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

SPSS

2012-11-15T05:42:00Z

Phillipkent:

SPSS is a widely-used statistical package, developed and sold since 1968. Now owned by IBM, it's official name is "IBM SPSS Statistics".

Four file formats are used by SPSS:

* [[SAV]] Binary "SPSS data format"
* [[SPO]] Output file - version 14
* [[SPS]] "Syntax file", plain text command script
* [[SPV]] Output file - version 17 and later

== References ==

* [http://en.wikipedia.org/wiki/SPSS Wikipedia:SPSS]

* [https://www-304.ibm.com/support/docview.wss?uid=swg21480797 Compatibility of SPSS files (.sav, .sps, .spv, .spo) between different versions] (Technical support note, 2011-12-07)

Computer-assisted qualitative data analysis

2012-11-15T05:30:34Z

Phillipkent: Created page

Computer-assisted qualitative data analysis, abbreviated as CAQDAS, denotes a type of software which is used to analyse combinations of text-based, audio-based and video-based data. Data can be "marked up" thematically, connected and searched via themes, keywords, etc. It is most often used in the social sciences.

Packages commonly in use are:
* [[Atlas.ti]]
* [[NVivo]]
* [[Transana]]

==References==
[http://www.surrey.ac.uk/sociology/research/researchcentres/caqdas/index.htm CAQDAS Networking Project]

Scientific Data formats

2012-11-15T05:22:14Z

Phillipkent: /* Social Sciences */

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
|}

== 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]]
* [[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)
* [[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)
* [[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 [http://www.ch.ic.ac.uk/chemime/ 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)
* [[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)

SPSS

2012-11-15T05:19:59Z

Phillipkent: Created page

SPSS is a widely-used statistical package, developed and sold since 1968. Now owned by IBM, it's official name is "IBM SPSS Statistics".

Four file formats are used by SPSS:

* [[SAV]] Binary "SPSS data format"
* [[SPO]] Output file - version 14
* [[SPS]] "Syntax file", plain text command script
* [[SPV]] Output file - version 17 and later

== References ==

* [http://en.wikipedia.org/wiki/SPSS Wikipedia]

* [https://www-304.ibm.com/support/docview.wss?uid=swg21480797 Compatibility of SPSS files (.sav, .sps, .spv, .spo) between different versions] (Technical support note, 2011-12-07)

Bibliographic data

2012-11-14T06:40:38Z

Phillipkent:

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Bibliographic data]]
|}

Formats specific to the storage and transmission of bibliographic data, finding aids and reference lists.

* [[BIB]] (BibTeX files)
* [[DCX]] (Dublin core)
* [[EAD]] (Encoded Archival Data, for archival finding aids)
* [[ENL]] (EndNote file format)
* [[MARC]]
* [[MARCXML]]
* [[MODS]]
* [[MPEG21-DIDL]]
* [[ONIX]]
* [[RIS]] (RefMan bibliographic (plain text) format - can be used to import/export content to proprietary EndNote/ReferenceManager)

MP3

2012-11-14T06:36:41Z

Phillipkent:

{{FormatInfo
|formattype=electronic
|subcat=Audio
|extensions={{ext|mp3}}
|mimetypes={{mimetype|audio/mpeg}}
}}
'''MP3''' is the name commonly given to the audio formats specified by MPEG-1 Layer III and MPEG-2 Layer III, standardized as ISO/IEC 11172-3:1993. It uses lossy compressed data. It is based in part on work by the Fraunhofer Institute, which still holds patents in the format. Other companies may also hold patents encumbering its implementation.

ID3 tags are often used to provide metadata in MP3 files, though they aren't part of the MP3 specification. ID3 V1 defines a fixed-length data block that is always placed at the end of the file. ID3 V2, which has very little in common with V1, defines a block with variable-length frames and allows more flexibility and verbosity.

