Scientific Data formats

Revision as of 16:48, 20 November 2012

General

• cdf (Common Data Format)
• EAS3 (binary file format for structured data)
• hdf (Hierarchical Data Format, originally from NCSA, now maintained by The HDF Group)
  • HDF4
  • HDF5
• NRRD (Nearly Raw Raster Data -- a simple format for n-dimensional raster data)
• NetCDF (Network Common Data Format)
• There are several formats abbreviated as SDF, including:
  • 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-DPT A new format from the Data Protocols Team for publishing and sharing data
  • Standard Delay Format A standard data structure for timing data
  • Structure Data File A file format for a chemical table file
• 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

• Flexible Image Transport System (FITS)
• PDS/ODL (Planetary Data System)
• VOTable (IVOA standard table format)
• SDF (Starlink Data Format) and NDF (Starlink's Extensible N-Dimensional Data Format).

Biological

• AB1 (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
• ABCD (Access to Biological Collection Data)
• ABCDDNA (Access to Biological Collection Data DNA extension)
• ABCDEFG (Access to Biological Collection Data Extension For Geosciences)
• ACE (Sequence assembly format)
• Affymetrix Raw Intensity Format
• ARLEQUIN Project Format
• Axt Alignment Format
• BAM (Binary compressed SAM format)
• BED (Browser extensible display format describing genes and other features of DNA sequences)
• BEDgraph
• Big Browser Extensible Data Format
• Big Wiggle Format
• Binary Alignement Map Format
• Binary Probe Map Format
• Binary sequence information Format
• Biological Pathway eXchange
• BLAT alignment Format
• BRIX generated O Format
• CAF (Common Assembly Format for sequence assembly)
• CellML
• CHADO XML interchange Format
• Chain Format for pairwise alignment
• CHARMM Card File Format
• CLUSTAL-W Alignment Format
• CLUSTAL-W Dendrogram Guide File Format
• Clustered Data Table Format
• DELTA (DEscription Language for TAxonomy)
• DAS (Distributed Sequence Annotation System)
• DBN (Dot Bracket Notation (DBN) - Vienna Format)
• EMBL (Flatfile format used by the EMBL for nucleotide and peptide sequences)
• EML (Environmental Markup Language) not to be confused with EML (Ecological Metadata Language)
• ENCODE (Peak information Format)
• FASTA and FASTQ (File format for sequence data, FASTQ with quality)
• FuGEFlow
• FuGE-ML (Functional Genomics Experiment Markup Language)
• Gating-ML
• GCDML (Genomic Contextual Data Markup Language)
• GelML Gel electrophoresis Markup Language
• GenBank (Flatfile format used by NCBI for nucleotide and peptide sequences)
• 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
• GenePattern GeneSet Table Format
• Genome Annotation File (version 1 and 2)
• GTF (Gene transfer format holds information about gene structure)
• HMMER
• ICB (ICM binary file Format)
• imzML (imaging mz Markup Language)
• ISA-Tab (Investigation Study Assay Tabular)
• ISND sequence record XML
• KGML (KEGG Mark-up Language)
• MAGE-Tab (MicroArray Gene Expression Tabular)
• MCL (Microbiological Common Language)
• MIARE-TAB (Minimum Information About a RNAi Experiment Tabular)
• microarray track data Browser Extensible Data Format
• MINiML (MIAME Notation in Markup Language)
• mini Protein Data Bank Format
• MIQAS-TAB (Minimal Information for QTLs and Association Studies Tabular)
• MITAB
• mmCIF (macromolecular Crystallographic Information File)
• Multiple Alignment Forma
• mzData (deprecated)
• mzIdentML
• mzML
• mzQuantML
• mzXML (deprecated)
• NCD (Natural Collections Descriptions)
• NDTF (Neurophysiology Data Translation Format)
• net alignment annotation Format
• NeuroML (Neuroscience eXtensible Markup Language)
• New Hampshire eXtended Format
• Newick tree Format
• NEXUS (Encodes mixed information about genetic sequence data in a block structured format)
• Nimblegen Design File Format
• Nimblegen Gene Data Format
• NMR-STAR (NMR Self-defining Text Archive and Retrieval format)
• nucleotide inFormation binary Format
• ODM (Operational Data Model)
• Open Biomedical Ontology Flat File Format
• PDB (Structures of biomolecules deposited in Protein Data Bank)
• Personal Genome SNP Format
• PHD (Output from the basecalling software Phred)
• phyloXML (XML for evolutionary biology and comparative genomics)
• Pre-Clustering File Format
• Protein InFormation Resource Format
• PRM (Protocol Representation Model (Medical Research))
• PSI-MI XML
• PSI-PAR
• RDML (Real-time PCR Data Markup Language)
• 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)
• SDD (Structured Descriptive Data)
• SED-ML (Simulation Experiment Description Markup Language)
• Sequence Alignment Map Format
• SOFT (Simple Omnibus Format in Text)
• spML (Separation Markup Language)
• SRA-XML (Short Read Archive eXtensible Markup Language)
• Standard Flowgram Format
• Stockholm Multiple Alignment Format (Representing multiple sequence alignments)
• SBML (System Biology Markup Language)
• SBGN (Systems Biology Graphical Notation)
• SBRML (Systems Biology Results Markup Language)
• Swiss-Prot (Flatfile format used for protein sequences from the Swiss-Prot database)
• TAIR annotation data Format
• TAPIR (TDWG Access Protocol for Information Retrieval)
• TCS (Taxonomic Concept transfer Schema)
• TraML (Transition Markup Language)
• UniProtKB XML Format
• VCF (Variant Call Format)
• Wiggle Format

