Data JCAMP

A computer file of about 19,000 peak wavenumbers and intensities, along with search software, is distributed by the Infrared Data Committee of Japan (IRDC). Donated spectra, which are evaluated by the Coblentz Society in coUaboration with the Joint Committee on Atomic and Molecular Physical Data (JCAMP), are digitized and made avaUable (64). Almost 25,000 ir spectra are avaUable on the SDBS system developed by the NCLl as described. A project was initiated at the University of California, Riverside, in 1986 for the constmction of a database of digitized ftir spectra. The team involved also developed algorithms for spectra evaluation (75). Other sources of spectral Hbraries include Sprouse Scientific, Aston Scientific, and the American Society for Testing and Materials (ASTM). 

In this article the two most modem standard formats will be addressed. The text will deal with the standards produced by the Joint Committee on Atomic and Molecular Physical Data (JCAMP) and those of the Analytical Instruments Association (AIA). In a short article such as this there is not enough space to attempt a full description of either the format types or their potential. If you wish to implement these standards or to understand more about the standards you already have in use it is essential to refer back to the original literature cited herein. 

To aid in sharing spectra obtained using equipment from different vendors, a number of efforts have been made to establish standard exchange formats. In 1987, the Joint Committee on Atomic and Molecular Physical Data (JCAMP) published the JCAMP-DX format as a standard for exchange of infrared spectra. This general format was subsequently extended to Include mass and NMR spectra. Although JCAMP-DX files are created with small variations from vendor to vendor, it is supported as an export format by most infrared and mass spectroscopy instrument vendors. 

JCAMP. jdx,. dx,. cs Joint Committee on Atomic and Molecular Physical Data structure and spectroscopic format nmm.jcamp. org/ 56... 

The JCAMP-DX file format is split into the sections CORE and NOTES with the intention of keeping less important data separated from the essential content. The CORE itself contains CORE HEADER and CORE DATA. NOTES are just between HEADER and DATA (see Figure 4-4 for an example). 

Data Analysis. The computerization of spectrometers and the concomitant digitization of spectra have caused an explosive increase in the use of advanced spectmm analysis techniques. Data analysis in infrared spectrometry is a very active research area and software producers are constantly releasing more sophisticated algorithms. Each instmment maker has adopted an independent format for spectmm files, which has created difficulties in transferring data. The Joint Committee on Atomic and Molecular Physical Data has developed a universal format for infrared spectmm files called JCAMP-DX (52). Most instmment makers incorporate in thek software a routine for translating thek spectmm files to JCAMP-DX format. 

If you have installed MAPI (mail application interface) software on your PC, you may exploit the MS-WINDOWS mailslot-function to e-mail NMR data directly to and from your PC. The full version of ID-WIN-NMR allows you to export/irnport FlDs, spectra, tables, text-files, relaxation data and metafiles to/from other users of (the full version of) ID WIN-NMR. Both JCAMP-DX5 and Bruker specific binary format are supported. Compared to the procedure outlined in section 2.6.5 this is an even more convenient way for exporting/importing NMR data via Internet. For further details refer to the ID WIN-NMR manual [2.1] or contact your Bruker/Spectrospin representative. 

With recent rapid increases in the size of computer hard disks and memory, another format, JCAMP.DX (Joint Committee of Atomic Molecular and Physical Data), has become more widespread. It preserves all the numerical values in the original spectrum as well as information regarding the spectrum in an ASCII file. One of the advantages of this format is that it allows all comparison algorithms to be used for further identification of the spectrum (Fig. 10.22). 

TITLE=polystyrene (film 38.lMm) JCAMP-DX=4.24 Nicolet v. 1 DATATYPE=INFRARED SPECTRUM ORIGIN= OWNER=IUT Le Mans DATE=1999/12/16 TIME=13 09 20 DATA PROCESSING=Ratio against background XUNITS=1/CM YUNITS=TRANSMITTANCE... 

