Scientific Data formats

From Just Solve the File Format Problem
(Difference between revisions)
Jump to: navigation, search
(add CIF to neutron and X-ray category)
(→‎Biological)
 
(43 intermediate revisions by 4 users not shown)
Line 6: Line 6:
 
}}
 
}}
  
−
See also [[Health and Medicine]] for medical/biomedical data formats.
+
See also [[Health and Medicine]] for medical/biomedical data formats, and also see [[Engineering]].
  
 
== General ==
 
== General ==
Line 14: Line 14:
 
** [[HDF4]]
 
** [[HDF4]]
 
** [[HDF5]]
 
** [[HDF5]]
 +
* [[IGOR]] (.ibw)
 
* [[NRRD]] (Nearly Raw Raster Data -- a simple format for n-dimensional raster data)
 
* [[NRRD]] (Nearly Raw Raster Data -- a simple format for n-dimensional raster data)
 
* [[NetCDF]] (Network Common Data Format)
 
* [[NetCDF]] (Network Common Data Format)
Line 21: Line 22:
 
* [[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]] (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
 
* [[Standard Delay Format]] (SDF) A standard data structure for timing data
−
* [[XDF]] (eXtensible Data Format)
+
* [[XDF (Extensible Data Format)]] [https://en.wikipedia.org/wiki/Extensible_Data_Format]
 
* [[XSIL]] (Extensible Scientific Interchange Language)
 
* [[XSIL]] (Extensible Scientific Interchange Language)
  
Line 50: Line 51:
 
* [[ACE (Sequence assembly)|ACE]] (Sequence assembly format)
 
* [[ACE (Sequence assembly)|ACE]] (Sequence assembly format)
 
* [[Affymetrix Raw Intensity Format]]
 
* [[Affymetrix Raw Intensity Format]]
 +
* [[AnnData Object]] (.h5ad)
 
* [[ARF (Axon Raw Format)]]
 
* [[ARF (Axon Raw Format)]]
 
* [[ARLEQUIN Project Format]]
 
* [[ARLEQUIN Project Format]]
Line 65: Line 67:
 
* [[BRIX generated O Format]]  
 
* [[BRIX generated O Format]]  
 
* [[CAF (Common Assembly Format)|CAF]] (Common Assembly Format for sequence assembly)
 
* [[CAF (Common Assembly Format)|CAF]] (Common Assembly Format for sequence assembly)
 +
* [[CASTEP]]
 
* [[CellML]]
 
* [[CellML]]
 
* [[CHADO XML interchange Format]]
 
* [[CHADO XML interchange Format]]
Line 73: Line 76:
 
* [[Clustered Data Table Format]]
 
* [[Clustered Data Table Format]]
 
* [[Complete Genomics]]
 
* [[Complete Genomics]]
 +
* [[CRAM]]
 
* [[DELTA]] (DEscription Language for TAxonomy)
 
* [[DELTA]] (DEscription Language for TAxonomy)
 
* [[DAS]] (Distributed Sequence Annotation System)
 
* [[DAS]] (Distributed Sequence Annotation System)
Line 80: Line 84:
 
* [[ENCODE]] (Peak information Format)
 
* [[ENCODE]] (Peak information Format)
 
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality)
 
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality)
 +
* [[FAST5]] (.fast5)
 
* [[FuGEFlow]]
 
* [[FuGEFlow]]
 
* [[FuGE-ML]] (Functional Genomics Experiment Markup Language)
 
* [[FuGE-ML]] (Functional Genomics Experiment Markup Language)
Line 87: Line 92:
 
* [[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]]
 
* [[ICB]] (ICM binary file Format)
 
* [[ICB]] (ICM binary file Format)
 +
* [[Image Cytometry Experiment]] (ICE)
 +
* [[Image Cytometry Standard]] (ICS)
 
* [[imzML]] (imaging mz Markup Language)
 
* [[imzML]] (imaging mz Markup Language)
 
* [[ISA-Tab]] (Investigation Study Assay Tabular)
 
* [[ISA-Tab]] (Investigation Study Assay Tabular)
Line 141: Line 149:
 
* [[SDD]] (Structured Descriptive Data)
 
* [[SDD]] (Structured Descriptive Data)
 
