JCAMP-DX format

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. 

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 ... 

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. 

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. 

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). 

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). 

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). 

JCAMP-DX, a standard format for the exchange of spectra in computer readable form. 

In contrast to typical expert systems, ARC is written in C-h- and includes a rules base in binary format, which can be created with information from different file formats, such as MDL Molfile, Brookhaven Protein Database, Gasteiger Cleartext, JCAMP (DX, JDX, JCM, and CS), binary files (molecule sets, databases, code... 

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]. 

JCAMP-DX is a standardized file format for the representation of spectra, chromatograms, and International Union of Pure and Applied Chemistry (lUPAC). 

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). 

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). 

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. 

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. ... 

AIA = Analytical Instruments Association AFFN = ASCII free format numeric API = application programming interface ASDF = ASCII squeezed difference form ASMS = American Society of Mass Spectrometry ASTM = American Society for Testing and Materials CCDB = Committee on Chemical Databases CDF = common data form CPEP = Committee on Printed and Electronic Publications CS = chemical structure EPA = United States Environmental Protection Agency lUPAC = International Union of Pure and Applied Chemistry JCAMP-DX = Joint Committee on Atomic and Molecular Physical Data - Data Exchange LDR = labeled data record netCDF = network common data form SMD = standardized molecular data UCAR = University Corporation for Atmospheric Research XDR = external data representation. 

It is important to note that although the size of the JCAMP-DX file is substantially reduced by use of the ASDF compressed data format there is absolutely no loss of data resolution. 

A major advance Introduced in the JCAMP-CS protocol was interblock linking. Although the compound data file format had been described in JCAMP-DX version 4.24 there was no mechanism provided to cross-reference between blocks. This problem was solved by the introduction of the LDR BLOCKJD=, which could be used to link a spectrum or peak table block to the chemical structure block for instance. 

The generic version 5.0 JCAMP-DX standard was launched to enable multidimensional data sets to be codeable with interblock linking. The problem of interblock linking had been partially addressed by the authors of the JCAMP-CS protocol, but version 5.0 includes features such as the n-tuple format for n-dimensional spectra. This standard also lays down the guidelines for integrating new protocols for techniques not as yet covered. The version 5.0 draft was used as the base protocol for the NMR and MS standards as at the time it was assumed it would shortly reach publication. 

The major development in the JCAMP-DX file structure in version 5.0 is the use of the n-tuple form. This version is. still in the draft form, and the same restrictions apply to its implementation as are stated for the NMR version 5.01 in Section 2.4.3 above. In a file built to this format the DATACLASS= NTUPLES. There follows an attribute table... 

JCAMP-DX, a standard format for exchange of infrared spectra in computer readable form (Recommendations 1991), Pure Appl. Chem., 1991, 63, 1781-1792. 

This format has been developed to cover the core functionality of the first version of SMD using the syntactical structure of JCAMP-DX (see Standard Exchange Formats for Spectral... 

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

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. 

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