== References ==
* [http://en.wikipedia.org/wiki/MP3 MP3 (Wikipedia)]

== Software ==
* [http://mpesch3.de1.cc/ MP3DirectCut] -- MP3 editor

Bibliographic data

2012-11-14T06:15:11Z

Phillipkent: Added RIS

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Bibliographic data]]
|}

Formats specific to the storage and transmission of bibliographic data, finding aids and reference lists.

* [[bib]] (BibTeX files)
* [[DCX]] (Dublin core)
* [[EAD]] (Encoded Archival Data, for archival finding aids)
* [[enl]] (EndNote file format)
* [[MARC]]
* [[MARCXML]]
* [[MODS]]
* [[MPEG21-DIDL]]
* [[ONIX]]
* [[RIS]] (RefMan bibliographic format - can be used to import/export content to proprietary EndNote/ReferenceManager)

Scientific Data formats

2012-11-11T16:19:26Z

Phillipkent: /* Social Sciences */

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
|}

== 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]]
* [[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 [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 ==

* [[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)

Scientific Data formats

2012-11-11T16:16:53Z

Phillipkent: /* Social Sciences */

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
|}

== 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]]
* [[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 [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 ==

* [[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 files for the [[SPSS]] Statistical package)
* [[SPV]] (Output file for the [[SPSS]] Statistical package - version 17 and later)
* [[Transana]] (Computer-assisted qualitative data analysis package)

Scientific Data formats

2012-11-11T16:05:02Z

Phillipkent: /* Social Sciences */

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
|}

== 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]]
* [[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 [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 ==

* [[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)
* [[SPSS]] (Statistical package)
* [[Transana]] (Computer-assisted qualitative data analysis package)

Scientific Data formats

2012-11-11T03:20:50Z

Phillipkent: /* Social Sciences */

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
|}

== 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]]
* [[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 [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 ==

* [[Atlas.ti]] (Computer-assisted qualitative data analysis package)
* [[DDI]] (Data Documentation Initiative)
* [[NVivo]] (Computer-assisted qualitative data analysis package)
* [[R]] (Statistical package)
* [[SAS]] (Statistical package)
* [[SPSS]] (Statistical package)
* [[Stata]] (Statistical package)
* [[Transana]] (Computer-assisted qualitative data analysis package)

Talk:Scientific Data formats

2012-11-11T03:14:25Z

Phillipkent: Created page with "I think 'Statistical' should have its own section, although arguably the statistical formats could be listed under Mathematical - but everyday folk are likely to think of stat..."

I think 'Statistical' should have its own section, although arguably the statistical formats could be listed under Mathematical - but everyday folk are likely to think of statistics by itself, not part of mathematics. --[[User:Phillipkent|Phillipkent]] ([[User talk:Phillipkent|talk]]) 03:14, 11 November 2012 (UTC)

Document

2012-11-04T19:55:28Z

Phillipkent: /* Word Processor */

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|Document
|}

== Markup ==
* [[HTML]] (HyperText Markup Language)
* [[Markdown]]
* [[SGML]] (Standard Generalised Markup Format)
* [[TEI]] (Specialised dialect of SGML)
* [[TEX]] (TeX)
* [[XHTML]] (Extensible HTML)
* [[XML]]

== Presentation ==
* [[ODP]] (OpenDocument presentation)
* [[PPT]] (PowerPoint presentation)
* [[PPTX]] PowerPoint presentation, XML format)

== Spreadsheet ==
* [[ODS]] (OpenDocument spreadsheet)
* [[XLS]] (Excel spreadsheet format)
* [[XLSX]] (Excel spreadsheet format, XML version)

== Word Processor ==
* [[ABW]] (Abiword word processor)
* [[CHI]] (ChiWriter word processor)
* [[DOC]] (Word document)
* [[DOCX]] (Word document, XML format)
* [[DOT]] (Word template)
* [[DOTX]] (Word template, XML format)
* [[TechWriter|EasiWriter]] (Word processor file format)
* [[ODT]]
* [[OTT]]

