JCAMP - The continuing saga of a "Standard" File Format for NMR

April 9th, 1998

Dear Barry,

In the continuing exchange of commentary and opinion within the NMR newsletter regarding the JCAMP standard file format for NMR, let me now add my statements on behalf of Advanced Chemistry Development Inc. During recent exchanges (NMR Newsletter and the JCAMP meeting at ENC '98) Virginia and Woody expressed concern regarding the need for the NMR industry to finally decide what the acceptable JCAMP format should be. In response, Mick Grzonka was kind enough to give us a historical overview regarding attempts to declare and invoke an NMR standard which, according to Mick's note, was actually declared to be the JCAMP format at a meeting in 1990.

Recently at ENC '98 yet another attempt was made to define and defend both the need and the details of a universally acceptable NMR data format appropriate to both 1D and multi-D spectroscopy. During this conversation Tony Davies of the IUPAC JCAMP sub-committee gave a seminar detailing development of the JCAMP standard which can actually take five separate forms: Fixed Length, DIF, PAC, SQZ and DIFDUP. The conclusion of the meeting appeared to lead to the decision that there was a need to develop a form of JCAMP which would deal with the complexities of multi-dimensional NMR data and, assuming funding, we can only wish Tony and the committee the best of luck in developing an appropriate standard.

During the same meeting concern was expressed regarding the need for the vendors to decide on which of the five JCAMP formats would become the standard export format. The driving force behind this discussion appeared to be the need to limit the number of JCAMP import filters that need to be coded into home-grown and third party vendor spectroscopy software. As was so elegantly summarized by Tony Davies, the idea behind the JCAMP format is to allow access to stored data years from now when vendor file formats will have shifted dramatically. Since the JCAMP format has already been around for a number of years and has delivered the five iterations named above, it is therefore necessary for third party software vendors to support all present JCAMP versions as imports as well as any new issues which may occur. Since the number of desktop packages for both 1D and multi-dimensional processing has increased it would be expected that these packages would also support the export of the JCAMP formats. In the initial communication in this series the availability of time domain data in JCAMP format was questioned. Since there may be a need to reprocess data using modified processing parameters it would certainly be appropriate for software to support the export of time domain data.

With all of these issues in mind, and with our present development of SLIMS, a fully web-based LIMS environment for Samples, Structure and Spectra, we have ensured that our desktop processing and spectral management package ACD/NMR Manager has both import and export capability for ALL of the JCAMP formats defined to date for NMR. As the dialog box below indicates, we have the capability to export both time domain data, and frequency domain data as both REAL and REAL/IMAGINARY data.

Using the capability for the spectral export of NMR spectra from ACD/NMR Manager, spectra can be exported to the spectral database within the SLIMS package for direct display on the web in our Java-based spectral display applet as shown below.

This applet is a platform independent Java application that runs within a web browser and therefore offers platform independent viewing of any spectra populated into the database. The standard applet toolset includes zooming, changing axis units, display of discrete lines and integration capability. The applet has the capability to display NMR, MS, IR, UV-Vis, Raman, X-ray spectra and LC curves using the data formats of SPC, JCAMP and NetCDF. Use hyperlink download capabilities platform dependent processing packages can be triggered as helper applications for remanipulation of the data. The window below displays the NMR spectrum shown in the Java applet above, when the NMR manager is loaded as the helper application by the browser. Note that the spectrum is indeed the one shown in the spectrum applet. In this case additional manipulation included baseline correction, adding a structure through the integrated ChemSketch interface and performing on-screen annotations.

With the continuing development of the Java Development Kit and the increasing installation of intranet enterprise capabilities, we can only assume that third party processing and spectral display software vendors will be developing plug-in or Java applet capabilities for browsers in the near future. In this venture ACD Inc. are finding that established data standards such as JCAMP are extremely useful in enabling this technology. To support this enabling technology, all spectrometer vendors are invited to make JCAMP export a simple option in their standard software.

Best wishes,

Tony Williams