* [[SED-ML]] (Simulation Experiment Description Markup Language)
 
* [[SED-ML]] (Simulation Experiment Description Markup Language)
−
* [[Sequence Alignment Map Format]]
 
 
* [[SOFT]] (Simple Omnibus Format in Text)
 
* [[SOFT]] (Simple Omnibus Format in Text)
 
* [[spML]] (Separation Markup Language)
 
* [[spML]] (Separation Markup Language)
Line 174: Line 181:
 
* [[MST]] ACD/ChemSketch v1 file format
 
* [[MST]] ACD/ChemSketch v1 file format
 
* [[Protein Data Bank]] (PDB)
 
* [[Protein Data Bank]] (PDB)
−
* [[RPT]] ACD/ChemSketch v1 file format
+
* [[RPT (OpenLynx)]] Waters OpenLynx reports
 
* [[RXN]] (Reaction file format)
 
* [[RXN]] (Reaction file format)
 
* [[SK2]] (ACD/ChemSketch v2 file format)
 
* [[SK2]] (ACD/ChemSketch v2 file format)
Line 182: Line 189:
 
* [[Structure Data File]] (SDF)
 
* [[Structure Data File]] (SDF)
 
* [[TGF]] (ISIS/Draw reaction file format)
 
* [[TGF]] (ISIS/Draw reaction file format)
 +
* [[XYZ Chem]] [https://en.wikipedia.org/wiki/XYZ_file_format Wiki]
  
 
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.
Line 190: Line 198:
 
* [[QuakeML]]
 
* [[QuakeML]]
 
* [[SEED]]
 
* [[SEED]]
 +
* [[SEG-D]] (formats, mostly tape based, for seismic data)
 
* [[SEG Y]] (Reflection seismology data format)
 
* [[SEG Y]] (Reflection seismology data format)
 
* [[SEIS-PROV]]
 
* [[SEIS-PROV]]
Line 212: Line 221:
 
* [[GeoTIFF]] (Geospatial extensions to TIFF)
 
* [[GeoTIFF]] (Geospatial extensions to TIFF)
 
* [[GML]] (Geography Markup Language)
 
* [[GML]] (Geography Markup Language)
−
* [[HDFEOS, HD2, HD4]] (Hierarchical Data Format-Earth Observing System)
+
* [[HDF-EOS]] (Hierarchical Data Format-Earth Observing System)[https://hdfeos.org/ 1] (HD2, HD4, HD5)
 
* [[KML]] (KML (formerly Keyhole Markup Language), Version 2.2)
 
* [[KML]] (KML (formerly Keyhole Markup Language), Version 2.2)
 
* [[NDF]] (National Landsat Archive Production System (NLAPS) Data Format)
 
* [[NDF]] (National Landsat Archive Production System (NLAPS) Data Format)
Line 220: Line 229:
 
* [[MrSID]] (MrSID- Multi-resolution Seamless Image Database)
 
* [[MrSID]] (MrSID- Multi-resolution Seamless Image Database)
 
* [[TAB]] (MapInfo dataset format, must have component)
 
* [[TAB]] (MapInfo dataset format, must have component)
 +
* [[Bathymetric Attributed Grid]] (.bag)
  
 
== Mathematical ==
 
== Mathematical ==
Line 227: Line 237:
 
* [[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)
 +
* GraphPad Prism
 +
** [[PZM]]
 +
** [[PZF]]
 +
** [[PZFX]]
 +
** [[PRISM]]
 +
* [[JMP]] (.jmp)
 +
* [[KaleidaGraph]] (.qda, .qdc)
 +
* [[Life 1.05]]
 +
* [[Life 1.06]]
 
* [[MacWavelets]]
 
* [[MacWavelets]]
 
* Mathematica
 
* Mathematica
Line 233: Line 252:
 
** [[Mathematica package file]] (M)
 
** [[Mathematica package file]] (M)
 
** [[Wolfram Language]]
 
** [[Wolfram Language]]
 +
* [[Macrocell]]
 +
* [[MCell]]
 
* [[MathML]]
 
* [[MathML]]
 
* MATLAB
 
* MATLAB
Line 238: Line 259:
 
