Scientific Data formats

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== Astronomical and Space ==
 
== Astronomical and Space ==
 
* [[Advanced Scientific Data Format]]
 
* [[Advanced Scientific Data Format]]
 +
* [[CPA (PRISM)]]
 
* [[Flexible Image Transport System]] (FITS)
 
* [[Flexible Image Transport System]] (FITS)
 
** [[PSRFITS]] (Pulsar data storage standard)
 
** [[PSRFITS]] (Pulsar data storage standard)
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* [[ARLEQUIN Project Format]]
 
* [[ARLEQUIN Project Format]]
 
* [[Axt Alignment Format]]
 
* [[Axt Alignment Format]]
* [[BAM]] (Binary compressed SAM format)
+
* [[BAM (Binary Alignment Map)|BAM]] (Binary compressed SAM format)
 
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
 
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
 
* [[BEDgraph]]
 
* [[BEDgraph]]
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== Chemical ==
 
== Chemical ==
 
* [[CCP4]] (X-ray crystallography voxels (electron density))
 
* [[CCP4]] (X-ray crystallography voxels (electron density))
* [[CDX]] (ChemDraw file format)
+
* [[CDX (ChemDraw Exchange)|CDX]] (ChemDraw file format)
 
* [[CDXML]] (ChemDraw file format)
 
* [[CDXML]] (ChemDraw file format)
 
* [[CHM (ChemDraw)|CHM]] (ChemDraw file format)
 
* [[CHM (ChemDraw)|CHM]] (ChemDraw file format)
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Chemical data may be distinguished in various ways, including [http://www.ch.ic.ac.uk/chemime/ Chemical MIME] types.
 
Chemical data may be distinguished in various ways, including [http://www.ch.ic.ac.uk/chemime/ Chemical MIME] types.
 +
 +
== Earth Sciences ==
 +
* [[Adaptable Seismic Data Format]]
 +
* [[Network-Day Tape]]
 +
* [[QuakeML]]
 +
* [[SEED]]
 +
* [[SEG Y]] (Reflection seismology data format)
 +
* [[SEIS-PROV]]
 +
* [[StationXML]]
  
 
== Ecological ==
 
== Ecological ==
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* [[Electronic Data Deliverable]] (EDD; EPA Superfund)
 
* [[Electronic Data Deliverable]] (EDD; EPA Superfund)
 
* [[EML (Ecological Metadata Language)]], not to be confused with [[EML (Environmental Markup Language)]]
 
* [[EML (Ecological Metadata Language)]], not to be confused with [[EML (Environmental Markup Language)]]
 +
 +
== Environmental ==
 +
* [[HYT]] (AquiferTest)
  
 
== Geographic and Geospatial ==
 
== Geographic and Geospatial ==
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* [[BioRad confocal image]]
 
* [[BioRad confocal image]]
 
* [[DeltaVision]]
 
* [[DeltaVision]]
* [[dm2]] (Gatan Digital Micrograph 2)
+
* [[DM2]] (Gatan Digital Micrograph 2)
* [[dm3]] (Gatan Digital Micrograph 3) ({{PRONOM|fmt/1131}})
+
* [[DM3]] (Gatan Digital Micrograph 3)
 +
* [[DM4]] (Gatan Digital Micrograph 4)
 
* [[GATAN]]
 
* [[GATAN]]
 
* [[Image Cytometry Standard]] (ICS)
 
* [[Image Cytometry Standard]] (ICS)
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* [[REC]] (ATI Vision recorder file)
 
* [[REC]] (ATI Vision recorder file)
 
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
 
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SEG Y]] (Reflection seismology data format)
 
 
* [[SIGIF]] (SIGnal Interchange Format)
 
* [[SIGIF]] (SIGnal Interchange Format)
  
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* [[Atlas.ti]] ([[Computer-assisted qualitative data analysis]] package)
 
* [[Atlas.ti]] ([[Computer-assisted qualitative data analysis]] package)
* [[DDI]] (Data Documentation Initiative)
+
* [[DDI (Data Documentation Initiative)|DDI]] (Data Documentation Initiative)
 
* [[DO]] ("DO file" command script for the [[Stata]] Statistical package)
 
* [[DO]] ("DO file" command script for the [[Stata]] Statistical package)
 
* [[DTA]] (Binary data file for the [[Stata]] Statistical package)
 
* [[DTA]] (Binary data file for the [[Stata]] Statistical package)
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* [[AIML]] (Artificial Intelligence Markup Language)
 
* [[AIML]] (Artificial Intelligence Markup Language)
 +
* [[IES]] (IESNA LM-63 Photometric Data File)
 
* [[Jupyter Notebook]] (.ipynb)
 
* [[Jupyter Notebook]] (.ipynb)
* [[QuakeML]]
 
  
 
== 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 15:07, 26 October 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] Earth Sciences

[edit] Ecological

[edit] Environmental

  • HYT (AquiferTest)

[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)
  • SIGIF (SIGnal Interchange Format)

[edit] Social Sciences

[edit] Miscellaneous

[edit] Links

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