Games of Daze/Infomagic - Games of Daze (Summer 1995) (Disc 1 of 2).iso/x2ftp/msdos/faq/scidata.faq

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From: [e-mail] (Ilana Stern)
Newsgroups: sci.data.formats,news.answers,sci.answers
Subject: Scientific Data Format Information FAQ
Followup-To: sci.data.formats
Date: 12 Apr 1995 11:00:06 GMT
Organization: NCAR/UCAR
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Summary: Where to find information on scientific data formats
Xref: senator-bedfellow.mit.edu sci.data.formats:906 news.answers:41769 sci.answers:2426

Archive-name: sci-data-formats
Last-modified: 6 Apr 1995

Recent changes:

  ==within last two weeks==
Added CIF (Crystallographic Information File)
Added JCAMP format for chemical spectra
Added information about CDF mailing list
Added CXF Chemical eXchange Format
Changed subscription procedure for netCDF mailing list

  ==within last four weeks==


This is the FAQ for the sci.data.formats newsgroup.  Contents:

-2)  How to use this document
-1)  How to get a current copy of this document
 0)  Resources for format information
 1)  Resources for visualization software information
 2)  How to use the data retrieval methods
 3)  Why isn't my favorite format on this list?

Each (major) section has a "Subject:" line, so you can search on the
subject title above to find the section quickly.

This article is copyright (c) 1993 by Ilana Stern.  It may be freely
distributed provided that this copyright notice and the information
on retrieving a current copy are not removed.

Comments, corrections, or additions should be sent to Ilana Stern
at [e-mail].

---------------
Subject:  How to use this document

  Most FAQ (Frequently Asked Questions) documents list many questions and
their answers.  This FAQ is (mostly) devoted to answering only one question:

"Where can I find documentation and software for [X] data format?"

  As the amount of information available over the networks has been
increasing, so have the methods by which this information can be obtained.
No longer is direct usage of FTP the only, or even the most frequent, method
of obtaining data;  we now have Gopher, Wais, and WWW, as well as many
site-specific interfaces.  Because the information itself may be accessible
in many different ways, this FAQ will identify resources in terms of
URLs (Uniform Resource Locators).  This will also help us convert this
FAQ to a hypertext document, so that it can be used with a WWW browser
to go directly to any of the listed sources.
  Here's a glossary, so you can decode the URLs if necessary to reach
the sites:

    ftp://host.name.domain/directory/[filename]    ftp site
    http://host.name.domain/directory/[filename]    www server
    telnet://host.name.domain            telnet site
    gopher://host.name.domain            gopher server
    wais://host.name.domain                wais server
    news:newsgroup.name                newsgroup

  So, for example, if a document is available at ftp://ncardata.ucar.edu/
it means that you should ftp to ncardata.ucar.edu, and the information is
in the top-level directory.
  If you don't know what these information retrieval methods are, see
the section "How to use the data retrieval methods".

---------------
Subject:  How to get a current copy of this document

  If you are reading this document after 26 Apr 1995, you are reading an
outdated copy. A current copy of this document can be obtained by anonymous
FTP to ftp://rtfm.mit.edu/pub/usenet/news.answers/sci-data-formats.
If you don't know what FTP is, see the section "How to use the data retrieval
methods".

If you can't use FTP, send email to [e-mail] with
    send /pub/usenet/news.answers/sci-data-formats
  as the only text in the message (leave the subject blank).

A current hypertext version of this document can be obtained from
http://fits.cv.nrao.edu/traffic/scidataformats/faq.html,
or (for European users in particular) from
http://info.mcc.ac.uk:80/CGU/Visualisation/sdf.html.  If
you would like to archive this FAQ in either hypertext or plaintext
format, and want to receive a new copy automatically at every update,
please send me email.