== Other ==
* [[602]]
* [[ACL]]
* [[AFP]]
* [[ANS]]
* [[ASC]]
* [[AWW]]
* [[AZW]]
* [[CCF]]
* [[CSV]]
* [[CWK]]
* [[DJVU]]
* [[DOX]] (Mutimate document, and others)
* [[EGT]]
* [[EPUB]]
* [[FDX]]
* [[FTM]]
* [[FTX]]
* [[GM6]] (Game Maker 6 source)
* [[GMK]] (Game Maker 7-8 source)
* [[HWP]]
* [[HWPML]]
* [[Impression]] (Desktop Publishing file format)
* [[LWP]]
* [[MBP]]
* [[MCW]]
* [[MOBI]]
* [[NB]]
* [[NBP]]
* [[ODM]]
* [[OMM]]
* [[PAGES]]
* [[PAP]]
* [[PAT]] (Multimate document, and many others)
* [[PDAX]]
* [[PDF]] (Portable Document Format)
* [[QUOX]]
* [[RTF]] (Rich Text Format)
* [[RTFD]] (Rich Text Format Directory)
* [[RPT]]
* [[scriv]] (Scrivener document format)
* [[SDW]]
* [[STW]]
* [[SXW]]
* [[TechWriter]] (Scientific word processor file format)
* [[TXT]] (Un-structured text document)
* [[UOF]]
* [[UOML]]
* [[VIA]]
* [[WPD]]
* [[WPS]]
* [[WPT]]
* [[WRD]]
* [[WRF]]
* [[WRI]]
* [[XPS]]

ChiWriter

2012-11-04T19:54:58Z

Phillipkent:

== ChiWriter - Description ==

'''.CHI''' files are a proprietary file format for the software ChiWriter.

ChiWriter was a popular word-processor for scientific purposes, circa 1990. Its popularity was based on the ability to type mathematical formulae in a WYSIWYG editor running in the MS-DOS operating system.

ChiWriter was created by Horstmann Software (Cay Horstmann) in 1986, and officially discontinued in 1996.

== Identifiers ==
* File extension: '''.CHI'''

== References ==

[http://en.wikipedia.org/wiki/ChiWriter Wikipedia entry for ChiWriter]

ChiWriter

2012-11-04T19:53:46Z

Phillipkent:

== ChiWriter - Description ==

ChiWriter was a popular word-processor for scientific purposes, circa 1990. Its popularity was based on the ability to type mathematical formulae in a WYSIWYG editor running in the MS-DOS operating system.

ChiWriter was created by Horstmann Software (Cay Horstmann) in 1986, and officially discontinued in 1996.

== Identifiers ==
* File extension: '''.CHI'''

== References ==

[http://en.wikipedia.org/wiki/ChiWriter Wikipedia entry for ChiWriter]

ChiWriter

2012-11-04T19:53:31Z

Phillipkent: created page for file format: CHI

== Chiwriter - Description ==

ChiWriter was a popular word-processor for scientific purposes, circa 1990. Its popularity was based on the ability to type mathematical formulae in a WYSIWYG editor running in the MS-DOS operating system.

ChiWriter was created by Horstmann Software (Cay Horstmann) in 1986, and officially discontinued in 1996.

== Identifiers ==
* File extension: '''.CHI'''

== References ==

[http://en.wikipedia.org/wiki/ChiWriter Wikipedia entry for ChiWriter]

Document

2012-11-04T19:38:59Z

Phillipkent: /* Word Processor */

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|Document
|}

== Markup ==
* [[HTML]] (HyperText Markup Language)
* [[Markdown]]
* [[SGML]] (Standard Generalised Markup Format)
* [[TEI]] (Specialised dialect of SGML)
* [[TEX]] (TeX)
* [[XHTML]] (Extensible HTML)
* [[XML]]

== Presentation ==
* [[ODP]] (OpenDocument presentation)
* [[PPT]] (PowerPoint presentation)
* [[PPTX]] PowerPoint presentation, XML format)

== Spreadsheet ==
* [[ODS]] (OpenDocument spreadsheet)
* [[XLS]] (Excel spreadsheet format)
* [[XLSX]] (Excel spreadsheet format, XML version)

