Scientific Data formats

From Just Solve the File Format Problem
(Difference between revisions)
Jump to: navigation, search
(Microscopy)
(Astronomical and Space)
 
(10 intermediate revisions by 4 users not shown)
Line 25: Line 25:
  
 
== Astronomical and Space ==
 
== Astronomical and Space ==
 +
* [[Advanced Scientific Data Format]]
 
* [[Flexible Image Transport System]] (FITS)
 
* [[Flexible Image Transport System]] (FITS)
 
** [[PSRFITS]] (Pulsar data storage standard)
 
** [[PSRFITS]] (Pulsar data storage standard)
 
* [[ICER]]
 
* [[ICER]]
 +
* [[NASA Raster Metafile]]
 +
* [[ODL (NASA Object Description Language)]]
 
* [[PDS]] (Planetary Data System)
 
* [[PDS]] (Planetary Data System)
 
* [[PDS4]]
 
* [[PDS4]]
 
* [[VOTable]] (IVOA standard table format)
 
* [[VOTable]] (IVOA standard table format)
 
* [[SBIG CCDOPS image]]
 
* [[SBIG CCDOPS image]]
 +
* [[Standard Archive Format]] (used for USAF missile data)
 
* [[Starlink_Data_Format|SDF]] (Starlink Data Format) and [[N-Dimensional_Data_Format|NDF]] (Starlink's Extensible N-Dimensional Data Format).
 
* [[Starlink_Data_Format|SDF]] (Starlink Data Format) and [[N-Dimensional_Data_Format|NDF]] (Starlink's Extensible N-Dimensional Data Format).
 
* [[VICAR]]
 
* [[VICAR]]
Line 206: Line 210:
 
== Mathematical ==
 
== Mathematical ==
 
* [[AsciiMath]]
 
* [[AsciiMath]]
* [[Computable Document Format]] (.cdf)
 
 
* [[DOT (graph description language)]]
 
* [[DOT (graph description language)]]
 +
* [[GEXF]] (Graph Exchange XML Format)
 
* [[graph6, sparse6]] (ASCII encoding of Adjacency matrices (.g6, .s6))
 
* [[graph6, sparse6]] (ASCII encoding of Adjacency matrices (.g6, .s6))
 
* [[graphML]] (Graph Markup Language)
 
* [[graphML]] (Graph Markup Language)
 
* [[MacWavelets]]
 
* [[MacWavelets]]
 
* Mathematica
 
* Mathematica
 +
** [[Computable Document Format]] (.cdf)
 
** [[Mathematica notebook]] (.nb, .nbp)
 
** [[Mathematica notebook]] (.nb, .nbp)
 
** [[Mathematica package file]] (M)
 
** [[Mathematica package file]] (M)
 +
** [[Wolfram Language]]
 
* [[MathML]]
 
* [[MathML]]
 
* MATLAB
 
* MATLAB
Line 226: Line 232:
  
 
* [[Amber ARR Bitmap Image]]
 
* [[Amber ARR Bitmap Image]]
 +
* [[Aperio SVS]]
 
* [[Bio]]
 
* [[Bio]]
 
* [[BioRad confocal image]]
 
* [[BioRad confocal image]]
 
* [[DeltaVision]]
 
* [[DeltaVision]]
 
* [[dm2]] (Gatan Digital Micrograph 2)
 
* [[dm2]] (Gatan Digital Micrograph 2)
* [[dm3]] (Gatan Digital Micrograph 3)
+
* [[dm3]] (Gatan Digital Micrograph 3) ({{PRONOM|fmt/1131}})
 
* [[GATAN]]
 
* [[GATAN]]
 
* [[Image Cytometry Standard]] (ICS)
 
* [[Image Cytometry Standard]] (ICS)
Line 264: Line 271:
 
* [[EDF]] (European data format)
 
* [[EDF]] (European data format)
 
* [[FEF]] (File Exchange Format for Vital signs)
 
* [[FEF]] (File Exchange Format for Vital signs)
* [[GDF]] (General data formats for biomedical signals)
+
* [[General Data Format for Biosignals]] (GDF)
 
* [[GMS]] (Gesture And Motion Signal format)
 
* [[GMS]] (Gesture And Motion Signal format)
 
* [[IROCK]] (intelliRock Sensor Data File Format)
 
* [[IROCK]] (intelliRock Sensor Data File Format)
Line 288: Line 295:
 
* [[SPV]] (Output file for the [[SPSS]] Statistical package - version 17 and later)
 
* [[SPV]] (Output file for the [[SPSS]] Statistical package - version 17 and later)
 
* [[Transana]] ([[Computer-assisted qualitative data analysis]] package)
 
* [[Transana]] ([[Computer-assisted qualitative data analysis]] package)
 +
 +
== Miscellaneous ==
 +
 +
* [[AIML]] (Artificial Intelligence Markup Language)
 +
* [[Jupyter Notebook]] (.ipynb)
  
 
== Links ==
 
== Links ==
 
* [http://cameronneylon.net/blog/improving-on-access-to-research/ Improving on “Access to Research”]
 
* [http://cameronneylon.net/blog/improving-on-access-to-research/ Improving on “Access to Research”]

Latest revision as of 01:57, 16 February 2019

File Format
Name Scientific Data formats
Ontology

Mad scientist from 1940 movie

Mad scientist from 1940 movie

See also Health and Medicine for medical/biomedical data formats.

Contents

[edit] General

  • Common Data Format (CDF)
  • 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)
  • ROOT (CERN data-analysis package and related formats, used in their Open Data initiative)
  • SDXF (Structured Data Exchange Format)
  • Silo (a storage format for visualization developed at Lawrence Livermore National Laboratory)
  • 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)
  • Standard Delay Format (SDF) A standard data structure for timing data
  • XDF (eXtensible Data Format)
  • XSIL (Extensible Scientific Interchange Language)

[edit] Astronomical and Space

[edit] Biological

[edit] 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
  • Protein Data Bank (PDB)
  • 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.

[edit] Ecological

[edit] 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)
  • Shapefile (ESRI, shp/shx)
  • MrSID (MrSID- Multi-resolution Seamless Image Database)
  • TAB (MapInfo dataset format, must have component)

[edit] Mathematical

[edit] Microscopy

[edit] Oceanographic, Atmospheric and Meteorological

  • GRIB (Gridded Binary)
  • BUFR (Binary Universal Format Representation)
  • IOAPI (netCDF augmented with metadata from the I/O API)
  • Meteosat data
  • PP (UK Met Office format for weather model data)

[edit] Physics

See subcategory Physics data

[edit] 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)
  • General Data Format for Biosignals (GDF)
  • 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)

[edit] Social Sciences

[edit] Miscellaneous

[edit] Links

Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox