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

BibTeX

2013-07-04T10:50:46Z

Crusbridge: Inital entry

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== General description ==

This page describes the BibTeX file format, .bib. BibTeX was originally devised by Oren Patashnik and Leslie Lamport in 1985, to be used with LaTeX, but can now be used with many word and text processing systems. It is "available under the same terms as Donald Knuth's TeX program".

The web site http://www.bibtex.org/ seems to be an authoritative source of information. The format is described at http://www.bibtex.org/Format/. BibTeX files are plain text files formatted according to the BibTeX specifications.

Detailed technical information at the TeX level is available at http://www.tex.ac.uk/tex-archive/bibliography/bibtex/base/bibtex.web.

== Other information ==

BibTeX has a Wikipedia page at http://en.wikipedia.org/wiki/BibTeX. There does not appear to be an entry for BibTeX in the PRONOM database.

There were no new versions of BibTeX between 1988 and 2010, when version 0.99d was released.

== Software ==

BibTeX files can be converted "to anything" using Bib2X according to http://www.bibtex.org/Convert/.

== Sample files ==

A list of BibTeX style examples is at https://verbosus.com/bibtex-style-examples.html.



== Identification ==



The file extension is usually .bib (sometimes .bibtex) and the MIME Type is application/x-bibtex.

== References ==

<references/>

LaTeX: A Document Preparation System by Leslie Lamport, 1986, Addison-Wesley.

There are many guides to BibTeX available on the web.

Databases

2012-11-30T11:47:43Z

Crusbridge: /* Triplestores */

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Classes of databases:

== CODASYL databases ==

* [[DBMS32]] (DEC)
* [[DMS1100]] (Univac)
* [[IDS/2]] (Honeywell)
* [[IDMS]] (Cullinet, and later Computer Associates)

== General databases ==

Specific database types:

* [[Ability]]
* [[Access]]
* [[dBase II]]
* [[dBase III]]
* [[FoxPro]]
* [[Paradox]]

== Hierarchical databases ==

* [[IMS]]

== NoSQL databases ==

* [[CouchDB]]
* [[MongoDB]]

== Object-oriented databases ==

* [[Cache]]
* [[db40]]
* [[Gemstone]]
* [[Objectivity]]
* [[ObjectStore]]
* [[Versant]]

== Relational databases ==

* [[Derby]]
* [[HSQLDB]]
* [[IBM DB2]]
* [[Ingres]]
* [[MySQL]]
* [[Oracle]]
** [[ARC (database backup format)]]
* [[PostGRESQL]]
* [[DB (SQLite)|SQLite]]

== Triplestores ==

* [[3store]]
* [[Apache Jena]]
* [[Mulgara]]

[[Category:Databases| ]]

Databases

2012-11-30T11:44:22Z

Crusbridge: /* NoSQL databases */

Databases

2012-11-30T11:42:30Z

Crusbridge: /* CODASYL databases */ added some examples of this obsolete type ofa database

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Classes of databases:

== CODASYL databases ==

* [[DBMS32]] (DEC)
* [[DMS1100]] (Univac)
* [[IDS/2]] (Honeywell)
* [[IDMS]] (Cullinet, and later Computer Associates)

== General databases ==

Specific database types:

* [[Ability]]
* [[Access]]
* [[dBase II]]
* [[dBase III]]
* [[FoxPro]]
* [[Paradox]]

== Hierarchical databases ==

* [[IMS]]

== NoSQL databases ==

== Object-oriented databases ==

* [[Cache]]
* [[db40]]
* [[Gemstone]]
* [[Objectivity]]
* [[ObjectStore]]
* [[Versant]]

== Relational databases ==

* [[Derby]]
* [[HSQLDB]]
* [[IBM DB2]]
* [[Ingres]]
* [[MySQL]]
* [[Oracle]]
** [[ARC (database backup format)]]
* [[PostGRESQL]]
* [[DB (SQLite)|SQLite]]

== Triplestores ==

[[Category:Databases| ]]

Databases

2012-11-30T11:37:07Z

Crusbridge: Added some OO databases and Triplestore heading

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Classes of databases:

== CODASYL databases ==

== General databases ==

Specific database types:

* [[Ability]]
* [[Access]]
* [[dBase II]]
* [[dBase III]]
* [[FoxPro]]
* [[Paradox]]

== Hierarchical databases ==

* [[IMS]]

== NoSQL databases ==

== Object-oriented databases ==

* [[Cache]]
* [[db40]]
* [[Gemstone]]
* [[Objectivity]]
* [[ObjectStore]]
* [[Versant]]

== Relational databases ==

* [[Derby]]
* [[HSQLDB]]
* [[IBM DB2]]
* [[Ingres]]
* [[MySQL]]
* [[Oracle]]
** [[ARC (database backup format)]]
* [[PostGRESQL]]
* [[DB (SQLite)|SQLite]]

== Triplestores ==

[[Category:Databases| ]]

Document

2012-11-30T11:20:59Z

Crusbridge: /* Markup */ added LaTeX

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== Collaboration ==

* [[Microsoft OneNote]] (ONE, ONEPKG)

== Desktop Publishing ==

* [[Impression]]
* [[Microsoft Publisher]] (.pub)
* [[PageMaker]] (originally from Aldus, later Adobe)
* [[PageMagic]] (.dtp)
* [[The Print Shop]] (Broderbund)
* [[Publish It!]] (.dtp)

== Document storage/exchange formats (non-program-specific)==
* [[CSV]] (Comma Separated Values)
* [[PDF]] (Portable Document Format)
* [[RTF]] (Rich Text Format)
* [[RTFD]] (Rich Text Format Directory)
* [[TXT]] (Un-structured text document)

== eBook / ePublication formats ==
* [[AZW]]
* [[EPUB]]
* [[MOBI]]

== Markup ==
* [[HTML]] (HyperText Markup Language)
* [[LaTeX]] (User-friendly version of [[TeX]] used by mathematicians, computer scientists etc)
* [[Markdown]]
* [[Scribe]]
* [[SGML]] (Standard Generalised Markup Format)
* [[Text Encoding Initiative|TEI]] (Text Encoding Initiative; Specialised dialect of SGML)
* [[TeX]] (TeX type-setting language created by Donald Knuth)
* [[XHTML]] (Extensible HTML)
* [[XML]]

== Multi-function office suites ==
* [[UOF]]

== Presentation ==
* OpenDocument
** [[OpenDocument presentation]] (ODP)
** [[OTP]] (OpenDocument Presentation Template)
* PowerPoint
** [[PPS]] (PowerPoint slide show- autoplay)
** [[PPSM]] (PowerPoint macro-enabled slide show)
** [[PPSX]] (PowerPoint slide show, XML format- autoplay)
** [[POT]] (PowerPoint template)
** [[POTM]] (PowerPoint macro-enabled template)
** [[POTX]] (PowerPoint template, XML format)
** [[PPT]] (PowerPoint presentation)
** [[PPTM]] (PowerPoint macro-enabled presentation)
** [[PPTX]] (PowerPoint presentation, XML format)
* [[STI]] (OpenOffice.org 1.0 presentation template)
* [[SXI]] (StarOffice / OpenOffice.org)

== Spreadsheet ==
* Excel
** [[XLS]] (Excel spreadsheet format)
** [[XLSB]] (Excel binary workbook)
** [[XLSM]] (Excel macro-enabled spreadsheet format)
** [[XLSX]] (Excel spreadsheet format, XML version)
** [[XLT]] (Excel template)
** [[XLTM]] (Excel macro-enabled template)
** [[XLTX]] (Excel template, XML version)
* [[Lotus 1-2-3]]
* [[Lotus Symphony]]
* OpenDocument
** [[OpenDocument Spreadsheet]]
** [[OpenDocument Spreadsheet Template]]
** [[ODS files created by Microsoft Office 2007 SP2]]
* OpenOffice.org
** [[SXC]] (OpenOffice.org 1.0 Spreadsheet)
** [[STC]] (OpenOffice.org 1.0 Spreadsheet Template)
* [[SDC]] (StarOffice spreadsheet)
* [[SuperCalc 3]]
* [[VisiCalc]]
* [[WB2]] (Quattro Pro 6.0)

== Word Processor ==
* [[ABW]] (Abiword word processor)
* [[CHI]] (ChiWriter word processor)
* [[TechWriter|EasiWriter / TechWriter]] (Word processor file format)
* [[HWP]] (Hangul WP 97)
* [[IBM Displaywriter]] (dedicated word processing machine)
* [[Kingsoft Office]] (.wps, .wpt)
* [[Locoscript]]
** [[LWP]] (Lotus WordPro Document)
* [[MCW]]
* Microsoft Word
** [[DOC]] (Word document)
** [[DOCM]] (Word macro-enabled document)
** [[DOCX]] (Word document, XML format)
** [[DOT]] (Word template)
** [[DOTM]] (Word macro-enabled template)
** [[DOTX]] (Word template, XML format)
** [[XML]] (Word 2003 XML - also uses [[DOC]])
* [[Microsoft Works]] (.wps, .wpt)
* [[MultiMate Professional Word Processor]] (.dox, .pat)
* [[OpenDocument Text]] (.odt)
* OpenOffice.org
** [[STW]] (OpenOffice.org 1.0 Text Document Template)
* [[PC-Write]]
* [[Samna Word]]
* [[Scrivener]] (.scriv)
* [[ScreenWriter II]] (for Apple II; formerly SuperScribe II)
* Star Office Writer
** [[SDW]]
** [[SXW]] (Also used by OpenOffice.org)
* [[TechWriter]] (Scientific word processor file format)
* Wang (dedicated word processing machines)
** [[Wang 1200]] (1972; used cassette storage)
** [[Wang OIS]] (1977; used disks)
* [[WordPerfect]]
* [[WordStar]]
** [[WordStar 2000]]

== Other ==
* [[602]]
* [[ACL]]
* [[AFP]]
* [[ANS]]
* [[ASC]]
* [[AWW]]
* [[CCF]]
* [[CWK]]
* [[DJVU]]
* [[EGT]]
* [[FDX]]
* [[FTM]]
* [[FTX]]
* [[HWP]]
* [[HWPML]]
* [[LWP]]
* [[MBP]]
* [[NB]]
* [[NBP]]
* [[ODM]]
* [[OMM]]
* [[OTT]]
* [[PAGES]]
* [[PAP]]
* [[PDAX]]
* [[QUOX]]
* [[RPT]]
* [[STW]]
* [[UOML]]
* [[VIA]]
* [[WRD]]
* [[WRF]]
* [[WRI]]
* [[XPS]]

[[Category:Document| ]]

MINC

2012-11-29T20:01:56Z

Crusbridge: Initial population thanks to Andrew Janke

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== General description ==


This page describes the MINC (Medical Imaging NetCDF) file format, a medical imaging data format and an associated set of tools and libraries initially created by Peter Neelin at the [[http://www.bic.mni.mcill.ca//| Montreal Neurological Institute]]. It is now developed by an international group of researchers who maintain an interest in such things. The MINC2 format is based upon HDF5 and MINC1 upon netCDF, the switch to HDF5 was motivated by support for large datasets (~1TB histology) and block compression. The format is described at http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC.

== Other information ==







== Software ==

The file format can be created, read and manipulated using the libminc Library and minc-tools packages. There are also many other packages available for specific image analysis tasks, these are generally focussed on the analysis of MRI data.

Development is on github:

https://github.com/BIC-MNI

Documentation and information is on wikibooks

http://en.wikibooks.org/wiki/MINC

Official downloads (releases) are here:

http://packages.bic.mni.mcgill.ca/tgz

== Sample files ==

Some sample MINC files are available in the mni-atlases packages here:
http://packages.bic.mni.mcgill.ca/tgz

== Identification ==



The file extension is .mnc and the MIME Type is application/x-minc ??.

== References ==
<references/>

MzML

2012-11-08T23:40:07Z

Crusbridge:

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== General description ==

This stub page describes the mzML file format for encoding raw spectrometer output. It is described in the [http://www.psidev.info/mzml mzML specification] at the HUPO Proteomics Standards Initiative site. MzML replaces two previous file formats, [[mzDATA]] developed by PSI and [[mzXML]] developed by the Seattle Proteome Center at the Institute for Systems Biology.

The current version is mzML version 1.1, releaseed in 2009.



== Other information ==







== Software ==

The [http://www.psidev.info/mzml specification page] lists many software packages that produce or can process mzML files.





== Sample files ==



== Identification ==



The file extension is .mzml and the MIME Type is not known.

== References ==
<references/>

MzML

2012-11-08T23:38:58Z

Crusbridge: Quick and dirty initial population

{|
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| xxMzMLxxx
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== General description ==

This stub page describes the mzML file format for encoding raw spectrometer output. It is described in the [http://www.psidev.info/mzml mzML specification] at the HUPO Proteomics Standards Initiative site. MzML replaces two previous file formats, [[mzDATA]] developed by PSI and [[mzXML]] developed by the Seattle Proteome Center at the Institute for Systems Biology.

The current version is mzML version 1.1, releaseed in 2009.



== Other information ==







== Software ==

The [http://www.psidev.info/mzml specification page] lists many software packages that produce or can process mzML files.





== Sample files ==



== Identification ==



The file extension is .mzml and the MIME Type is not known.

== References ==
<references/>

MzML

2012-11-08T23:38:27Z

Crusbridge: Qu

{|
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| xxMzMLxxx
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== General description ==

This stub page describes the mzML file format for encoding raw spectrometer output. It is described in the [http://www.psidev.info/mzml mzML specification] at the HUPO Proteomics Standards Initiative site. <zML replaces two previous file formats, [[mzDATA]] developed by PSI and [[mzXML]] developed by the Seattle Proteome Center at the Institute for Systems Biology.

The current version is mzML version 1.1, releaseed in 2009.



== Other information ==







== Software ==

The [http://www.psidev.info/mzml specification page] lists many software packages that produce or can process mzML files.





== Sample files ==



== Identification ==



The file extension is .mzml and the MIME Type is not known.

== References ==
<references/>

Scientific Data formats

2012-11-08T23:29:44Z

Crusbridge: /* Biological */

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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]]
* [[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 ==

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

PSI-PAR

2012-11-08T22:04:41Z

Crusbridge: Quick and dirty initial population

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

== General description ==

The PSI-PAR format is a standardized means of representing protein affinity reagent data. The PSI-PAR format consists of the PSI-MI XML2.5 schema (originally designed for molecular interactions) and the PSI-PAR controlled vocabulary. Strictly speaking it is not a separate file format; the Proteomics Standards Initiative [http://psidev.info/psi-par page describing PSI-PAR] says there are no changes to the structure of the [[PSI-MI XML2.5]] schema, although some schema element descriptions have been modified.



== Other information ==







== Software ==





== Sample files ==



== Identification ==





== References ==

Gloriam, D. E., Orchard, S., Bertinetti, D., Björling, E., Bongcam-Rudloff, E., Borrebaeck, C. a K., Bourbeillon, J., et al. (2010, January). A community standard format for the representation of protein affinity reagents. Molecular & cellular proteomics : MCP. doi:10.1074/mcp.M900185-MCP200
<references/>

MITAB

2012-11-08T18:04:19Z

Crusbridge: /* General description */

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

== General description ==

This stub page describes the MITAB file format, derived from the tabular format provided by BioGrid.
The MITAB25 format is part of the [[PSI-MI XML]] 2.5 standard. The sponsor is the Protemics Standard Initiative.

The MITAB25 specification is available by FTP at [ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README].

The MITAB27 specification (for version 2.7) is available at [http://code.google.com/p/psicquic/wiki/MITAB27Format http://code.google.com/p/psicquic/wiki/MITAB27Format].



== Other information ==







== Software ==





The PSI-MI workgroup has developed a parser for PSIMITAB, more information can be found on the [http://www.psidev.info/index.php?q=node/60#tools PSI web site].

== Sample files ==



== Identification ==





== References ==
<references/>

MITAB

2012-11-08T18:03:45Z

Crusbridge: Quick and dirty initial population

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

== General description ==

This stub page describes the MITAB file format, derived from the tabular format provided by BioGrid.
The MITAB25 format is part of the [[PSI-MI XML]] 2.5 standard. The sponsor is the Protemics Standard Initiative.

The MITAB25 specification is available by FTP at [ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README].

The MITAB27 specification (for vesion 2.7) is available at [http://code.google.com/p/psicquic/wiki/MITAB27Format http://code.google.com/p/psicquic/wiki/MITAB27Format].



== Other information ==







== Software ==





The PSI-MI workgroup has developed a parser for PSIMITAB, more information can be found on the [http://www.psidev.info/index.php?q=node/60#tools PSI web site].

== Sample files ==



== Identification ==





== References ==
<references/>

Scientific Data formats

2012-11-08T18:02:12Z

Crusbridge: /* Biological */

{|
|[[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]]
* [[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]] (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)

Scientific Data formats

2012-11-08T17:48:33Z

Crusbridge: /* Biological */

{|
|[[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)
* [[MITAB25]]
* [[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]] (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)

PSI-MI XML

2012-11-08T14:09:08Z

Crusbridge: Quick and dirty initial population

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
| >
| PSI-MI XML
|}

== General description ==

This page describes the PSI-MI XML file format, also known as MIF. The PSI MI format is a data exchange format for molecular interactions.

The file format is described at the HUPO Proteomics Standards Initiative site, see the [http://psidev.info/mif specification]. The current version is 2.5.

Released December 5, 2005; last maintenance update June 1, 2006, to version 2.5.3.



== Other information ==







== Software ==





== Sample files ==



== Identification ==

The newer OBO file type appears to be .obo; previously DAG file types of .dag and .def were used. <Uncertain.>




== References ==
<references/>

Talk:Electronic File Formats

2012-11-08T02:51:22Z

Crusbridge: /* ASN.1 */ new section

There should probably be an agreed definition of an electronic file format to aid in selecting content and automating reasoning based on format IDs etc (if we are not all talking about the same things then we will not be able to generalise from the results of our work).

What is an Electronic File format?

Options:

1) a knowable, repeatable set of rules for structuring content in a computer file

2) a documented standard way of structuring computer files

3) the options that appear in the save-as drop-down menus in software applications

4) a file extension

5) a mime type

6) ???

''preceeding question was written by [[User:Euanc|Euanc]].''

: For the moment, I can make this very simple. An Electronic File Format is a file format that can only be accessed through the use of electrical charge. The rest of what you're discussing is a matter of hierarchy below the "Electronic File Format" heading, which will definitely be sticky and hard to keep on top of, but can be done. --[[User:Jason Scott|Jason Scott]] ([[User talk:Jason Scott|talk]]) 06:15, 1 November 2012 (UTC)

: If an electronic file format is an "electronic" file format, then what is a file format? --[[User:Euanc|Euanc]] ([[User talk:Euanc|talk]]) 06:27, 1 November 2012 (UTC)

== ASN.1 ==

Is it a file format and if so, where should it go? [[Crusbridge]]

Scientific Data formats

2012-11-08T00:28:59Z

Crusbridge: /* General */

{|
|[[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]]
* [[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))
* [[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)
* [[PDB]] (Protein Data Bank)
* [[SMILES]] (Simplified molecular input line entry specification, .smi)
* [[SPC]] (spectroscopic data)
* [[Structure Data File]] (SDF)

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]] (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)

Scientific Data formats

2012-11-08T00:27:37Z

Crusbridge: /* Mathematical */

{|
|[[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]]
* [[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))
* [[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)
* [[PDB]] (Protein Data Bank)
* [[SMILES]] (Simplified molecular input line entry specification, .smi)
* [[SPC]] (spectroscopic data)
* [[Structure Data File]] (SDF)

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]] (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)

Scientific Data formats

2012-11-08T00:26:08Z

Crusbridge: Added rest of BioSharing formats

{|
|[[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]]
* [[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))
* [[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)
* [[PDB]] (Protein Data Bank)
* [[SMILES]] (Simplified molecular input line entry specification, .smi)
* [[SPC]] (spectroscopic data)
* [[Structure Data File]] (SDF)

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))
* [[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)

Scientific Data formats

2012-11-07T15:39:00Z

Crusbridge: /* Biological */ Adding HUP and BioSharing formats

{|
|[[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)
* [[SDXF]] (Structured Data Exchange Format)
* [[Silo]] (a storage format for visualization developed at Lawrence Livermore National Laboratory)* [[XDF]] (eXtensible Data Format)
* [[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
* [[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)
* [[EMBL]] (Flatfile format used by the EMBL for nucleotide and peptide sequences)
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality).
* [[GelML]]
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
* [[GTF]] (Gene transfer format holds information about gene structure)
* [[MITAB]]
* [[mzData]] (deprecated)
* [[mzIdentML]]
* [[mzML]]
* [[mzQuantML]]
* [[NEXUS]] (Encodes mixed information about genetic sequence data in a block structured format)
* [[PDB]] (Structures of biomolecules deposited in Protein Data Bank)
* [[PHD]] (Output from the basecalling software Phred)
* [[PSI-MI XML]]
* [[PSI-PAR]]
* [[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)
* [[spML]]
* [[Stockholm]] (Representing multiple sequence alignments)
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database)
* [[TraML]]
* [[VCF]] (Variant Call 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))
* [[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)
* [[PDB]] (Protein Data Bank)
* [[SMILES]] (Simplified molecular input line entry specification, .smi)
* [[SPC]] (spectroscopic data)
* [[Structure Data File]] (SDF)

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))
* [[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)

Standard Delay Format

2012-11-06T23:59:01Z

Crusbridge: Initial population

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
| >
|[[SDF]]
| >
| Standard Delay Format
|}

== General description ==

This page describes one of several data formats known as [[SDF]], in this case the Standard Delay Format file. It is a "textual file format for representing the delay and timing information of electronic systems". It has been approved as an IEEE standard P1497 in December 2001. A pre-approval version is available at [http://www.eda.org/sdf/sdf_1497_draft_0.10.pdf http://www.eda.org/sdf/sdf_1497_draft_0.10.pdf].

