Difference between revisions of "Main Page"

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Direct link to page describing the [[NMReDATA tag format|format of the "<NMREDATA_...>" tags]].
 
  
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Direct link to the the[[1D attributes|1D spectra attributes page]].
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'''Quick links'''
  
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= Introduction =
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Direct link to the page describing the [[NMReDATA tag format|format of the NMREDATA tags (version 1.0/1.1)]] and [[NMReDATA tag format 2.0|format of the NMREDATA tags (version 2.0)]].
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The [http://www.nmredata.org NMReDATA working group] decided to include data extracted from NMR spectra of small molecules using "tags" in SDF files.  
 
  
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[[sdf files| More details about SDF files including NMReDATA here!]].
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List of [[compatible software|compatible software and webtools]]
  
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An important task of the group is to define the format of the content of the "<NMREDATA_...>" tags.  [[NMReDATA tag format|More details here!]].
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Tentative instruction for [[Submission NMReDATA|journal submission of NMReDATA]].
  
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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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Link to the [https://github.com/NMReDATAInitiative GitHub page] of the NMReDATA Initiative.
  
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= NMR records =
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= Introduction =
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<!-- [[commented_example_nmredata|Example of commented and simplified NMREDATA 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.  
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We call "NMR record", a folder (or .zip file including the folder) or database record including:
 
  
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1) All the NMR spectra (including FID, acquisition and processing parameters)
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Link to the [https://onlinelibrary.wiley.com/doi/abs/10.1002/mrc.4737 MRC article] on the NMReDATA format.
  
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2) The .nmredata.sdf file
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An important task of the group is to define the format of the content of the "<NMREDATA_...>" tags.  [[NMReDATA tag format|More details here!]].
  
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[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.
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The version 1.0 has been decided in September at the "Round table" of the Smash 2017 conference at Baveno, Italy.
  
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= Currect version of the format of NMReDATA =
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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.
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The format can be found here : [[NMReDATA tag format]]
 
  
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[[V0.98|Changes to V 0.98]]
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A 1.1 version was released to fix a problem in 1.0.
  
 +
Version 2.0 adds extensions and was released after the [[Symposium2019|'''1st NMReDATA symposium''']] (Sept. 16, Porto, Portugal).
  
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= Certification=
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= NMR records =
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<!-- [[commented_example_nmredata|Examples of commented and simplified NMREDATA tags ]] -->
  
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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. ?)
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We call "NMR record", a folder (or .zip file including the folder) or a database record including:
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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).
 
  
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>  <NMREDATA_CERTIFICATION>
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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''.  
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Software=CMC_assist
 
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Author=Bruker
 
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Confidence_level=4.6
 
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Confidence_level_certificate=”ADFS678AG67DFG6SD5F7GS5DFGSD8F5GSD7FG7”
 
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Unique_solution=YES
 
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Unique_solution_certificate=”ADFS678AG67DFG6SD5F7GS5DFGSD8F5GSD7FG7”
 
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ETC...
 
  
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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.
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2) The SDF file(s) including the NMReDATA (''.nmredata.sdf'' file)
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= Role(s) and scope of the “assignment records”  =
 
  
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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.
 
  
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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.
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[[File:nmr_record.png|600px|center|NMR record]]
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A more detailed picture (see [[File:test-2.pdf|600px|center|pictorial representation of NMR record and example of SDF file]]) was 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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==Report assignment from experimental data==
 
  
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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:
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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) are able to grenerate MNR records.  
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- only 1D 1H NMR data (with or without integration, coupling, etc).
 
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- only 1D 13C data (just from a simple peak peaking)
 
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- only 1D data  but for multiple isotopes (from NMRshiftDB ?)
 
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- full analysis based on computer-assisted software (such as Bruker cmc-se ACDLabs Structure Elucidator or Mestrelab Mnova) or web-platform (cheminfo.org)
 
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- 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)
 
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- 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).
 
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- 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
 
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( from http://onlinelibrary.wiley.com/doi/10.1002/mrc.4527/full).
 
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Scripts could be written to convert such a "pure text" description into .sdf file and include the .mol file.
 
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- 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.  
 
  
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Synthetic/predicted data
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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.
  
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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:
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The full description can be found [[NMReDATA tag format|in the NMReDATA tag format page]].
  
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>  <NMREDATA_ORIGIN>
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An example ('''probably obsolete''') of .nmredata.sdf files with the spectra can be found [https://www.dropbox.com/sh/hu0qudy2bt56ix0/AACc8UiUoeEskSDVhYnP-cZna?dl=0 here]
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Source=Calculation
 
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method=DFT
 
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Geometry=method/basis set
 
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Shielding=method_basis set
 
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Coupling=method_basis set
 
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Software=...
 
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Version=...
 
  
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==Literature data==
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A better source is the [https://github.com/NMReDATAInitiative/Examples-of-NMR-records GitHub example page] of the [https://github.com/nmredatainitiative GitHub page of the Initiative].
  
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When the NMR data originate from publications, a reference to the published paper/book/thesis are given in the NMREDATA_LITERATURE tag.
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== Mixtures of compounds ==
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When more than one compound is present in a sample, multiple .sdf are produced and called compound1.nmredata.sdf, compound2.nmredata.sdf, etc.
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>  <NMREDATA_LITERATURE>
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= Current version of the format of NMReDATA =
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Source=Journal
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The format can be found here : [[NMReDATA tag format]]
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DOI=DOI_HERE (if Reference field is DOI specify it here)
 
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CompoundNumber=label used in the reference to designate the compound (typically a number in boldface)
 
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>  <NMREDATA_LITERATURE>
 
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Source=Book
 
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ISBN=ISBN_HERE (if Reference field is DOI specify it here)
 
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CompoundNumber=label used in the reference to designate the compound (typically a number in boldface)
 
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>  <NMREDATA_LITERATURE>
 
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Source=Thesis
 
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Thesis=HTML link here (if available if not "LastName, Firstname(s), institution providing the degree, city, country, year of publication.
 
