Scientific Data formats

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* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
 
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
 
* [[Gene Feature File]] (Versions 1 and 3)
 
* [[Gene Feature File]] (Versions 1 and 3)
−
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
 
 
* [[Gene Prediction File Format]]
 
* [[Gene Prediction File Format]]
 
* [[GenePattern GeneSet Table Format]]
 
* [[GenePattern GeneSet Table Format]]
 
* [[Genome Annotation File]] (version 1 and 2)
 
* [[Genome Annotation File]] (version 1 and 2)
 +
* [[Genozip]]
 +
* [[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)
 
* [[GTF]] (Gene transfer format holds information about gene structure)
 
* [[HMMER]]
 
* [[HMMER]]

Latest revision as of 14:20, 18 December 2024

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, and also see Engineering.

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)
  • IGOR (.ibw)
  • 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) [1]
  • 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 (OpenLynx) Waters OpenLynx reports
  • 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)
  • XYZ Chem Wiki

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)
  • HDF-EOS (Hierarchical Data Format-Earth Observing System)1 (HD2, HD4, HD5)
  • 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)
  • Bathymetric Attributed Grid (.bag)

[edit] Mathematical

[edit] Microscopy

[edit] Neutron and X-ray Scattering

  • canSAS (tools for small-angle scattering)
  • CIF (Crystallographic Information File, standardised by IUCr)
  • NeXus (NeXus is a common data format for neutron, x-ray, and muon science)

[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] Spectra

[edit] Miscellaneous

  • AIML (Artificial Intelligence Markup Language)
  • EMD-DF64 (used for high frequency energy monitoring)
  • IES (IESNA LM-63 Photometric Data File)
  • Jupyter Notebook (.ipynb)

[edit] Links

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