== Other information ==

The format is referenced in the Wikipedia [http://en.wikipedia.org/wiki/Standard_Delay_Format stub page on Standard Delay Format].

A Standard Delay Format file contains its own version number as part of its header, see below.

== Software ==

The file format can be created, read and manipulated with many different software packages..

== Sample files ==

Not known.

== Identification ==

Each Standard Delay Format file is a text file that starts with a header, starting with the string (DELAYFILE . The header next has a strong defining the version, eg (SDFVERSION "4.0"). Version 4.0 is the earliest version defined by the IEEE standard.

There is no specific naming convention for Standard Delay Format files, but more usually the file extention .sdf is used. Apparently .sdo for Standard Delay Format Output File can also be used. The MIME Type is not known.

== References ==

A pre-approval specification is available at [http://www.eda.org/sdf/sdf_1497_draft_0.10.pdf http://www.eda.org/sdf/sdf_1497_draft_0.10.pdf].

Structure Data File

2012-11-06T20:04:54Z

Crusbridge:

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

== General description ==
The Structure Data file is one of several scientific dta file formats known as [[SDF]]. It is a component of the [[CTab]] format for chemical and molecular data originally created by MDL. For more detail, see CTab.

Structure Data File

2012-11-06T20:04:12Z

Crusbridge: Initial population lining to CTab

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

== General description ==
The Structure Data file is one of several scientific dta file formats known as [[SDF]]. It is a compnent of the [[CTab]] format originally created by MDL. For more detail, see CTab.

Tabular Data Package

2012-11-06T19:45:57Z

Crusbridge:

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
| >
|[[SDF]]
| >
| Simple Data format-DPT
|}

== General description ==

This page describes one of several known [[SDF]] file formats, and at least two formats called simple data format. This one is described as a "simple data publishing format (Simple Data Format) for publishing and sharing data". (Note: in this wiki the characters "-DPT" have been arbitrarily added to distibguish this Simple Data Format from the [[Simple Data format]] created earlier by George H Fisher). It is created by the Data Protocols Team (in 2011?), whose manifesto is at [http://www.dataprotocols.org/en/latest/manifesto.html http://www.dataprotocols.org/en/latest/manifesto.html]. This does not however identify the Data Protocols Team or its affiliations.

The draft specification is at [http://www.dataprotocols.org/en/latest/simple-data-format.html http://www.dataprotocols.org/en/latest/simple-data-format.html]. The format's focus is simlicity and web usage. It is based on [[CSV]] for the base data and [[JSON]] for schema, metadata and lined data aspects.

== Other information ==

There is no know Wikipedia page for the Data Protocols Team or this version of the Simple Data Format.

== Software ==

Not known.
== Sample files ==

Not known.

== Identification ==

The file extension and MIME Type are not known.

== References ==

Apart from the manifesto and specification, nothing is known.

Simple Data format

2012-11-06T19:44:38Z

Crusbridge:

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

== General description ==

This page describes one of several known [[SDF]] file formats, and at least two formats called simple data format. This is the Simple Data Format by George H Fisher, Space Sciences Lab, UC Berkeley. It provides a simple "way of reading and writing output data from numerical simulations that preserves full precision, is simple, easy to use, that supports large (> 2GB) files, works in C, Fortran77, Fortran95, and IDL/GDL, compiles out of the box in the most common operating systems
(Linux, Windows, OS X, Solaris), and is not affected by platform endian-ness".

The format is described in [http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF/SDF_MANIFESTO.txt the Manifesto]. That document and [http://swan.gsfc.nasa.gov/RoR_WWW/workshops/2007/presentations/day4/fisher-sdf-ccmc-2007.pdf http://swan.gsfc.nasa.gov/RoR_WWW/workshops/2007/presentations/day4/fisher-sdf-ccmc-2007.pdf] seem to provide its main specification.

Version 0.74 (the latest known) dates from September 2007.

== Other information ==

There is a [http://en.wikipedia.org/wiki/Simple_Data_Format Wikipedia page about this version of the Simple Data Format] but it has very little information.

== Software ==

SDF has been tested on many different platforms including Linux and other UNIX variants, Windows and MacOSX. It can be used from C, different versions of FORTAN, and IDL. The software can be downloaded as a tarball from [http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF].

== Sample files ==

Not Known.

== Identification ==
Bytes 0-10 of a SDF file contain the string "SDF Format" including null terminator.

The file extension is .sdf and the MIME Type is not known.

== References ==

As noted, the format is described inthe Manifesto at [http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF/SDF_MANIFESTO.txt http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF/SDF_MANIFESTO.txt].

Simple Data format

2012-11-06T19:43:27Z

Crusbridge:

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

== General description ==

This page describes one of several known [[SDF]] file formats. This is the Simple Data Format by George H Fisher, Space Sciences Lab, UC Berkeley. It provides a simple "way of reading and writing output data from numerical simulations that preserves full precision, is simple, easy to use, that supports large (> 2GB) files, works in C, Fortran77, Fortran95, and IDL/GDL, compiles out of the box in the most common operating systems
(Linux, Windows, OS X, Solaris), and is not affected by platform endian-ness".

The format is described in [http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF/SDF_MANIFESTO.txt the Manifesto]. That document and [http://swan.gsfc.nasa.gov/RoR_WWW/workshops/2007/presentations/day4/fisher-sdf-ccmc-2007.pdf http://swan.gsfc.nasa.gov/RoR_WWW/workshops/2007/presentations/day4/fisher-sdf-ccmc-2007.pdf] seem to provide its main specification.

Version 0.74 (the latest known) dates from September 2007.

== Other information ==

There is a [http://en.wikipedia.org/wiki/Simple_Data_Format Wikipedia page about this version of the Simple Data Format] but it has very little information.

== Software ==

SDF has been tested on many different platforms including Linux and other UNIX variants, Windows and MacOSX. It can be used from C, different versions of FORTAN, and IDL. The software can be downloaded as a tarball from [http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF].

== Sample files ==

Not Known.

== Identification ==
Bytes 0-10 of a SDF file contain the string "SDF Format" including null terminator.

The file extension is .sdf and the MIME Type is not known.

== References ==

As noted, the format is described inthe Manifesto at [http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF/SDF_MANIFESTO.txt http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF/SDF_MANIFESTO.txt].

Tabular Data Package

2012-11-06T19:42:30Z

Crusbridge: Initial population

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
| >
|[[SDF]]
| >
| Simple Data format-DPT
|}

== General description ==

This page describes one of two scientific data file formats known as Simple Data Format. This one is described as a "simple data publishing format (Simple Data Format) for publishing and sharing data". (Note: in this wiki the characters "-DPT" have been arbitrarily added to distibguish this Simple Data Format from the [[Simple Data format]] created earlier by George H Fisher). It is created by the Data Protocols Team (in 2011?), whose manifesto is at [http://www.dataprotocols.org/en/latest/manifesto.html http://www.dataprotocols.org/en/latest/manifesto.html]. This does not however identify the Data Protocols Team or its affiliations.

