Just Solve the File Format Problem - User contributions [en]

Category:File formats with extension .whl

2016-04-06T09:53:53Z

DavidFichtmueller: Created page with "W"

[[Category:File formats by extension|W]]

Python

2016-04-06T09:53:04Z

DavidFichtmueller: added whl for python packages

{{FormatInfo
|formattype=Languages
|subcat=Programming Languages
|extensions={{ext|py}}, {{ext|pyc}}, {{ext|pyo}}, {{ext|pyd}}, {{ext|whl}}
|released=1991
}}
'''Python''' is a [[Programming Languages|programming language]].

It is one of the possibilities for the P in LAMP (a set of technologies used in many web back-ends, including Linux, Apache, and MySQL, notable for being free, open-source software in contrast to proprietary technologies such as those from Microsoft) along with [[Perl]] and [[PHP]].

Media reports of [http://www.cbc.ca/news/canada/story/2013/08/06/f-exotic-animals-laws-canada.html python-linked deaths] have nothing to do with the safety of this language, honest! Actually, the name of the language was inspired by [[Wikipedia:Monty Python|Monty Python]], not any actual reptile (or even [http://www.youtube.com/watch?v=R4yBv4sSKTw fictional ones]).

A notable feature of Python is its use of whitespace as a syntactically-significant part of its structure; the level of indenting of code blocks actually determines its place structurally, in contrast to most other languages which use explicit items such as curly braces or keywords such as [[Pascal]]'s '''begin''' and '''end''' (though in those languages it is still customary to indent code blocks for readability). Other novel features of Python include native support of complex arithmetic (involving both real and imaginary numbers and sums of them).

The easy learnability of the language is enhanced by the fact that it has a command-line interpreter which lets you type commands from a prompt in immediate mode, much like the old-time [[BASIC]] interpreters on which so many people first learned to program back in the days of the Apple II and Commodore 64. However, any program of significant length is likely to be created in a text editor and saved in files.

Python is often affiliated with [[reStructuredText]] documents. Python comments are often formatted with reStructuredText markup.

Versions 2 and 3 of Python (with various sub-versions of each) are both in wide use, with version 2 still usually being the default version included in Linux/Unix distributions, but version 3 gaining popularity; there are a number of minor syntax differences between the two.

O'Reilly's technical books are famous for having animals on their covers. Their book, ''Programming Python'', has a snake on the cover, logically enough. However, other Python-related books from this publisher have different animals, and, in particular, the introductory book ''Learning Python'' has a rodent. Pythons ''eat'' rodents, so is this trying to imply that the Python community will eat newbies whole?

== File extensions ==

Python has a number of file endings associated with it, including .py, .pyc, .pyo, and .pyd. When people have desired a MIME type for Python code, they run into the fact that no standard has been established, and even the nonstandard types don't seem to have reached any degree of consistency; people have tried ''text/python'', ''text/python3'', ''application/python'', ''text/x-python'', and others.

;.py
: A text file that contains python source code. It is often [[utf-8]] encoded, but it does not have to be.
;.pyc
: Compiled [[bytecode]] of a python source file
;.pyo
: Optimized compiled [[bytecode]]
;.pyd
: A python version of a Windows [[Dynamic-link library (Windows)|.dll]] file
;.whl
: A python wheel which is a package distribution for using a "[[ZIP|ZIP-formated]] archive with a specially formatted filename" <ref>Wheel, Python Package Index https://pypi.python.org/pypi/wheel</ref>

== See also ==
* [[Pickle]]

== Links ==

=== References ===
<references/>

=== Specifications and file format info ===
* [http://daeken.com/2010-02-20_Python_Marshal_Format.html Python Marshal Format (bytecode)]

=== Programming tips and tutorials ===
* [http://docs.python.org/2/tutorial/index.html Python 2 tutorial]
* [http://docs.python.org/3/tutorial/index.html Python 3 tutorial]
* [http://www.python.org/dev/peps/pep-0008/ PEP 8: Style guide for Python code]
* [http://hubsec.eu/blog/introduction-to-python.html Python for Investigative Journalists: An introduction]
* [http://www.greenteapress.com/thinkpython/thinkpython.html Think Python (free online book)]

=== Program code, libraries, and APIs ===
* [https://pypi.python.org/pypi/internetarchive Python interface to archive.org]
* [https://github.com/LindseyB/starwars-dot-gif Python script to generate GIFs from Star Wars based on input dialogue line]
* [http://www.pkcarlisle.com/blog.html#tth Python script to create 'Tweet this' link that doesn't require JavaScript]
* [http://www.brython.info/ Brython: Python implemented in JavaScript]

=== Online utilities ===
* [http://pypyjs.org/ In-browser Python interpreter]

=== Metaformat files ===

* [https://www.synalysis.net/Grammars/pyc.grammar Synalysis grammar file for Python bytecode] (for Hexinator / Synalize It!; [[Synalysis grammar file|more details]])

=== Commentary ===
* [http://blogs.computerworlduk.com/simon-says/2013/02/responding-to-pythons-batsignal/index.htm Python trademark filer ignorant of Python?]
* [http://www.linuxjournal.com/article/3882 Why Python?]
* [http://www.developerdrive.com/2014/11/should-you-be-using-python-for-web-development/ Should you be using Python for web development?]

=== Other links and references ===
* [http://www.python.org/ Official website]
* [[Wikipedia:Python (programming_language)|Python (Wikipedia)]]
* [http://www.quora.com/Why-does-the-lifetime-of-a-variable-defined-in-a-loop-last-after-the-loop-in-Python/ Why does the lifetime of a variable defined in a loop last after the loop in Python?]
* [http://cacm.acm.org/blogs/blog-cacm/176450-python-is-now-the-most-popular-introductory-teaching-language-at-top-us-universities/fulltext Python is now the most popular introductory teaching language at top U.S. universities]

DBase III

2015-02-20T08:36:58Z

DavidFichtmueller: link formatting

{{FormatInfo
| subcat = Databases
| extensions = {{ext|dbf}}
| pronom = {{PRONOM|x-fmt/9}}
}}

This article describes how to export data out of a dBase III Table File (*.dbf).

== Opening the data with Libre Office ==
It is possible to import *.dbf files into Libre Office (or Open Office) Calc or Base: http://help.libreoffice.org/Calc/Importing_and_Exporting_dBASE_Files .

Libre Office will try to recognize the character encoding of the data and preselect this option in the import window. Once a file imported, it can be saved in/exported to a variety of different formats.

== Importing the data directly into a mySQL database ==
Alternatively the data can directly be imported into a running mySQL database using the linux program <code>[http://manpages.ubuntu.com/manpages/lucid/man1/dbf2mysql.1.html dbf2mysql]</code>. Importing the data directly however could cause some problems with the character encoding for non ASCII characters.

If the mysql server is already running, the following commands will import the data:
user@linux:~$ mysql -u root -p
mysql> create database database_name;
mysql> exit
user@linux:~$ sudo apt-get install dbf2mysql
user@linux:~$ dbf2mysql -vvv -c -f -d database_name -U root -P password DATA_FILE.DBF

The data can then be exported using <code>mysqldump</code>
user@linux:~$ mysqldump -u root -p database_name > data_export.sql

== Specifications ==

* [http://www.dbase.com/Knowledgebase/INT/db7_file_fmt.htm dBase version 7 file header format]

== Metaformat files ==

* [https://www.synalysis.net/Grammars/dbase.grammar Synalysis grammar file] (for Hexinator / Synalize It!; [[Synalysis grammar file|more details]])

== See also ==
* [[dBase programming language]]

== Additional Weblinks ==
* [http://en.wikipedia.org/wiki/DBase Wikipedia article about dBase]
* [http://www.nationalarchives.gov.uk/pronom/x-fmt/9 dBase III entry in PRONOM]
* [http://www.digitalpreservation.gov/formats/fdd/fdd000325.shtml dBase entry at digitalpreservation.gov]
* [http://www.dbf2002.com/dbf-file-format.html DBF File structure]
* [http://www.dbase.com/Knowledgebase/INT/db7_file_fmt.htm dBase File Structure at dBase knowledge base]
* [http://www.clicketyclick.dk/databases/xbase/format/index.html Xbase file format description]
* [http://www.dbase.com/ Current dBase product]
* [http://www.textfiles.com/programming/FORMATS/dbasefil.inf dBase III file structure]
* [http://stackoverflow.com/questions/14008534/opening-and-searching-dbase-iii-dbf-databases-in-python Opening and searching dBase III (DBF) databases in Python]

File identification software

2014-12-01T16:22:46Z

DavidFichtmueller: updated DROID requirements

{|
|[[Software]]
| >
|[[File identification software]]
|}

Software that automates the process of [[Identifying Files]].

* [[Apache Tika]] (cross-platform, open source, [http://tika.apache.org/ website]): "The Apache Tika™ toolkit detects and extracts metadata and structured text content from various documents using existing parser libraries." Written in [[Java]].
* [[DROID]] (cross-platform, open source, [http://digital-preservation.github.com/droid/ website]): ''"DROID is a software tool developed by The National Archives [of the United Kingdom] to perform automated batch identification of file formats."'' Requires [[Java]] 7 or 8 (Version 6.1.5).
* [[FIDO]] (cross-platform, open source) [http://www.openplanetsfoundation.org/software/fido website]: Format Identification for Digital Objects, written in [[Python]].
* [[FIDOO]] (web-based online file identification): [http://www.techmaurice.com/fidoo/ website]
* [[File command]] (various implementations): a standard Unix command, found on almost all Unix and Unix-like (i.e., Linux) systems. See the [http://manpages.debian.net/cgi-bin/man.cgi?query=file&apropos=0&sektion=0&manpath=Debian+6.0+squeeze&format=html&locale=en Debian man page] for an overview.
* [[File Information Tool Set]]: software from the Harvard University library to identify file formats and extract metadata
*[[FI Tools]] (Windows, commercial, [http://www.forensicinnovations.com/fitools.html website])
* [[G-Spot]] (Windows, freeware, [http://www.headbands.com/gspot/ website]): Identifies [[audio]] and [[video]] codecs need to play a media file.
* [[JHOVE]] (tool to classify/identify/validate file formats)
* [[MediaInfo]] (cross-platform, open source, [http://mediainfo.sourceforge.net/en website]): "MediaInfo is a convenient unified display of the most relevant technical and tag data for video and audio files."
* [[Siegfried]] (signature-based file identification tool) [http://www.itforarchivists.com/siegfried website] [http://www.openplanetsfoundation.org/blogs/2014-09-27-siegfried-pronom-based-file-format-identification-tool blog post]
* [[TrID]] (Windows/Linux, free for non-commercial use, [http://mark0.net/soft-trid-e.html website]): identifies files using a database of filetype signatures. Also has an [http://mark0.net/onlinetrid.aspx online version].

== References ==
* http://www.forensicswiki.org/wiki/File_Format_Identification

Databases

2014-01-20T15:27:20Z

DavidFichtmueller: XML databases added as well as two others

{{FormatInfo
|formattype=electronic
|thiscat=Databases
|image=File manager.png
}}

Classes of databases:

== CODASYL databases ==

* [[DBMS32]] (DEC)
* [[DMS1100]] (Univac)
* [[IDS/2]] (Honeywell)
* [[IDMS]] (Cullinet, and later Computer Associates)

== General databases ==

* [[dBase II]]
* [[dBase III]]
* [[FoxPro]]
* [[Mork]]

== Hierarchical databases ==

* [[IMS]]

== ISAM (Indexed Sequential Access Method) ==

* [[Ability Database]] (.adb)
* [[Access]] (was also known as Jet)
* [[Extensible Storage Engine]] (ESE, EDB)
* [[Paradox]]

== NoSQL databases ==

* [[CouchDB]]
* [[MongoDB]]
* [[Clusterpoint]]

== Object-oriented databases ==

* [[Cache]]
* [[db40]]
* [[Gemstone]]
* [[Objectivity]]
* [[ObjectStore]]
* [[Versant]]

== Relational databases ==

* [[Derby]]
* [[HSQLDB]]
* [[IBM DB2]]
* [[Ingres]]
* [[MemSQL]]
* [[MySQL]]
* [[Oracle]]
** [[ARC (database backup format)]]
* [[PostGRESQL]]
* [[DB SQL Anywhere|SQL Anywhere]]
* [[DB (SQLite)|SQLite]]
* [[Virtuoso]]
* [[DB (Watcom-SQL)|Watcom SQL]]

== Triplestores ==

* [[3store]]
* [[Apache Jena]]
* [[Mulgara]]

== XML databases ==
* [[BaseX]]
* [[Documentum xDB]]
* [[eXist-db]]
* [[MarkLogic]]
* [[Oracle XML DB]]
* [[Qizx]]
* [[Sedna]]
* [[Tamino]]
* [[TEXTML]]
* [[TigerLogic XDMS]]
* [[Xpriori XMS]]
* [[XQuantum]]

== Links ==

* [http://blog.okfn.org/2013/04/24/frictionless-data-making-it-radically-easier-to-get-stuff-done-with-data/ Frictionless data]
* [http://oddc.opendataresearch.org/ Open Data Research Network]
* [http://www.chrisstucchio.com/blog/2013/hadoop_hatred.html Don't use Hadoop - your data isn't that big]
* [http://www.itnews.com.au/News/357842,social-networks-stick-with-mysql.aspx Social networks stick with MySQL]
* [http://scholarworks.umass.edu/cpo/vol1/iss1/4/ From Punched Cards to "Big Data": A Social History of Database Populism]
* [http://support.microsoft.com/kb/168702 If you move your mouse continually the query may not fail. Do not stop moving] (that's Microsoft for you)

DOC

2012-12-05T13:48:11Z

DavidFichtmueller: added section: Opening Word for DOS files in a modern Microsoft Word

{{FormatInfo
|subcat=Document
|extensions={{ext|doc}}
|mimetypes=
{{mimetype|application/msword}}
}}

'''MS Word Doc''' format is a family of formats used by older versions of MS Word (they now use [[DOCX]] as a default as of Office 2007).