Biomedical signals (time series)

• ACQ (AcqKnowledge)
• BCI2000 (The BCI2000 project)
• BioSemi (BDF) data format
• 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))
• 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
• PDB (Protein Data Bank)
• 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.

Ecological

• Darwin Core (Standard for sharing information about biological diversity)
• EML (Ecological Metadata Language), not to be confused with EML (Environmental Markup 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 Shapefile must have components; other optional components as well, see entry)
• MrSID (MrSID- Multi-resolution Seamless Image Database)
• TAB (MapInfo dataset format, must have component)

Mathematical

• graph6, sparse6 (ASCII encoding of Adjacency matrices (.g6, .s6))
• graphML (Graph Markup Language)
• m (MATLAB script file)
• M (Mathematica package file)
• MAT (MATLAB matrix data format)
• MathML
• OPJ (Origin data format)
• WP2 WinPlot

Medical Imaging

• BRIK/HEAD (Voxel data from AFNI programs, dual-file (data and metadata, repectively))
• MGH (uncompressed)
• MGZ (zip-compressed)
• 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-XML (Open Microscopy Imaging format)
• OST (Open Spatio-Temporal) (extensible, open alternative for microscope images)
• NII (Neuroimaging Informatics Technology Initiative (NIfTI) voxel data, single-file (combined data and metadata))
• IMG/HDR (ANALYZE or NIfTI voxel data, dual-file (separate data and metadata, respectively))
• gii (NIfTI offspring for brain surface data, single-file (combined data and meta-data) style)
• TRK (Vector data describing tracts of neurons, used by TrackVis)
• 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)
• BioSemi (BDF) data format
• BKR (EEG 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)
• REC (ATI Vision recorder file)
• SCP-ECG (Standard Communication Protocol for Computer assisted electrocardiography)
• SEG Y (Reflection seismology data format)
• SIGIF (SIGnal Interchange Format)

Social Sciences

• Atlas.ti (Computer-assisted qualitative data analysis package)
• DDI (Data Documentation Initiative)
• DO ("DO file" command script for the Stata Statistical package)
• DTA (Binary data file for the Stata Statistical package)
• NVivo (Computer-assisted qualitative data analysis package)
• R (Statistical package)
• SAS (Statistical package)
• SAV (Binary "SPSS data format" for the SPSS Statistical package)
• SPO (Output file for the SPSS Statistical package - version 14)
• SPS ("Syntax file" (plain text command script) for the SPSS Statistical package)
• SPV (Output file for the SPSS Statistical package - version 17 and later)
• Transana (Computer-assisted qualitative data analysis package)