The draft specification is at [http://www.dataprotocols.org/en/latest/simple-data-format.html http://www.dataprotocols.org/en/latest/simple-data-format.html]. The format's focus is simlicity and web usage. It is based on [[CSV]] for the base data and [[JSON]] for schema, metadata and lined data aspects.

== Other information ==

There is no know Wikipedia page for the Data Protocols Team or this version of the Simple Data Format.

== Software ==

Not known.
== Sample files ==

Not known.

== Identification ==

The file extension and MIME Type are not known.

== References ==

Apart from the manifesto and specification, nothing is known.

Simple Data format

2012-11-06T19:09:01Z

Crusbridge: Initial population

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

== General description ==

This page describes one of several known [[SDF]] file formats. This is the Simple Data Format by George H Fisher, Space Sciences Lab, UC Berkeley. It provides a simple "way of reading and writing output data from numerical simulations that preserves full precision, is simple, easy to use, that supports large (> 2GB) files, works in C, Fortran77, Fortran95, and IDL/GDL, compiles out of the box in the most common operating systems
(Linux, Windows, OS X, Solaris), and is not affected by platform endian-ness".

The format is described in [http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF/SDF_MANIFESTO.txt the Manifesto]. That document and [http://swan.gsfc.nasa.gov/RoR_WWW/workshops/2007/presentations/day4/fisher-sdf-ccmc-2007.pdf http://swan.gsfc.nasa.gov/RoR_WWW/workshops/2007/presentations/day4/fisher-sdf-ccmc-2007.pdf] seem to provide its main specification.

Version 0.74 (the latest known) dates from September 2007.

== Other information ==

There is a [http://en.wikipedia.org/wiki/Simple_Data_Format Wikipedia page about this version of the Simple Data Format] but it has very little information.

== Software ==

SDF has been tested on many different platforms including Linux and other UNIX variants, Windows and MacOSX. It can be used from C, different versions of FORTAN, and IDL. The software can be downloaded as a tarball from [http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF].

== Sample files ==

Not Known.

== Identification ==
Bytes 0-10 of a SDF file contain the string "SDF Format" including null terminator.

The file extension is .sdf and the MIME Type is not known.

== References ==

As noted, the format is described inthe Manifesto at [http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF/SDF_MANIFESTO.txt http://solarmuri.ssl.berkeley.edu/~fisher/public/software/SDF/SDF_MANIFESTO.txt].

SDF

2012-11-05T14:54:00Z

Crusbridge:

This is a disambiguation page. SDF as a Scientific Data format could refer to

* [[Simple Data format]] By George H. Fisher, Space Sciences Lab, UC Berkeley,
* [[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.

SDF

2012-11-04T21:57:21Z

Crusbridge: Initial creation

This is a disambiguation page. SDF as a Scientific Data format could refer to

* [[Simple Data format- Fisher]] by George H. Fisher, Space Sciences Lab, UC Berkeley
* [[Simple Data format- Data Protocols Team]]
* [[Standard Delay Format]] A standard data structure for timing data
* [[Structure Data File]] A file format for a chemical table file

EAS3

2012-11-04T20:40:50Z

Crusbridge: Initial page population

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific Data formats]]
| >
| EAS3
|}

== General description ==

This page describes the EAS3 file format. It is the product of a toolkit intended to help transfer floating point data between computers, to convert it to other formats and process it. It is intended to help deal with problems such as endianness and floating point implementation differences between computers. EAS stands for Ein Ausgabe System.

The format was designed by the Institut für Aerodynamik und Gasdynamik (IAG) of the Universität Stuttgart, and is described in their [https://www.iag.uni-stuttgart.de/eas3wiki/index.php/Main_Page EAS3 web pages]. (This site has an out-of-date certificate; it claims that a new wiki is under development but not yet available.)

== Other information ==

The format is referenced in the Wikipedia [http://en.wikipedia.org/wiki/EAS3 page on EAS3].

EAS3 is a successor to EAS2. The EAS3 web site shows a version history. It is published under the GPL-compatible MIT licence, and therefore can be considered Open.

== Software ==

Include processing and/or migration information, eg:

The file format can be processed using the EAS3 command-line software program from the same source..

== Sample files ==

Many sample xxxxx files are available in the yyyyy

== Identification ==

Factors that can help identify a candidate file as of this format. Include magic numbers, signatures etc if available. Eg:

The file extension is .eas and the MIME Type is ??. The Magic number is EAS3_I8R8.

== References ==

List articles, books or web pages describing the format or supporting the evidence: NA.

NetCDF

2012-11-04T20:14:00Z

Crusbridge:

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

== General description ==

The Network Common Data Form (netCDF) is a long-lived set of file formats and associated APIs designed by UCAR for multi-dimensional datasets. (Though its name resembles that of [[cdf]], and their original designs were similar, the two products have greatly diverged.) The various versions are widely used in environmental science, especially atmospheric and oceanographic research. Currently it has two main versions, netCDF-3 and netCDF-4, which are quite different in implementation, and moderately different in API. There are also "subversions" of netCDF-3, notably "netCDF Classic." Tool support for netCDF-3 continues to exceed that for netCDF-4; but the latter, based on [[HDF5]], is generally considered technically superior, so its tool support is increasing rapidly.

Notable features of netCDF include

* incorporation of metadata. netCDF is said to be "self-describing," in that the file format provides for a header describing the structure of the data. In practice, the utility of its metadata depends on the extent to which the data author provides and maintains it.
* platform independence via API: provided the user manipulates netCDF files via supported APIs (which are numerous), the user can effectively ignore issues such as endianness.
* backward compatibility. Software and API capable of manipulating netCDF-4 is also capable of manipulating netCDF-3, though of course advanced features of the later version are not accessible to files written for the earlier version.

According to the FAQ,there are 4 main versions of NetCDF:

* the classic format
* the 64-bit offset format
* the netCDF-4 format
* the netCDF-4 classic model format
Either of the first two may be referred to as NetCDF-3.

NetCDF is described on the [http://www.unidata.ucar.edu/software/netcdf/ Unidata pages] of the UCAR web site. A short document [http://www.esdswg.org/spg/rfc/esds-rfc-011/ESDS-RFC-011v1.00.pdf describing early versions] has been accepted as a standard by NASA.

== Other information ==

The format is referenced in the Wikipedia [http://en.wikipedia.org/wiki/NetCDF page on NetCDF].

NetCDF claims full backwards compatibility.

Software and information is made available according to [http://www2.ucar.edu/terms-of-use UCAR Terms of Use], which indicate they are not usable for commercial purposes.

== Software ==
There is a wide range of software available to create and process NetCDF files. The Wikipedia article mentioned above has a starter list.

== Sample files ==

Sample NetCDF files are available on the [http://www.unidata.ucar.edu/software/netcdf/examples/files.html Unidata web site].

== Identification ==

The magic number is CDF\001 .

The file extension is .nc (originally .cdf) and the MIME Type is application/netcdf or
application/x-netcdf.

== References ==

The User's Guide is: Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies, NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.

NetCDF

2012-11-04T18:56:02Z

Crusbridge:

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

== General description ==

The Network Common Data Form (netCDF) is a long-lived set of file formats and associated APIs designed by UCAR for multi-dimensional datasets. (Though its name resembles that of [[CDF]], and their original designs were similar, the two products have greatly diverged.) The various versions are widely used in environmental science, especially atmospheric and oceanographic research. Currently it has two main versions, netCDF-3 and netCDF-4, which are quite different in implementation, and moderately different in API. There are also "subversions" of netCDF-3, notably "netCDF Classic." Tool support for netCDF-3 continues to exceed that for netCDF-4; but the latter, based on [[HDF5]], is generally considered technically superior, so its tool support is increasing rapidly.

