Standard Guide for Analytical Data Interchange Protocol for Mass Spectrometric Data

SIGNIFICANCE AND USE
General Coding Guidelines—The NetCDF libraries are supplied to developers as source code. End users receive the libraries in compiled binary form as part of a vendor's application.
Developers setting out to write a program to convert their data files to the Mass Spectrometric Data Protocol should consider using the NetCDF utilities ncgen and ncdump. After developers create the NetCDF file they should use the ncdump program to generate the ASCII representation of the data file, and examine it to ensure the data are being correctly put into the file.
Make Files for NetCDF Libraries and Utilities—In general the compilation is straightforward. The make files were modified after they were received from the Unidata Corporation, because they did not compile the first time on PCs. The changes needed to get the Unidata distribution to run on DOS are (1) rename the file MAKEFILE to UNIX.MK, and (2) rename MSOFT.MK to MAKEFILE, and then run NMAKE. The default switches in the Unidata distribution use the switches for the floating point coprocessor and Microsoft Windows options.
The protocol kit contains some complete makefile examples for Microsoft C V6.0 running on DOS. The Microsoft C V6.0 compiler manual should be consulted for the exact meaning of the compiler and linker options.
The VMS and SunOS compilation instructions are in directories for those operating systems.
NetCDF Library Build Order—The NetCDF libraries must be built in a specific order. The correct order to build the NetCDF directories is:
UTIL XDR SRC NCDUMP NCGEN NCTEST
The UTIL and XDR makefiles work as distributed using NMAKE with Microsoft C V6.0.
SCOPE
1.1 This guide covers the implementation of the Mass Spectrometric Data Protocol in analytical software applications. Implementation of this protocol requires:
1.1.1 Specification E2077, which contains the full set of data definitions. The mass spectrometric data protocol is not based upon any specific implementation; it is designed to be independent of any particular implementation so that implementations can change as technology evolves. The protocol is implemented in categories to speed its acceptance through actual use.
1.1.2 Specification E2077 contains a full description of the contents of the data communications protocol, including the analytical information categories with data elements and their attributes for most aspects of mass spectrometric tests.
1.2 The analytical information categories are a practical convenience for breaking down the standardization process into smaller, more manageable pieces. It is easier for developers to build consensus and produce working systems based on smaller information sets, without the burden and complexity of the hundreds of data elements contained in all the categories. The categories also assist vendors and end users in using the guide in their computing environments.
1.3 The network common data format (NetCDF) data interchange system is the container used to communicate data between applications in a way that is independent of both computer architectures and end-user applications. In essence, it is a special type of application designed for data interchange.
1.4 The common data language (CDL) template for mass spectrometry is a language specification of the mass spectrometry dataset being interchanged. With the use of the NetCDF utilities, this human-readable template can be used to generate an equivalent binary file and the software subroutine calls needed for input and output of data in analytical applications.

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31-Oct-2010
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NOTICE: This standard has either been superseded and replaced by a new version or withdrawn.
Contact ASTM International (www.astm.org) for the latest information
Designation: E2078 − 00(Reapproved 2010)
Standard Guide for
Analytical Data Interchange Protocol for Mass
1
Spectrometric Data
This standard is issued under the fixed designation E2078; the number immediately following the designation indicates the year of
original adoption or, in the case of revision, the year of last revision. A number in parentheses indicates the year of last reapproval. A
superscript epsilon (´) indicates an editorial change since the last revision or reapproval.
1. Scope 2. Referenced Documents
2
2.1 ASTM Standards:
1.1 This guide covers the implementation of the Mass
Spectrometric Data Protocol in analytical software applica- E2077 Specification for Analytical Data Interchange Proto-
col for Mass Spectrometric Data
tions. Implementation of this protocol requires:
1.1.1 Specification E2077, which contains the full set of 2.2 Other Standard:
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data definitions. The mass spectrometric data protocol is not
NetCDF User’s Guide
4
based upon any specific implementation; it is designed to be
2.3 ISO Standards:
independent of any particular implementation so that imple-
8601:1988 Data elements and interchange formats, (First
mentations can change as technology evolves. The protocol is
edition published 1988-06-15; with Technical Corrigen-
implemented in categories to speed its acceptance through
dum 1 published 1991-05-01)
actual use.
3. List of Contents and Use
1.1.2 Specification E2077 contains a full description of the
contents of the data communications protocol, including the
3.1 NetCDF Toolkit—The protocol is an application pro-
analytical information categories with data elements and their
gramming interface (API) layered on top of the public domain
attributes for most aspects of mass spectrometric tests.
NetCDF toolkit. NetCDF is a set of tools that facilitate reading
or writing platform-independent, self-describing data files. All
1.2 The analytical information categories are a practical
data in a NetCDF file is written using the external data
convenience for breaking down the standardization process
representation (XDR). XDR was developed by Sun Microsys-
into smaller, more manageable pieces. It is easier for develop-
tems and is used for platform-independent file systems for all
ers to build consensus and produce working systems based on
workstations and personal computers. Each NetCDF data
smaller information sets, without the burden and complexity of
element is self-describing - it has a name, type, and dimen-
the hundreds of data elements contained in all the categories.
sionality. A NetCDF file contains three parts: a dimensions
The categories also assist vendors and end users in using the
section, which defines the names and size of all dimensions
guide in their computing environments.
used to describe variables; a variables section, which defines
1.3 The network common data format (NetCDF) data inter-
the names, data types, dimensionality, and attributes for all
change system is the container used to communicate data
variables used in the file; and finally, a data section, which
between applications in a way that is independent of both
contains the actual values assigned to the variables. Attributes
computerarchitecturesandend-userapplications.Inessence,it
are numbers or strings which augment the description of
is a special type of application designed for data interchange.
variables or the file as a whole.
1.4 The common data language (CDL) template for mass
3.1.1 For example, a variable “x_axis_ values” might con-
spectrometry is a language specification of the mass spectrom-
tain an array of numbers representing the abscissa of a
etry dataset being interchanged. With the use of the NetCDF
two-dimensional data set. It would have a dimension, possibly
utilities, this human-readable template can be used to generate
named “x_axis_size,” which would specify the number of
an equivalent binary file and the software subroutine calls
abscissa points. The variable might have some descriptive
needed for input and output of data in analytical applications.
2
For referenced ASTM standards, visit the ASTM website, www.astm.org, or
contact ASTM Customer Service at service@astm.org. For Annual Book of ASTM
1
This guide is under the jurisdiction of ASTM Committee E13 on Molecular Standards volume information, refer to the standard’s Document Summary page on
Spectroscopy and Separation Science and is the direct responsibility of Subcom- the ASTM website.
3
mittee E13.15 on Analytical Data. Available for Russell K. Rew, Unidata Program Center, University Corporation
Current edition approved Nov. 1, 2010. Published November 2010. Originally for Atmospheric Research, P.O. Box 3000, Boulder, CO 80307-3000.
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approved in 2000. Last previous edition approved in 2005 as E2078 – 00 (2005). Available from ISO, 1 Rue de Varembe, Case Postale 56, CH 1211, Gen
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