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):
1. The author info is missing - this can probably be added by the
submitter afterwards.
2. The entity entry is not complete - relax needs to add a few
additional tags for this.
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?
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?
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)?
6. The citations section of the software saveframe appears to be
missing. Is this not metadata?
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?
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.
9. Save as 6. for the heteronuclear NOE saveframes.
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.
11. I'm not sure what _Heteronucl_NOE_list.NOE_ref_val is or why it
is compulsory.
12. relax should produce the _Heteronucl_NOE_experiment tags.
Sorry about the length of this, though I think that covers almost
everything except for the missing information that requires new
saveframes.
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)
_______________________________________________________
Additional Item Attachment:
File name: adit-nmr_bmr15437_3.str Size:47 KB
_______________________________________________________
Reply to this item at:
<http://gna.org/task/?6438>
_______________________________________________
Message sent via/by Gna!
http://gna.org/
Re: [task #6438] To relax the BMRB.