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CompoundNumber=label used in the reference to designate the compound (typically a number in boldface)
 
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For revised/update data
 
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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.
 
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>  <NMREDATA_UPDATE>
 
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Source=Record
 
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Record_number=ref_to_the_original_record (multiple reference is allowed for aggregation of records – separated by “,”).
 
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Date =date.... standard format for date
 
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Correction="fixed assignments of C(13) and C(15)"
 
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This is also to be refined according to future developments.
 
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= Problems related to symmetry =
 
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This section is tentative... to be worked on in the future....
 
  
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For symmetrical molecules a difficulty arises to code coupling and 2D correlations.
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Various examples of NMReDATA files can be found in the [https://github.com/NMReDATAInitiative/Examples-of-NMR-records github repository].
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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…
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= Database =
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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.
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The NMReDATA Inititiative define the format and rules for hosting and provide data, but hosting data is not part of our mission.  
  
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We have three different possibilities:
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Discussion on [[database_policy | about database providers ]]
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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.
 
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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.
 
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3) Try to face the problem and develop a serious method to include symmetry… Could be the object of future work.
 
  
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=  Versions =
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==Changes to Versions 1.1 ==
  
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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.
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*[[end-of-line | Addition of backslash]] at the end of the line of  NMReDATA tags.
  
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= Why not adding more data in NMReDATA tags? =
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==Changes to Versions 2.0 ==
  
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We consider that our task is to focus on NMR data. But SDF files could (and should!) also include other experimental data such as:
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*Possibility to include Jcamp spectra on top of original data from the instrument.
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*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 metadata in repositories).
  
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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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For details, see [[NMReDATA_tag_format_2.0|the specification]].
  
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2) MS data  
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==Changes to Versions 2.1 (future version)==
 +
<span style="color:#FF8C00">  ''Future version of the format! Suggestions are welcome! '' </span>
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*Possibility to include [[Jassign|J-coupling assignment data]] (coupling network and J-graph data).
  
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3) other spectral data
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Discussion and complete list on [[Future version| future versions of the NMReDATA format ]]
  
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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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= Jmol integration in this wiki =
 +
NMReDATA is being integrated with [[Jmol |  Jmol/JspecView ]]
  
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The software producing SDF files including NMReDATA, should read SDF files and write SDF files only adding (or modifying/reviewing) the NMReDATA data.
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= Publications =
 +
* NMReDATA, a standard to report the NMR assignment and parameters of organic compounds. M. Pupier et al. (2018) Magnetic Resonance in Chemistry 56:703-715. doi: [https://doi.org/10.1002/mrc.4737 10.1002/mrc.4737]  PMID: 29656574
 +
* NMReDATA: Tools and applications. S. Kuhn et al. (2021) Magnetic Resonance in Chemistry 59:792-803. doi: [https://doi.org/10.1002/mrc.5146 10.1002/mrc.5146]  PMID: 33729627

Latest revision as of 21:42, 17 February 2024

Quick links

Direct link to the page describing the format of the NMREDATA tags (version 1.0/1.1) and format of the NMREDATA tags (version 2.0).

List of compatible software and webtools

Tentative instruction for journal submission of NMReDATA.

Link to the GitHub page of the NMReDATA Initiative.

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 has been 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.

A 1.1 version was released to fix a problem in 1.0.

Version 2.0 adds extensions and was released after the 1st NMReDATA symposium (Sept. 16, Porto, Portugal).

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(s) including the NMReDATA (.nmredata.sdf file)


NMR record

A more detailed picture (see File:Test-2.pdf) was 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) are able to grenerate MNR records.

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 (probably obsolete) of .nmredata.sdf files with the spectra can be found here

A better source is the GitHub example page of the GitHub page of the Initiative.

Mixtures of compounds

When more than one compound is present in a sample, multiple .sdf are produced and called compound1.nmredata.sdf, compound2.nmredata.sdf, etc.

Current version of the format of NMReDATA

The format can be found here : NMReDATA tag format

Various examples of NMReDATA files can be found in the github repository.

Database

The NMReDATA Inititiative define the format and rules for hosting and provide data, but hosting data is not part of our mission.

Discussion on about database providers

Versions

Changes to Versions 1.1

Changes to Versions 2.0

  • Possibility to include Jcamp spectra on top of original data from the instrument.
  • 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 metadata in repositories).

For details, see the specification.

Changes to Versions 2.1 (future version)

Future version of the format! Suggestions are welcome!

Discussion and complete list on future versions of the NMReDATA format

Jmol integration in this wiki

NMReDATA is being integrated with Jmol/JspecView

Publications

  • NMReDATA, a standard to report the NMR assignment and parameters of organic compounds. M. Pupier et al. (2018) Magnetic Resonance in Chemistry 56:703-715. doi: 10.1002/mrc.4737 PMID: 29656574
  • NMReDATA: Tools and applications. S. Kuhn et al. (2021) Magnetic Resonance in Chemistry 59:792-803. doi: 10.1002/mrc.5146 PMID: 33729627
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