== Word Processor ==
* [[ABW]] (Abiword word processor)
* [[CHI]] (Chiwriter word processor)
* [[DOC]] (Word document)
* [[DOCX]] (Word document, XML format)
* [[DOT]] (Word template)
* [[DOTX]] (Word template, XML format)
* [[TechWriter|EasiWriter]] (Word processor file format)
* [[ODT]]
* [[OTT]]

== Other ==
* [[602]]
* [[ACL]]
* [[AFP]]
* [[ANS]]
* [[ASC]]
* [[AWW]]
* [[AZW]]
* [[CCF]]
* [[CSV]]
* [[CWK]]
* [[DJVU]]
* [[DOX]] (Mutimate document, and others)
* [[EGT]]
* [[EPUB]]
* [[FDX]]
* [[FTM]]
* [[FTX]]
* [[GM6]] (Game Maker 6 source)
* [[GMK]] (Game Maker 7-8 source)
* [[HWP]]
* [[HWPML]]
* [[Impression]] (Desktop Publishing file format)
* [[LWP]]
* [[MBP]]
* [[MCW]]
* [[MOBI]]
* [[NB]]
* [[NBP]]
* [[ODM]]
* [[OMM]]
* [[PAGES]]
* [[PAP]]
* [[PAT]] (Multimate document, and many others)
* [[PDAX]]
* [[PDF]] (Portable Document Format)
* [[QUOX]]
* [[RTF]] (Rich Text Format)
* [[RTFD]] (Rich Text Format Directory)
* [[RPT]]
* [[scriv]] (Scrivener document format)
* [[SDW]]
* [[STW]]
* [[SXW]]
* [[TechWriter]] (Scientific word processor file format)
* [[TXT]] (Un-structured text document)
* [[UOF]]
* [[UOML]]
* [[VIA]]
* [[WPD]]
* [[WPS]]
* [[WPT]]
* [[WRD]]
* [[WRF]]
* [[WRI]]
* [[XPS]]

Org mode

2012-11-04T19:20:41Z

Phillipkent:

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Text-based data]]
| >
| Org mode
|}

See: [[Org-mode]]

Org mode

2012-11-04T19:20:28Z

Phillipkent: format 'Org mode' links to 'Org-mode'

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Text-based data]]
| >
| Org-mode
|}

See: [[Org-mode]]

Org-mode

2012-11-04T19:16:18Z

Phillipkent: changed format 'Org mode' to 'Org-mode' because latter is more commonly used

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Text-based data]]
| >
| Org-mode
|}

== Org-mode - Description ==

[http://orgmode.org Org-mode] is a multi-purpose plain-text system which is displayed and manipulated via an
[http://www.gnu.org/software/emacs/manual/html_node/emacs/Modes.html#Modes editing mode] of the [http://www.gnu.org/software/emacs Emacs text editor].

Outside of Emacs, Org-mode files can be viewed as human-readable plain text.

It can be used for: structured note-taking, TO DO lists, project planning, authoring of "executable documents" that combine markup language (for example, LaTeX) with embedded executable code.

== Identifiers ==
* File extension: '''.ORG'''

== References ==

[http://orgmode.org Official website]

Text-based data

2012-11-04T19:14:47Z

Phillipkent:

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|Text-based data
|}
* [[Attribute-Relation File Format]]
* [[Column Delimited]]
* [[CSV]] (Comma Separated Values; comma-delimited)
* [[FidoNet nodelists]]
* [[Org-mode]]
* [[Softdisk Publishing UDF files]]
* [[Tab delimited]]
* [[Text Encoding Initiative]]

== See Also ==
* [[TXT]]
* Some text-based formats are listed in [[Document]] or [[Serialization]]

Org mode

2012-11-04T19:14:29Z

Phillipkent: changed 'Org mode' to 'Org-mode' because latter is more commonly used

User:Phillipkent

2012-11-04T15:35:47Z

Phillipkent:

Find out about me at: [http://www.phillipkent.net www.phillipkent.net]

User:Phillipkent

2012-11-04T15:35:16Z

Phillipkent:

Find out about me at: [http://www.phillipkent.net]

Just Solve the File Format Problem:Community portal

2012-11-04T14:34:16Z

Phillipkent:

= Issues =

Below is a list of "issues" which would ordinarily be in a ticketing system of some kind, but are here on the Wiki instead, because that's how we roll. When things are resolved feel free to remove or strike out the issue.

