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Direct link to page describing the [[NMReDATA tag format|format of the NMREDATA tags]].
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'''Quick links'''
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<span style="color:#008F00">  Important annoncement: </span>On Sept 26, 2019 the First [[Symposium2019|''' NMReDATA symposium''']] will take place in Porto, Portugal.
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Direct link to the page describing the [[NMReDATA tag format|format of the NMREDATA tags]].
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List of [[compatible software]]
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Tentative instruction for [[Submission NMReDATA|journal submission of NMReDATA]].
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Link to the [https://github.com/NMReDATAInitiative GitHub page] of the NMReDATA Initiative.
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Discussion on [[Future version| future versions of the NMReDATA format ]]
  
 
= Introduction =
 
= Introduction =
The [http://www.nmredata.org NMReDATA working group] decided to include data extracted from NMR spectra of small molecules in SDF files using SD tags.  
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The [http://www.nmredata.org/partners.html NMReDATA working group] decided to include data extracted from NMR spectra of small molecules in [[sdf files|  SDF files]] using SD tags.  
  
[[sdf files| More details about SDF files!]]
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Link to the [https://onlinelibrary.wiley.com/doi/abs/10.1002/mrc.4737 MRC article] on the NMReDATA format.
  
 
An important task of the group is to define the format of the content of the "<NMREDATA_...>" tags.  [[NMReDATA tag format|More details here!]].
 
An important task of the group is to define the format of the content of the "<NMREDATA_...>" tags.  [[NMReDATA tag format|More details here!]].
  
 
The version 1.0 will be decided in September at the "Round table" of the Smash 2017 conference at Baveno, Italy.
 
The version 1.0 will be decided in September at the "Round table" of the Smash 2017 conference at Baveno, Italy.
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The SDF file alone (that is without the spectra) cannot be used to verify that the assignment corresponds to the spectra. It is therefore important to always have the spectra with the SDF file! We call ''"NMR Record"'' the combination of the spectra and the SDF file.
  
 
= NMR records =
 
= NMR records =
<!-- [[commented_example_nmredata|Example of commented and simplified NMREDATA tags ]] -->
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<!-- [[commented_example_nmredata|Examples of commented and simplified NMREDATA tags ]] -->
The SDF file alone (that is whithout the spectra) canot be used to verify that the assignment corresponds to the spectra. It is therefore important to always have the spectra with the SDF file!
 
  
 
We call "NMR record", a folder (or .zip file including the folder) or a database record including:
 
We call "NMR record", a folder (or .zip file including the folder) or a database record including:
  
1) All the NMR spectra (including FID, acquisition and processing parameters). The format of these data is as produced by the manufacturer of the instrument which acquired the data. That means that software generating the data either has these crude data available or it will ask the user to point to the crude data in order to include them in the records.  
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1) All the NMR spectra (including FID, acquisition and processing parameters). The format of these data is as produced by the manufacturer of the instrument which acquired the data. That means that software generating the data either has these crude data available or it will ask the user to point to the crude data in order to include them in the ''NMR record''.  
  
 
2) The SDF file including the NMReDATA (''.nmredata.sdf'' file)
 
2) The SDF file including the NMReDATA (''.nmredata.sdf'' file)
  
 
[[File:nmr_record.png|600px|center|NMR record]]
 
[[File:nmr_record.png|600px|center|NMR record]]
A more detailed [http://www.nmredata.org/test-2.pdf pictural representation of NMR record and example of SDF file] presented in the [http://nmredata.org/euromar_2017_v5_optimized.pdf poster] presented in July at the Euromar 2017. '''Note:''' The NMREDATA tag "SIGNALS" was renamed "ASSIGNMENT" in Version 0.98.
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A more detailed [http://www.nmredata.org/test-2.pdf pictorial representation of NMR record and example of SDF file] presented in the [http://nmredata.org/euromar_2017_v5_optimized.pdf poster] presented in July at the Euromar 2017. '''Note:''' The NMREDATA tag "SIGNALS" was renamed "ASSIGNMENT" in Version 0.98.
  
NMR records will be requested by ''Magnetic Resonance in Chemistry'' in 2018 (add link when the editorial will be published). The editors of software (Bruker, Mestrelab, ADC/Labs, cheminfo) will be ready by the end of 2017 to produce MNR records for submission to MRC.  
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NMR records will be [http://onlinelibrary.wiley.com/doi/10.1002/mrc.4631/full requested by ''Magnetic Resonance in Chemistry''] from 2018 on. The editors of software (ADC/Labs, Bruker, cheminfo, Mestrelab) will be ready by the end of 2017 to produce MNR records for submission to MRC.  
  
Records will be either analysed on web pages, or downloaded, and the nmrdata.sdf file opened by the software which will access automatically to the associaced spectra.  
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Records will be either analysed on web pages, or downloaded, and the nmredata.sdf file opened by the software which will access automatically to the associated spectra.  
  
 
The full description can be found [[NMReDATA tag format|in the NMReDATA tag format page]].
 
The full description can be found [[NMReDATA tag format|in the NMReDATA tag format page]].
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An example of .nmredata.sdf files with the spectra can be found [https://www.dropbox.com/sh/hu0qudy2bt56ix0/AACc8UiUoeEskSDVhYnP-cZna?dl=0 here]
 
An example of .nmredata.sdf files with the spectra can be found [https://www.dropbox.com/sh/hu0qudy2bt56ix0/AACc8UiUoeEskSDVhYnP-cZna?dl=0 here]
  
= Currect version of the format of NMReDATA =
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= Current version of the format of NMReDATA =
 
The format can be found here : [[NMReDATA tag format]]
 
The format can be found here : [[NMReDATA tag format]]
  
A small set of simple exemples of .nmredata.sdf files can be found [https://www.dropbox.com/sh/sqk1583gyaj52yz/AADzTUQQwXALlm5Geu3swYPqa?dl= here] ('''Version 0.95'''). ('''Note:''' the field called "NMREDATA_SIGNALS" was renamed "NMREDATA_ASSIGNMENT" in V 0.98).
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A small set of simple examples of .nmredata.sdf files can be found [https://www.dropbox.com/sh/sqk1583gyaj52yz/AADzTUQQwXALlm5Geu3swYPqa?dl= here] ('''Version 0.95'''). ('''Note:''' the field called "NMREDATA_SIGNALS" was renamed "NMREDATA_ASSIGNMENT" in V 0.98).
 
It includes .nmredata.sdf files for ethanol with diverse formats (explicit or implicit hydrogen atoms, etc.)
 
It includes .nmredata.sdf files for ethanol with diverse formats (explicit or implicit hydrogen atoms, etc.)
  
= Development Version 0.98 =
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Versions =
[[V0.98|Changes to V 0.98]]
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==Changes to Versions 1.1 ==
 
 
= 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.
 
 
 
'''To be refined by the  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 ''Logic for Stucture Determination'' (LSD) tool. Software producers can include here the specifications of their product. Multiple certification can be listed one after the other. The “Software=...” assignment separates them all in the same <CERTIFICATION> tag.
 
 
 
= Role(s) and scope of the “assignment records”  =
 
 
 
The NMR record can be generated from experimental (this is how the format was designed), but data may also originate 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 formats or spectral description without loss.
 
== Multiple records ==
 
We should see as an advantage if  databases include multiple "assignment records" associated to the same molecule or the same set of NMR spectra. 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.
 
 
 
==SDF files generated from from experimental data==
 
 
 
When the NMR data originate from experimental spectra, they may be quite crude (simple automated integration, peak-picking). At the other extreme, the data may follow complex automated or carefull and expert manual analysis. The NMReDATA muss have to flexibility to code diverse quality of data: They may be partial, incomplete, contain inconsistencies, impossible features, etc. 
 
 
 
- only 1D <sup>1</sup>H NMR data (with or without integration, coupling, etc).
 
 
 
- only 1D <sup>13</sup>C 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 figure 5 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 tool allowing to draw a molecule, enter lists of signal names and 2D correlations could be easily made. We could consider to accept .pdf or pictures of the spectra when the original files do not exist anymore.
 
 
 
An example of .nmredata.sdf files originating from experimental data can be found [https://www.dropbox.com/sh/hu0qudy2bt56ix0/AACc8UiUoeEskSDVhYnP-cZna?dl=0 here]
 
 
 
==SDF files generated from calculated 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=...
 
 
 
Examples of .nmredata.sdf files originating from gaussian can be found here: [https://www.dropbox.com/sh/yfx82u28qpitiuz/AACVJ8J1Ozgzq82I4GQzXrwUa?dl=0 androsten data]
 
 
 
==SDF files generated from 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)
 
 
 
==SDF files generated after revision of existing SDF files==
 
 
 
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.
 
 
 
 
= Concerning symmetry =
 
== Magnetic non-equivalence ==
 
For symmetrical molecules a difficulty may arises to code coupling and 2D correlations.
 
 
 
Reminder: Coupling are not directly associated to atoms, but are associated to labels (in the NMREDATA_ASSIGNMENT tag). Labels are associated to one or more atoms (in case of symetry/fast rotation, etc.).
 