---------------
Subject:  Resources for format information

1) CDF
2) FITS
3) GRIB
4) HDF
5) netCDF
6) VICAR
7) PDS
8) Miscellaneous graphics formats
9) SAIF
10) SDTS
11) HDS
12) MedFileS
13) CXF
14) JCAMP
15) CIF

1. CDF
  CDF (Common Data Format) is a library and toolkit for storing, manipulating,
and accessing multi-dimensional data sets.  The basic component of CDF is a
software programming interface that is a device independent view of the
CDF data model.
  A user's guide and software are on ftp://nssdca.gsfc.nasa.gov/cdf.dir/ for
VMS and ftp://ncgl.gsfc.nasa.gov/pub/cdf/ for all others.
  Some general information on CDF, including a FAQ, is available from
http://nssdc.gsfc.nasa.gov/cdf/cdf_home.html.
  A recent paper for CDF is available from ftp://ncgl.gsfc.nasa.gov/pub/cdf/
doc/papers/CDF-nssdc.ps.Z.
  A mailing list, [e-mail], exists for discussion of CDF.
To subscribe, please send email to "[e-mail]" with the
command "SUBSCRIBE cdf-users" in the body of your message.
  Questions can be directed to [e-mail].
  A client-server software layer called CSCDF, which can be used with
the CDF library to provide applications access to remote CDF datasets,
can be obtained from its author, Hillel Steinberg, by email at
[e-mail].

2. FITS

  FITS (Flexible Image Transport System) is the standard data interchange
and archival format of the worldwide astronomy community.  The NOST Standard
and User's Guide, some software, and test files are available from
ftp://nssdc.gsfc.nasa.gov/pub/fits.
  The site ftp://fits.cv.nrao.edu/fits (accessible via WWW at
http://fits.cv.nrao.edu/) has other software and a different set of test files,
and electronic copies of FITS proposals that are under development or in the
international approval process.  Archives of news:sci.data.formats and
news:sci.astro.fits (which is devoted to discussion of FITS) that are of
interest to astronomers can be found in ftp://fits.cv.nrao.edu/fits/traffic/.
  A WAIS index that can be searched for FITS information is at
http://info.cern.ch:8001/fits.cv.nrao.edu:210/nrao-fits.
  If you've searched all these resources and still have questions, you
can direct them to [e-mail].

3. GRIB

  GRIB (GRid In Binary) is the World Meteorological Organization (WMO)
standard for gridded meteorological data.  Unfortunately it is still not
very "standard", as some organizations use their own versions.  A format
description for WMO GRIB can be found at
ftp://ncardata.ucar.edu/datasets/ds084.5/format_grib.new,
and read code is in the file access_grib.f in the same directory.
The format description can also be found at
ftp://nic.fb4.noaa.gov/pub/nws/nmc/docs/gribguide/guide.txt.

  If you need GRIB to read ECMWF data, the above format description, along
with the ECMWF-specific parameter table, and a list of differences between
WMO and ECMWF GRIB, is in ftp://ncardata.ucar.edu/datasets/ds111.2/format.
Read code can be found in ftp://ncardata.ucar.edu/datasets/ds111.2/software.
  If all else fails, contact Ilana Stern at [e-mail].

4. HDF

  HDF (Hierarchical Data Format) is a self-defining file format for transfer
of various types of data between different machines. The HDF library contains
interfaces for storing and retrieving compressed or uncompressed raster images
with palettes, and an interface for storing and retrieving n-Dimensional
scientific datasets together with information about the data, such as labels,
units, formats, and scales for all dimensions.
  Source code and documentation are on ftp://ftp.ncsa.uiuc.edu/HDF.
Some general information on HDF, including a FAQ, is available from
http://www.ncsa.uiuc.edu/SDG/Software/HDF/HDFIntro.html.
  The HDF World Wide Web(WWW) information server, with links to the above plus
an in-progress HTML reference manual is on http://hdf.ncsa.uiuc.edu:8001/.