== File Types ==
[https://en.wikipedia.org/wiki/Microsoft_Word#File_formats Wikipedia says] the following four types exist
* Word for DOS
* Word 1 & Word 2 for MS Windows, and Word 4 & 5 for Mac
* Word 6 & Word 95 for MS Windows, and Word 6 for Mac
* Word 97, 2000, 2002, 2003, 2007 & 2010 for MS Windows, and Word 98, 2001, X, & 2004 for Mac

== What's up, DOC? ==

But just because the file you stumbled onto has a DOC extension doesn't mean it is necessarily actually an MS Word file, though if it's not that old it probably is. Older files, like from the 1980s or 1990s, might be something else entirely. Several other word processors in that era used .DOC file extensions, even though their format was nothing like MS Word's. Also, it was fairly common for people to save plain text files with that extension when they were DOCumenting something, like the instructions for a program that was packed up in an [[ARC]] or [[ZIP]] file for download on a bulletin board system (BBS). But you might still try opening them with Word (as will normally happen in Windows if you have Word installed and double-click on a DOC file), since it will open plain-text files all right (even ancient ones).

== Opening Word for DOS files in a modern Microsoft Word ==
Word for DOS files can't be opened natively with the current versions of Microsoft Word anymore. However it is possible to import such old Word files with an additional converter for Word.
# Download the file ftp://ftp.microsoft.com/Softlib/MSLFILES/WDSUPCNV.EXE, open it (it is a self extracting zip file) and select a directory to save the files.
# Copy all the resulting *.cnv files (but most importantly <code>Doswrd32.cnv</code>) to <code>C:\Program Files (x86)\Common Files\microsoft shared\TextConv</code> (For users with a 32-bit Windows it is just <code>C:\Program Files\Common Files\microsoft shared\TextConv</code>)
# (Re)Start Microsoft Word
# Open the old Word file via the Open-dialog within Word.
# Word will show a prompt informing you that a text converter has to be started and that this might impose a security risk which you should only do if you trust the source where you got the files from. Press OK (if you trust the source of the files).
# Word will most likely show a prompt like "Style Sheet D:/STANDARD.DFV not found". Press Ok. Now a file selector dialog will open asking you to select a style sheet (*.sty) file. If you do have a style sheet for the file then select this. Otherwise create a new empty file in the regular Windows Explorer, rename it "empty.sty" and select it in the file selector. Selecting such an empty file could cause opened file to loose some general properties like print margins etc.
# Now you should be able to see the Word for DOS file within the modern Microsoft Word.

== References ==
* [http://msdn.microsoft.com/en-us/library/cc313153.aspx Microsoft's specification on the .DOC format]

MzML

2012-11-20T17:26:43Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Scientific Data formats
|extensions={{ext|mzml}}
}}

== General description ==

This stub page describes the mzML file format for encoding raw spectrometer output. It is described in the [http://www.psidev.info/mzml mzML specification] at the HUPO Proteomics Standards Initiative site. MzML replaces two previous file formats, [[mzDATA]] developed by PSI and [[mzXML]] developed by the Seattle Proteome Center at the Institute for Systems Biology.

The current version is mzML version 1.1, releaseed in 2009.



== Other information ==







== Software ==

The [http://www.psidev.info/mzml specification page] lists many software packages that produce or can process mzML files.





== Sample files ==



== Identification ==



The file extension is .mzml and the MIME Type is not known.

== References ==
<references/>


[[Category:XML based file formats]]

AAS

2012-11-20T17:17:15Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Interactive Fiction
|extensions={{ext|aas}}
|mimetypes=application/x-authorware-seg
}}

AAS (Advanced Authoring System) is an [[Interactive Fiction]] development system, created as a hoax. The GUI editor and game interpreter both run in Java. The game source is an XML file that is run directly by the interpreter.

== Software ==
* [http://ifarchive.org/indexes/if-archiveXprogrammingXaas.html IF Archive: AAS Programming]

== Sample Files ==
* [http://ifarchive.org/if-archive/games/aas/aasmasters.aas aasmasters.aas]: AAS Masters, by "David Banner" (Stephen Granade)
* [http://ifarchive.org/if-archive/games/aas/darkness.aas darkness.aas]: Cloak of Ultimate Darkness, by "Roddy Ramieson" (Ian Merrick)

== Resources ==
* [http://diden.net/if/aas/ AAS homepage]: an archive of the original hoax site
* [http://www.ifwiki.org/index.php/AAS IFwiki: AAS]

[[Category:XML based file formats]]

KML

2012-11-20T17:16:16Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Geospatial
|extensions={{ext|kml}} {{ext|kmz}}
|pronom={{PRONOM|fmt/244}}
}}

'''[[KML]]''' is derived from Keyhole Markup Language. KML is an [[XML]] notation for geographic annotation and visualization of features for use in two-dimensional maps and three-dimensional Earth browsers used on the Internet. The KML file specifies a set of features (place marks, images, polygons, 3D models, textual descriptions, etc.) for display in applications such as Google Earth and Google Maps or any other geospatial software implementing the KML encoding. Positions are located using longitude and latitude as defined by the World Geodetic System of 1984 (WGS84). KML became an international standard of the Open Geospatial Consortium in 2008.

== References ==
* [http://www.opengeospatial.org/standards/kml/ KML specification from OGC]
* [http://schemas.opengis.net/kml/ KML schemas from OGC]
* [https://developers.google.com/kml/documentation/ KML documentation and examples from Google]
* [http://en.wikipedia.org/wiki/Keyhole_Markup_Language Keyhole Markup Language : Wikipedia]
* [http://www.digitalpreservation.gov/formats/fdd/fdd000340.shtml KML, Version 2.2, from Library of Congress resource on Sustainability of Digital Formats]

[[Category:XML based file formats]]

VOTable

2012-11-20T17:15:51Z

DavidFichtmueller: added category Category:XML based file formats

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
| >
|[[VOTable]]
|}

== General description ==

VOTable is an XML-based table format used for interchange within the International Virtual Observatory Alliance ([http://www.ivoa.net IVOA]) suite of standards.

The current version (as of late 2012) is VOTable 1.2, standardised in an IVOA Recommendation<ref>Francois Ochsenbein and Roy Williams, ''VOTable Format Definition, Version 1.2''. Online: http://www.ivoa.net/Documents/VOTable/</ref>

== Other information ==

The [http://en.wikipedia.org/wiki/International_Virtual_Observatory_Alliance IVOA] acts as a standardisation body for [http://en.wikipedia.org/wiki/Virtual_observatory Virtual Observatory] projects. In a process modelled on the W3C's, it provides a forum for standards documents to be proposed, discussed, and eventually promoted to Recommendations.

The IVOA's [http://wiki.ivoa.net/twiki/bin/view/IVOA/IvoaVOTable VOTable Working Group] maintains an informal list of versions and implementations.

The MIME type <code>application/x-votable+xml</code> is often used for VOTable documents, but has not been registered with the IETF.

File extensions <code>.vot</code> and <code>.xml</code> are reasonably common, but there is no recommendation or fixed convention.

== Software ==

See the IVOA Working Group page mentioned above.

== Sample files ==

No collections known.

== Identification ==

The v1.2 VOTable XML-Schema uses the namespace <code>http://www.ivoa.net/xml/VOTable/v1.2</code>

== References ==

<references/>

[[Category:XML based file formats]]

QCDml

2012-11-20T17:15:05Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Scientific Data formats
}}

'''QCDml''' is an XML Schema defined by the [http://www.usqcd.org/ildg/ International Lattice Data Grid] Metadata Working Group in order to make is easy to share data generated by Lattice QCD simulations.

== References ==
* [http://cdsweb.cern.ch/record/793008/files/0409055.pdf?version=1 QCDml: First milestone for building an International Lattice Data Grid]
* [http://www.lqcd.org/ildg/QCDml/ XML Schemas]
* [http://buphy.bu.edu/~brower/SciDAC/doc/QCDML.pdf QCDML, summary of discussion, proposed solution]
* [http://code.google.com/p/qcdutils/ qcdutils] related software that can handle QCD data formats.

[[Category:XML based file formats]]

Mm

2012-11-20T17:14:38Z

DavidFichtmueller: added category Category:XML based file formats

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Mind maps, Topic maps etc]]
| >
|[[mm]]
|}

This page describes the FreeMind file format, which is reportedly used by several other mind mapping software programs (at least for import and/or export). The file format can be created, read and manipulated using the [http://freemind.sourceforge.net/wiki/index.php/Main_Page FreeMind Open Source software application]. Tools and mechanisms for [http://freemind.sourceforge.net/wiki/index.php/Import_and_export import and export of maps] and [http://freemind.sourceforge.net/wiki/index.php/Accessories conversion to other formats] are listed.

The format is referenced in the Wikipedia [http://en.wikipedia.org/wiki/List_of_mind_mapping_software#File_format page on mind mapping software]. The XML schema for version 0.9.0 beta 2 (the latest "production version as of November 2012) is at [http://freemind.cvs.sourceforge.net/viewvc/freemind/freemind/freemind.xsd?pathrev=fm_0_9_0_beta2&revision=1.1.2.4 http://freemind.cvs.sourceforge.net/viewvc/freemind/freemind/freemind.xsd?pathrev=fm_0_9_0_beta2&revision=1.1.2.4]. The schema for the latest development version as of November 2012 is identical.

Many sample FreeMind maps are available in the [http://freemind.sourceforge.net/wiki/index.php/Mind_Map_Gallery FreeMind Map Gallery]. Some of these are shown in a [http://freemind.sourceforge.net/wiki/index.php/Flash_browser Flash-based browser].

The file extension is .mm and the MIME Type is application/freemind or application/x-freemind.

[[Category:XML based file formats]]

XML

2012-11-20T17:11:06Z

DavidFichtmueller: character fix

{{FormatInfo
|formattype=electronic
|subcat=Document
|extensions={{ext|xml}}
|mimetypes=
{{mimetype|application/xml}}<br>
{{mimetype|text/xml}}
}}
'''Extensible Markup Language''' (XML) is a markup language used to encode data.

XML is a language from which languages are made. A body of rules for how an XML document for specific purpose may be constructed is often called a "language" or a "format" in its own right. These rules may be specified in several different ways, the most common being Document Type Definition (DTD) and Schema. A document which follows the syntactic rules of XML is considered "well-formed." A document which is well-formed and also conforms to its DTD or schema declarations is considered "valid."

A Document Type Definition may be included in an XML document or be referenced by a Document Type Declaration, or both approaches may be combined. An external reference to a DTD is provided by a Document Type Declaration, which confusingly has the same initials.

A Schema, unlike a DTD, is itself written in XML. A document can have a Schema for each of its namespaces. DTDs have been largely superseded by Schemas because of the former's limitation of one DTD per document and the latter's greater capacity for describing rules and namespace support.

XML documents refer to both Schemas and DTDs by a URI. It is crucial to remember that this reference is a Universal Resource Identifier, nor a Universal Resource Locator (URL). There is no requirement that the URI point to a resource on the Internet, or even that such a resource exist. This is a potential preservation risk with XML documents, as they may outlive the DTD and Schema documents that characterize them, or the documents may move and be difficult to locate.

There are variants of [[HTML]] which are expressed in XML-compliant syntax (which, for instance, requires the tags to be consistently lowercase, and elements with no closing tag have a slash before the right angle bracket at the end of the tag, like <BR /> instead of <BR>), and these are known as XHTML. This format may be served under the XML or HTML MIME types, and browsers might treat them differently in these cases.

== Specifications ==

* [http://www.w3.org/TR/xml/ XML 1.0]
** [http://www.w3.org/TR/2008/REC-xml-20081126/ XML 1.0, Fifth Edition (2008-11-26)]
** [http://www.w3.org/TR/2006/REC-xml-20060816/ XML 1.0, Fourth Edition (2006-09-29)]
** [http://www.w3.org/TR/2004/REC-xml-20040204/ XML 1.0, Third Edition (2004-02-04)]
** [http://www.w3.org/TR/2000/REC-xml-20001006 XML 1.0, Second Edition (2000-10-06)]
** [http://www.w3.org/TR/1998/REC-xml-19980210 XML 1.0, First Edition (1998-02-10)]
* [http://www.w3.org/TR/xml11/ XML 1.1]
** [http://www.w3.org/TR/2006/REC-xml11-20060816/ XML 1.1, Second Edition (2006-09-29)]
** [http://www.w3.org/TR/2004/REC-xml11-20040204/ XML 1.1, First Edition (2004-04-15)]

== External links ==

* [http://www.w3.org/XML/ W3C XML Homepage]
* [http://www.w3.org/XML/Core/ W3C XML Core Working Group Public Page]

[[Category:Text-based data]]
[[Category:XML based file formats| ]]

XML

2012-11-20T17:10:11Z

DavidFichtmueller: added category ! as the general overview page of the category

CML

2012-11-20T17:09:27Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Scientific Data formats
|subcat2=Chemical data
|extensions={{ext|cml}}
|mimetypes={{mimetype|chemical/x-cml}}
}}
'''Chemical Markup Language''' ('''CML''') is an XML-based format for encoding detailed information about a wide range of chemical concepts. It has existed in several versions, originally based on a XML DTD and latterly on a XML Schema. Some aspects of v1 are now deprecated. Schemas and other information are now hosted on [http://cml.sourceforge.net/ the CML SourceForge pages].

The [http://en.wikipedia.org/wiki/Chemical_Markup_Language Wikipedia page for CML] describes several Open Source libraries and tools for creating, reading and processing CML.