Figure 10.22—Example of a JCAMP.DX file read by a word processor. This file corresponds to the spectrum in Fig. 10.1. The header contains information about the spectrum and the data points are organised in sequences of 6 values. Only a few values have been retained.

Before reaching the point of complete data integration as given above, there are intermediary levels of data integration that are beneficial to better analysis of data from process analyzers. The best case would be to have all the data in a human readable form that is independent of the application data format. Over the years several attempts have been made to have a universal format for spectroscopic data, including JCAMP-DX and extensible markup language (XML). Because many instrument vendors use proprietary databases, and there is not a universal standard, the problem of multiple data formats persists. This has led to an entire business of data integration by third parties who aid in the transfer of data from one source to another, such as between instruments and the plant s distributed control system (DCS). 

To facilitate the validation process on the basis of the above approach, the MS electronic data is contributed to the OPCW Laboratory in any of the following electronic formats JCAMP, NIST ASCII, AMDIS, and NIST MS Database. Contributing laboratories provide mostly the NIST MS Database format, with structures. The OPCW Code and the Schedule number are placed in the synonym field of the database. The file is submitted to the OPCW Laboratory either as the NIST MS User Database or the corresponding set of text files representing the MSP (Spectral) and MOL (Structure) information. The NIST MS Search/Analysis programs are used for the management of the MS electronic data and also GC(RI) once merged with the MS data. 

In the case where MS analytical data has been contributed in the other formats, it is prepared into a NIST MS Database, using the NIST MS Search program. This program is used to create MS spectral files from the following electronic formats JCAMP, NIST ASCH, AMDIS, and NIST MS Database. If the analytical data contains no chemical structure, the structure is created in ISIS Draw and then imported into the database as an MOL file. The information associated with the MS analytical data is handled by the NIST program. 

Neural network methods require a fixed length representation of the data to be processed. Vibrational spectra recorded usually fulfill this requirement. With most applications in vibrational spectroscopy, the spectral range and resolution are fixed, and a comparison of spectra from different sources is directly possible. Appropriate scaling of the spectra allows handling different resolutions to obtain the same number of components in a descriptor. Digitized vibrational spectra typically contain absorbance or transmission values in wave-number format. Most of the spectrometers provide the standardized spectral data format JCAMP-DX developed by the Working Party on Spectroscopic Data Standards from the International Union of Pure and Applied Chemistry (lUPAC) [48]. 

Supporting data formats for nontextual sections Additional proprietary or standardized open data formats that are required by the ELN for appropriate visualization of nontext data. Examples are Molhle format for structure display, JCAMP format for spectra and chromatograms, or native binary formats for representing sections in proprietary visual format. In contrast to attachments, these data formats are required by the ELN for the appropriate visualization of contents. 

Agents provide an interface to plug in different types of converters. File converters translate data from instrument vendor-specific or indnstry-standard formats into native or human-readable formats. Common indnstry standardized formats are, for instance, JCAMP (e.g., DX, JDX, CS), ANDI, AIA, NetCDF, MDL Molflle and related formats (e.g., SD, SDF), ASCII formats (ASC, TXT, CSV), and XML-based formats. Most of the commercially available instrument software can import or export one of these formats. Conversion can either be done using an implemented converter in the application server of the target software or by specifying an executable for streaming conversion. 

Structure registration is the process of entering structural information in a centralized repository, usually a structure database. These repositories serve as a pool for providing structure information that has been created in other departments of a company. Structure databases are set up according to the individual needs of a department or company. They consist of a common representation of a structure in a standardized file format, such as MolFile, SDF, reaction (RXN) (MDL), JCAMP (International Union of Pure and Applied Chemistry), or simplified molecular input line entry specification. Any additional data can be stored with the structure depending on the context typical examples are structure properties, reaction conditions, and literature references. 

