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The format can be found here : [[NMReDATA tag format]]
 
The format can be found here : [[NMReDATA tag format]]
  
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[V0.98|Changes to V 0.98]
  
 
= Comments about the content of NMReDATA tags =
 
= Comments about the content of NMReDATA tags =

Revision as of 14:14, 31 July 2017

Direct link to page describing the format of the "<NMREDATA_...>" tags.

Direct link to the the1D spectra attributes page.

Introduction

The NMReDATA working group decided to include data extracted from NMR spectra of small molecules using "tags" in SDF files.

More details about SDF files including NMReDATA here!.

An important task of the group is to define the format of the content of the "<NMREDATA_...>" tags. More details here!.

The version 1.0 will be decided in September at the "Round table" of the Smash 2017 conference at Baveno, Italy.

NMR records

We call "NMR record", a folder (or .zip file including the folder) or database record including:

1) All the NMR spectra (including FID, acquisition and processing parameters)

2) The .nmredata.sdf file

Pictural representation of NMR record and example of SDF file presented in the poster presented in July at the Euromar 2017.

Comments and changes to version 0.98

Concerning the intensity in 2D spectra, it was not a good idea to ask to strictly give the intensity at the coordinates of the peak. This may fall in the middle of a doublet (in a HSQC for example). So this was slightly rephrased in this version

1) For all 2D spectra, the intensity of the spectrum at (or very close to) the coordinates of the correlated peaks should be given when the spectrum is available. If the signals has a shape such that the intensity is zero at that center (phase sensitive COSY, for in the middle of a well resolved doublet in HSQC, for example) the intensity can be measure at the maximum amplitude of the multiplet. This intensity is not pretending to be “quantitative”. Optional integration of the volume is possible using the "E=" attribute.

Currect version of the format of NMReDATA

The format can be found here : NMReDATA tag format

[V0.98|Changes to V 0.98]

Comments about the content of NMReDATA tags

We consider that our task is to focus on NMR data. But SDF files could (and should!) also include other experimental data such as:

1) The origin of the molecule. This may include the extraction method and the plant it originates from, in phytochemistry, or the reaction producing it.

2) MS data

3) other spectral data

In principle authors can add any tag provided they have tools to do it and requests from the Journals... such data could have the following form...

The software producing SDF files including NMReDATA, should read SDF files and write SDF files only adding (or modifying/reviewing) the NMReDATA data.

Certification

When the assignment is made using a computer assisted manner, the software may want to add a certification of the validity of the data. This should be (up to the manufacturers) to somehow encode it to make it impossible to forge the certification (using hashtag, etc. ?) Certificates TAGS could be listed at the end of the .sdf file. They can originate from the CASE software or from the database hosting the data and spectra, from the journal (to say data were peered reviewed). They can be cumulated. If the text of the .sdf file needs to be hashed for certification, the list of TAG used for hashing could be listed. (I’m not sure what needs to be done to certify the validity of certificates. To be refined by the certificate specialists).

>  <NMREDATA_CERTIFICATION>
Software=CMC_assist
Author=Bruker
Confidence_level=4.6
Confidence_level_certificate=”ADFS678AG67DFG6SD5F7GS5DFGSD8F5GSD7FG7”
Unique_solution=YES
Unique_solution_certificate=”ADFS678AG67DFG6SD5F7GS5DFGSD8F5GSD7FG7”
ETC...

This is only a very vague example. The uniqueness of the structure proposed may be understood in the sense of J.-M. Nuzillard’s LSD tool. Software producers can tell what needs to be done for their format. Multiple certification can be listed one after the other. The “Software=...” assignment separates them all in the same <CERTIFICATION> tag.

4 Role(s) and scope of the “assignment records”

The NMR record can be generated from experimental data but also from simulations, predictions, etc. Tools to compare, evaluate, validate, and check consistency of “assignment records” will certainly be developed. Assignment records can be generated by commercial software, but also by diverse tools analysing NMR data, homemade processing tools, simulation software, etc. This is why it is important to have a format of data including a maximum of options to be as flexible as possible, even if not all possible uses are clearly defined and used immediately. Ideally, the .sdf files should be converted into other file format or spectral description without loss.

We should see as an advantage if the databases include multiple "assignment records" associated to the same molecule. Some could be old, originating from, incomplete literature data. Others could include errors because they originate from bulk data processed automatically. But finally a computer could verify and nicely validated record combining all the other data. Aggregated record could be generated by NMR software/database scoring available data for consistency, calculated chemical shifts and spectral simulations. They could refine chemical shifts and couplings, etc.

