Hi,
Below are a few answers to your items.
Cheers,
Eldon
Edward d'Auvergne wrote:
Ah, ok. That's what is happening. So a good aim for relax would be
to get it into a form where the annotator needs only to check the
data. Another aim would be so that the submitter does as little as
possible as well.
For testing deposition against the new dictionary, is there a
non-production machine that could be used? If I can submit and check
against your changes, this should speed up development. I have made a
few improvements since the file at
https://gna.org/support/download.php?file_id=7140, and using the new
file, a few of the issues identified by ADIT-NMR include (I'll number
these for future reference):
ADIT-NMR is a relatively complex (several components and lots of legacy
code) system. Updating an instance of the system with a new dictionary
requires a bit of work that is carried out by Steve Mading in the group.
Other parts of the system also are under development to handle mandatory
chemical shift deposition with PDB depositions. Unfortunately, this all
makes it difficult to create a unique test system for this project that
I could keep up to date with changes.
1. The author info is missing - this can probably be added by the
submitter afterwards.
That would be the normal procedure.
2. The entity entry is not complete - relax needs to add a few
additional tags for this.
OK
3. In the Molecular assembly saveframe supergroup 3, three saveframes
appear to be required - Molecular assembly, Natural source, and
Experimental source. Should relax create these?
Natural source and experimental source would normally be filled in by
the depositor. For simple single polymer systems, the molecular assembly
might be filled in by relax. But if the system is more complex (ligands,
multiple polymer, etc.), it might be easier to have the depositor enter
the information.
4. For the Experimental_descriptions saveframe supergroup, only the
software saveframe is being created by relax. I have used $sample_1
and $conditions_1 in the other saveframes so these exist but are
empty. Should relax do more with this?
This should be all you need to do. Sample and conditions information is
usually hidden in a lab book and the depositor has to dig it out and
enter it at the time of deposition.
5. _Software.Version is only allowed to be 31 characters. For
non-released software (a number of users utilise the repository code
rather than released versions) I would like to have something like
"repository checkout r9832
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb". Can this be
extended into VARCHAR(127)?
This has been changed to VARCHAR(127).
6. The citations section of the software saveframe appears to be
missing. Is this not metadata?
I will need to do more investigating on this one. I do not know of
anyone who has provided this information and there is probably a flag
set somewhere that is causing the problem.
7. The chemical shift anisotropy saveframe requires the deposited
data file name. I've tried supplying '?', but nothing I do appears
remove this issue from the user. Is there some way I can specify that
it all comes from the same file?
I uploaded your temp_bmrb file and then entered it as the deposited data
file name in both the CSA and the Het NOE fields and this was accepted
and the green check marks appeared.
8. The chemical shift anisotropy saveframe is asking for the NMR
experiment used. You usually set this to -160 or -172 ppm in
model-free analyses. Can this be made non-compulsory or at least put
a tick in the ADIT-NMR system for it.
Data had to be collected from an experiment run on an NMR spectrometer.
One or more NMR experiments like a '1H-15N het NOE' experiment needs to
be entered by the depositor and linked to the sample, sample conditions,
and NMR spectrometer used. This is filled in in the 'NMR experiments and
samples' section after the Sample, Sample conditions, and NMR
spectrometer list have been completed. The deposition system is asking
for the name of an NMR experiment not for parameters.
9. Save as 6. for the heteronuclear NOE saveframes.
Not sure about this one.
10. _Heteronucl_NOE_list.Heteronuclear_NOE_val_type appears to be
compulsory in ADIT-NMR but not in the dictionary at
http://www.bmrb.wisc.edu/dictionary/3.1html_frame/frame_HeteronuclNOEList.html#_Heteronucl_NOE_list.Heteronuclear_NOE_val_type.
This information is not available from legacy data and so in the
dictionary the field is allowed to have a null value, however it was
felt that the NOE val type should be a mandatory item in the deposition
system so that this information would be collected for all future
depositions.
11. I'm not sure what _Heteronucl_NOE_list.NOE_ref_val is or why it
is compulsory.
It is no longer compulsory. I think it was intended as an intensity
value that is used to normalize the data or as a reference to compare
with other values in the spectrum.
12. relax should produce the _Heteronucl_NOE_experiment tags.
OK
Sorry about the length of this, though I think that covers almost
everything except for the missing information that requires new
saveframes.
No problem. I hope the answers help. It may be a little while before the
dictionary changes are incorporated into the production system.
Cheers,
Edward
2009/10/28 Eldon Ulrich <elu@xxxxxxxxxxxxx>:
Hi,
Now I understand the issue. The fact that you can upload your file and do
not receive a parse error is a very good sign. The file generated by
ADIT-NMR as a preview only contains the meta data and has never contained
the experimental data. The experimental data is deposited in many different
formats and is often difficult to parse. The uploaded experimental data is
processed by annotators and concatenated to the meta data before being sent
back to the depositor for review and release to the public.
Eldon
Edward d Auvergne wrote:
Follow-up Comment #5, task #6438 (project relax):
This file is the result of taking file #5194, submitting it to the
ADIT-NMR
system, and then asking to see the preview. It demonstrates the loss of
certain data types - i.e. relaxation data and chemical shifts.
(file #7157)
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Re: [task #6438] To relax the BMRB.