Hi all,
It appears that during my time here at Cold Spring Harbor, I have missed a
small debate on CCP4BB (in which my name has been used in vain to boot).
I have not yet had time to read all the contributions, but would like to make
a few points that hopefully contribute to the discussion and keep it with two
feet on Earth (as opposed to La La Land where the people live who think that
image archiving can be done on a shoestring budget... more about this in a
bit).
Note: all of this is on personal title, i.e. not official wwPDB gospel. Oh,
and sorry for the new subject line, but this way I can track the replies more
easily.
It seems to me that there are a number of issues that need to be separated:
(1) the case for/against storing raw data
(2) implementation and resources
(3) funding
(4) location
I will say a few things about each of these issues in turn:
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(1) Arguments in favour and against the concept of storing raw image data, as
well as possible alternative solutions that could address some of the issues
at lower cost or complexity.
I realise that my views carry a weight=1.0 just like everybody else's, and
many of the arguments and counter-arguments have already been made, so I will
not add to these at this stage.
-----------
(2) Implementation details and required resources.
If the community should decide that archiving raw data would be scientifically
useful, then it has to decide how best to do it. This will determine the level
of resources required to do it. Questions include:
- what should be archived? (See Jim H's list from (a) to (z) or so.) An
initial plan would perhaps aim for the images associated with the data used in
the final refinement of deposited structures.
- how much data are we talking about per dataset/structure/year?
- should it be stored close to the source (i.e., responsibility and costs for
depositors or synchrotrons) or centrally (i.e., costs for some central
resource)? If it is going to be stored centrally, the cost will be
substantial. For example, at the EBI -the European Bioinformatics Institute-
we have 15 PB of storage. We pay about 1500 GBP (~2300 USD) per TB of storage
(not the kind you buy at Dixons or Radio Shack, obviously). For stored data,
we have a data-duplication factor of ~8, i.e. every file is stored 8 times (at
three data centres, plus back-ups, plus a data-duplication centre, plus
unreleased versus public versions of the archive). (Note - this is only for
the EBI/PDBe! RCSB and PDBj will have to acquire storage as well.) Moreover,
disks have to be housed in a building (not free!), with cooling, security
measures, security staff, maintenance staff, electricity (substantial cost!),
rental of a 1-10 Gb/s connection, etc. All hardware has a life-cycle of three
years (barring failures) and then needs to be replaced (at lower cost, but
still not free).
- if the data is going to be stored centrally, how will it get there? Using
ftp will probably not be feasible.
- if it is not stored centrally, how will long-term data availability be
enforced? (Otherwise I could have my data on a public server until my paper
comes out in print, and then remove it.)
- what level of annotation will be required? There is no point in having
zillions of files lying around if you don't know which
structure/crystal/sample they belong to, at what wavelength they were
recorded, if they were used in refinement or not, etc.
- an issue that has not been raised yet, I think: who is going to validate
that the images actually correspond to the structure factor amplitudes or
intensities that were used in the refinement? This means that the data will
have to be indexed, integrated, scaled, merged, etc. and finally compared to
the deposited Fobs or Iobs. This will have to be done for *10,000 data sets a
year*... And I can already imagine the arguments that will follow between
depositors and "re-processors" about what software to use, what resolution
cut-off, what outlier-rejection criteria, etc. How will conflicts and
discrepancies be resolved? This could well end up taking a day of working time
per data set, i.e. with 200 working days per year, one would need 50 *new*
staff for this task alone. For comparison: worldwide, there is currently a
*total* of ~25 annotators working for the wwPDB partners...
Not many of you know that (about 10 years ago) I spent probably an entire year
of my life sorting out the mess that was the PDB structure factor files
pre-EDS... We were apparently the first people to ever look at the tens of
thousands of structure factor files and try to use all of them to calculate
maps for the EDS server. (If there were others who attempted this before us,
they had probably run away screaming.) This went well for many files, but
there were many, many files that had problems. There were dozens of different
kinds of issues: non-CIF files, CIF files with wrong headers, Is instead of
Fs, Fcalc instead of Fobs, all "h" equal to 0, non-space-separated columns,
etc. For a list, see: http://eds.bmc.uu.se/eds/eds_help.html#PROBLEMS
Anyway, my point is that simply having images without annotation and without
reprocessing is like having a crystallographic kitchen sink (or bit bucket)
which will turn out to be 50% useless when the day comes that somebody wants
to do archive-wide analysis/reprocessing/rerefinement etc. And if the point is
to "catch cheaters" (which in my opinion is one of the weakest, least-fundable
arguments for storage), then the whole operation is in fact pointless without
reprocessing by a "third party" at deposition time.
