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NFDI4Chem / nmrxiv

nmrXiv is currently developed as the FAIR, consensus-driven NMR data repository and computational platform. The ultimate goal is to accelerate broader coordination and data sharing among researchers by enabling storage, management, sharing and analysis of NMR data.
https://nmrxiv.org
MIT License
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NMRium in nmrXiv does not read NMRium files #649

Open tilfischer opened 1 year ago

tilfischer commented 1 year ago

There is a dataset in RADAR4Chem also having the NMR data in NMRrium file format. https://dx.doi.org/10.22000/786

Thanks to Johannes Liermann for preparing this data.

If this data is added to nmrXiv i.e. a NMRium file in a folder, the NMRium spectral viewer does not read this NMRium file and the folder is not considered as being a nmrXiv Study (or "Sample" from another point of view).

NRayya commented 1 year ago

Hi @tilfischer Could you please share the project with me on nmrXiv? It would be easier than duplicating the work

tilfischer commented 1 year ago

As ever before, the data is available in RADAR: https://dx.doi.org/10.22000/786

tilfischer commented 1 year ago

While NMRium does not read nmrium files added in Step 1 (File Upload) of a submission, NMRium itself in Step 2 is happy to read this files via Import -> Import file from file system.

That is how that may look like:

nmrXiv_nmrrium_files

On the left you see data obtained with one sample. Data is available in Bruker format and in JCAMP-DX format. On the right in NMRium you see the data in NMRium format, which is not added as spectra listed on the left.

NishaSharma14 commented 1 year ago

Duplicate #531

tilfischer commented 9 months ago

Issue still present in current version of nmrXiv. If I upload the nmrium file mentioned and linked above and want to proceed to step 2/3 I get the following error message Spectra files needs to be organised into folders. Please create a folder corresponding to each sample and add all your NMR spectroscopic experiment output files are added to the corresponding folders. If I wrap the nmrium file with a folder I get Please upload spectral data to proceed..

Possible this issue is of minor importance. The nmrium format is possibly of minor importance. The description of the format is very limited and there are vendor formats, JCAMP-DX formats, nmrML and formats by Mestrelab out there. That's possibly already more than enough.

CS76 commented 9 months ago

Quick update:

TLDR; NMRium format is constantly evolving and updated without retrospective compatibility. Therefore, we cannot enable this feature unless a stable release is provided by the core NMRium team.

At nmrXiv, we use sources and source selectors to link spectra instead of embedding them in the nmrium file due to file size issues affecting loading times. Parsing the NMRium file to extract metadata is possible. For example, in this project, we found zones defined for 2D spectra and correlation data.

tilfischer commented 9 months ago

This is totally a'right from my perspective. We do not need another exchange format but one which lab users have in their hand and which they may use to also provide data on peaks, integrals, multiplets/ranges and chemical structures + assignments.

The documentation of the NMRium format is very limited anyhow. It seems to me that it is is not intended to be an exchange format.