The CML file extension is .cml and the MIME-type is chemical/x-cml.

[[Category:XML based file formats]]

Scalable Vector Graphics

2012-11-20T17:07:20Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Graphics
|extensions={{ext|svg}}
|mimetypes={{mimetype|image/svg+xml}}
}}

Scalable Vector Graphics (SVG) is an [[XML]] based method for storing [[Graphics|vector images]].

The [http://www.w3.org/TR/SVG/ specification] is open and there is a [http://www.w3.org/Graphics/SVG/ working group].

The following is an example of a simple svg file:

<svg xmlns="http://www.w3.org/2000/svg" version="1.1">
<circle cx="100" cy="50" r="40" stroke="black" stroke-width="2" fill="red" />
</svg>

== References ==
* [http://www.w3.org/TR/SVG/ Official specification]

[[Category:XML based file formats]]

AbiWord

2012-11-20T17:05:54Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Document
|extensions={{ext|abw}}, {{ext|zabw}}, {{ext|abw.gz}}
}}

'''ABW''' is the format used by AbiWord a Free multi-platform word processor.
It is a [[XML]] based format. The .zabw and .abw.gz versions are compressed using [[GZIP]].

* [http://abisource.com/ AbiWord website]
* [http://www.abisource.com/wiki/File_format info about the file format]
* [http://www.abisource.com/wiki/AbiWord page has a sample file]
* [http://www.abisource.com/wiki/FaqAbiWordNativeFormatToText to convert to plain text]

[[Category:XML based file formats]]

EPUB

2012-11-20T17:05:17Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Electronic Publishing formats
|extensions={{ext|epub}}
}}

== Description ==

ePub is an open format defined by the Open eBook Forum of the International Digital Publishing Forum ([[IDPF]]). It is based on [[XHTML]] and [[XML]] along with optional [[CSS]] style sheets. Its predecessor was the [[OEB]] standard.

Quoted from the IDPF web site:

: '.epub' is the file extension of an XML format for reflowable digital books and publications. '.epub' is composed of three open standards, the Open Publication Structure (OPS), Open Packaging Format (OPF) and Open Container Format (OCF), produced by the IDPF. '.epub' allows publishers to produce and send a single digital publication file through distribution and offers consumers interoperability between software/hardware for unencrypted reflowable digital books and other publications. The Open eBook Publication Structure or 'OEB', originally produced in 1999, is the precursor to OPS.

The intent of ePub is to serve both as a source file format and an end user format. For this reason the files are collected into a container for easy dissemination and use. This container is generally a zip file but the extension has been renamed to .epub. It has special requirements by including an uncompressed mime type file while the rest of the data in the file is compressed. An ePub reader should be capable of reading the content in its compressed format. <sup>http://wiki.mobileread.com/wiki/EPUB</sup>

== Version 2 ==

[http://www.idpf.org/specs.htm The IDPF specification page] contains the specifications for this format. In particular check the version 2.01 OPS and OPF specifications and the version 1.01 OCF specifications. The informational documents are also quite useful in understanding the standard's intent and content.

=== References ===

* http://wiki.mobileread.com/wiki/EPUB
* http://www.idpf.org/specs.htm

== Version 3 ==

ePub version 3 is the newest version of the standard and has now been recommended by the idpf standards committee.

In version 2.01 there were three defining documents, the [[OPF]] (Open Packaging Format), the [[OCF]] (Open Container Format), and the [[OPS]] (Open Publications Structure). The OPS referenced a [[DAISY]] standard for the [[NCX]] file. The new 3.0 standard has 4 defining documents with new names. The OPF becomes the [[ePub Publications standard]]. The OCF remains the same and the OPS received the most changes to become the [[ePub Content Documents]]. This now includes the old NCX specifications which are no longer used. A fourth document is concerned with [[Media Overlays]] and is a new feature of ePub version 3. <sup>http://wiki.mobileread.com/wiki/EPub_3</sup>

=== References ===

* http://wiki.mobileread.com/wiki/EPub_3
* http://idpf.org/epub/30/spec/epub30-overview.html

[[Category:XML based file formats]]

HTML

2012-11-20T17:03:46Z

DavidFichtmueller: removed category Category:XML based file formats, it was moved to XHTML

{{FormatInfo
|formattype=electronic
|subcat=Document
|extensions={{ext|html}}, {{ext|htm}}
|mimetypes={{mimetype|text/html}}
}}

'''HTML''' ('''h'''yper'''t'''ext '''m'''arkup '''l'''anguage) originally was a [[SGML]] based markup language. XHTML is HTML redeveloped using the stricter [[XML]] rules. Disagreement over the direction of W3C developments from some of the browser vendors lead to the formation of the Web Hypertext Application Technology Working Group (WHATWG). They maintain the spec for the HTML5 or HTML Next or HTML Living Standard, which is not based on SGML any more. The W3C standardisation group will work to formalise the WHATWG specification as a series of standardised [http://wiki.whatwg.org/wiki/HTML_snapshots 'snapshots'] of the living standard.

== Identifiers ==
* File extension: '''.HTML''', '''.HTM'''
* MIME type (Internet media type): '''text/html'''

== Resources ==
* W3C specifications:
** [http://www.w3.org/MarkUp/HTMLPlus/htmlplus_1.html HTML (1) specification]
** [http://www.w3.org/MarkUp/html-spec/ HTML 2.0 specification] (see also the [http://tools.ietf.org/html/rfc1866 RFC])
** [http://www.w3.org/TR/REC-html32 HTML 3.2 specification]
** [http://www.w3.org/TR/REC-html40/ HTML 4.01 specification]
** [http://www.w3.org/TR/html5/ HTML5 working draft]
** [http://www.w3.org/TR/xhtml1 XHTML 1.0 specification]
** [http://www.w3.org/TR/xhtml11 XHTML 1.1 specification]
* Web Hypertext Application Technology Working Group (WHATWG) specifications:
** [http://wiki.whatwg.org/ The WHATWG Wiki]
** [http://www.whatwg.org/specs/web-apps/current-work/multipage/ HTML Living Standard]
** [http://blog.whatwg.org/html-is-the-new-html5 Blog post describing the background information of the living standard]
** [http://www.whatwg.org/specs/ List of all WHATWG specifications]
** [http://wiki.whatwg.org/wiki/HTML_derivatives List of 'HTML derivatives' and other spin-off specifications]
** [http://wiki.whatwg.org/wiki/HTML_snapshots HTML Snapshots]
* [http://www.w3.org/community/webhistory/ W3C Web History Community Group]

XHTML

2012-11-20T17:03:33Z

DavidFichtmueller: added category Category:XML based file formats

#REDIRECT [[HTML]]

[[Category:XML based file formats]]

XLSX

2012-11-20T17:02:12Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Document
|extensions={{ext|xlsx}}
}}

Office Open XML Spreadsheet (.XLSX) is the default file format for documents used by Microsoft Excel as of Excel 2007. In prior versions, the default version was [[XLS]].

== History ==

This (along with the other Office Open XML items [[DOCX]] and [[PPTX]]) was initially standardized as ECMA-376 in 2006. Three formats of this standard have been produced; the second version also corresponds to ISO/IEC 29500.

== References ==
* [http://www.ecma-international.org/publications/standards/Ecma-376.htm ECMA-376 specification ]
* [http://standards.iso.org/ittf/PubliclyAvailableStandards/index.html ISO/IEC 29500 specification]

[[Category:XML based file formats]]

DOCX

2012-11-20T17:02:00Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Document
|extensions={{ext|docx}}
|mimetypes={{mimetype|application/msword}}
}}
Office Open XML (OOXML) representation (.DOCX) is the default file format for documents created by Microsoft Word as of Word 2007. The format is based on [[XML]] component files in a container based on the [[ZIP]] format.

== History ==

This (along with the other Office Open XML document types [[PPTX]] and [[XLSX]]) was initially standardized as ECMA-376 in 2006. Three versions of ECMA-376 have been produced; the second version corresponds to ISO/IEC 29500:2008, approved as an ISO/IEC standard in April 2008. Changes to the standard between 2008 and 2012 were primarily corrections based on individual defects reported as implementation of the standard proceeded and required to ensure functional interoperability with existing applications. They do not introduce new functionality.

== References ==
* [http://www.ecma-international.org/publications/standards/Ecma-376.htm ECMA-376 specification ]
* [http://standards.iso.org/ittf/PubliclyAvailableStandards/index.html ISO publicly available standards, including the latest ISO/IEC 29500 specification] (as of November 2012, this is ISO/IEC 29500:2012)
* [http://en.wikipedia.org/wiki/Office_Open_XML Office Open XML : Wikipedia]

[[Category:XML based file formats]]

PPTX

2012-11-20T17:01:47Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Document
|extensions={{ext|pptx}}
|mimetypes={{mimetype|application/vnd.openxmlformats-officedocument.presentationml.presentation}}
}}

Office Open XML (OOXML) Powerpoint (.PPTX) is the default file format for documents used by Microsoft Powerpoint as of Powerpoint 2007. The format can be read by the Open Source OpenOffice and LibreOffice suites.

The file extension is .pptx and the approved MIME type is application/vnd.openxmlformats-officedocument.presentationml.presentation.

== History ==

This (along with the other Office Open XML items [[DOCX]] and [[XLSX]]) was initially standardized as ECMA-376 in 2006. Three formats of this standard have been produced; the second version also corresponds to ISO/IEC 29500. OOXML may not completely comply with the latter as of 2012.

== References ==
* [http://www.ecma-international.org/publications/standards/Ecma-376.htm ECMA-376 specification ]
* [http://standards.iso.org/ittf/PubliclyAvailableStandards/index.html ISO/IEC 29500 specification]

[[Category:XML based file formats]]

HTML

2012-11-20T17:00:38Z

DavidFichtmueller: added category XHTML, since XHTML redirects here

CapXML

2012-11-20T16:58:39Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Audio
|extensions={{ext|capx}}
}}

== Description ==

CapXML is used by the Capella notation software to represent musical scores. It is an evolution of the previous binary format, [[CAP]]. There are two versions: CapXML 1.0 and CapXML 2.0.

== Information ==

* [http://www.capella.de/download/mehr/workshops/capxml.pdf Some info on the CapXML format] (PDF, German)
* [http://mfi.math.uni-siegen.de/barcelona.pdf CapXML Design Goals] (PDF)

[[Category:XML based file formats]]

PSI-MI XML

2012-11-20T16:57:01Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Scientific Data formats
|extensions={{ext|obo}}, {{ext|dag}}, {{ext|def}}
}}

== General description ==

This page describes the PSI-MI XML file format, also known as MIF. The PSI MI format is a data exchange format for molecular interactions.

The file format is described at the HUPO Proteomics Standards Initiative site, see the [http://psidev.info/mif specification]. The current version is 2.5.

Released December 5, 2005; last maintenance update June 1, 2006, to version 2.5.3.



== Other information ==







== Software ==





== Sample files ==



== Identification ==

The newer OBO file type appears to be .obo; previously DAG file types of .dag and .def were used. <Uncertain.>




== References ==
<references/>


[[Category:XML based file formats]]

OME-XML

2012-11-20T16:56:31Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Scientific Data formats
|extensions={{ext|ome.xml}}
}}

== General description ==
This page describes the OME-XML file format for Open Microscopy, defined to make it simple to move microscopy data from one site and user to another. This format is related to [[OME-TIFF]], which was developed from it. The format is described on the [http://www.openmicroscopy.org/site/support/file-formats/the-ome-xml-file OME-XML page] at the Open Microscopy site.

== Other information ==
NA

== Software ==
The file format can be created, read and manipulated using the [http://loci.wisc.edu/software/bio-formats Bio-Formats Library] and the [http://www.openmicroscopy.org/site/support/omero4 OMERO Server]. There is an [http://validator.openmicroscopy.org.uk/ OME Validator] to check files, which can lso tell you the OME-XML version. However, almost any software can read the files; you don't need OME software to use OME-XML.

== Sample files ==
NA

== Identification ==
The file extension is .ome.xml and the MIME Type is xxxxx.

== References ==
The original paper describing the concept is Goldberg, I. G., Allan, C., Burel, J.-M., Creager, D., Falconi, A., Hochheiser, H., Johnston, J., et al. (2005). The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome biology, 6(5), R47. doi:10.1186/gb-2005-6-5-r47 .

[[Category:XML based file formats]]

Early Mind Manager XML format

2012-11-20T16:55:10Z

DavidFichtmueller: added category Category:XML based file formats

{{FormatInfo
|formattype=electronic
|subcat=Mind maps, Topic maps etc
|subcat2=Mind Manager formats
|extensions={{ext|xml}}
}}

The Commercial mind mapping software Mind Manager has had at least two different XML-based file formats. From about 2003 Mind Manager seems to have produced XML files with a file extension of .xml. The schema for these files is at [http://schemas.mindjet.com/MindManager/Application/2003/ http://schemas.mindjet.com/MindManager/Application/2003/].