=== Time zone setting ===

OK, to get this community portal going... is this the place to report issues with the wiki server configuration? Anyway, its time-zone setting seems to be a bit odd. It's set (apparently) to UTC + 4 hours (somewhere in Asia?), but it thinks it's in UTC, so if you set up your user configuration to adjust it to your local time zone, it ends up 4 hours off. I had to use "-08:00" to get my current EDT time. (That will change by one hour in a week or two when Daylight Saving Time ends.) [[User:Dan Tobias|Dan Tobias]] ([[User talk:Dan Tobias|talk]]) 22:23, 28 October 2012 (UTC)

=== index.php ===

The Wiki is obviously working (yay), but it would be nice if the MediaWiki .htaccess file was [http://www.mediawiki.org/wiki/Manual:Short_URL/Apache adjusted] so that the index.php disappears from wiki URLs.

=== Licensing ===

I'm not lawyer but I don't think declaring the content here Public Domain (US) as discussed in the [[FAQ]] will have desirable consequences outside the United States. It's been my experience working with datasets published by the US federal government that people outside the US are uncertain about whether or not they can use the data. I think using CC0 would be preferable to just saying Public Domain, if you really want to encourage reuse. [[User:Edsu|Edsu]] ([[User talk:Edsu|talk]]) 14:26, 1 November 2012 (UTC)

=== Using templates ===

I'm a newbie with Mediawiki. Could someone add a quick help note about using the templates for this site?
--[[User:Phillipkent|Phillipkent]] ([[User talk:Phillipkent|talk]]) 14:34, 4 November 2012 (UTC)

Org mode

2012-11-04T14:24:48Z

Phillipkent: Reformat of external links

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Text-based data]]
| >
| Org mode
|}

== Org mode - Description ==

[http://orgmode.org Org mode] is a multi-purpose plain-text system which is displayed and manipulated via an
[http://www.gnu.org/software/emacs/manual/html_node/emacs/Modes.html#Modes editing mode] of the [http://www.gnu.org/software/emacs Emacs text editor].

Outside of Emacs, Org mode files can be viewed as human-readable plain text.

It can be used for: structured note-taking, TO DO lists, project planning, authoring of "executable documents" that combine markup language (for example, LaTeX) with embedded executable code.

== Identifiers ==
* File extension: '''.ORG'''

== References ==

[http://orgmode.org Official website]

Org mode

2012-11-04T14:06:05Z

Phillipkent: Created page for file format: Org mode

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Text-based data]]
| >
| Org mode
|}

== Org mode - Description ==

Org mode is a multi-purpose plain-text system which runs as a mode of the EMACS editor.

It can be used for: structured note-taking, TO DO lists, project planning, authoring of "executable documents" that combine markup language (for example, LaTeX) with embedded executable code.

== References ==

http://orgmode.org

Text-based data

2012-11-04T13:52:28Z

Phillipkent: Added item for Org mode

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|Text-based data
|}
* [[Attribute-Relation File Format]]
* [[Column Delimited]]
* [[CSV]] (Comma Separated Values; comma-delimited)
* [[FidoNet nodelists]]
* [[Org mode]]
* [[Softdisk Publishing UDF files]]
* [[Tab delimited]]
* [[Text Encoding Initiative]]

== See Also ==
* [[TXT]]
* Some text-based formats are listed in [[Document]] or [[Serialization]]

User:Phillipkent

2012-10-30T17:31:26Z

Phillipkent:

Find out about me at: http://www.phillipkent.net

User:Phillipkent

2012-10-30T17:30:04Z

Phillipkent: link to personal website

Find out about me at: [http://www.phillipkent.net]