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- From: ilana@kiowa.scd.ucar.edu (Ilana Stern)
- Newsgroups: sci.data.formats,news.answers,sci.answers
- Subject: Scientific Data Format Information FAQ
- Followup-To: sci.data.formats
- Date: 14 Nov 1995 21:17:37 GMT
- Organization: NCAR/UCAR
- Lines: 511
- Approved: news-answers-request@MIT.Edu
- Distribution: world
- Expires: Tue, 28 Nov 1995 07:00:00 GMT
- Message-ID: <48b11h$8c7@ncar.ucar.edu>
- Reply-To: ilana@ncar.ucar.edu
- NNTP-Posting-Host: kiowa.scd.ucar.edu
- Summary: Where to find information on scientific data formats
- Xref: senator-bedfellow.mit.edu sci.data.formats:1324 news.answers:57687 sci.answers:3412
-
- Archive-name: sci-data-formats
- Last-modified: 13 Oct 1995
-
- Recent changes:
-
- ==within last two weeks==
- Format changes to document
- Correction to CDF information
- Corrected URL of JCAMP standard
- New URL for GeoTIFF information
-
- ==within last four weeks==
- Added DLG-3 information
- Added DEM information
- Corrected location of CIF information
-
- This is the FAQ for the sci.data.formats newsgroup. Contents:
-
- 1) How to use this document
- 2) How to get a current copy of this document
- 3) Resources for format information
- 4) Resources for visualization software information
- 5) How to use the data retrieval methods
- 6) 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) 1995 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 ilana@ncar.ucar.edu.
-
- ---------------
-
- Subject: 1) 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:
-
- <URL:ftp://host.name.domain/[directory/[filename]]> ftp site
- <URL:http://host.name.domain/[directory/[filename]]> www server
- <URL:telnet://host.name.domain> telnet site
- <URL:gopher://host.name.domain/[directory/[filename]]> gopher server
- <URL:wais://host.name.domain> wais server
- <URL: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: 2) How to get a current copy of this document
-
- If you are reading this document after 11 Oct 1995, you are reading an
- outdated copy. A current copy of this document can be obtained by anonymous
- FTP to <URL: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 mail-server@rtfm.mit.edu with
- send /pub/usenet/news.answers/sci-data-formats
- as the only text in the message (leave the subject blank).
-
- A current somewhat hypertext version of this document can be obtained
- from <URL:http://www.smartpages.com/faqs/sci-data-formats/faq.html>.
- Real hypertext versions are available at
- <URL:http://ncardata.ucar.edu/dss/faq/data-formats.html>,
- <URL:http://fits.cv.nrao.edu/traffic/scidataformats/faq.html>,
- and (for European users in particular) at
- <URL: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: 3) 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
- 16) OpenMath
- 17) GeoTIFF
- 18) DLG-3
- 19) DEM
-
- Format: 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.
- All software and related information, including a FAQ and hypertext User's
- Guide with searchable WAIS index, are available from the WWW site:
- <URL:http://nssdc.gsfc.nasa.gov/cdf/cdf_home.html>.
- A user's guide and software are on <URL:ftp://nssdca.gsfc.nasa.gov/cdf.dir/>
- for VMS and <URL:ftp://ncgl.gsfc.nasa.gov/pub/cdf/> for all others.
- A recent paper for CDF is available from
- <URL:ftp://ncgl.gsfc.nasa.gov/pub/cdf/doc/papers/CDF-nssdc.ps.Z>.
- A mailing list, cdf-users@nssdc.gsfc.nasa.gov, exists for discussion of CDF.
- To subscribe, please send email to "Majordomo@nssdc.gsfc.nasa.gov" with the
- command "SUBSCRIBE cdf-users" in the body of your message.
- Questions can be directed to cdfsupport@nssdca.gsfc.nasa.gov.
- 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
- zeus@cs.umd.edu.
-
- Format: 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
- <URL:ftp://nssdc.gsfc.nasa.gov/pub/fits>.
- The site <URL: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 the
- USENET newsgroups sci.data.formats, sci.astro.fits (which is devoted
- to discussion of FITS), and others that are of interest to astronomers can
- be found here. This site is also accessible via ftp at
- <URL:ftp://fits.cv.nrao.edu/fits>.