5. netCDF

  NetCDF (Network Common Data Form) is an interface for scientific data
access which implements a machine-independent, self-describing, extendible
file format.  All netCDF information is available via the WWW site
http://www.unidata.ucar.edu/packages/netcdf/.
  Source code and documentation for the netCDF data access library
is available from ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf.tar.Z.
  A FAQ is available from http://www.unidata.ucar.edu/packages/netcdf/faq.html
or in text from ftp://ftp.unidata.ucar.edu/pub/netcdf/FAQ.
  Past netCDF support inquiries have been archived and can be searched from
gopher://groucho.unidata.ucar.edu/7waissrc%3a/systems/netcdf/unidata-support-netcdf.src.
  The netCDF User's Guide is available as a hypertext (HTML) document
from http://www.unidata.ucar.edu/packages/netcdf/guide.txn_toc.html,
in compressed PostScript at ftp://ftp.unidata.ucar.edu/pub/netcdf/guide.ps.Z,
or in source form with the netCDF source distribution.
  A recent paper (Jenter and Signell, 1992) which provides a good introduction
to netCDF is available as ftp://crusty.er.usgs.gov/pub/netcdf.asce.ps.
  A visual browser for netCDF format data files is available from
ftp://ftp.unidata.ucar.edu/pub/netcdf/contrib/ncview.tar.Z.
  A mailing list, [e-mail], exists for discussion of the
netCDF interface, and for announcements of netCDF news:  to subscribe, send
a message to [e-mail] containing the line:
"subscribe netcdfgroup".  The archives of netcdfgroup are available from
ftp://ftp.unidata.ucar.edu/mail-archives/netcdfgroup, and can be searched
at wais://wais.unidata.ucar.edu:210/netcdf-group.src.
  For more information, contact [e-mail].

6. VICAR

  VICAR (Video Image Communication and Retrieval) is a collection of image
processing programs supported by the Multimission Image Processing
Laboratory (MIPL) at the Jet Propulsion Laboratory (JPL), for use
in manipulating and analyzing spacecraft images.  The image format
used by VICAR programs, and for all or most data from JPL-managed
missions, is referred to as VICAR format.  An independent third-party
description of the VICAR image format is available at
ftp://lager.geo.brown.edu/pub/doc/vicar_fmt.txt.
  A much more comprehensive and official description of the VICAR
image format was recently spotted at
http://www-mipl.jpl.nasa.gov/vic_file_fmt.html.  Contact
[e-mail] for more information.

7. PDS

  In recent years, the Planetary Data System (PDS) has been responsible
for archiving space mission data on CD-ROM media, using its own self-
describing data format, variously know as PDS or ODL (Object Description
Language).  At least some of the current projects (e.g. Magellan, Galileo)
are using the PDS format as a "pointer" to detached VICAR-format imagery on
the mission CDROM volumes.
  The PDS Standards Reference Document can be found at
http://stardust.jpl.nasa.gov/stdref/stdref.htm.  For more information,
contact [e-mail].

8. Miscellaneous graphics formats

  These formats for storing graphics files -- TIFF, GIF, JPEG, FLI, CGM,
and so on -- are more properly discussed in news:comp.graphics.  A small
amount of documentation on these and other graphics formats is on
ftp://zamenhof.cs.rice.edu/pub/graphics.formats;  other archive sites
are ftp://ftp.ncsa.uiuc.edu/misc/file.formats/graphics.formats, and
ftp://telva.ccu.uniovi.es/pub/graphics/Image.
  The site http://www.crs4.it/HTML/LUIGI/MPEG/mpegfaq.html has information
on the MPEG format.
  The comp.graphics FAQ and resource file have more information on where
to find read and conversion programs for these formats.  You can find
them at ftp://rtfm.mit.edu/pub/usenet/news.answers.
  A good (hardcopy) reference for graphics formats is  _Graphics
File Formats_, by David C. Kay and John R. Levine (Windcrest Books,
ISBN 0-8306-3060-0, about US$30.00 in paperback).

9. SAIF

  SAIF (Spatial Archive and Interchange Format) is a Canadian standard
for the exchange of geographic data.  It uses an object oriented data
model, and consists of definitions of the underlying building blocks,
including tuples, sets, lists, enumerations, and primitives.
  A company has formed to provide tools and training for the SAIF data
standard.  Safe Software may be contacted by email at [e-mail]
or by phone at either [phone] or [phone].  They maintain
a WWW page for SAIF at http://www.wimsey.com/~infosafe/saif/saifHome.html
which will be continually updated.
  The SAIF specification is also available by FTP at
ftp://s2k-ftp.cs.berkeley.edu/pub/sequoia/schema/STANDARDS/SAIF and
ftp://moon.cecer.army.mil/ogis/related/SAIF3.1.
  There is a SAIF Mailing List:  send email to "[e-mail]" with
the subject "SAIF Request" to be added to the list.