Notable features of netCDF include

* incorporation of metadata. netCDF is said to be "self-describing," in that the file format provides for a header describing the structure of the data. In practice, the utility of its metadata depends on the extent to which the data author provides and maintains it.
* platform independence via API: provided the user manipulates netCDF files via supported APIs (which are numerous), the user can effectively ignore issues such as endianness.
* backward compatibility. Software and API capable of manipulating netCDF-4 is also capable of manipulating netCDF-3, though of course advanced features of the later version are not accessible to files written for the earlier version.

There are 4 main versions of NetCDF:

* the classic format
* the 64-bit offset format
* the netCDF-4 format
* the netCDF-4 classic model format
Either of the first two may be referred to as NetCDF-3.

NetCDF is described on the [http://www.unidata.ucar.edu/software/netcdf/ Unidata pages] of the UCAR web site. A short document [http://www.esdswg.org/spg/rfc/esds-rfc-011/ESDS-RFC-011v1.00.pdf describing early versions] has been accepted as a standard by NASA.

== Other information ==

The format is referenced in the Wikipedia [http://en.wikipedia.org/wiki/NetCDF page on NetCDF].

NetCDF claims full backwards compatibility.

Software and information is made available according to [http://www2.ucar.edu/terms-of-use UCAR Terms of Use], which indicate they are freely usable for non-commercial purposes.

== Software ==
There is a wide range of software available to create and process NetCDF files. The Wikipedia article mentioned above as a good starter list.

== Sample files ==

Sample NetCDF files are available on the [http://www.unidata.ucar.edu/software/netcdf/examples/files.html Unidata web site].

== Identification ==

The magic number is CDF\001 .

The file extension is .nc (originally .cdf) and the MIME Type is application/netcdf or
application/x-netcdf.

== References ==

The User's Guide is: Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies, NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.

NetCDF

2012-11-04T18:55:01Z

Crusbridge: Restructured page to new template and added more information

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

== General description ==

The Network Common Data Form (netCDF) is a long-lived set of file formats and associated APIs designed by UCAR for multi-dimensional datasets. (Though its name resembles that of [[CDF]], and their original designs were similar, the two products have greatly diverged.) The various versions are widely used in environmental science, especially atmospheric and oceanographic research. Currently it has two main versions, netCDF-3 and netCDF-4, which are quite different in implementation, and moderately different in API. There are also "subversions" of netCDF-3, notably "netCDF Classic." Tool support for netCDF-3 continues to exceed that for netCDF-4; but the latter, based on [[HDF5]], is generally considered technically superior, so its tool support is increasing rapidly.

Notable features of netCDF include

* incorporation of metadata. netCDF is said to be "self-describing," in that the file format provides for a header describing the structure of the data. In practice, the utility of its metadata depends on the extent to which the data author provides and maintains it.
* platform independence via API: provided the user manipulates netCDF files via supported APIs (which are numerous), the user can effectively ignore issues such as endianness.
* backward compatibility. Software and API capable of manipulating netCDF-4 is also capable of manipulating netCDF-3, though of course advanced features of the later version are not accessible to files written for the earlier version.

There are 4 main versions of NetCDF:

* the classic format
* the 64-bit offset format
* the netCDF-4 format
* the netCDF-4 classic model format
Either of the first two may be referred to as NetCDF-3.

NetCDF is described on the [http://www.unidata.ucar.edu/software/netcdf/ Unidata pages] of the UCAR web site. A short document [http://www.esdswg.org/spg/rfc/esds-rfc-011/ESDS-RFC-011v1.00.pdf describing early versions] has been accepted as a standard by NASA.

== Other information ==

Include other information describing the format, eg Wikipedia pages, PRONOM or LoC identifiers, etc. Eg

The format is referenced in the Wikipedia [http://en.wikipedia.org/wiki/NetCDF page on NetCDF].

NetCDF claims full backwards compatibility.

Software and information is made available according to [http://www2.ucar.edu/terms-of-use UCAR Terms of Use], which indicate they are freely usable for non-commercial purposes.

== Software ==
There is a wide range of software available to create and process NetCDF files. The Wikipedia article mentioned above as a good starter list.

== Sample files ==

Sample NetCDF files are available on the [http://www.unidata.ucar.edu/software/netcdf/examples/files.html Unidata web site].

== Identification ==

The magic number is CDF\001 .

The file extension is .nc (originally .cdf) and the MIME Type is application/netcdf or
application/x-netcdf.

== References ==

The User's Guide is: Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies, NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.

OME-TIFF

2012-11-04T18:23:07Z

Crusbridge: Restructured page to new template

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

== General description ==
This page describes the OME-TIFF file format, created by the Open Microscopy Environment Consortium to combine the strengths of [[OME-XML]] and [[TIFF]]. The format is described at the [http://www.openmicroscopy.org/site/support/file-formats/ome-tiff OME-TIFF Overview and Rationale page], where there is also a link to the specification.

== Other information ==
NA

== Software ==
The file format can be created, read and manipulated using the [http://loci.wisc.edu/software/bio-formats Bio-Formats Library] and the [http://www.openmicroscopy.org/site/support/omero4 OMERO Server]. There is an [http://validator.openmicroscopy.org.uk/ OME Validator to check files].

== Sample files ==
Some sample [http://www.openmicroscopy.org/site/support/file-formats/ome-tiff/ome-tiff-data OME-TIFF files] are available.

== Identification ==
The file extension is .ome.tif and the MIME Type is xxxxx.

== References ==
Linkert, M., Rueden, C. T., Allan, C., Burel, J.-M., Moore, W., Patterson, A., Loranger, B., et al. (2010). Metadata matters: access to image data in the real world. The Journal of cell biology, 189(5), 777–82. doi:10.1083/jcb.201004104

Geospatial

2012-11-04T18:19:07Z

Crusbridge: Added cross reference

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|Geospatial
|}
== Cross reference ==
See also [http://justsolve.archiveteam.org/index.php/Scientific_Data_formats#Geographic_and_Geospatial the Scientific Data formats section].

== Raster Formats ==

* [[GeoTIFF]]
* [[MrSID]]

== Vector Formats ==
* [[SHP]] -- shapefile
* [[KML]]
* [[E00]] -- ArcInfo interchange file

== Grid Formats -- see raster formats, above ==

== Point cloud ==
* [[LAS]]

OME-XML

2012-11-04T18:15:47Z

Crusbridge: Restructured page to new template

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

== General description ==
This page describes the OME-XML file format for Open Microscopy, defined to make it simple to move microscopy data from one site and user to another. This format is related to [[OME-TIFF]], which was developed from it. The format is described on the [http://www.openmicroscopy.org/site/support/file-formats/the-ome-xml-file OME-XML page] at the Open Microscopy site.

== Other information ==
NA

== Software ==
The file format can be created, read and manipulated using the [http://loci.wisc.edu/software/bio-formats Bio-Formats Library] and the [http://www.openmicroscopy.org/site/support/omero4 OMERO Server]. There is an [http://validator.openmicroscopy.org.uk/ OME Validator] to check files, which can lso tell you the OME-XML version. However, almost any software can read the files; you don't need OME software to use OME-XML.