- The "FITS Support Office" which contains many useful documents and links
- to other information, is at
- <URL:http://www.gsfc.nasa.gov/astro/fits/fits_home.html>.
- A WAIS index that can be searched for FITS information is at
- <URL: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 fits@nssdca.gsfc.nasa.gov.
-
- Format: 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, and software to read general GRIB grids, can be
- found at <URL:ftp://ncardata.ucar.edu/libraries/grib/>. The format
- description can also be found at
- <URL: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
- the WMO and the ECMWF versions of GRIB, is in
- <URL:ftp://ncardata.ucar.edu/datasets/ds111.2/format>. Read code can be
- found in <URL:ftp://ncardata.ucar.edu/datasets/ds111.2/software>.
- If all else fails, contact Ilana Stern at ilana@ncar.ucar.edu.
-
- Format: 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 <URL:ftp://ftp.ncsa.uiuc.edu/HDF>.
- Some general information on HDF, including a FAQ, is available from
- <URL:http://www.ncsa.uiuc.edu/SDG/Software/HDF/HDFIntro.html>.
- The HDF WWW information server, with links to the above plus an in-progress
- HTML reference manual is on <URL:http://hdf.ncsa.uiuc.edu:8001/>.
-
- Format: 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
- <URL:http://www.unidata.ucar.edu/packages/netcdf/>.
- Source code and documentation for the netCDF data access library
- is available from <URL:ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf.tar.Z>.
- A FAQ is available from
- <URL:http://www.unidata.ucar.edu/packages/netcdf/faq.html> or in text from
- <URL:ftp://ftp.unidata.ucar.edu/pub/netcdf/FAQ>.
- Past netCDF support inquiries have been archived and can be searched from
- <URL: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 <URL:http://www.unidata.ucar.edu/packages/netcdf/guide.txn_toc.html>,
- in compressed PostScript at
- <URL: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 <URL:ftp://crusty.er.usgs.gov/pub/netcdf.asce.ps>.
- A visual browser for netCDF format data files is available from
- <URL:ftp://ftp.unidata.ucar.edu/pub/netcdf/contrib/ncview.tar.Z>.
- A mailing list, netcdfgroup@unidata.ucar.edu, exists for discussion of the
- netCDF interface, and for announcements of netCDF news: to subscribe, send
- a message to majordomo@unidata.ucar.edu containing the line:
- "subscribe netcdfgroup". The archives of netcdfgroup are available from
- <URL:ftp://ftp.unidata.ucar.edu/mail-archives/netcdfgroup>, and can be searched
- at <URL:wais://wais.unidata.ucar.edu:210/netcdf-group.src>.
- For more information, contact support@unidata.ucar.edu.
-
- Format: 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
- <URL: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
- <URL:http://www-mipl.jpl.nasa.gov/vic_file_fmt.html>. Contact
- Bob_Deen@iplmail.jpl.nasa.gov for more information.
-
- Format: 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
- <URL:http://stardust.jpl.nasa.gov/stdref/stdref.htm>. For more information,
- contact pds_operator@jplpds.jpl.nasa.gov.
-
- Format: 8) Miscellaneous graphics formats
-
- These formats for storing graphics files -- TIFF, GIF, JPEG, FLI, CGM,
- and so on -- are more properly discussed in the newsgroup comp.graphics.
- A small amount of documentation on these and other graphics formats is on
- <URL:ftp://zamenhof.cs.rice.edu/pub/graphics.formats>; other archive sites
- are <URL:ftp://ftp.ncsa.uiuc.edu/misc/file.formats/graphics.formats>, and
- <URL:ftp://telva.ccu.uniovi.es/pub/graphics/Image>.
- The site <URL: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 <URL: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).
- See section 17 for information on GeoTIFF.
-
- Format: 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 infosafe@safe.com
- or by phone at either (604) 241-4424 or (604) 583-2016. They maintain a
- WWW page for SAIF at <URL:http://www.wimsey.com/~infosafe/saif/saifHome.html>
- which will be continually updated.
- The SAIF specification is also available by FTP at
- <URL:ftp://s2k-ftp.cs.berkeley.edu/pub/sequoia/schema/STANDARDS/SAIF> and
- <URL:ftp://moon.cecer.army.mil/ogis/related/SAIF3.1>.
- There is a SAIF Mailing List: send email to "infosafe@safe.com" with
- the subject "SAIF Request" to be added to the list.
