Scientific Data formats
From Just Solve the File Format Problem
(Difference between revisions)
Crusbridge (Talk | contribs) m (→Medical Imaging) |
Crusbridge (Talk | contribs) (Listed a bunch more formats, sourced from Wikipedia) |
||
| Line 9: | Line 9: | ||
== General == | == General == | ||
* [[cdf]] (Common Data Format) | * [[cdf]] (Common Data Format) | ||
| + | * [[EAS3]] (binary file format for structured data) | ||
* [[hdf]] (Hierarchical Data Format, from NASA) | * [[hdf]] (Hierarchical Data Format, from NASA) | ||
* [[NetCDF]] (Network Common Data Format) | * [[NetCDF]] (Network Common Data Format) | ||
| + | * [[SDF]] (Simple Data Format, a platform-independent, precision-preserving binary data I/O format capable of handling large, multi-dimensional arrays) | ||
* [[SDXF]] (Structured Data Exchange Format) | * [[SDXF]] (Structured Data Exchange Format) | ||
| − | * [[XDF]] (eXtensible Data Format) | + | * [[Silo]] (a storage format for visualization developed at Lawrence Livermore National Laboratory)* [[XDF]] (eXtensible Data Format) |
* [[XSIL]] (Extensible Scientific Interchange Language) | * [[XSIL]] (Extensible Scientific Interchange Language) | ||
| Line 40: | Line 42: | ||
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database) | * [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database) | ||
* [[VCF]] (Variant Call Format) | * [[VCF]] (Variant Call Format) | ||
| + | |||
| + | == Biomedical signals (time series) == | ||
| + | |||
| + | * [[ACQ]] (AcqKnowledge) | ||
| + | * [[BCI2000]] (The BCI2000 project) | ||
| + | * [[BDF]] (BioSemi data format0 | ||
| + | * [[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 == | == Chemical == | ||
| + | * [[CCP4]] (X-ray crystallography voxels (electron density)) | ||
* [[Chemical data]] | * [[Chemical data]] | ||
| + | * [[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) | ||
| + | * [[MRC]] (voxels in cryo-electron microscopy) | ||
| + | * [[SMILES]] (Simplified molecular input line entry specification, .smi) | ||
| + | * [[SPC]] (spectroscopic data) | ||
== Ecological == | == Ecological == | ||
| Line 68: | Line 97: | ||
== Mathematical == | == Mathematical == | ||
| − | + | * [[graph6, sparse6]] (ASCII encoding of Adjacency matrices (.g6, .s6)) | |
| + | * [[M]] (Mathematica package file) | ||
* [[MathML]] | * [[MathML]] | ||
== Medical Imaging == | == Medical Imaging == | ||
| − | * [[DICOM]] | + | * [[AFNI]] (data, meta-data (.BRIK,.HEAD)) |
| + | * [[.MGH]] (uncompressed) | ||
| + | * [[.MGZ]] (zip-compressed) | ||
| + | * [[Analyze data, meta-data]] (.img,.hdr) | ||
| + | * [[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-TIFF]] (Open Microscopy Imaging format) | ||
| + | * [[OST (Open Spatio-Temporal)]] (extensible, open alternative for microscope images) | ||
| + | * [[nii]] (Neuroimaging Informatics Technology Initiative (NIfTI) single-file (combined data and meta-data)) | ||
| + | * [[gii]] (NIfTI offspring for brain surface data, single-file (combined data and meta-data) style) | ||
| + | * [[.img,.hdr]] (NIfTI offspring for brain surface data, dual-file (separate data and meta-data, respectively) style) | ||
| + | * [[SDM]] (Signed Differential Mapping- brain maps(.sdm)) | ||
| + | |||
== Oceanographic, Atmospheric and Meteorological == | == Oceanographic, Atmospheric and Meteorological == | ||
| Line 87: | Line 128: | ||
* [[NeXuS]] (Common data format for neutron, x-ray and muon science) | * [[NeXuS]] (Common data format for neutron, x-ray and muon science) | ||
* [[QCDml]] (Lattice QCD gauge configuration markup language) | * [[QCDml]] (Lattice QCD gauge configuration markup language) | ||
| + | |||
| + | == Scientific Signal data == | ||
| + | |||
| + | * [[ACQ]] (AcqKnowledge File Format for Windows) | ||
| + | * [[BKR]] (EEG data format) | ||
| + | * [[BDF]] (BioSemi 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) | ||
| + | * [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography) | ||
| + | * [[SEG Y]] (Reflection seismology data format) | ||
| + | * [[SIGIF]] (SIGnal Interchange Format) | ||
== Social Sciences == | == Social Sciences == | ||
Revision as of 16:23, 3 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, from NASA)
- NetCDF (Network Common Data Format)
- SDF (Simple Data Format, a platform-independent, precision-preserving binary data I/O format capable of handling large, multi-dimensional arrays)
- 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
- AB1 (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
- ACE (Sequence assembly format)
- BAM (Binary compressed SAM format)
- BED (Browser extensible display format describing genes and other features of DNA sequences)
- CAF (Common Assembly Format for sequence assembly)
- EMBL (Flatfile format used by the EMBL for nucleotide and peptide sequences)
- FASTA and FASTQ (File format for sequence data, FASTQ with quality).
- GenBank (Flatfile format used by NCBI for nucleotide and peptide sequences)
- 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)
- NEXUS (Encodes mixed information about genetic sequence data in a block structured format)
- PDB (Structures of biomolecules deposited in Protein Data Bank)
- PHD (Output from the basecalling software Phred)
- SAM (Sequence Alignment/Map format)
- SCF (Staden chromatogram files used to store data from DNA sequencing)
- SBML (Systems Biology Markup Language used to store biochemical network computational models)
- Stockholm (Representing multiple sequence alignments)
- Swiss-Prot (Flatfile format used for protein sequences from the Swiss-Prot database)
- VCF (Variant Call Format)
Biomedical signals (time series)
- ACQ (AcqKnowledge)
- BCI2000 (The BCI2000 project)
- BDF (BioSemi data format0
- 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))
- Chemical data
- 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)
- MRC (voxels in cryo-electron microscopy)
- SMILES (Simplified molecular input line entry specification, .smi)
- SPC (spectroscopic data)
Ecological
- Darwin Core (Standard for sharing information about biological diversity)
- EML (Ecological Metadata Language)
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 Shaepfile must have components; other optional components as well, see entry)
- SID (MrSID- Multi-resolution Seamless Image Database)
- TAB (MapInfo dataset format, must have component)
Mathematical
- graph6, sparse6 (ASCII encoding of Adjacency matrices (.g6, .s6))
- M (Mathematica package file)
- MathML
Medical Imaging
- AFNI (data, meta-data (.BRIK,.HEAD))
- .MGH (uncompressed)
- .MGZ (zip-compressed)
- Analyze data, meta-data (.img,.hdr)
- 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)
- OST (Open Spatio-Temporal) (extensible, open alternative for microscope images)
- nii (Neuroimaging Informatics Technology Initiative (NIfTI) single-file (combined data and meta-data))
- gii (NIfTI offspring for brain surface data, single-file (combined data and meta-data) style)
- .img,.hdr (NIfTI offspring for brain surface data, dual-file (separate data and meta-data, respectively) style)
- 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)
- BKR (EEG data format)
- BDF (BioSemi 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)
- SCP-ECG (Standard Communication Protocol for Computer assisted electrocardiography)
- SEG Y (Reflection seismology data format)
- SIGIF (SIGnal Interchange Format)
