Scientific Data formats

Revision as of 02:54, 3 November 2012

General

• cdf (Common Data Format)
• hdf (Hierarchical Data Format, from NASA)
• NetCDF (Network Common Data Format)
• SDXF (Structured Data Exchange Format)
• XDF (eXtensible Data Format)
• XSIL (Extensible Scientific Interchange Language)

Astronomical and Space

• FITS (Flexible Image Transport System)
• PDS/ODL (Planetary Data System)

Biological

• AB1 (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
• ACE (Sequence assembly format)
• BAM (Binary compressed SAM format)
• BED (Browser extensible display format describing genes and other features of DNA sequences)
• CAF (Common Assembly Format for sequence assembly)
• EMBL (Flatfile format used by the EMBL for nucleotide and peptide sequences)
• FASTA and FASTQ (File format for sequence data, FASTQ with quality).
• GenBank (Flatfile format used by NCBI for nucleotide and peptide sequences)
• GFF (General feature format for describing genes and other features of DNA, RNA and protein sequences)
• GTF (Gene transfer format holds information about gene structure)
• NEXUS (Encodes mixed information about genetic sequence data in a block structured format)
• PDB (Structures of biomolecules deposited in Protein Data Bank)
• PHD (Output from the basecalling software Phred)
• 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)
• Stockholm (Representing multiple sequence alignments)
• Swiss-Prot (Flatfile format used for protein sequences from the Swiss-Prot database)
• VCF (Variant Call Format)

Chemical

• Chemical data

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

• MathML

Medical Imaging

• DICOM
• [[OME-TIFF] (Open Microscopy Imaging format)

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)

Social Sciences

• DDI (Data Documentation Initiative)
• SAS (Statistical package)
• SPSS (Statistical package)