Different methods are used to store spectra with less memory space than the original files. The experimental data points are mathematically treated by a deresolution procedure in order to replace them by a smaller number of calculated values (e.g. a point calculated each 4 or 2cm reduces a spectrum to less than 1 Ko). Another standard format is the JCAMP-DX (Joint Committee on Atomic and Molecular Physical Data) for exchange spectra in computer readable form. It preserves all of the numerical values of the original spectrum, as well as all of the related information regarding the spectrum in an ASCII file. Most FTIR spectrometers have JCAMP.DX import/export utilities. This format is compatible with all of the comparison algorithms to enable further identification (Figure 10.20). 

TITLE= CAFFEINE JCAMP-DX= 4.24 DATA TYPE= INFFIARED SPECTRUM ORIGIN= EPA1100.SPC converted Galactic SPC file... 

Figure 10.20 Example of a JCAMP-DX file read hy a word processor. This type of file enables the reproduction of the original spectrum by treatment with a suitable software. Experimental points are arranged in sequences of six data points. Only the beginning and the end of the file have been retained.

To transfer data between different bulk storage media, files of fixed exchange formats are created. The most important exchange format in spectroscopy is that elaborated by the JCAMP/DX format, which was elaborated by the Joint Committee on Atomic and Molecular Data with the following objectives ... 

Table 7.2 demonstrates an example of a JCAMP/DX data file for storing the IR spectrum of epichlorohydrin vapor. Here, the minimum information is given. Further items concern information about the compound, for example, the molecular mass or the... 

JCAMP Joint Committee on Atomic and Molecular Data... 

All spectra were converted to the JCAMP format using the Bruker ATS-JCAMP-DX (4.24) conversion program (Version 1.3). Data transfer to a personal computer was initialized by the Bruker-Kermit program. 

JSpecView is a viewer for spectral data in the JCAMP-DX and AnIML/CML format [75], The program was initially developed at the Department of Chemistiy of the University of the West Indies, Mona, Jamaica, West Indies and is available via sourceforge net under the GNU Lesser General Public License. It is an open-source viewer and converter for multiple spectra (Fig. 7.31). 

All H NMR spectra were obtained with three signals suppression, i. e., water, methyl and methylene of ethanol signals in a 5 mm inverse-detection probe head. Eight FIDs were collected as 65536 data points using a 8.5 ps pulse (90°) spectral width, 8013 Hz acquisition time, 4.1 s and relaxation delay, 6.4 s. Spectra were processed using 32768 data points by applying an exponential line broadening of 0.3 Hz for sensitivity enhancement before Fourio transformation and were accurately phased, baseline adjusted and converted into JCAMP format to build the data matrix. 

The formatting of a database involves the creation of several types of files that are manipulated with specialized software. A source file containing raw analytical data is converted to a library file by reducing noise, eliminating unimportant data and compression. Associated exchange files enable data to be transferred in a standard format such as JCAMP/DX for spectrometric data and JCAMP/CS for chemical structures. 

The necessary provision of computers in FT-IR soon led to much more than simple data manipulation. After much unfulfilled promise and wasted effort, data transfer systems became fairly standardized and reliable by the late 1980s. With the universal adoption of the JCAMP format, spectra in digital form became truly portable and could become part of the business of laboratory information management systems (LIMS). More interestingly, they could be directly matched into large digital spectral databases... 

In most investigations dealing with structure-IR spectrum correlations, digitized spectra containing absorbance values in a wavenumber range from 400 to 4000 cm were used. A standard spectral data format that has gained global acceptance is the JCAMP-DX format. In this ASCII format, the wavenumbers, absorbance values, and other information about the measurement process can be stored. 

JGAMP - Joint Committee on Atomic and Molecular Properties. JCAMP is a format for spectroscopic data and associated structure information, including bridging information such as peak assignments. The JCAMP-DX standard concerns spectral data encoding, JCAMP-CS describes structure information. Both information blocks can be combined. ... 

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