[[Category:XML based file formats]]

Category:XML based file formats

2012-11-20T16:54:36Z

DavidFichtmueller: Created page with "Category:Electronic File Formats"

[[Category:Electronic File Formats]]

Scientific Data formats

2012-11-20T16:48:51Z

DavidFichtmueller: /* Biological */ ABCDDNA and ABCDEFG now linked to the sections in ABCD

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
|}

== General ==
* [[cdf]] (Common Data Format)
* [[EAS3]] (binary file format for structured data)
* [[hdf]] (Hierarchical Data Format, originally from NCSA, now maintained by The HDF Group)
** [[HDF4]]
** [[HDF5]]
* [[NRRD]] (Nearly Raw Raster Data -- a simple format for n-dimensional raster data)
* [[NetCDF]] (Network Common Data Format)
* There are several formats abbreviated as [[SDF]], including:
** [[Simple Data format]] (SDF) By George H. Fisher, Space Sciences Lab, UC Berkeley (A platform-independent, precision-preserving binary data I/O format capable of handling large, multi-dimensional arrays)
** [[Simple Data format-DPT]] A new format from the Data Protocols Team for publishing and sharing data
** [[Standard Delay Format]] A standard data structure for timing data
** [[Structure Data File]] A file format for a chemical table file
* [[SDXF]] (Structured Data Exchange Format)
* [[Silo]] (a storage format for visualization developed at Lawrence Livermore National Laboratory)
* [[XDF]] (eXtensible Data Format)
* [[XSIL]] (Extensible Scientific Interchange Language)

== Astronomical and Space ==
* [[Flexible Image Transport System]] (FITS)
* [[PDS/ODL]] (Planetary Data System)
* [[VOTable]] (IVOA standard table format)
* [[Starlink_Data_Format|SDF]] (Starlink Data Format) and [[N-Dimensional_Data_Format|NDF]] (Starlink's Extensible N-Dimensional Data Format).

== Biological ==

* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
* [[ABCD]] (Access to Biological Collection Data)
* [[ABCD#ABCDDNA|ABCDDNA]] (Access to Biological Collection Data DNA extension)
* [[ABCD#ABCDEFG|ABCDEFG]] (Access to Biological Collection Data Extension For Geosciences)
* [[ACE (Sequence assembly)|ACE]] (Sequence assembly format)
* [[Affymetrix Raw Intensity Format]]
* [[ARLEQUIN Project Format]]
* [[Axt Alignment Format]]
* [[BAM]] (Binary compressed SAM format)
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
* [[BEDgraph]]
* [[Big Browser Extensible Data Format]]
* [[Big Wiggle Format]]
* [[Binary Alignement Map Format]]
* [[Binary Probe Map Format]]
* [[Binary sequence information Format]]
* [[Biological Pathway eXchange]]
* [[BLAT alignment Format]]
* [[BRIX generated O Format]]
* [[CAF]] (Common Assembly Format for sequence assembly)
* [[CellML]]
* [[CHADO XML interchange Format]]
* [[Chain Format for pairwise alignment]]
* [[CHARMM Card File Format]]
* [[CLUSTAL-W Alignment Format]]
* [[CLUSTAL-W Dendrogram Guide File Format]]
* [[Clustered Data Table Format]]
* [[DELTA]] (DEscription Language for TAxonomy)
* [[DAS]] (Distributed Sequence Annotation System)
* [[DBN]] (Dot Bracket Notation (DBN) - Vienna Format)
* [[EMBL]] (Flatfile format used by the EMBL for nucleotide and peptide sequences)
* [[EML (Environmental Markup Language)]] not to be confused with [[EML (Ecological Metadata Language)]]
* [[ENCODE]] (Peak information Format)
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality)
* [[FuGEFlow]]
* [[FuGE-ML]] (Functional Genomics Experiment Markup Language)
* [[Gating-ML]]
* [[GCDML]] (Genomic Contextual Data Markup Language)
* [[GelML]] Gel electrophoresis Markup Language
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
* [[Gene Feature File]] (Versions 1 and 3)
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
* [[Gene Prediction File Format]]
* [[GenePattern GeneSet Table Format]]
* [[Genome Annotation File]] (version 1 and 2)
* [[GTF]] (Gene transfer format holds information about gene structure)
* [[HMMER]]
* [[ICB]] (ICM binary file Format)
* [[imzML]] (imaging mz Markup Language)
* [[ISA-Tab]] (Investigation Study Assay Tabular)
* [[ISND sequence record XML]]
* [[KGML]] (KEGG Mark-up Language)
* [[MAGE-Tab]] (MicroArray Gene Expression Tabular)
* [[MCL]] (Microbiological Common Language)
* [[MIARE-TAB]] (Minimum Information About a RNAi Experiment Tabular)
* [[microarray track data Browser Extensible Data Format]]
* [[MINiML]] (MIAME Notation in Markup Language)
* [[mini Protein Data Bank Format]]
* [[MIQAS-TAB]] (Minimal Information for QTLs and Association Studies Tabular)
* [[MITAB]]
* [[mmCIF]] (macromolecular Crystallographic Information File)
* [[Multiple Alignment Forma]]
* [[mzData]] (deprecated)
* [[mzIdentML]]
* [[mzML]]
* [[mzQuantML]]
* [[mzXML]] (deprecated)
* [[NCD]] (Natural Collections Descriptions)
* [[NDTF]] (Neurophysiology Data Translation Format)
* [[net alignment annotation Format]]
* [[NeuroML]] (Neuroscience eXtensible Markup Language)
* [[New Hampshire eXtended Format]]
* [[Newick tree Format]]
* [[NEXUS]] (Encodes mixed information about genetic sequence data in a block structured format)
* [[Nimblegen Design File Format]]
* [[Nimblegen Gene Data Format]]
* [[NMR-STAR]] (NMR Self-defining Text Archive and Retrieval format)
* [[nucleotide inFormation binary Format]]
* [[ODM]] (Operational Data Model)
* [[Open Biomedical Ontology Flat File Format]]
* [[PDB]] (Structures of biomolecules deposited in Protein Data Bank)
* [[Personal Genome SNP Format]]
* [[PHD]] (Output from the basecalling software Phred)
* [[phyloXML]] (XML for evolutionary biology and comparative genomics)
* [[Pre-Clustering File Format]]
* [[Protein InFormation Resource Format]]
* [[PRM]] (Protocol Representation Model (Medical Research))
* [[PSI-MI XML]]
* [[PSI-PAR]]
* [[RDML]] (Real-time PCR Data Markup Language)
* [[SAM]] (Sequence Alignment/Map format)
* [[SCF]] (Staden chromatogram files used to store data from DNA sequencing)
* [[SBML]] (Systems Biology Markup Language used to store biochemical network computational models)
* [[SDD]] (Structured Descriptive Data)
* [[SED-ML]] (Simulation Experiment Description Markup Language)
* [[Sequence Alignment Map Format]]
* [[SOFT]] (Simple Omnibus Format in Text)
* [[spML]] (Separation Markup Language)
* [[SRA-XML]] (Short Read Archive eXtensible Markup Language)
* [[Standard Flowgram Format]]
* [[Stockholm Multiple Alignment Format]] (Representing multiple sequence alignments)
* [[SBML]] (System Biology Markup Language)
* [[SBGN]] (Systems Biology Graphical Notation)
* [[SBRML]] (Systems Biology Results Markup Language)
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database)
* [[TAIR annotation data Format]]
* [[TAPIR]] (TDWG Access Protocol for Information Retrieval)
* [[TCS]] (Taxonomic Concept transfer Schema)
* [[TraML]] (Transition Markup Language)
* [[UniProtKB XML Format]]
* [[VCF]] (Variant Call Format)
* [[Wiggle Format]]

== Biomedical signals (time series) ==

* [[ACQ]] (AcqKnowledge)
* [[BCI2000]] (The BCI2000 project)
* [[BioSemi]] (BDF) data format
* [[BKR]] (EEG data format)
* [[CFWB]] (Chart Data File Format)
* [[DICOM-Waveform]] (An extension of Dicom for storing waveform data)
* [[ecgML]] (A markup language for electrocardiogram data acquisition and analysis)
* [[EDF/EDF+]] (European Data Format)
* [[FEF]] (File Exchange Format for Vital signs, CEN TS 14271)
* [[GDF v1.x]] (General Data Format for biomedical signals - Version 1.x)
* [[GDF v2.x]] (The General Data Format for biomedical signals - Version 2.x)
* [[HL7aECG]] (Health Level 7 v3 annotated ECG)
* [[OpenXDF]] (Open Exchange Data Format)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SIGIF]] (A digital SIGnal Interchange Format)
* [[WFDB]] (Format of Physiobank)

== Chemical ==
* [[CCP4]] (X-ray crystallography voxels (electron density))
* [[CDX]] (ChemDraw file format)
* [[CDXML]] (ChemDraw file format)
* [[CHM (ChemDraw)|CHM]] (ChemDraw file format)
* [[CIF]] (Crystallographic Information File, standardised by IUCr)
* [[CML]] (Chemical markup language)
* [[CTab]] (Chemical table file .mol, .sd, .sdf)
* [[HITRAN]] (spectroscopic data with one optical/infrared transition per line in the ASCII file (.hit))
* [[JCAMP]] (Joint Committee on Atomic and Molecular Physical Data, .dx, .jdx)
* [[MOL]] (MDL Molfile)
* [[MOP]] (MOPAC format)
* [[MRC]] (voxels in cryo-electron microscopy)
* [[MST]] ACD/ChemSketch v1 file format
* [[PDB]] (Protein Data Bank)
* [[RPT]] ACD/ChemSketch v1 file format
* [[RXN]] (Reaction file format)
* [[SK2]] (ACD/ChemSketch v2 file format)
* [[SKC]] (ISIS/Draw file format)
* [[SMILES]] (Simplified molecular input line entry specification, .smi)
* [[SPC]] (spectroscopic data)
* [[Structure Data File]] (SDF)
* [[TGF]] (ISIS/Draw reaction file format)

Chemical data may be distinguished in various ways, including [http://www.ch.ic.ac.uk/chemime/ Chemical MIME] types.

== Ecological ==
* [[Darwin Core]] (Standard for sharing information about biological diversity)
* [[EML (Ecological Metadata Language)]], not to be confused with [[EML (Environmental Markup Language)]]

== Geographic and Geospatial ==

See also [[Geospatial]]

* [[DEM]] (Digital Elevation Model)
* [[DOQ]] (Digital Orthophotos)
* [[e00]] (ESRI ArcInfo Interchange File)
* [[FGDC]] (Content Standard for Digital Geospatial Metadata??)
* [[GeoTIFF]] (Geospatial extensions to TIFF)
* [[GML]] (Geography Markup Language)
* [[HDFEOS, HD2, HD4]] (Hierarchical Data Format-Earth Observing System)
* [[KML]] (KML (formerly Keyhole Markup Language), Version 2.2)
* [[NDF]] (National Landsat Archive Production System (NLAPS) Data Format)
* [[SAIF]] (Spatial Archive and Interchange Format, Canadian)
* [[SDTS]] (Spatial Data Transfer Standard)
* [[shp and shx]] (ESRI [[Shapefile]] must have components; other optional components as well, see entry)
* [[MrSID]] (MrSID- Multi-resolution Seamless Image Database)
* [[TAB]] (MapInfo dataset format, must have component)

== Mathematical ==
* [[graph6, sparse6]] (ASCII encoding of Adjacency matrices (.g6, .s6))
* [[graphML]] (Graph Markup Language)
* [[m]] (MATLAB script file)
* [[M]] (Mathematica package file)
* [[MAT]] (MATLAB matrix data format)
* [[MathML]]
* [[OPJ]] (Origin data format)
* [[WP2]] WinPlot

== Medical Imaging ==
* [[BRIK/HEAD]] (Voxel data from AFNI programs, dual-file (data and metadata, repectively))
* [[MGH]] (uncompressed)
* [[MGZ]] (zip-compressed)
* [[DICOM]] (Digital Imaging and Communications in Medicine (.dcm))
* [[MINC]] (Medical Imaging NetCDF format; since version 2.0, based on HDF5 (.mnc))
* [[OME-TIFF]] (Open Microscopy Imaging format)
* [[OME-XML]] (Open Microscopy Imaging format)
* [[OST (Open Spatio-Temporal)]] (extensible, open alternative for microscope images)
* [[NII]] (Neuroimaging Informatics Technology Initiative (NIfTI) voxel data, single-file (combined data and metadata))
* [[IMG/HDR]] (ANALYZE or NIfTI voxel data, dual-file (separate data and metadata, respectively))
* [[gii]] (NIfTI offspring for brain surface data, single-file (combined data and meta-data) style)
* [[TRK]] (Vector data describing tracts of neurons, used by TrackVis)
* [[SDM]] (Signed Differential Mapping- brain maps(.sdm))

== Oceanographic, Atmospheric and Meteorological ==

* [[GRIB]] (Grid in Binary)
* [[BUFR]] (Binary Universal Format Representation)
* [[IOAPI]] (netCDF augmented with metadata from the I/O API)
* [[PP]] (UK Met Office format for weather model data)

== Physics ==

* [[CGNS]] (Computational Fluid Dynamics General Notation System)
* [[NeXuS]] (Common data format for neutron, x-ray and muon science)
* [[QCDml]] (Lattice QCD gauge configuration markup language)

== Scientific Signal data ==

* [[ACQ]] (AcqKnowledge File Format for Windows)
* [[BioSemi]] (BDF) data format
* [[BKR]] (EEG data format)
* [[CFWB]] (Chart Data File Format)
* [[EDF]] (European data format)
* [[FEF]] (File Exchange Format for Vital signs)
* [[GDF]] (General data formats for biomedical signals)
* [[GMS]] (Gesture And Motion Signal format)
* [[IROCK]] (intelliRock Sensor Data File Format)
* [[MFER]] (Medical waveform Format Encoding Rules)
* [[REC]] (ATI Vision recorder file)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SEG Y]] (Reflection seismology data format)
* [[SIGIF]] (SIGnal Interchange Format)

== Social Sciences ==

* [[Atlas.ti]] ([[Computer-assisted qualitative data analysis]] package)
* [[DDI]] (Data Documentation Initiative)
* [[DO]] ("DO file" command script for the [[Stata]] Statistical package)
* [[DTA]] (Binary data file for the [[Stata]] Statistical package)
* [[NVivo]] ([[Computer-assisted qualitative data analysis]] package)
* [[R]] (Statistical package)
* [[SAS]] (Statistical package)
* [[SAV]] (Binary "[[SPSS]] data format" for the [[SPSS]] Statistical package)
* [[SPO]] (Output file for the [[SPSS]] Statistical package - version 14)
* [[SPS]] ("Syntax file" (plain text command script) for the [[SPSS]] Statistical package)
* [[SPV]] (Output file for the [[SPSS]] Statistical package - version 17 and later)
* [[Transana]] ([[Computer-assisted qualitative data analysis]] package)

ABCD

2012-11-20T16:46:57Z

DavidFichtmueller: initial version

{{FormatInfo
|formattype=electronic
|subcat=Scientific Data formats
}}

== General description ==

ABCD stands for '''Access to Biological Collection Data''' and is an XML based format. It is a ratified TDWG (Biodiversity Information Standards, formerly Taxonomic Databases Working Group) standard and the current version is 2.06b (though 2.06 is most commonly used).