-
- Format: 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 <URL: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 <URL:ftp://sdts.er.usgs.gov/pub/sdts>.
- For more information, contact sdts@usgs.gov.
-
- Format: 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 <URL:http://star-www.rl.ac.uk/> or in a LaTex document at
- <URL:ftp://starlink-ftp.rl.ac.uk/pub/doc/star-docs/sun92.tex>.
-
- Format: 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 "medfiles@delphi.com". 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.
-
- Format: 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 <URL:ftp://info.cas.org/pub/cxf>.
- For more information, interested users should contact Thomas Steckert
- (tsteckert@cas.org) or Joseph Mockus (jmockus@cas.org). Questions and
- comments also are welcome.
-
- Format: 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 <URL:http://wwwchem.uwimona.edu.jm:1104/software/jcampdx.html>
- The mass spectrometry standard is available at
- <URL:ftp://ftp.pe-nelson.com/andi-MS/ms_doc.zip> (192.52.153.11)
-
- Format: 15) CIF
-
- CIF (Crystallographic Information File) is becoming standard in the
- crystallography world and related fields:
- <URL:http://www.iucr.ac.uk/cif/home.html>
-
- Format: 16) OpenMath
-
- The OpenMath effort aims at developing a standard exchange format for
- mathematical objects (such as formulae processed by computer algebra systems).
- The OpenMath home page is located at
- <URL:http://www.uni-koeln.de/themen/Computeralgebra/OpenMath/index.html>
-
- Format: 17) GeoTIFF
-
- A new set of TIFF tag extensions for georeferencing raster data within
- TIFF 6.0, GeoTIFF, was announced July 1995. Information is available
- at <URL:http://www-mipl.jpl.nasa.gov/cartlab/geotiff/geotiff.html> and
- specifications and source code are available via ftp at
- <URL:ftp://mtritter.jpl.nasa.gov/pub/geotiff/>. A mailing list for discussion
- of the development of this standard is geotiff@tazboy.jpl.nasa.gov; to
- subscribe send email to geotiff-request@tazboy.jpl.nasa.gov with
- subscribe geotiff your-name-here
- as the body of the message.
-
- Format: 18) DLG-3
-
- The Digital Line Graph (DLG) format is used by USGS to store geographical
- vector data. Documentation on this format is available at
- <URL:ftp://spectrum.xerox.com/depts/markc/demtools/demwork/dlg/doc/dlgguide.txt.Z>.
-
- Format: 19) DEM
-
- A Digital Elevation Model (DEM) consists of a sampled array of elevations
- for ground positions that are normally at regularly spaced intervals.
- <URL:http://edcwww.cr.usgs.gov/glis/hyper/guide/1_dgr_dem> has information
- about this format (along with data availability) from the USGS.
-
- ---------------
-
- Subject: 4) 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 <URL:http://www.unidata.ucar.edu/packages/netcdf/utilities.html>.
- A page of links to many scientific visualization and graphics software
- packages is at <URL: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 <URL:http://sslab.colorado.edu:2222/sw_list.html>.
- An article comparing several scientific visualization techniques and
- packages is available at <URL:http://www.sara.nl/Consumer.Report/Report.html>.
-
- ---------------
-
- Subject: 5) 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.
-
- 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:
-
- ftpmail@decwrl.dec.com
- ftpmail@src.doc.ic.ac.uk
- ftpmail@cs.uow.edu.au
- ftpmail@grasp.insa-lyon.fr
- ftpmail@ftp.uni-stuttgart.de
-
- Send an e-mail message to the closest address, with the lines:
-
- reply your_address@some.where <- 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!
-
- 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.
-
- Gopher information
-
- Available by ftp at ftp://rtfm.mit.edu/pub/usenet/news.answers/gopher-faq.
-
- Wais information
-
- Available by ftp at
- ftp://rtfm.mit.edu/pub/usenet/news.answers/wais-faq/getting-started.
-
- 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 or
- Netscape.
-
- ---------------
-
- Subject: 6) 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.
-
- --
- /\ Backcountry skiing is for anarchists and coyote angels. Your feet
- \_][ get cold and no one admires your new outfit. [C. L. Rawlins]
- \__Ilana Stern | ilana@ncar.ucar.edu | http://www.ucar.edu/dss/ilana.html
-