nmrshiftdb2 / News: Recent posts

We have made available an updated version of the "NMR prediction history" originally published in our review paper. The online version will be updated with new data as they become available. Ideas and suggestions are welcome!

We can proudly say we have been FAIR even before the term existed. I compiled an overview of the FAIRness of nmrshiftdb2.

We have got new hardware to run the database for about three weeks now. We believe everything is running smoothly and occasional speed issues, which occured on the old hardware, have been resolved. The database should be fit to run for the foreseeable future.

We can celebrate the 20th anniversary of the database. We published a paper in MRC reviewing the development of the database.

We have added a 13C/1H correlation search. This searches for structures which have pairs of directly connected carbon and hydrogen atoms with certain shifts. For example, "135;5" would search for a structure which has a carbon with a shift of 135 ppm with a hydrogen attached with a shift of 5 ppm. Search is via the spectrum search, choose "13C/1H correlation" as "Spectrum type". Total/subspectrum search work as normal.

We recently worked with Jean-Marc Nuzillard on a paper about using predicted data for structure dereplication. Those data are part of nmrshiftdb2 and can be used for searches (if calculated spectra are used for searches, which is the case by default).

nmrium is a sister project of nmrshiftdb2. It is a web-based visualizer and editor for 1D and 2D NMR spectra. On the website, you can already test 1D and 2D NMR functionalities like peak picking, integration, assignment, and more, without installing software, completely in the browser. A close integration with the next version of nmrshiftdb2 is planned.

We have added links to the raw data to the downloads, where raw data are available. In the sd files, there is an additional tag rawdata, the NMReDATA file has the link in the Spectrum_Location, and the cml files have an attribute rawdata in spectrum. This all is only the case if there are rawdata. We currently have more than 500 spectra with raw data for 1H and 13C, and about 300 2D spectra of various nuclei. The raw data so far were available only via the web interface.

It turned out that due to a size limitation on sourceforge's svn, the download of the full data no longer worked. We have changed that to a file download, the new links are on the help page. For interested developers, the svn repository still exists and can be used. Only the http download is affected by the limit.

nmrshiftdb2 entries can now be resolved using identifiers.org. The prefix is nmrshiftdb2 and the id is the molecule id. For example, the identifier nmrshiftdb2:234 identifies the first entry in NMRShiftDB. A link via identifiers.org would be http://identifiers.org/resolve?query=nmrshiftdb2:234

We are pleased to announce that from 2020 the section with NMR challenges, 'problem of the month', will be developed and maintained by Dr. Rainer Haessner (Technical University Munich). He will be happy about feedback and suggestions.

A paper with complete NMReDATA assignment and nmrshiftdb2 deposition was published as part of the integration of the NMReDATA standard and nmrshiftdb2. The dataset can be found here. It contains raw data as well as peak lists. Notice there is also a DOI for the dataset, namely 10.18716/nmrshiftdb2/60004113/nmredata_mrc_cd3od. The nmrshiftdb2 entry links back to the paper, and the paper gives the nmrshiftdb2 entry. An NMReDATA file and NMR Record can be downloaded.

We have a new prediction mechanism available, using deep learning techniques. It should offer improved results - see the paper for details. The prediction is available on the Prediction tab by choosing the methos "13C NN" or "1H NN". Currently it is a bit slow due to the way it is integrated, this will hopefully be improved soon.

nmrshiftdb2 contains structures published in the journal 'Chemie in Unserer Zeit' as part of a series on extraction and spectroscopy of natural products. The corresponding raw data as well as assigned structures are available. The compounds can be found here. DOIs (digital object identifiers) are assigned to these datasets. For example, data for Quinine are identified by DOI 10.18716/nmrshiftdb2/60004827/chiuz_cdcl3.

We have funding for further development of nmrshiftdb2, with a focus on the user interface. Therefore we have a job opening for a developer. If you are interested in working in an international open science environment, you find the announcement here

The QuickCheck now allows for export of the assigned data in the NMReDATA format. The NMReDATA inititiative, which we are part of, strives for establishing the format as a new standard for NMR data exchange.

We have been working with Sciformation to integrate nmrshiftdb2 functionalities into their ELN (elecronic lab notebook). We hope this will be a useful addition for ELN users.

We have released a new version of the software. The main new feature is the Quick Check (still experimental), which is part of a wider initiative about NMR data quality (information in German).

We published a paper about the use of nmrshiftdb2 and its lab system, specifically to increase data quality control for spectra assignments. See our Magnetic Resonance in Chemistry paper for details.

Since 1.2.2015 a new release is live on the servers. This is mainly a bugfix release with quite a few minor improvements.

nmrshiftdb2 is now part of the Unichem network, a cross-referencing databases between (currently) 24 molecular databases. In practice, this means that all the databases now show nmrshiftdb2 links (e. g. ChEMBL) and nmrshiftdb2 shows links to other databases in the additonal data of each molecule. This is updated without a need to exchange links with each individual database. This is part of the new 1.4.6 release.

A new nmrshiftdb2 release was done. It includes most prominently MarvinJS for input, since the Java applets cause increasing problems. There is also partial handling of diastereotopic atoms in the prediction and other small improvements.

It might have lost a bit because of other historic celebrations this year, like the 200th anniversary of the Battle of Leipzig, but this project respectively its predecessor NMRShiftDB celebrates its 10th anniversary this year. It was on the 3rd of November 2003 that the 1.0 release of NMRShiftDB was announced (beta releases had been online before). There were around 6000 spectra available then, most of them calculated. So we have made some progress since then.

A new nmrshiftdb2 is live on the servers. Main change is a rework of the submit process, with a hopefully much improved usability. See the changelog for details.

A new release of the software has been deployed to the servers. Apart from some bugfixes, the most important change is the improved handling of stereochemistry in predictions.