Hi,
Seb, we should discuss and make a list of the necessary tags. We can
have relax ask the user to input the required data, this will be the
easiest for the user and BMRB input. Adding new tags appears to be
quite a lot easier with the BMRB than modifying existing designs, but
we should be certain of these tags and design the list to be the
highest quality possible. So for example in your list:
* the use of heat compensation (or is this included in the temperature
control tag ?)
This is the _Auto_relaxation_list.Temp_control_method tag.
* the number of different relaxation delays (including some
information on duplicates)
* the order with which the different relaxation delays were recorded
(and the use of interleaving)
This is a good idea, but is hard to implement as a strict definition.
Maybe a single tag with free-formatted text could be used. For
example:
_Auto_relaxation.Delay_interleaving
where the free text could be something like "300, 20, 1000, 10, 1500,
200". Eldon, is there another way of storing this info?
* the number of samples used (if not a single one)
A single Auto_relaxation or Heteronuc_NOE saveframe should really come
from a single sample. If there are different samples for different
experiments, then _Auto_relaxation_list.Sample_condition_list_ID
should point to the different samples for each saveframe.
Regards,
Edward
On 6 March 2011 19:55, Eldon Ulrich <elu@xxxxxxxxxxxxx> wrote:
Hi,
The suggestion on how to validate relaxation data is extremely helpful. We
will look into this and try to implement it.
Adding tags to gather additional information about the experimental details,
etc. is not difficult to do. What is difficult is getting people to provide
the information. If it can be extracted by software with little difficulty
for the depositor, this would be the best way to go. I will be updating the
dictionary with the tags that were suggested earlier and will try to
implement those mentioned here. Not being an expert in the intricacies of
the relaxation data and experimental details, suggestions for specific tag
names along with definitions for the tag values would be helpful.
Thank you very much for all the help and suggestions.
Eldon
On 3/5/11 2:02 AM, Sébastien Morin wrote:
Hi,
Including information on the recycle delay would be quite valuable indeed.
Additionally, many other such tags might also be valuable such as for:
* the use of heat compensation (or is this included in the temperature
control tag ?)
* the number of different relaxation delays (including some information
on duplicates)
* the order with which the different relaxation delays were recorded
(and the use of interleaving)
* the number of samples used (if not a single one)
Maybe also there could be some automatic checkup by the BMRB upon data
deposition on the consistency of the R2 data, as judged by the ratio of
J(0) calculated for the different fields (Morin and Gagné, 2009, JBNMR,
45:361–372). Indeed,this can be used as a global consistency probe for
the complete dataset, potentially reporting on sample and/or temperature
issues between data from different magnetic fields. The mean value of
the J(0) ratio (+- StdDev) for different pairs of R2 data (from
different magnetic fields) could be included in a tag...
Best regards,
Séb :)
On 11-03-04 3:58 PM, Edward d'Auvergne wrote:
Great! I would be perfect if we had all the entries updated by the
time the relax-BMRB integration paper is ready. One thing I've
recently thought about which is important for the relaxation data
(just like the temperature control and calibration tags which were
added) is the recycle delay. This is another experimental detail
which is very good to know, so that the quality of the data can be
judged. Is there a tag or place for this already? Or could a new tag
for the heteronucl_NOE or auto_relaxation saveframes be created?
Cheers,
Edward
On 3 March 2011 19:30, Eldon Ulrich<elu@xxxxxxxxxxxxx> wrote:
Hi,
I have begun to edit the entries according to the changes in the
diffs. This
is a focus for this and next week. Hopefully the edited files will
all be
released by sometime next week. I will let you know.
Thanks,
Eldon
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Re: Finished the reading of all the BMRB model-free data - necessary corrections to the database entries.