== Sample files ==
NA

== Identification ==
The file extension is .ome.xml and the MIME Type is xxxxx.

== References ==
The original paper describing the concept is Goldberg, I. G., Allan, C., Burel, J.-M., Creager, D., Falconi, A., Hochheiser, H., Johnston, J., et al. (2005). The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome biology, 6(5), R47. doi:10.1186/gb-2005-6-5-r47 .

Crtemplate

2012-11-04T15:05:09Z

Crusbridge: Created page with "{| |File Formats | > |Electronic File Formats | > |xxxxx | > | xxxxx |} == General description == This page describes the xxxxx file format, xxxxx (include brief..."

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

== General description ==

This page describes the xxxxx file format, xxxxx (include brief information about the format, including name(s) by which it is commonly known.

Include link to any authoritative web site(s) about the format, particularly the prime sponsor, and if possible a direct link to a specification, schema etc.

== Other information ==

Include other information describing the format, eg Wikipedia pages, PRONOM or LoC identifiers, etc. Eg

The format is referenced in the Wikipedia [http://en.wikipedia.org/wiki/xxxxx page on xxxxx].

Indicate any version-specific information that may be available. Indicate openness (or otherwise) of the format.

== Software ==

Include processing and/or migration information, eg:

The file format can be created, read and manipulated using the [http://url xxx Open Source software application].

== Sample files ==

Many sample xxxxx files are available in the yyyyy

== Identification ==

Factors that can help identify a candidate file as of this format. Include magic numbers, signatures etc if available. Eg:

The file extension is .xx and the MIME Type is xxxxx.

== References ==

List articles, books or web pages describing the format or supporting the evidence.

User:Crusbridge

2012-11-04T15:04:07Z

Crusbridge:

I don't really have a web site, but I do blog at [http://unsustainableideas.wordpress.com/ Unsustainable Ideas]. I'm also @carusb on Twitter.

Here's a suggested simpler template: [[crtemplate]]

OME-XML

2012-11-04T02:42:30Z

Crusbridge: Initial page population

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

This page describes the OME-XML file format for Open Microscopy, defined to make it simple to move microscopy data from one site and user to another. This format is related to [[OME-TIFF]], which was developed from it. The format is described on the [http://www.openmicroscopy.org/site/support/file-formats/the-ome-xml-file OME-XML page] at the Open Microscopy site.

The file format can be created, read and manipulated using the [http://loci.wisc.edu/software/bio-formats Bio-Formats Library] and the [http://www.openmicroscopy.org/site/support/omero4 OMERO Server]. There is an [http://validator.openmicroscopy.org.uk/ OME Validator] to check files, which can lso tell you the OME-XML version. However, almost any software can read the files; you don't need OME software to use OME-XML.

The file extension is .ome.xml and the MIME Type is xxxxx.

The original paper describing the concept is Goldberg, I. G., Allan, C., Burel, J.-M., Creager, D., Falconi, A., Hochheiser, H., Johnston, J., et al. (2005). The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome biology, 6(5), R47. doi:10.1186/gb-2005-6-5-r47 .

OME-TIFF

2012-11-04T02:16:56Z

Crusbridge:

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

This page describes the OME-TIFF file format, created by the Open Microscopy Environment Consortium to combine the strengths of [[OME-XML]] and [[TIFF]]. The format is described at the [http://www.openmicroscopy.org/site/support/file-formats/ome-tiff OME-TIFF Overview and Rationale page], where there is also a link to the specification.

The file format can be created, read and manipulated using the [http://loci.wisc.edu/software/bio-formats Bio-Formats Library] and the [http://www.openmicroscopy.org/site/support/omero4 OMERO Server]. There is an [http://validator.openmicroscopy.org.uk/ OME Validator to check files].

Some sample [http://www.openmicroscopy.org/site/support/file-formats/ome-tiff/ome-tiff-data OME-TIFF files] are available.

The file extension is .ome.tif and the MIME Type is xxxxx.

Reference: Linkert, M., Rueden, C. T., Allan, C., Burel, J.-M., Moore, W., Patterson, A., Loranger, B., et al. (2010). Metadata matters: access to image data in the real world. The Journal of cell biology, 189(5), 777–82. doi:10.1083/jcb.201004104

OME-TIFF

2012-11-04T02:16:08Z

Crusbridge:

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

This page describes the OME-TIFF file format, created by the Open Microscopy Environment Consortium to combine the strengths of [[OME-XML]] and [[TIFF]]. The format is described at the [http://www.openmicroscopy.org/site/support/file-formats/ome-tiff OME-TIFF Overview and Rationale page], where there is also a link to the specification.

The file format can be created, read and manipulated using the [http://loci.wisc.edu/software/bio-formats Bio-Formats Library] and the [http://www.openmicroscopy.org/site/support/omero4 OMERO Server]. There is a [http://validator.openmicroscopy.org.uk/ OME Validator to check files].

Some sample [http://www.openmicroscopy.org/site/support/file-formats/ome-tiff/ome-tiff-data OME-TIFF files] are available.

The file extension is .ome.tif and the MIME Type is xxxxx.

Reference: Linkert, M., Rueden, C. T., Allan, C., Burel, J.-M., Moore, W., Patterson, A., Loranger, B., et al. (2010). Metadata matters: access to image data in the real world. The Journal of cell biology, 189(5), 777–82. doi:10.1083/jcb.201004104

OME-TIFF

2012-11-04T02:15:38Z

Crusbridge: Initial creation

{|
|[[File Formats]]
| >
|[[Electronic File Formats]]
| >
|[[Scientific data]]
| >
| OME-TIFF
|}

This page describes the OME-TIFF file format, created by the Open Microscopy Environment Consortium to combine the strengths of [[OME-XML]] and [[TIFF]]. The format is described at the [http://www.openmicroscopy.org/site/support/file-formats/ome-tiff OME-TIFF Overview and Rationale page], where there is also a link to the specification.

The file format can be created, read and manipulated using the [http://loci.wisc.edu/software/bio-formats Bio-Formats Library] and the [http://www.openmicroscopy.org/site/support/omero4 OMERO Server]. There is a [http://validator.openmicroscopy.org.uk/ OME Validator to check files].

Some sample [http://www.openmicroscopy.org/site/support/file-formats/ome-tiff/ome-tiff-data OME-TIFF files] are available.

The file extension is .ome.tif and the MIME Type is xxxxx.

