Scientific Data formats

2012-11-08T19:10:11Z

Jessebikman: /* Mathematical */ added MATLAB m-file.

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|[[File Formats]]
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|[[Electronic File Formats]]
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|[[Scientific Data formats]]
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== General ==
* [[cdf]] (Common Data Format)
* [[EAS3]] (binary file format for structured data)
* [[hdf]] (Hierarchical Data Format, from NASA)
* [[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 ==
* [[FITS]] (Flexible Image Transport System)
* [[PDS/ODL]] (Planetary Data System)
* [[VOTable]] (IVOA standard table format)
* [[Starlink_Data_Format|SDF]] (Starlink Data Format) and [[N-Dimensional_Data_Format|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)
* [[ACE]] (Sequence assembly format)
* [[ABCDDNA]] (Access to Biological Collection Data DNA extension)
* [[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)
* [[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]]
* [[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 [http://www.ch.ic.ac.uk/chemime/ Chemical MIME] types.

== 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))
* [[graphML]] (Graph Markup Language)
* [[m]] (MATLAB script file)
* [[M]] (Mathematica package file)
* [[MAT]] (MATLAB matrix data format)
* [[MathML]]
* [[WP2]] WinPlot

== 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)
* [[OME-XML]] (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)
* [[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 ==

* [[DDI]] (Data Documentation Initiative)
* [[SAS]] (Statistical package)
* [[SPSS]] (Statistical package)
* [[Stata]] (Statistical package)

Just Solve the File Format Problem - User contributions [en]

Scientific Data formats