10. SDTS
  SDTS (Spatial Data Transfer Standard) is a Federal standard (Federal
Information Processing Standard (FIPS) 173) for transfer of geologic and
other spatial data.  Documentation and examples are available from the USGS
at ftp://sdts.er.usgs.gov/pub/sdts/www/html/sdts.html (for WWW users;
this is an html interface to the ftp site, which can also be accessed
directly, although not as nicely, at ftp://sdts.er.usgs.gov/pub/sdts.
  For more information, contact [e-mail].

11. HDS

  HDS (Hierarchical Data System) is a freely available database system.
It is particularly suited to the storage of large multi-dimensional arrays
(with their ancillary data) where efficiency of access is a requirement.
It is presently used in astronomy, for storing (in particular) images,
spectra and time series.
  Documentation, and information on obtaining the source code, is
available at http://star-www.rl.ac.uk/ or in a LaTex document at
ftp://starlink-ftp.rl.ac.uk/pub/doc/star-docs/sun92.tex.

12. MedFileS
  The Medical File Standard (MedFileS) is a global project coordinated
via the internet to provide a standard for the recording of clinical medical
information.  Anyone may participate in the project or obtain the current
standard by e-mail to "[e-mail]".  Information is obtained by
sending commands in the subject line of e-mail messages.  The command
"send distrib." will provide a full description of the e-mail distribution
system.  The command "send overview." will provide a document detailing the
MedFileS project.
  NOTE:  an attempt on 19 Dec 1994 to obtain MedFileS failed.

13. CXF

  CXF provides representation of chemical substances and queries,
including atoms, fragments, molecules, and reactions.  Also available are
various substance types, including organics, inorganics, polymers, salts,
hydrates, multi-component mixtures and biosequences.
  The specification is available at ftp://info.cas.org/pub/cxf
  For more information, interested users should contact Thomas Steckert
([e-mail]) or Joseph Mockus ([e-mail]).  Questions and
comments also are welcome.

14. JCAMP

  JCAMP is a draft standard for spectra data (IR & NMR) and chemical stuff
which is related to netCDF.  Some references:
  JCAMP-DX for NMR, A. N. Davies, P. Lampen, Applied Spectroscopy,
1993, 47, 1093-1099;
  A proposed European Implementation of the JCAMP-DX Format, D. N. Rutledge,
P. Mcintyre, Chemometrics and Intelligent Laboratory Systems, 1992, 16, 95-101
  JCAMP-DX, A standard format for exchange of infrared-spectra in computer
readable form, J. G. Grasselli, Pure and Applied Chemistry  1991, 63, 1781-1792
  JCAMP-CS A standard exchange format for chemical-structure information,
J.Gasteiger, B. M.  P. Hendriks, P. Hoever, C. Jochum, H. Somberg, Applied
spectroscopy, 1991, 45, 4-11
  Also, see the DEC 1994 issue of Applied Spectroscopy.
  A viewer is at http://wwwchem.uwimona.edu.jm:1104/software/jcampdx.html
  The mass spectrometry standard is available at
ftp://ftp.pe-nelson.com/pub/andi-MS/ms_doc.zip (192.52.153.11)

15. CIF

  CIF (Crystallographic Information File) is becoming standard in the
crystallography world and related fields:
http://www.icur.ac.uk/cif/home.html


---------------
Subject: Resources for visualization software information

  Many visualization software packages exist which are intended to be
used with data in one or more of these standard formats.  Here are
pointers to some lists of information about this software.  (Note that
this is somewhat outside the scope of this document, which is really
only intended to discuss data formats, but I think this will be
useful to many.)
  Brief descriptions and pointers to software that can be used with
netCDF is at http://www.unidata.ucar.edu/packages/netcdf/utilities.html.
  A page of links to many scientific visualization and graphics software
packages is at http://www.msi.umn.edu/SciVis/Packages/packages.html.
  A page of links to both graphics software and various scientific data
format descriptions is at http://sslab.colorado.edu:2222/sw_list.html.
  An article comparing several scientific visualization techniques and
packages is available at http://www.sara.nl/Consumer.Report/Report.html.