The ABCD documentation can be found on the TDWG Wiki: http://wiki.tdwg.org/twiki/bin/view/ABCD/WebHome

There are over 1400 different concepts that can be expressed in ABCD of which 1100 can contain data.

== Extensions ==
ABCD allows for extension to the schema for special purposes that are not covered by ABCD. The two most notable extensions are ABCDDNA and ABCDEFG.

=== ABCDDNA ===
ABCDDNA is the ABCD extension for DNA data and is also a ratified TDWG standard. It is maintained by the [http://wiki.bgbm.org/dnabankwiki/index.php/ABCDDNA DNA Bank Network].

=== ABCDEFG ===
ABCDEFG is the ABCD Extension For Geosciences and it is maintained by the [http://www.geocase.eu/efg GeoCASe Project].

== Software ==

The ABCD format is used by biodiversity networks like [http://www.gbif.org/ GBIF] and [http://www.biocase.org BioCASe].

ABCD files can be created using the [http://www.biocase.org/products/provider_software/index.shtml BioCASe Provider Software] (it also works for the DNA and EFG extensions).

== Sample files ==
A sample document can be found in the documentation wiki for the BioCASe Provider Software: http://wiki.bgbm.org/bps/index.php/SampleABCDDocument

== Identification ==

The XML namespace for ABCD 2.06 is <code><nowiki>http://www.tdwg.org/schemas/abcd/2.06</nowiki></code>.

The XML namespace for elements from the DNA extension is <code><nowiki>http://www.dnabank-network.org/schemas/ABCDDNA</nowiki></code>.

The XML namespace for elements from the EFG is <code><nowiki>http://www.synthesys.info/ABCDEFG/1.0</nowiki></code>.

== References ==
<references/>


[[Category:XML based file formats]]

Template:FormatInfo

2012-11-14T19:30:01Z

DavidFichtmueller: /* Potential Parameters */ namespace added as potential parameter

<table class="infobox formatinfo" border="0" style="float: right; border: 1px solid #666666; max-width: 15%; background-color: #F8F8F8; padding: 0.25em; margin: 0.25em 1em;">
<tr>
<th colspan="2">[[File Formats|File Format]]<includeonly>[[Category:File Formats]]</includeonly></th>
</tr>
{{FormatInfo/row|Name|{{{name|{{PAGENAME}}}}}{{DEFAULTSORT:{{{name|{{PAGENAME}}}}}}}}}
{{FormatInfo/row
| Ontology
|
<ul><li>
{{#switch: {{{formattype}}}
|electronic=[[Electronic File Formats]]<includeonly>[[Category:Electronic File Formats]]</includeonly>
|physical=[[Physical File Formats]]<includeonly>[[Category:Physical File Formats]]</includeonly>
|organic=[[Organic File Formats]]<includeonly>[[Category:Organic File Formats]]</includeonly>
|[[{{{formattype|Electronic File Formats}}}]]<includeonly>[[Category:{{{formattype|Electronic File Formats}}}]]</includeonly>
}}
<ul><li>
{{#if:{{{subcat|}}}
|[[{{{subcat}}}]]<includeonly>[[Category:{{{subcat}}}]]</includeonly>
<ul><li>
{{#if:{{{subcat2|}}}
|[[{{{subcat2}}}]]<includeonly>[[Category:{{{subcat2}}}]]</includeonly>
<ul><li>
{{#if:{{{subcat3|}}}
|[[{{{subcat3}}}]]<includeonly>[[Category:{{{subcat3}}}]]</includeonly>
<ul><li>
{{#if:{{{subcat4|}}}
|[[{{{subcat4}}}]]<includeonly>[[Category:{{{subcat4}}}]]</includeonly>
<ul><li>
{{#if:{{{subcat5|}}}
|[[{{{subcat5}}}]]<includeonly>[[Category:{{{subcat5}}}]]</includeonly>
<ul><li>
[[{{{name|{{PAGENAME}}}}}]]
</li></ul>
|[[{{{name|{{PAGENAME}}}}}]]
}}
</li></ul>
|[[{{{name|{{PAGENAME}}}}}]]
}}
</li></ul>
|[[{{{name|{{PAGENAME}}}}}]]
}}
</li></ul>
|[[{{{name|{{PAGENAME}}}}}]]
}}
</li></ul>
|[[{{{name|{{PAGENAME}}}}}]]
}}
</li></ul>
</li></ul>
}}{{#if:{{{extensions|}}}|
{{FormatInfo/row|Extension(s)|{{{extensions}}}}}
}}{{#if:{{{mimetypes|}}}|
{{FormatInfo/row|MIME Type(s)|{{{mimetypes}}}}}
}}{{#if:{{{fourccs|}}}|
{{FormatInfo/row|FourCC|{{{fourccs}}}}}
}}{{#if:{{{pronom|}}}|
{{FormatInfo/row|PRONOM|{{{pronom}}}}}
}}
</table>
<includeonly>{{#if:{{{formattype|}}}||[[Category:FormatInfo without formattype]]}}{{#if:{{{subcat|}}}||[[Category:FormatInfo without subcat]]}}{{#if:{{{extensions|}}}||[[Category:FormatInfo without extensions]]}}{{#if:{{{mimetypes|}}}||[[Category:FormatInfo without mimetypes]]}}</includeonly><noinclude>
== Usage ==
<pre>
{{FormatInfo
| name =
| formattype =
| subcat =
| subcat2 =
| subcat3 =
| subcat4 =
| subcat5 =
| extensions =
| mimetypes =
| pronom =
}}
</pre>

===Parameters===
;name: '''(optional)''' The name of the file format. ''Default: <nowiki>{{PAGENAME}}</nowiki>''
;formattype: '''(optional)''' The [[File Formats|type]] of the file format. Choose 'electronic', 'physical', or 'organic', or specify your own. ''Default: electronic''
;subcat: '''(optional)''' The subcategory of the file format.
;subcat2: '''(optional)''' An additional subcategory of the file format.
;subcat3: '''(optional)''' An additional subcategory of the file format.
;subcat4: '''(optional)''' An additional subcategory of the file format.
;subcat5: '''(optional)''' An additional subcategory of the file format.
;extensions: '''(optional)''' The format's known filename extensions. Use [[Template:ext|<nowiki>{{ext}}</nowiki>]].
;mimetypes: '''(optional)''' The MIME type of the format. Use [[Template:mimetype|<nowiki>{{mimetype}}</nowiki>]].
;pronom: '''(optional)''' The [[Sources/PRONOM|PRONOM]] ID of the format, e.g. "fmt/45". Use [[Template:PRONOM|<nowiki>{{PRONOM}}</nowiki>]].

===Potential Parameters===
This is a list of parameters that could be included in this template.

;mime & mime aliases: Split mimetypes into primary type and known aliases.
;charset: For character encodings, the value of the charset parameter used to identify it in MIME headers
;version: The version of the format, e.g. "1.4" for PDF 1.4
;previous version: Link to page about the previous version of this format.
;next version: Link to page about the next version of this format.
;back compat: Whether this version is backwards compatible with the previous version.
;wikipedia: Name of the Wikipedia page that describes this format, e.g. "JPEG 2000" will be rendered as [[Wikipedia:JPEG 2000|JPEG 2000]]
;locfdd: Identifier for this format from the Library of Congress Sustainability of Digital Formats, e.g. "fdd000314" will be rendered as [http://www.digitalpreservation.gov/formats/fdd/fdd000314.shtml fdd000314].
;type code: The Type Code of the file, used by Mac OS Classic.
;uniform type: The Uniform Type Identifier (UTI), used by Mac OS X and iOS.
;conforms to: The UTI of the parent format in the conformance hierarchy.
;magic: A sequence of byte values that can be used to identify the file contents, usually located close to the start of the file.
;released: The date the format was publicly released.
;container for: A list of formats this format can contain.
;contained by: A list of formats that may contain this format.
;extended from: Any formats this one was based upon.
;extended to: Any formats that have been derived from this one.
;spec: URL of the format specification.
;spec availability: Type of availability the specification, e.g. commercial, free.
;patent license: Unknown, Disputed, Encumbered, (F)RAND, Royalty-Free, Unencumbered.
;compression: Types of compression. Whether Lossy, Lossless, or Both, and whether Optional or Always compressed. i.e. JPEG is Always Lossy.
;endianness: Big-endian or Little-endian byte ordering.
;developed by: Who developed the format.
;maintained by: Who now maintains the format.
;reference impl: Link to page about the reference implementation of this format, if any.
;embeddable metadata: Kinds of metadata that can be embedded in this format.
;tpm: Technical Protection Mechanisms supported by the format, e.g. encryption.
;dependencies: External resources that files in this format may depend upon, e.g. fonts, or even hardware.
;error resiliance: Is this format able to detect damage or recover from damage to the bitstream.
;namespace: The namespace-uri that defines the file format if it is XML-based.

==Examples==

[[Category:File Formats| ]]
</noinclude>

DBase III

2012-11-12T17:04:35Z

DavidFichtmueller: Template for PRONOM-Link

{{FormatInfo
| name = dBase Database File
| subcat = Database
| extensions = *.dbf
| pronom = {{PRONOM|x-fmt/9}}
}}

This article describes how to export data out of a dBase III Table File (*.dbf).

=== Opening the data with Libre Office ===
It is possible to import *.dbf files into Libre Office (or Open Office) Calc or Base: http://help.libreoffice.org/Calc/Importing_and_Exporting_dBASE_Files .

Libre Office will try to recognize the character encoding of the data and preselect this option in the import window. Once a file imported, it can be saved in/exported to a variety of different formats.

=== Importing the data directly into a mySQL database ===
Alternatively the data can directly be imported into a running mySQL database using the linux program <code>[http://manpages.ubuntu.com/manpages/lucid/man1/dbf2mysql.1.html dbf2mysql]</code>. Importing the data directly however could cause some problems with the character encoding for non ASCII characters.

If the mysql server is already running, the following commands will import the data:
user@linux:~$ mysql -u root -p
mysql> create database database_name;
mysql> exit
user@linux:~$ sudo apt-get install dbf2mysql
user@linux:~$ dbf2mysql -vvv -c -f -d database_name -U root -P password DATA_FILE.DBF

The data can then be exported using <code>mysqldump</code>
user@linux:~$ mysqldump -u root -p database_name > data_export.sql

=== Additional Weblinks ===
* [http://en.wikipedia.org/wiki/DBase Wikipedia article about dBase]
* [http://www.nationalarchives.gov.uk/pronom/x-fmt/9 dBase III entry in PRONOM]
* [http://www.digitalpreservation.gov/formats/fdd/fdd000325.shtml dBase entry at digitalpreservation.gov]
* [http://www.dbf2002.com/dbf-file-format.html DBF File structure]
* [http://www.dbase.com/Knowledgebase/INT/db7_file_fmt.htm dBase File Structure at dBase knowledge base]

Scientific Data formats

2012-11-12T16:54:31Z

DavidFichtmueller: there are two different EML formats, I added the other one and clarified the links

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
|}

== General ==
* [[cdf]] (Common Data Format)
* [[EAS3]] (binary file format for structured data)
* [[hdf]] (Hierarchical Data Format, from NASA)
* [[NetCDF]] (Network Common Data Format)
* There are several formats abbreviated as [[SDF]], including:
** [[Simple Data format]] (SDF) By George H. Fisher, Space Sciences Lab, UC Berkeley (A platform-independent, precision-preserving binary data I/O format capable of handling large, multi-dimensional arrays)
** [[Simple Data format-DPT]] A new format from the Data Protocols Team for publishing and sharing data
** [[Standard Delay Format]] A standard data structure for timing data
** [[Structure Data File]] A file format for a chemical table file
* [[SDXF]] (Structured Data Exchange Format)
* [[Silo]] (a storage format for visualization developed at Lawrence Livermore National Laboratory)
* [[XDF]] (eXtensible Data Format)
* [[XSIL]] (Extensible Scientific Interchange Language)

== Astronomical and Space ==
* [[Flexible Image Transport System]] (FITS)
* [[PDS/ODL]] (Planetary Data System)
* [[VOTable]] (IVOA standard table format)
* [[Starlink_Data_Format|SDF]] (Starlink Data Format) and [[N-Dimensional_Data_Format|NDF]] (Starlink's Extensible N-Dimensional Data Format).

== Biological ==

* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
* [[ABCD]] (Access to Biological Collection Data)
* [[ABCDDNA]] (Access to Biological Collection Data DNA extension)
* [[ABCDEFG]] (Access to Biological Collection Data Extension For Geosciences)
* [[ACE]] (Sequence assembly format)
* [[Affymetrix Raw Intensity Format]]
* [[ARLEQUIN Project Format]]
* [[Axt Alignment Format]]
* [[BAM]] (Binary compressed SAM format)
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
* [[BEDgraph]]
* [[Big Browser Extensible Data Format]]
* [[Big Wiggle Format]]
* [[Binary Alignement Map Format]]
* [[Binary Probe Map Format]]
* [[Binary sequence information Format]]
* [[Biological Pathway eXchange]]
* [[BLAT alignment Format]]
* [[BRIX generated O Format]]
* [[CAF]] (Common Assembly Format for sequence assembly)
* [[CellML]]
* [[CHADO XML interchange Format]]
* [[Chain Format for pairwise alignment]]
* [[CHARMM Card File Format]]
* [[CLUSTAL-W Alignment Format]]
* [[CLUSTAL-W Dendrogram Guide File Format]]
* [[Clustered Data Table Format]]
* [[DELTA]] (DEscription Language for TAxonomy)
* [[DAS]] (Distributed Sequence Annotation System)
* [[DBN]] (Dot Bracket Notation (DBN) - Vienna Format)
* [[EMBL]] (Flatfile format used by the EMBL for nucleotide and peptide sequences)
* [[EML (Environmental Markup Language)]] not to be confused with [[EML (Ecological Metadata Language)]]
* [[ENCODE]] (Peak information Format)
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality)
* [[FuGEFlow]]
* [[FuGE-ML]] (Functional Genomics Experiment Markup Language)
* [[Gating-ML]]
* [[GCDML]] (Genomic Contextual Data Markup Language)
* [[GelML]] Gel electrophoresis Markup Language
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
* [[Gene Feature File]] (Versions 1 and 3)
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
* [[Gene Prediction File Format]]
* [[GenePattern GeneSet Table Format]]
* [[Genome Annotation File]] (version 1 and 2)
* [[GTF]] (Gene transfer format holds information about gene structure)
* [[HMMER]]
* [[ICB]] (ICM binary file Format)
* [[imzML]] (imaging mz Markup Language)
* [[ISA-Tab]] (Investigation Study Assay Tabular)
* [[ISND sequence record XML]]
* [[KGML]] (KEGG Mark-up Language)
* [[MAGE-Tab]] (MicroArray Gene Expression Tabular)
* [[MCL]] (Microbiological Common Language)
* [[MIARE-TAB]] (Minimum Information About a RNAi Experiment Tabular)
* [[microarray track data Browser Extensible Data Format]]
* [[MINiML]] (MIAME Notation in Markup Language)
* [[mini Protein Data Bank Format]]
* [[MIQAS-TAB]] (Minimal Information for QTLs and Association Studies Tabular)
* [[MITAB]]
* [[mmCIF]] (macromolecular Crystallographic Information File)
* [[Multiple Alignment Forma]]
* [[mzData]] (deprecated)
* [[mzIdentML]]
* [[mzML]]
* [[mzQuantML]]
* [[mzXML]] (deprecated)
* [[NCD]] (Natural Collections Descriptions)
* [[NDTF]] (Neurophysiology Data Translation Format)
* [[net alignment annotation Format]]
* [[NeuroML]] (Neuroscience eXtensible Markup Language)
* [[New Hampshire eXtended Format]]
* [[Newick tree Format]]
* [[NEXUS]] (Encodes mixed information about genetic sequence data in a block structured format)
* [[Nimblegen Design File Format]]
* [[Nimblegen Gene Data Format]]
* [[NMR-STAR]] (NMR Self-defining Text Archive and Retrieval format)
* [[nucleotide inFormation binary Format]]
* [[ODM]] (Operational Data Model)
* [[Open Biomedical Ontology Flat File Format]]
* [[PDB]] (Structures of biomolecules deposited in Protein Data Bank)
* [[Personal Genome SNP Format]]
* [[PHD]] (Output from the basecalling software Phred)
* [[phyloXML]] (XML for evolutionary biology and comparative genomics)
* [[Pre-Clustering File Format]]
* [[Protein InFormation Resource Format]]
* [[PRM]] (Protocol Representation Model (Medical Research))
* [[PSI-MI XML]]
* [[PSI-PAR]]
* [[RDML]] (Real-time PCR Data Markup Language)
* [[SAM]] (Sequence Alignment/Map format)
* [[SCF]] (Staden chromatogram files used to store data from DNA sequencing)
* [[SBML]] (Systems Biology Markup Language used to store biochemical network computational models)
* [[SDD]] (Structured Descriptive Data)
* [[SED-ML]] (Simulation Experiment Description Markup Language)
* [[Sequence Alignment Map Format]]
* [[SOFT]] (Simple Omnibus Format in Text)
* [[spML]] (Separation Markup Language)
* [[SRA-XML]] (Short Read Archive eXtensible Markup Language)
* [[Standard Flowgram Format]]
* [[Stockholm Multiple Alignment Format]] (Representing multiple sequence alignments)
* [[SBML]] (System Biology Markup Language)
* [[SBGN]] (Systems Biology Graphical Notation)
* [[SBRML]] (Systems Biology Results Markup Language)
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database)
* [[TAIR annotation data Format]]
* [[TAPIR]] (TDWG Access Protocol for Information Retrieval)
* [[TCS]] (Taxonomic Concept transfer Schema)
* [[TraML]] (Transition Markup Language)
* [[UniProtKB XML Format]]
* [[VCF]] (Variant Call Format)
* [[Wiggle Format]]

== Biomedical signals (time series) ==

* [[ACQ]] (AcqKnowledge)
* [[BCI2000]] (The BCI2000 project)
* [[BioSemi]] (BDF) data format
* [[BKR]] (EEG data format)
* [[CFWB]] (Chart Data File Format)
* [[DICOM-Waveform]] (An extension of Dicom for storing waveform data)
* [[ecgML]] (A markup language for electrocardiogram data acquisition and analysis)
* [[EDF/EDF+]] (European Data Format)
* [[FEF]] (File Exchange Format for Vital signs, CEN TS 14271)
* [[GDF v1.x]] (General Data Format for biomedical signals - Version 1.x)
* [[GDF v2.x]] (The General Data Format for biomedical signals - Version 2.x)
* [[HL7aECG]] (Health Level 7 v3 annotated ECG)
* [[OpenXDF]] (Open Exchange Data Format)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SIGIF]] (A digital SIGnal Interchange Format)
* [[WFDB]] (Format of Physiobank)

== Chemical ==
* [[CCP4]] (X-ray crystallography voxels (electron density))
* [[CDX]] (ChemDraw file format)
* [[CDXML]] (ChemDraw file format)
* [[CHM]] (ChemDraw file format)
* [[CIF]] (Crystallographic Information File, standardised by IUCr)
* [[CML]] (Chemical markup language)
* [[CTab]] (Chemical table file .mol, .sd, .sdf)
* [[HITRAN]] (spectroscopic data with one optical/infrared transition per line in the ASCII file (.hit))
* [[JCAMP]] (Joint Committee on Atomic and Molecular Physical Data, .dx, .jdx)
* [[MOL]] (MDL Molfile)
* [[MOP]] (MOPAC format)
* [[MRC]] (voxels in cryo-electron microscopy)
* [[MST]] ACD/ChemSketch v1 file format
* [[PDB]] (Protein Data Bank)
* [[RPT]] ACD/ChemSketch v1 file format
* [[RXN]] (Reaction file format)
* [[SK2]] (ACD/ChemSketch v2 file format)
* [[SKC]] (ISIS/Draw file format)
* [[SMILES]] (Simplified molecular input line entry specification, .smi)
* [[SPC]] (spectroscopic data)
* [[Structure Data File]] (SDF)
* [[TGF]] (ISIS/Draw reaction file format)

Chemical data may be distinguished in various ways, including [http://www.ch.ic.ac.uk/chemime/ Chemical MIME] types.

== Ecological ==
* [[Darwin Core]] (Standard for sharing information about biological diversity)
* [[EML (Ecological Metadata Language)]], not to be confused with [[EML (Environmental Markup Language)]]

== Geographic and Geospatial ==

See also [[Geospatial]]

* [[DEM]] (Digital Elevation Model)
* [[DOQ]] (Digital Orthophotos)
* [[e00]] (ESRI ArcInfo Interchange File)
* [[FGDC]] (Content Standard for Digital Geospatial Metadata??)
* [[GeoTIFF]] (Geospatial extensions to TIFF)
* [[GML]] (Geography Markup Language)
* [[HDFEOS, HD2, HD4]] (Hierarchical Data Format-Earth Observing System)
* [[KML]] (KML (formerly Keyhole Markup Language), Version 2.2)
* [[NDF]] (National Landsat Archive Production System (NLAPS) Data Format)
* [[SAIF]] (Spatial Archive and Interchange Format, Canadian)
* [[SDTS]] (Spatial Data Transfer Standard)
* [[shp and shx]] (ESRI Shaepfile must have components; other optional components as well, see entry)
* [[SID]] (MrSID- Multi-resolution Seamless Image Database)
* [[TAB]] (MapInfo dataset format, must have component)

== Mathematical ==
* [[graph6, sparse6]] (ASCII encoding of Adjacency matrices (.g6, .s6))
* [[graphML]] (Graph Markup Language)
* [[m]] (MATLAB script file)
* [[M]] (Mathematica package file)
* [[MAT]] (MATLAB matrix data format)
* [[MathML]]
* [[WP2]] WinPlot

== Medical Imaging ==
* [[AFNI]] (data, meta-data (.BRIK,.HEAD))
* [[MGH]] (uncompressed)
* [[MGZ]] (zip-compressed)
* [[Analyze data, meta-data]] (.img,.hdr)
* [[DICOM]] (Digital Imaging and Communications in Medicine (.dcm))
* [[MINC]] (Medical Imaging NetCDF format; since version 2.0, based on HDF5 (.mnc))
* [[OME-TIFF]] (Open Microscopy Imaging format)
* [[OME-XML]] (Open Microscopy Imaging format)
* [[OST (Open Spatio-Temporal)]] (extensible, open alternative for microscope images)
* [[nii]] (Neuroimaging Informatics Technology Initiative (NIfTI) single-file (combined data and meta-data))
* [[gii]] (NIfTI offspring for brain surface data, single-file (combined data and meta-data) style)
* [[.img,.hdr]] (NIfTI offspring for brain surface data, dual-file (separate data and meta-data, respectively) style)
* [[SDM]] (Signed Differential Mapping- brain maps(.sdm))

== Oceanographic, Atmospheric and Meteorological ==

* [[GRIB]] (Grid in Binary)
* [[BUFR]] (Binary Universal Format Representation)
* [[IOAPI]] (netCDF augmented with metadata from the I/O API)
* [[PP]] (UK Met Office format for weather model data)

== Physics ==

* [[CGNS]] (Computational Fluid Dynamics General Notation System)
* [[NeXuS]] (Common data format for neutron, x-ray and muon science)
* [[QCDml]] (Lattice QCD gauge configuration markup language)

== Scientific Signal data ==

* [[ACQ]] (AcqKnowledge File Format for Windows)
* [[BioSemi]] (BDF) data format
* [[BKR]] (EEG data format)
* [[CFWB]] (Chart Data File Format)
* [[EDF]] (European data format)
* [[FEF]] (File Exchange Format for Vital signs)
* [[GDF]] (General data formats for biomedical signals)
* [[GMS]] (Gesture And Motion Signal format)
* [[IROCK]] (intelliRock Sensor Data File Format)
* [[MFER]] (Medical waveform Format Encoding Rules)
* [[REC]] (ATI Vision recorder file)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SEG Y]] (Reflection seismology data format)
* [[SIGIF]] (SIGnal Interchange Format)

== Social Sciences ==

* [[Atlas.ti]] (Computer-assisted qualitative data analysis package)
* [[DDI]] (Data Documentation Initiative)
* [[DO]] ("DO file" command script for the [[Stata]] Statistical package)
* [[DTA]] (Binary data file for the [[Stata]] Statistical package)
* [[NVivo]] (Computer-assisted qualitative data analysis package)
* [[R]] (Statistical package)
* [[SAS]] (Statistical package)
* [[SAV]] (Binary "[[SPSS]] data format" for the [[SPSS]] Statistical package)
* [[SPO]] (Output file for the [[SPSS]] Statistical package - version 14)
* [[SPS]] ("Syntax file" (plain text command script) for the [[SPSS]] Statistical package)
* [[SPV]] (Output file for the [[SPSS]] Statistical package - version 17 and later)
* [[Transana]] (Computer-assisted qualitative data analysis package)

DBase III

2012-11-12T14:34:02Z

DavidFichtmueller: added subcategory in template ontology

{{FormatInfo
| name = dBase Database File
| subcat = Database
| extensions = *.dbf
| pronom = x-fmt/9
}}

This article describes how to export data out of a dBase III Table File (*.dbf).

=== Opening the data with Libre Office ===
It is possible to import *.dbf files into Libre Office (or Open Office) Calc or Base: http://help.libreoffice.org/Calc/Importing_and_Exporting_dBASE_Files .

Libre Office will try to recognize the character encoding of the data and preselect this option in the import window. Once a file imported, it can be saved in/exported to a variety of different formats.

=== Importing the data directly into a mySQL database ===
Alternatively the data can directly be imported into a running mySQL database using the linux program <code>[http://manpages.ubuntu.com/manpages/lucid/man1/dbf2mysql.1.html dbf2mysql]</code>. Importing the data directly however could cause some problems with the character encoding for non ASCII characters.

If the mysql server is already running, the following commands will import the data:
user@linux:~$ mysql -u root -p
mysql> create database database_name;
mysql> exit
user@linux:~$ sudo apt-get install dbf2mysql
user@linux:~$ dbf2mysql -vvv -c -f -d database_name -U root -P password DATA_FILE.DBF

The data can then be exported using <code>mysqldump</code>
user@linux:~$ mysqldump -u root -p database_name > data_export.sql

=== Additional Weblinks ===
* [http://en.wikipedia.org/wiki/DBase Wikipedia article about dBase]
* [http://www.nationalarchives.gov.uk/pronom/x-fmt/9 dBase III entry in PRONOM]
* [http://www.digitalpreservation.gov/formats/fdd/fdd000325.shtml dBase entry at digitalpreservation.gov]
* [http://www.dbf2002.com/dbf-file-format.html DBF File structure]
* [http://www.dbase.com/Knowledgebase/INT/db7_file_fmt.htm dBase File Structure at dBase knowledge base]

Scientific Data formats

2012-11-12T14:29:04Z

DavidFichtmueller: /* Biological */ correct ordering and ABCDEFG added

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
|}

== General ==
* [[cdf]] (Common Data Format)
* [[EAS3]] (binary file format for structured data)
* [[hdf]] (Hierarchical Data Format, from NASA)
* [[NetCDF]] (Network Common Data Format)
* There are several formats abbreviated as [[SDF]], including:
** [[Simple Data format]] (SDF) By George H. Fisher, Space Sciences Lab, UC Berkeley (A platform-independent, precision-preserving binary data I/O format capable of handling large, multi-dimensional arrays)
** [[Simple Data format-DPT]] A new format from the Data Protocols Team for publishing and sharing data
** [[Standard Delay Format]] A standard data structure for timing data
** [[Structure Data File]] A file format for a chemical table file
* [[SDXF]] (Structured Data Exchange Format)
* [[Silo]] (a storage format for visualization developed at Lawrence Livermore National Laboratory)
* [[XDF]] (eXtensible Data Format)
* [[XSIL]] (Extensible Scientific Interchange Language)

== Astronomical and Space ==
* [[Flexible Image Transport System]] (FITS)
* [[PDS/ODL]] (Planetary Data System)
* [[VOTable]] (IVOA standard table format)
* [[Starlink_Data_Format|SDF]] (Starlink Data Format) and [[N-Dimensional_Data_Format|NDF]] (Starlink's Extensible N-Dimensional Data Format).

== Biological ==

* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
* [[ABCD]] (Access to Biological Collection Data)
* [[ABCDDNA]] (Access to Biological Collection Data DNA extension)
* [[ABCDEFG]] (Access to Biological Collection Data Extension For Geosciences)
* [[ACE]] (Sequence assembly format)
* [[Affymetrix Raw Intensity Format]]
* [[ARLEQUIN Project Format]]
* [[Axt Alignment Format]]
* [[BAM]] (Binary compressed SAM format)
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
* [[BEDgraph]]
* [[Big Browser Extensible Data Format]]
* [[Big Wiggle Format]]
* [[Binary Alignement Map Format]]
* [[Binary Probe Map Format]]
* [[Binary sequence information Format]]
* [[Biological Pathway eXchange]]
* [[BLAT alignment Format]]
* [[BRIX generated O Format]]
* [[CAF]] (Common Assembly Format for sequence assembly)
* [[CellML]]
* [[CHADO XML interchange Format]]
* [[Chain Format for pairwise alignment]]
* [[CHARMM Card File Format]]
* [[CLUSTAL-W Alignment Format]]
* [[CLUSTAL-W Dendrogram Guide File Format]]
* [[Clustered Data Table Format]]
* [[DELTA]] (DEscription Language for TAxonomy)
* [[DAS]] (Distributed Sequence Annotation System)
* [[DBN]] (Dot Bracket Notation (DBN) - Vienna Format)
* [[EMBL]] (Flatfile format used by the EMBL for nucleotide and peptide sequences)
* [[ENCODE]] (Peak information Format)
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality)
* [[FuGEFlow]]
* [[FuGE-ML]] (Functional Genomics Experiment Markup Language)
* [[Gating-ML]]
* [[GCDML]] (Genomic Contextual Data Markup Language)
* [[GelML]] Gel electrophoresis Markup Language
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
* [[Gene Feature File]] (Versions 1 and 3)
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
* [[Gene Prediction File Format]]
* [[GenePattern GeneSet Table Format]]
* [[Genome Annotation File]] (version 1 and 2)
* [[GTF]] (Gene transfer format holds information about gene structure)
* [[HMMER]]
* [[ICB]] (ICM binary file Format)
* [[imzML]] (imaging mz Markup Language)
* [[ISA-Tab]] (Investigation Study Assay Tabular)
* [[ISND sequence record XML]]
* [[KGML]] (KEGG Mark-up Language)
* [[MAGE-Tab]] (MicroArray Gene Expression Tabular)
* [[MCL]] (Microbiological Common Language)
* [[MIARE-TAB]] (Minimum Information About a RNAi Experiment Tabular)
* [[microarray track data Browser Extensible Data Format]]
* [[MINiML]] (MIAME Notation in Markup Language)
* [[mini Protein Data Bank Format]]
* [[MIQAS-TAB]] (Minimal Information for QTLs and Association Studies Tabular)
* [[MITAB]]
* [[mmCIF]] (macromolecular Crystallographic Information File)
* [[Multiple Alignment Forma]]
* [[mzData]] (deprecated)
* [[mzIdentML]]
* [[mzML]]
* [[mzQuantML]]
* [[mzXML]] (deprecated)
* [[NCD]] (Natural Collections Descriptions)
* [[NDTF]] (Neurophysiology Data Translation Format)
* [[net alignment annotation Format]]
* [[NeuroML]] (Neuroscience eXtensible Markup Language)
* [[New Hampshire eXtended Format]]
* [[Newick tree Format]]
* [[NEXUS]] (Encodes mixed information about genetic sequence data in a block structured format)
* [[Nimblegen Design File Format]]
* [[Nimblegen Gene Data Format]]
* [[NMR-STAR]] (NMR Self-defining Text Archive and Retrieval format)
* [[nucleotide inFormation binary Format]]
* [[ODM]] (Operational Data Model)
* [[Open Biomedical Ontology Flat File Format]]
* [[PDB]] (Structures of biomolecules deposited in Protein Data Bank)
* [[Personal Genome SNP Format]]
* [[PHD]] (Output from the basecalling software Phred)
* [[phyloXML]] (XML for evolutionary biology and comparative genomics)
* [[Pre-Clustering File Format]]
* [[Protein InFormation Resource Format]]
* [[PRM]] (Protocol Representation Model (Medical Research))
* [[PSI-MI XML]]
* [[PSI-PAR]]
* [[RDML]] (Real-time PCR Data Markup Language)
* [[SAM]] (Sequence Alignment/Map format)
* [[SCF]] (Staden chromatogram files used to store data from DNA sequencing)
* [[SBML]] (Systems Biology Markup Language used to store biochemical network computational models)
* [[SDD]] (Structured Descriptive Data)
* [[SED-ML]] (Simulation Experiment Description Markup Language)
* [[Sequence Alignment Map Format]]
* [[SOFT]] (Simple Omnibus Format in Text)
* [[spML]] (Separation Markup Language)
* [[SRA-XML]] (Short Read Archive eXtensible Markup Language)
* [[Standard Flowgram Format]]
* [[Stockholm Multiple Alignment Format]] (Representing multiple sequence alignments)
* [[SBML]] (System Biology Markup Language)
* [[SBGN]] (Systems Biology Graphical Notation)
* [[SBRML]] (Systems Biology Results Markup Language)
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database)
* [[TAIR annotation data Format]]
* [[TAPIR]] (TDWG Access Protocol for Information Retrieval)
* [[TCS]] (Taxonomic Concept transfer Schema)
* [[TraML]] (Transition Markup Language)
* [[UniProtKB XML Format]]
* [[VCF]] (Variant Call Format)
* [[Wiggle Format]]

== Biomedical signals (time series) ==

* [[ACQ]] (AcqKnowledge)
* [[BCI2000]] (The BCI2000 project)
* [[BioSemi]] (BDF) data format
* [[BKR]] (EEG data format)
* [[CFWB]] (Chart Data File Format)
* [[DICOM-Waveform]] (An extension of Dicom for storing waveform data)
* [[ecgML]] (A markup language for electrocardiogram data acquisition and analysis)
* [[EDF/EDF+]] (European Data Format)
* [[FEF]] (File Exchange Format for Vital signs, CEN TS 14271)
* [[GDF v1.x]] (General Data Format for biomedical signals - Version 1.x)
* [[ GDF v2.x]] (The General Data Format for biomedical signals - Version 2.x)
* [[ HL7aECG]] (Health Level 7 v3 annotated ECG)
* [[OpenXDF]] (Open Exchange Data Format)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SIGIF]] (A digital SIGnal Interchange Format)
* [[WFDB]] (Format of Physiobank)

== Chemical ==
* [[CCP4]] (X-ray crystallography voxels (electron density))
* [[CDX]] (ChemDraw file format)
* [[CDXML]] (ChemDraw file format)
* [[CHM]] (ChemDraw file format)
* [[CIF]] (Crystallographic Information File, standardised by IUCr)
* [[CML]] (Chemical markup language)
* [[CTab]] (Chemical table file .mol, .sd, .sdf)
* [[HITRAN]] (spectroscopic data with one optical/infrared transition per line in the ASCII file (.hit))
* [[JCAMP]] (Joint Committee on Atomic and Molecular Physical Data, .dx, .jdx)
* [[MOL]] (MDL Molfile)
* [[MOP]] (MOPAC format)
* [[MRC]] (voxels in cryo-electron microscopy)
* [[MST]] ACD/ChemSketch v1 file format
* [[PDB]] (Protein Data Bank)
* [[RPT]] ACD/ChemSketch v1 file format
* [[RXN]] (Reaction file format)
* [[SK2]] (ACD/ChemSketch v2 file format)
* [[SKC]] (ISIS/Draw file format)
* [[SMILES]] (Simplified molecular input line entry specification, .smi)
* [[SPC]] (spectroscopic data)
* [[Structure Data File]] (SDF)
* [[TGF]] (ISIS/Draw reaction file format)

Chemical data may be distinguished in various ways, including [http://www.ch.ic.ac.uk/chemime/ Chemical MIME] types.

== Ecological ==
* [[Darwin Core]] (Standard for sharing information about biological diversity)
* [[EML]] (Ecological Metadata Language)

== Geographic and Geospatial ==

See also [[Geospatial]]

* [[DEM]] (Digital Elevation Model)
* [[DOQ]] (Digital Orthophotos)
* [[e00]] (ESRI ArcInfo Interchange File)
* [[FGDC]] (Content Standard for Digital Geospatial Metadata??)
* [[GeoTIFF]] (Geospatial extensions to TIFF)
* [[GML]] (Geography Markup Language)
* [[HDFEOS, HD2, HD4]] (Hierarchical Data Format-Earth Observing System)
* [[KML]] (KML (formerly Keyhole Markup Language), Version 2.2)
* [[NDF]] (National Landsat Archive Production System (NLAPS) Data Format)
* [[SAIF]] (Spatial Archive and Interchange Format, Canadian)
* [[SDTS]] (Spatial Data Transfer Standard)
* [[shp and shx]] (ESRI Shaepfile must have components; other optional components as well, see entry)
* [[SID]] (MrSID- Multi-resolution Seamless Image Database)
* [[TAB]] (MapInfo dataset format, must have component)

== Mathematical ==
* [[graph6, sparse6]] (ASCII encoding of Adjacency matrices (.g6, .s6))
* [[graphML]] (Graph Markup Language)
* [[m]] (MATLAB script file)
* [[M]] (Mathematica package file)
* [[MAT]] (MATLAB matrix data format)
* [[MathML]]
* [[WP2]] WinPlot

== Medical Imaging ==
* [[AFNI]] (data, meta-data (.BRIK,.HEAD))
* [[MGH]] (uncompressed)
* [[MGZ]] (zip-compressed)
* [[Analyze data, meta-data]] (.img,.hdr)
* [[DICOM]] (Digital Imaging and Communications in Medicine (.dcm))
* [[MINC]] (Medical Imaging NetCDF format; since version 2.0, based on HDF5 (.mnc))
* [[OME-TIFF]] (Open Microscopy Imaging format)
* [[OME-XML]] (Open Microscopy Imaging format)
* [[OST (Open Spatio-Temporal)]] (extensible, open alternative for microscope images)
* [[nii]] (Neuroimaging Informatics Technology Initiative (NIfTI) single-file (combined data and meta-data))
* [[gii]] (NIfTI offspring for brain surface data, single-file (combined data and meta-data) style)
* [[.img,.hdr]] (NIfTI offspring for brain surface data, dual-file (separate data and meta-data, respectively) style)
* [[SDM]] (Signed Differential Mapping- brain maps(.sdm))

== Oceanographic, Atmospheric and Meteorological ==

* [[GRIB]] (Grid in Binary)
* [[BUFR]] (Binary Universal Format Representation)
* [[IOAPI]] (netCDF augmented with metadata from the I/O API)
* [[PP]] (UK Met Office format for weather model data)

== Physics ==

* [[CGNS]] (Computational Fluid Dynamics General Notation System)
* [[NeXuS]] (Common data format for neutron, x-ray and muon science)
* [[QCDml]] (Lattice QCD gauge configuration markup language)

== Scientific Signal data ==

* [[ACQ]] (AcqKnowledge File Format for Windows)
* [[BioSemi]] (BDF) data format
* [[BKR]] (EEG data format)
* [[CFWB]] (Chart Data File Format)
* [[EDF]] (European data format)
* [[FEF]] (File Exchange Format for Vital signs)
* [[GDF]] (General data formats for biomedical signals)
* [[GMS]] (Gesture And Motion Signal format)
* [[IROCK]] (intelliRock Sensor Data File Format)
* [[MFER]] (Medical waveform Format Encoding Rules)
* [[REC]] (ATI Vision recorder file)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SEG Y]] (Reflection seismology data format)
* [[SIGIF]] (SIGnal Interchange Format)

