An important component of scientific work is being able to take your data with you as you move from one position to another, and being able to work with the data files on the computer systems at your new institute. Similarly, it's vital to be able to exchange data files with colleagues or just read your own files in multiple different packages.

Therefore it is important to have standards-based data formats that are openly and well documented so that anyone can implement a reader and writer for the format. Please use this page to list:

hdf5

[http://hdf.ncsa.uiuc.edu/HDF5/ Hierarchical Data format] is an extremely flexible format, possibly too flexible for its own good

FITS

[http://fits.gsfc.nasa.gov/ Flexible Image Transport System] was developed for astronomy, but could be used by many disciplines. One notable feature is good support for World Coordinates, i.e. translation between pixel coordinates and physical coordinates such as Longitude & Latitude, Frequency, Stokes parameters (polarisation). Arbitrary numbers of dimensions are supported as well, but not so flexibly as in hdf5.

XML variants

Name

Open Spec?

Debian Packages

[http://www.ivoa.net/Documents/latest/VOT.html VOTable]

YES

[http://www.biodas.org/dtd/dasdna.dtd DASDNA]

[http://www.biodas.org/documents/spec.html YES]

[http://mipe.sourceforge.net/ MIPE]

GPL

[http://packages.debian.org/mipe/ YES]

[http://graphml.graphdrawing.org/ GraphML]

[http://www-lbit.iro.umontreal.ca/rnaml/ RNAML]

[http://www.biomedcentral.com/info/about/datamining ?BioMedCentral format]

Do not know

[http://schema.omg.org/lsr/gene_expression/1.1/MAGE-ML.dtd MAGE-ML]

Do not know

[http://www.loc.gov/standards/mods/ MODS]

Do not know

dicom

[http://en.wikipedia.org/wiki/DICOM Digital Imaging and Communications in Medicine] is a classical format for medical computing imaging.

Chemical MIME/file types

[http://www.ch.ic.ac.uk/chemime/ Chemical MIME types] can be introduced to the Linux desktop with [http://chemical-mime.sf.net/ chemical-mime-data]. You will find most information about these MIME types and the project in the source of the package.

All chemical applications (e.g. [http://packages.debian.org/xdrawchem xdrawchem] or [http://packages.debian.org/openbabel openbabel]), which can handle the freedesktop.org MIME specs benefit from this package. Older specs for e.g. GNOME <= 2.4 or KDE <= 3.x are a bit harder to support, because their magic databases are not expandable.

The MIME-types are not part of the official shared-mime-info package/projects, because these MIME-types have never been registered with IANA (see also [http://lists.freedesktop.org/archives/xdg/2005-May/006858.html]).

BioDAS

[http://www.biodas.org BioDAS] is a Distributed Annotation System for genome work - more a protocol than a data format. It uses XML for the sequence data.

General