Experimental data

When the NMR data originate from experimental spectra, they may be quite crude (simple automated integration, peak-picking) or follow complex automated or manual analysis. The data may be partial, incomplete, contain inconsistencies, impossible features, etc. The content may be diversely complex depending on the origin of the data: - only 1D 1H NMR data (with or without integration, coupling, etc). - only 1D 13C data (just from a simple peak peaking) - only 1D data but for multiple isotopes (from NMRshiftDB ?) - full analysis based on computer-assisted software (such as Bruker cmc-se ACDLabs Structure Elucidator or Mestrelab Mnova) or web-platform (cheminfo.org) - 1D and 2D data processed automatically with ambiguities on the signal assignment and partial (for example not all signals are assigned) and/or ambiguous (due to lack of resolution, or other problems) - The file may not contain the actual assignment, only the structure and the list of chemical shift (the assignment could be added by NMR tools). - The data may come from scientific report i.e. the text providing the description of the spectra. It could be like the one of the text of the following figure ( from http://onlinelibrary.wiley.com/doi/10.1002/mrc.4527/full).

Scripts could be written to convert such a "pure text" description into .sdf file and include the .mol file. - For assignment work made with only "paper and pencil", a simple webtool allowing to draw a molecule, enter lists of signal names and 2D correlation could be easily made. We could consider to accept .pdf or pictures of the spectra when the original files do not exist anymore.

Synthetic/predicted data

The NMR data may originate from DFT calculations or any other type of predictor of chemical shifts, and/or coupling. In such a case, a general tag is added to provide information about the software. For example:

>  <NMREDATA_ORIGIN>
Source=Calculation
method=DFT
Geometry=method/basis set
Shielding=method_basis set
Coupling=method_basis set
Software=...
Version=...

Literature data

When the NMR data originate from publications, a reference to the published paper/book/thesis are given in the NMREDATA_LITERATURE tag.

>  <NMREDATA_LITERATURE>
Source=Journal
DOI=DOI_HERE (if Reference field is DOI specify it here)
CompoundNumber=label used in the reference to designate the compound (typically a number in boldface)
>  <NMREDATA_LITERATURE>
Source=Book
ISBN=ISBN_HERE (if Reference field is DOI specify it here)
CompoundNumber=label used in the reference to designate the compound (typically a number in boldface)
>  <NMREDATA_LITERATURE> 
Source=Thesis
Thesis=HTML link here (if available if not "LastName, Firstname(s), institution providing the degree, city, country, year of publication.
CompoundNumber=label used in the reference to designate the compound (typically a number in boldface)

For revised/update data

Assignment records may be generated after revision from experimental, literature, prediction data, etc. Ideally, the original .sdf files should be also generated to facilitate comparison or exists somewhere and be referred to. In both cases reference should be given.

>  <NMREDATA_UPDATE>
Source=Record
Record_number=ref_to_the_original_record (multiple reference is allowed for aggregation of records – separated by “,”).
Date =date.... standard format for date
Correction="fixed assignments of C(13) and C(15)"

This is also to be refined according to future developments.  

Problems related to symmetry

This section is tentative... to be worked on in the future....

For symmetrical molecules a difficulty arises to code coupling and 2D correlations. 1) Problem for coupling: For the 1H spectrum of 1, 2 dichlorobenzene, we have two signals (two different protons in an AA’XX’ system) so if the SDF file includes two signals (one for A and one for X), in principle one can only give one coupling: the J(A,X). But we should be able to give other coupling constants with respect to the prime H. When only one symmetry property is present, it may not be too difficult to include in the format a manner to provide pairs of couplings instead of only one, but with more than one symmetry, it would become complicated… 2) Problem for correlations. Consider 1, 4 dichlorobenzene, a 3J(C,H) HMBC correlation will be visible between a proton that seems to be the directly bound-carbon. Because the carbons 1J and 3J bond, relative to a proton are symmetrical.

We have three different possibilities: 1) Ignore the problem. It may not be so serious in fact. In systems with non-magnetically equivalent spins, the coupling structures are complex and the coupling will probably not be measured in routine exp. Concerning the HMBC correlation, the HMBC correlation will be ambiguous and it will be to the person/software checking consistency, i.e. to see that when signals correspond to more than one proton or more than one carbone, it suffice that one of the possible combination of Hortho, H’ortho and Cortho and C’ortho corresponds to 3JCH and the check is passed… even if it also pass a check for 1JCH. 2) Duplicate all signals (or the subset with symmetry). If we list two signals (with two different labels) for Hortho and H’ortho, then we will have no problem anymore with coupling (one will be able to give a J(A, X) and (JAX’) and ambiguous correlations (they will be OK) . But the problem may be that for any chemical shifts, there will always be two labels/spins and that may cause confusion for the assignment software. The complications may be worse than the problem. 3) Try to face the problem and develop a serious method to include symmetry… Could be the object of future work.


P.S. Some names are somewhat tentative. We don’t necessarily mean to define 3D spectra here or projections of 3D to 2D (HSQC-TOCSY). The list is mostly to test the ability of the format to list as many experiments as possible with the same logic.