** [[Matlab figure]]
 
** [[Matlab figure]]
 
** [[MATLAB script file]] (m)
 
** [[MATLAB script file]] (m)
−
*[[Minitab]] (.mtw, .mpj)
+
** [[Matlab Model]] (.mdl, .slx)
 +
* [[Minitab]] (.mtw, .mpj)
 +
* [[NPY and NPZ (NumPy)]]
 
* [[OPJ]] (Origin data format)
 
* [[OPJ]] (Origin data format)
 
* [[PDL]] (Perl Data Language)
 
* [[PDL]] (Perl Data Language)
 +
* [[Plaintext (cellular automata)]]
 +
* [[RLE (cellular automata)]]
 +
* [[Rule (Golly)]]
 +
* [[Small Object Format]]
 
* [[Statistica]]
 
* [[Statistica]]
 
** [[CSS Software]] (Complete Statistical System)
 
** [[CSS Software]] (Complete Statistical System)
Line 257: Line 284:
 
* [[DM4]] (Gatan Digital Micrograph 4)
 
* [[DM4]] (Gatan Digital Micrograph 4)
 
* [[GATAN]]
 
* [[GATAN]]
 +
* [[HMSA]] (.msa)
 +
* [[Image Cytometry Experiment]] (ICE)
 
* [[Image Cytometry Standard]] (ICS)
 
* [[Image Cytometry Standard]] (ICS)
 
* [[KONTRON]]
 
* [[KONTRON]]
Line 309: Line 338:
 
* [[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)
 +
* [[Linguistic Annotation Framework]] (LAF; used by computational linguists to annotate language samples)
 
* [[M2k]] (MAXQDA)
 
* [[M2k]] (MAXQDA)
 
* [[NVivo]] ([[Computer-assisted qualitative data analysis]] package)
 
* [[NVivo]] ([[Computer-assisted qualitative data analysis]] package)
 
* [[R]] (Statistical package)
 
* [[R]] (Statistical package)
 
* [[SAS]] (Statistical package)
 
* [[SAS]] (Statistical package)
 +
** [[SAS Transport File]] (.xpt)
 
* [[SAV]] (Binary "[[SPSS]] data format" for the [[SPSS]] Statistical package)
 
* [[SAV]] (Binary "[[SPSS]] data format" for the [[SPSS]] Statistical package)
 
* [[SPO]] (Output file for the [[SPSS]] Statistical package - version 14)
 
* [[SPO]] (Output file for the [[SPSS]] Statistical package - version 14)
 
* [[SPS]] ("Syntax file" (plain text command script) for the [[SPSS]] Statistical package)
 
* [[SPS]] ("Syntax file" (plain text command script) for the [[SPSS]] Statistical package)
 
* [[SPV]] (Output file for the [[SPSS]] Statistical package - version 17 and later)
 
* [[SPV]] (Output file for the [[SPSS]] Statistical package - version 17 and later)
 +
* [[Statistix]] (.sx)
 
* [[Transana]] ([[Computer-assisted qualitative data analysis]] package)
 
* [[Transana]] ([[Computer-assisted qualitative data analysis]] package)
 +
 +
== Spectra ==
 +
* [[Bruker]] (XRF software, .pdz)
 +
* [[Niton]] (XRF software, .ndt)
 +
* [[EDAX Spectrum]] (.spc)
 +
* [[Thermo Scientific SPC]] (.spc)
 +
* [[EMSA/MAS]]
 +
* [[HMSA Hyper-Dimensional Data]]
  
 
== Miscellaneous ==
 
== Miscellaneous ==
  
 
* [[AIML]] (Artificial Intelligence Markup Language)
 
* [[AIML]] (Artificial Intelligence Markup Language)
 +
* [[EMD-DF64]] (used for high frequency energy monitoring)
 
* [[IES]] (IESNA LM-63 Photometric Data File)
 
* [[IES]] (IESNA LM-63 Photometric Data File)
 
* [[Jupyter Notebook]] (.ipynb)
 
* [[Jupyter Notebook]] (.ipynb)
−
* [[Bruker]] (XRF software, .pdz)
 
−
* [[Niton]] (XRF software, .ndt)
 
  
 
== 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”]
 +
* [[WikiBooks:Software Tools For Molecular Microscopy]]

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

Retrieved from "http://fileformats.archiveteam.org/index.php?title=Scientific_Data_formats&oldid=49788"
Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox