Scientific Data formats

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(Chemical)
(Biological: ABCDDNA and ABCDEFG now linked to the sections in ABCD)
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* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
 
* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
 
* [[ABCD]] (Access to Biological Collection Data)
 
* [[ABCD]] (Access to Biological Collection Data)
* [[ABCDDNA]] (Access to Biological Collection Data DNA extension)
+
* [[ABCD#ABCDDNA|ABCDDNA]] (Access to Biological Collection Data DNA extension)
* [[ABCDEFG]] (Access to Biological Collection Data Extension For Geosciences)
+
* [[ABCD#ABCDEFG|ABCDEFG]] (Access to Biological Collection Data Extension For Geosciences)
 
* [[ACE (Sequence assembly)|ACE]] (Sequence assembly format)
 
* [[ACE (Sequence assembly)|ACE]] (Sequence assembly format)
 
* [[Affymetrix Raw Intensity Format]]
 
* [[Affymetrix Raw Intensity Format]]

Revision as of 16:48, 20 November 2012

File Formats > Electronic File Formats > Scientific Data formats

Contents

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)
  • 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

Biological

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 Chemical MIME types.

Ecological

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

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