 
 
Example of difficulty/solution concerning scalar coupling: For the <sup>1</sup>H spectrum of 1, 2 dichlorobenzene, we have two multiplets in the 1D <sup>1</sup>H spectrum (two different protons in an AA’XX’ system) so if the SDF file includes two labels (one for A and one for X, each pointing to two atoms), in principle one can only give one coupling: the J<sub>A,X</sub>  (no J<sub>A,A</sub> or J<sub>A,X'</sub>). But if one desires to specify all the couplings, give two different "labels" to A and A' (each pointing to only one atom), so that different coupling can be given for J<sub>A,X</sub>, J<sub>A',X</sub>,J<sub>A,A'</sub>, J<sub>X,X'</sub>. This may desired so that the 1D spectrum can be simulated with the correct non-equivalence effect.
 
 
 
== HMBC correlations in symetrical molecules ==
 
 
 
Consider 1, 4 dichlorobenzene, a 3J<sub>C,H</sub> HMBC correlation will be visible between a proton that seems to be the directly bound-carbon. Because the carbons <sup>1</sup>J and <sup>3</sup>J bond, relative to a proton are symmetrical. A software may see the correlation as 1J, but, it should be able to analyse the NMREDATA_ASSIGNMENT tag and see that the H and C are poiting to two atoms, and that the correlation may correspond to any combination of the four possible pairs. Two pairs will seem as the actual <sup>3</sup>J and two as the <sup>1</sup>J.
 
 
 
= Why not adding more data in 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.  
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Addition of backslash at the end of the line in text of the NMReDATA tags. (This is to avoid the problem that CDK librairies ignore the NewLine character (ASCII 10). Since we need a line separator, we use backslash + NewLine in NMReDATA tags).  [[end-of-line | (More details.)]]
  
2) MS data
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==Changes to Versions 2.0 ==
  
3) other spectral data
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The version 2 is under development. It will probably include the following changes:
  
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...
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*Possibility to add a 3D structure (on top of the "flat" 2D structure).
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*Possibility to add author and institution information (to facilitate integration of these data in repositories).
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*etc.
  
The software producing SDF files including NMReDATA, should read SDF files and write SDF files only adding (or modifying/reviewing) the NMReDATA data. Any other SDF tags should be passed from the file which is read to the file which is generated.
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Discussion and complete list on [[Future version| future versions of the NMReDATA format ]]

Revision as of 11:45, 3 April 2019

Quick links

Important annoncement: On Sept 26, 2019 the First NMReDATA symposium will take place in Porto, Portugal.

Direct link to the page describing the format of the NMREDATA tags.

List of compatible software

Tentative instruction for journal submission of NMReDATA.

Link to the GitHub page of the NMReDATA Initiative.

Discussion on future versions of the NMReDATA format

Introduction

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

Link to the MRC article on the NMReDATA format.

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.

The SDF file alone (that is without the spectra) cannot be used to verify that the assignment corresponds to the spectra. It is therefore important to always have the spectra with the SDF file! We call "NMR Record" the combination of the spectra and the SDF file.

NMR records

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

1) All the NMR spectra (including FID, acquisition and processing parameters). The format of these data is as produced by the manufacturer of the instrument which acquired the data. That means that software generating the data either has these crude data available or it will ask the user to point to the crude data in order to include them in the NMR record.

2) The SDF file including the NMReDATA (.nmredata.sdf file)

NMR record

A more detailed pictorial representation of NMR record and example of SDF file presented in the poster presented in July at the Euromar 2017. Note: The NMREDATA tag "SIGNALS" was renamed "ASSIGNMENT" in Version 0.98.

NMR records will be requested by Magnetic Resonance in Chemistry from 2018 on. The editors of software (ADC/Labs, Bruker, cheminfo, Mestrelab) will be ready by the end of 2017 to produce MNR records for submission to MRC.

Records will be either analysed on web pages, or downloaded, and the nmredata.sdf file opened by the software which will access automatically to the associated spectra.

The full description can be found in the NMReDATA tag format page.

An example of .nmredata.sdf files with the spectra can be found here

Current version of the format of NMReDATA

The format can be found here : NMReDATA tag format

A small set of simple examples of .nmredata.sdf files can be found here (Version 0.95). (Note: the field called "NMREDATA_SIGNALS" was renamed "NMREDATA_ASSIGNMENT" in V 0.98). It includes .nmredata.sdf files for ethanol with diverse formats (explicit or implicit hydrogen atoms, etc.)

Versions

Changes to Versions 1.1

Addition of backslash at the end of the line in text of the NMReDATA tags. (This is to avoid the problem that CDK librairies ignore the NewLine character (ASCII 10). Since we need a line separator, we use backslash + NewLine in NMReDATA tags). (More details.)

Changes to Versions 2.0

The version 2 is under development. It will probably include the following changes:

  • Possibility to add a 3D structure (on top of the "flat" 2D structure).
  • Possibility to add author and institution information (to facilitate integration of these data in repositories).
  • etc.

Discussion and complete list on future versions of the NMReDATA format