-----------
(3) Funding.
This is one issue we can't really debate - ultimately, it is the funding
agencies who have to be convinced that the cost/benefit ratio is low enough.
The community will somehow have to come up with a stable, long-term funding
model. The outcome of (2) should enable one to estimate the initial investment
cost plus the variable cost per year. Funding could be done in different ways:
- centrally - e.g., a big application for funding from NIH or EU
- by charging depositors (just like they are charged Open Access charges,
which can often be reclaimed from the funding agencies) - would you be willing
to pay, say, 5000 USD per dataset to secure "perpetual" storage?
- by charging users (i.e., Gerard Bricogne :-) - just kidding!
Of course, if the consensus is to go for decentralised storage and a DOI-like
identifier system, there will be no need for a central archive, and the
identifiers could be captured upon deposition in the PDB. (We could also check
once a week if the files still exist where they are supposed to be.)
-----------
(4) Location.
If the consensus is to have decentralised storage, the solution is quite
simple and very cheap in terms of "centralised" cost - wwPDB can capture
DOI-like identifiers upon deposition and make them searchable.
If central storage is needed, then there has to be an institution willing and
able to take on this task. The current wwPDB partners are looking at future
funding that is at best flat, with increasing numbers of depositions that also
get bigger and more complex. There is *no way on earth* that wwPDB can accept
raw data (be it X-ray, NMR or EM! this is not an exclusive X-ray issue)
without *at least* double the current level of funding (and not just in the US
for RCSB, but also in Japan for PDBj and in Europe for PDBe)! I am pretty
confident that this is simply *not* going to happen.
[Besides, in my own humble opinion, in order to remain relevant (and
fundable!) in the biomedical world, the PDB will have to restyle itself as a
biomedical resource instead of a crystallographic archive. We must take the
structures to the biologists, and we must expand in breadth of coverage to
include emerging hybrid methods that are relevant for structural cell (as
opposed to molecular) biology. This mission will be much easier to fund on
three continents than archiving TBs of raw data that have little or no
tangible (i.e., fundable) impact on our quest to find a cure for various kinds
of cancer (or hairloss) or to feed a growing population.]
However, there may be a more realistic solution. The role model could be NMR,
which has its own global resource for data storage in the BMRB. BMRB is a
wwPDB partner - if you deposit an NMR model with us, we take your ensemble
coordinates, metadata, restraints and chemical shifts - any other NMR data
(including spectra and FIDs) can subsequently be deposited with BMRB. These
data will get their own BMRB ID which can be linked to the PDB ID.
A model like this has advantages - it could be housed in a single place, run
by X-ray experts (just as BMRB is co-located with NMRFAM, the national NMR
facility at Madison), and there would be only one place that would need to
secure the funding (which would be substantially larger than the estimate of
$1000 per year suggested by a previous poster from La La Land). This could for
instance be a synchrotron (linked to INSTRUCT?), or perhaps one of the
emerging nations could be enticed to take on this challenging task. I would
expect that such a centre would be closely affiliated with the wwPDB
organisation, or become a member just like BMRB. A similar model could also be
employed for archiving raw EM image data.
-----------
I've said enough for today. It's almost time for the booze-up that kicks off
the PDB40 symposium here at CSHL! Heck, some of you who read this might be
here as well!
Btw - Colin Nave wrote:
"(in increasing order of influence/power do we have the Pope, US president,
the Bond Market and finally Gerard K?)"
I'm a tad disappointed to be only in fourth place, Colin! What has the Pope
ever done for crystallography?
--Gerard
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Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:[log in to unmask]
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
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