== Social Sciences ==

* [[Atlas.ti]] (Computer-assisted qualitative data analysis package)
* [[DDI]] (Data Documentation Initiative)
* [[DO]] ("DO file" command script for the [[Stata]] Statistical package)
* [[DTA]] (Binary data file for the [[Stata]] Statistical package)
* [[NVivo]] (Computer-assisted qualitative data analysis package)
* [[R]] (Statistical package)
* [[SAS]] (Statistical package)
* [[SAV]] (Binary "[[SPSS]] data format" for the [[SPSS]] Statistical package)
* [[SPO]] (Output file for the [[SPSS]] Statistical package - version 14)
* [[SPS]] ("Syntax file" (plain text command script) for the [[SPSS]] Statistical package)
* [[SPV]] (Output file for the [[SPSS]] Statistical package - version 17 and later)
* [[Transana]] (Computer-assisted qualitative data analysis package)

Character encoding

2012-11-12T14:16:30Z

DavidFichtmueller: /* External links */ Formatting Fix

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Character Encodings]]
|}

* [[Adobe Standard Encoding]]
* [[ARMSCII]]
* [[ASCII]]
* [[ANSEL]]
** [[MARC-8]]
* [[ATASCII]] (used by Atari computers)
* [[Baudot code]]
* [[Braille]]
* [[EBCDIC]]
* [[IBM PC code pages]]
* [[ISO 646]]
** [[ISO 646-CA]] (Canada / French)
** [[ISO 646-CA-2]] (Canada / French)
** [[ISO 646-CH]] (Switzerland)
** [[ISO 646-CN]] (China / Basic Latin)
** [[ISO 646-CU]] (Cuba / Spanish)
** [[ISO 646-DE]] (Germany)
** [[ISO 646-DK]] (Denmark)
** [[ISO 646-FI]] (Finland)
** [[ISO 646-FR]] (France)
** [[ISO 646-GB]] (Great Britain)
** [[ISO 646-HU]] (Hungary)
** [[ISO 646-IRV]] (International Reference Version)
** [[ISO 646-IT]] (Italy)
** [[ISO 646-JP]] (Japan / Romaji)
** [[ISO 646-JP OCR-B]] (Japan / Romaji)
** [[ISO 646-KR]] (Korea / Latin)
** [[ISO 646-MT]] (Malta)
** [[ISO 646-NL]] (Netherlands)
** [[ISO 646-NO]] (Norway)
** [[ISO 646-NO-2]] (Norway)
** [[ISO 646-PT]] (Portugal)
** [[ISO 646-SE]] (Sweden)
** [[ISO 646-SE-2]] (Sweden)
** [[ISO 646-US]] (Same as [[ASCII]])
** [[ISO 646-YU]] (Yugoslavia)
* [[ISO 2022]]
* [[ISO 8859]]
** [[ISO 8859-1]] (Latin-1)
** [[ISO 8859-2]] (Latin-2, Central/East European)
** [[ISO 8859-3]] (Latin-3, Esperanto, Galician, Maltese, and Turkish)
** [[ISO 8859-4]] (Latin-4, Scandinavian and Baltic)
** [[ISO 8859-5]] (Cyrillic)
** [[ISO 8859-6]] (Arabic)
** [[ISO 8859-7]] (Modern Greek)
** [[ISO 8859-8]] (Hebrew)
** [[ISO 8859-9]] (Latin-5, Turkish)
** [[ISO 8859-10]] (Latin-6, Lappish, Nordic, and Inuit)
** [[ISO 8859-11]] (Thai)
** [[ISO 8859-13]] (Latin-7, Baltic Rim)
** [[ISO 8859-14]] (Celtic)
** [[ISO 8859-15]] (Latin-9, Latin-1 with a Euro sign)
** [[ISO 8859-16]] (Romanian)
* [[JIS]]
** [[JIS X 0201]]
** [[JIS X 0208]]
** [[Shift-JIS]]
* [[KOI8]]
** [[KOI8-CS]] (Czechoslovakia)
** [[KOI8-R]] (Russia)
** [[KOI8-U]] (Ukraine)
* [[Macintosh encodings]]
** [[MacCE]]
** [[MacCyrillic]]
** [[MacDingbat]]
** [[MacGreek]]
** [[MacGujarati]]
** [[MacGurmukhi]]
** [[MacIceland]]
** [[MacRoman]]
** [[MacRomania]]
** [[MacSymbol]]
** [[MacThai]]
** [[MacTurkish]]
** [[MacUkraine]]
* [[Morse code]]
* [[MS-DOS encodings]]
** [[MS-DOS Latin US ]]
** [[MS-DOS Greek ]]
** [[MS-DOS Baltic Rim ]]
** [[MS-DOS Latin-1 ]]
** [[MS-DOS Greek 1 ]]
** [[MS-DOS Latin-2 ]]
** [[MS-DOS Cyrillic ]]
** [[MS-DOS Turkish ]]
** [[MS-DOS Portuguese ]]
** [[MS-DOS Icelandic ]]
** [[MS-DOS Hebrew ]]
** [[MS-DOS French Canada ]]
** [[MS-DOS Arabic ]]
** [[MS-DOS Nordic ]]
** [[MS-DOS Cyrillic CIS 1 ]]
** [[MS-DOS Greek 2 ]]
* [[PETSCII]] (or PET ASCII or CBM ASCII; used by Commodore computers)
* [[Unicode]]
** [[UTF-1]]
** [[UTF-7]]
** [[UTF-8]]
** [[UTF-EBCDIC]]
** [[UTF-9]]
** [[UTF-16]] / [[UCS-2]]
** [[UTF-18]]
** [[UTF-32]] / [[UCS-4]]
* [[VISCII]]
* [[Windows encodings]]
** [[Windows 1252]] (ISO 8859-1 plus additional characters)
** [[Windows 1255]] (Hebrew)
** [[Windows 1256]] (Arabic, Farsi, Urdu)
** [[Windows 1257]] (Baltic Rim)
** [[Windows 1258]] (Vietnamese)
== External links ==

* [http://www.transbay.net/~enf/ascii/ascii.pdf The Evolution of Character Codes, 1874–1968]
* [http://www.kreativekorp.com/charset/ Collection of character encodings]
* [http://www.joelonsoftware.com/articles/Unicode.html The Absolute Minimum Every Software Developer Absolutely, Positively Must Know About Unicode and Character Sets (No Excuses!)] by [http://en.wikipedia.org/wiki/Joel_Spolsky Joel Spolsky]
[[Category:Character Encodings]]

Character encoding

2012-11-12T14:15:55Z

DavidFichtmueller: /* External links */ Added the article "The Absolute Minimum Every Software Developer Absolutely, Positively Must Know About Unicode and Character Sets (No Excuses!)" by Joel Spolsky, as a general overview on the topic

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Character Encodings]]
|}

* [[Adobe Standard Encoding]]
* [[ARMSCII]]
* [[ASCII]]
* [[ANSEL]]
** [[MARC-8]]
* [[ATASCII]] (used by Atari computers)
* [[Baudot code]]
* [[Braille]]
* [[EBCDIC]]
* [[IBM PC code pages]]
* [[ISO 646]]
** [[ISO 646-CA]] (Canada / French)
** [[ISO 646-CA-2]] (Canada / French)
** [[ISO 646-CH]] (Switzerland)
** [[ISO 646-CN]] (China / Basic Latin)
** [[ISO 646-CU]] (Cuba / Spanish)
** [[ISO 646-DE]] (Germany)
** [[ISO 646-DK]] (Denmark)
** [[ISO 646-FI]] (Finland)
** [[ISO 646-FR]] (France)
** [[ISO 646-GB]] (Great Britain)
** [[ISO 646-HU]] (Hungary)
** [[ISO 646-IRV]] (International Reference Version)
** [[ISO 646-IT]] (Italy)
** [[ISO 646-JP]] (Japan / Romaji)
** [[ISO 646-JP OCR-B]] (Japan / Romaji)
** [[ISO 646-KR]] (Korea / Latin)
** [[ISO 646-MT]] (Malta)
** [[ISO 646-NL]] (Netherlands)
** [[ISO 646-NO]] (Norway)
** [[ISO 646-NO-2]] (Norway)
** [[ISO 646-PT]] (Portugal)
** [[ISO 646-SE]] (Sweden)
** [[ISO 646-SE-2]] (Sweden)
** [[ISO 646-US]] (Same as [[ASCII]])
** [[ISO 646-YU]] (Yugoslavia)
* [[ISO 2022]]
* [[ISO 8859]]
** [[ISO 8859-1]] (Latin-1)
** [[ISO 8859-2]] (Latin-2, Central/East European)
** [[ISO 8859-3]] (Latin-3, Esperanto, Galician, Maltese, and Turkish)
** [[ISO 8859-4]] (Latin-4, Scandinavian and Baltic)
** [[ISO 8859-5]] (Cyrillic)
** [[ISO 8859-6]] (Arabic)
** [[ISO 8859-7]] (Modern Greek)
** [[ISO 8859-8]] (Hebrew)
** [[ISO 8859-9]] (Latin-5, Turkish)
** [[ISO 8859-10]] (Latin-6, Lappish, Nordic, and Inuit)
** [[ISO 8859-11]] (Thai)
** [[ISO 8859-13]] (Latin-7, Baltic Rim)
** [[ISO 8859-14]] (Celtic)
** [[ISO 8859-15]] (Latin-9, Latin-1 with a Euro sign)
** [[ISO 8859-16]] (Romanian)
* [[JIS]]
** [[JIS X 0201]]
** [[JIS X 0208]]
** [[Shift-JIS]]
* [[KOI8]]
** [[KOI8-CS]] (Czechoslovakia)
** [[KOI8-R]] (Russia)
** [[KOI8-U]] (Ukraine)
* [[Macintosh encodings]]
** [[MacCE]]
** [[MacCyrillic]]
** [[MacDingbat]]
** [[MacGreek]]
** [[MacGujarati]]
** [[MacGurmukhi]]
** [[MacIceland]]
** [[MacRoman]]
** [[MacRomania]]
** [[MacSymbol]]
** [[MacThai]]
** [[MacTurkish]]
** [[MacUkraine]]
* [[Morse code]]
* [[MS-DOS encodings]]
** [[MS-DOS Latin US ]]
** [[MS-DOS Greek ]]
** [[MS-DOS Baltic Rim ]]
** [[MS-DOS Latin-1 ]]
** [[MS-DOS Greek 1 ]]
** [[MS-DOS Latin-2 ]]
** [[MS-DOS Cyrillic ]]
** [[MS-DOS Turkish ]]
** [[MS-DOS Portuguese ]]
** [[MS-DOS Icelandic ]]
** [[MS-DOS Hebrew ]]
** [[MS-DOS French Canada ]]
** [[MS-DOS Arabic ]]
** [[MS-DOS Nordic ]]
** [[MS-DOS Cyrillic CIS 1 ]]
** [[MS-DOS Greek 2 ]]
* [[PETSCII]] (or PET ASCII or CBM ASCII; used by Commodore computers)
* [[Unicode]]
** [[UTF-1]]
** [[UTF-7]]
** [[UTF-8]]
** [[UTF-EBCDIC]]
** [[UTF-9]]
** [[UTF-16]] / [[UCS-2]]
** [[UTF-18]]
** [[UTF-32]] / [[UCS-4]]
* [[VISCII]]
* [[Windows encodings]]
** [[Windows 1252]] (ISO 8859-1 plus additional characters)
** [[Windows 1255]] (Hebrew)
** [[Windows 1256]] (Arabic, Farsi, Urdu)
** [[Windows 1257]] (Baltic Rim)
** [[Windows 1258]] (Vietnamese)
== External links ==

* [http://www.transbay.net/~enf/ascii/ascii.pdf The Evolution of Character Codes, 1874–1968]
* [http://www.kreativekorp.com/charset/ Collection of character encodings]]
* [http://www.joelonsoftware.com/articles/Unicode.html The Absolute Minimum Every Software Developer Absolutely, Positively Must Know About Unicode and Character Sets (No Excuses!)] by [http://en.wikipedia.org/wiki/Joel_Spolsky Joel Spolsky]
[[Category:Character Encodings]]

DBase III

2012-11-09T21:17:22Z

DavidFichtmueller: initial version

{{FormatInfo
| name = dBase Database File
| extensions = *.dbf
| pronom = x-fmt/9
}}

This article describes how to export data out of a dBase III Table File (*.dbf).

=== Opening the data with Libre Office ===
It is possible to import *.dbf files into Libre Office (or Open Office) Calc or Base: http://help.libreoffice.org/Calc/Importing_and_Exporting_dBASE_Files .

Libre Office will try to recognize the character encoding of the data and preselect this option in the import window. Once a file imported, it can be saved in/exported to a variety of different formats.

=== Importing the data directly into a mySQL database ===
Alternatively the data can directly be imported into a running mySQL database using the linux program <code>[http://manpages.ubuntu.com/manpages/lucid/man1/dbf2mysql.1.html dbf2mysql]</code>. Importing the data directly however could cause some problems with the character encoding for non ASCII characters.

If the mysql server is already running, the following commands will import the data:
user@linux:~$ mysql -u root -p
mysql> create database database_name;
mysql> exit
user@linux:~$ sudo apt-get install dbf2mysql
user@linux:~$ dbf2mysql -vvv -c -f -d database_name -U root -P password DATA_FILE.DBF

The data can then be exported using <code>mysqldump</code>
user@linux:~$ mysqldump -u root -p database_name > data_export.sql

=== Additional Weblinks ===
* [http://en.wikipedia.org/wiki/DBase Wikipedia article about dBase]
* [http://www.nationalarchives.gov.uk/pronom/x-fmt/9 dBase III entry in PRONOM]
* [http://www.digitalpreservation.gov/formats/fdd/fdd000325.shtml dBase entry at digitalpreservation.gov]