
Vrije Universiteit Brussel and VIB