---------------
Subject:  How to use the data retrieval methods

  This section only describes FTP and telnet in any detail;  for other
methods, FTP sites are given, so you can get information on them yourself.

1) How to use FTP
2) How to use telnet
3) Gopher information
4) Wais information
5) WWW information

1. How to use FTP

FTP (File Transfer Protocol) allows transfer of files between two computers
which are on the Internet.  To access the FTP areas listed here, at your
system prompt type "ftp" followed by the name of the desired system.  For
example, to access ncardata.ucar.edu you'd type

    ftp ncardata.ucar.edu

Use "anonymous" as your login and your email address as the password (if
requested).

[Note: quotes ("like this") are used to set off names of directories and
files, or commands you'd type, and are not part of these names.]

Not all FTP systems accept the same commands, but here's a list of the
most useful:

    ls      list files in the current directory.
    cd      change directory, e.g. "cd wx" changes to the wx directory.
    binary  sets binary mode
    ascii   sets ascii mode (the default).  Use for retrieving text.
    get     retrieves a file, e.g. "get readme" gets a file called readme.
    bye     exits FTP.

If you can't seem to connect to the site, check to see if it is a telnet
site.  If it is, follow the instructions in the following section instead.

If you can't FTP from your site, use one of the following ftp-by-mail servers:

    [e-mail]
    [e-mail]
    [e-mail]
    [e-mail]
    [e-mail]

Send an e-mail message to the closest address, with the lines:

    reply [e-mail]     <- with your email address
    connect ncardata.ucar.edu         <- for example
    cd datasets/ds111.2/software
    get access_sun.f
    quit

For complete instructions, send a one-line message reading "help" to the
server.  Please don't ask me for help!

2. How to use telnet

Type "telnet" followed by the name or IP number of the desired system.  These
publicly accessible systems generally allow you to log in but put you in
a restricted shell, from which only a certain menu of commands is available.
The description for the site will include the login to use.

If you can't seem to connect to the site, re-check its description in the
document; if it's an FTP site, follow the instructions in the previous
section instead.

3. Gopher information

Available by ftp at ftp://rtfm.mit.edu/pub/usenet/news.answers/gopher-faq.

4. Wais information

Available by ftp at
ftp://rtfm.mit.edu/pub/usenet/news.answers/wais-faq/getting-started.

5. WWW information

Available by ftp at ftp://rtfm.mit.edu/pub/usenet/news.answers/www/faq.
WWW is so easy to use that you might as well just hop in and try it, so
ask your sysadmin if you have a WWW browser such as NCSA Mosaic.

---------------
Subject:  Why isn't my favorite format on this list?

  If you don't see a format you're interested in here, it could be one
of three reasons.  First of all, there are a lot of formats which are
out of the scope of this newsgroup:  it ain't named *sci*.data.formats
for nuthin', you know.  Formats used in commercial spreadsheet and
word-processing software aren't scientific data formats, and aren't
discussed in this group.

  Second, it may be that nobody has given the FAQ organizer any information
on sources for information on that format.  So ask the newsgroup -- and
if you do get a response, please let me know what it is!

  Finally, you may ask on the net, and hear nothing, because the
data format description just *isn't* publicly available.  For most
scientific data formats, this is a Bad Thing, and most archivists and
scientists *want* to have their format information available.  If
you have such information, but don't have resources to make it
available, please ask around and see if you can get it into an FTP
area or other resource.  Please don't publicize private or proprietary
formats without the permission of the author, though.
--
/\        | The immense vacuum of space is neither canister nor upright, and
  \_][    | has no upholstery attachments. -- Bob Rhubart
      \___http://www.ucar.edu/dss/ilana.html  [e-mail] | Ilana Stern