Reference: Linkert, M., Rueden, C. T., Allan, C., Burel, J.-M., Moore, W., Patterson, A., Loranger, B., et al. (2010). Metadata matters: access to image data in the real world. The Journal of cell biology, 189(5), 777–82. doi:10.1083/jcb.201004104

Scientific Data formats

2012-11-04T01:57:32Z

Crusbridge: /* Medical Imaging */

{|
|[[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)
* [[SDF]] (Simple Data Format, a platform-independent, precision-preserving binary data I/O format capable of handling large, multi-dimensional arrays)
* [[SDXF]] (Structured Data Exchange Format)
* [[Silo]] (a storage format for visualization developed at Lawrence Livermore National Laboratory)* [[XDF]] (eXtensible Data Format)
* [[XSIL]] (Extensible Scientific Interchange Language)

== Astronomical and Space ==
* [[FITS]] (Flexible Image Transport System)
* [[PDS/ODL]] (Planetary Data System)

== Biological ==

* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
* [[ACE]] (Sequence assembly format)
* [[BAM]] (Binary compressed SAM format)
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
* [[CAF]] (Common Assembly Format for sequence assembly)
* [[EMBL]] (Flatfile format used by the EMBL for nucleotide and peptide sequences)
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality).
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
* [[GTF]] (Gene transfer format holds information about gene structure)
* [[NEXUS]] (Encodes mixed information about genetic sequence data in a block structured format)
* [[PDB]] (Structures of biomolecules deposited in Protein Data Bank)
* [[PHD]] (Output from the basecalling software Phred)
* [[SAM]] (Sequence Alignment/Map format)
* [[SCF]] (Staden chromatogram files used to store data from DNA sequencing)
* [[SBML]] (Systems Biology Markup Language used to store biochemical network computational models)
* [[Stockholm]] (Representing multiple sequence alignments)
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database)
* [[VCF]] (Variant Call Format)

== Biomedical signals (time series) ==

* [[ACQ]] (AcqKnowledge)
* [[BCI2000]] (The BCI2000 project)
* [[BDF]] (BioSemi data format0
* [[BKR]] (EEG data format)
* [[CFWB]] (Chart Data File Format)
* [[ DICOM-Waveform]] (An extension of Dicom for storing waveform data)
* [[ecgML]] (A markup language for electrocardiogram data acquisition and analysis)
* [[EDF/EDF+]] (European Data Format)
* [[FEF]] (File Exchange Format for Vital signs, CEN TS 14271)
* [[GDF v1.x]] (General Data Format for biomedical signals - Version 1.x)
* [[ GDF v2.x]] (The General Data Format for biomedical signals - Version 2.x)
* [[ HL7aECG]] (Health Level 7 v3 annotated ECG)
* [[OpenXDF]] (Open Exchange Data Format)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SIGIF]] (A digital SIGnal Interchange Format)
* [[WFDB]] (Format of Physiobank)

== Chemical ==
* [[CCP4]] (X-ray crystallography voxels (electron density))
* [[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)
* [[PDB]] (Protein Data Bank)
* [[SDF]] (Structure Data File)
* [[SMILES]] (Simplified molecular input line entry specification, .smi)
* [[SPC]] (spectroscopic data)

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))
* [[M]] (Mathematica package file)
* [[MathML]]

== Medical Imaging ==
* [[AFNI]] (data, meta-data (.BRIK,.HEAD))
* [[MGH]] (uncompressed)
* [[MGZ]] (zip-compressed)
* [[Analyze data, meta-data]] (.img,.hdr)
* [[DICOM]] (Digital Imaging and Communications in Medicine (.dcm))
* [[MINC]] (Medical Imaging NetCDF format; since version 2.0, based on HDF5 (.mnc))
* [[OME-TIFF]] (Open Microscopy Imaging format)
* [[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)
* [[BKR]] (EEG data format)
* [[BDF]] (BioSemi data format)
* [[CFWB]] (Chart Data File Format)
* [[EDF]] (European data format)
* [[FEF]] (File Exchange Format for Vital signs)
* [[GDF]] (General data formats for biomedical signals)
* [[GMS]] (Gesture And Motion Signal format)
* [[IROCK]] (intelliRock Sensor Data File Format)
* [[MFER]] (Medical waveform Format Encoding Rules)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SEG Y]] (Reflection seismology data format)
* [[SIGIF]] (SIGnal Interchange Format)

== Social Sciences ==

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

Scientific Data formats

2012-11-04T01:53:53Z

Crusbridge: /* Chemical */ Added back elements from Chemical data page

{|
|[[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)
* [[SDF]] (Simple Data Format, a platform-independent, precision-preserving binary data I/O format capable of handling large, multi-dimensional arrays)
* [[SDXF]] (Structured Data Exchange Format)
* [[Silo]] (a storage format for visualization developed at Lawrence Livermore National Laboratory)* [[XDF]] (eXtensible Data Format)
* [[XSIL]] (Extensible Scientific Interchange Language)

== Astronomical and Space ==
* [[FITS]] (Flexible Image Transport System)
* [[PDS/ODL]] (Planetary Data System)

== Biological ==

* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
* [[ACE]] (Sequence assembly format)
* [[BAM]] (Binary compressed SAM format)
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
* [[CAF]] (Common Assembly Format for sequence assembly)
* [[EMBL]] (Flatfile format used by the EMBL for nucleotide and peptide sequences)
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality).
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
* [[GTF]] (Gene transfer format holds information about gene structure)
* [[NEXUS]] (Encodes mixed information about genetic sequence data in a block structured format)
* [[PDB]] (Structures of biomolecules deposited in Protein Data Bank)
* [[PHD]] (Output from the basecalling software Phred)
* [[SAM]] (Sequence Alignment/Map format)
* [[SCF]] (Staden chromatogram files used to store data from DNA sequencing)
* [[SBML]] (Systems Biology Markup Language used to store biochemical network computational models)
* [[Stockholm]] (Representing multiple sequence alignments)
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database)
* [[VCF]] (Variant Call Format)

== Biomedical signals (time series) ==

* [[ACQ]] (AcqKnowledge)
* [[BCI2000]] (The BCI2000 project)
* [[BDF]] (BioSemi data format0
* [[BKR]] (EEG data format)
* [[CFWB]] (Chart Data File Format)
* [[ DICOM-Waveform]] (An extension of Dicom for storing waveform data)
* [[ecgML]] (A markup language for electrocardiogram data acquisition and analysis)
* [[EDF/EDF+]] (European Data Format)
* [[FEF]] (File Exchange Format for Vital signs, CEN TS 14271)
* [[GDF v1.x]] (General Data Format for biomedical signals - Version 1.x)
* [[ GDF v2.x]] (The General Data Format for biomedical signals - Version 2.x)
* [[ HL7aECG]] (Health Level 7 v3 annotated ECG)
* [[OpenXDF]] (Open Exchange Data Format)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SIGIF]] (A digital SIGnal Interchange Format)
* [[WFDB]] (Format of Physiobank)

== Chemical ==
* [[CCP4]] (X-ray crystallography voxels (electron density))
* [[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)
* [[PDB]] (Protein Data Bank)
* [[SDF]] (Structure Data File)
* [[SMILES]] (Simplified molecular input line entry specification, .smi)
* [[SPC]] (spectroscopic data)

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))
* [[M]] (Mathematica package file)
* [[MathML]]

== Medical Imaging ==
* [[AFNI]] (data, meta-data (.BRIK,.HEAD))
* [[.MGH]] (uncompressed)
* [[.MGZ]] (zip-compressed)
* [[Analyze data, meta-data]] (.img,.hdr)
* [[DICOM]] (Digital Imaging and Communications in Medicine (.dcm))
* [[MINC]] (Medical Imaging NetCDF format; since version 2.0, based on HDF5 (.mnc))
* [[OME-TIFF]] (Open Microscopy Imaging format)
* [[OST (Open Spatio-Temporal)]] (extensible, open alternative for microscope images)
* [[nii]] (Neuroimaging Informatics Technology Initiative (NIfTI) single-file (combined data and meta-data))
* [[gii]] (NIfTI offspring for brain surface data, single-file (combined data and meta-data) style)
* [[.img,.hdr]] (NIfTI offspring for brain surface data, dual-file (separate data and meta-data, respectively) style)
* [[SDM]] (Signed Differential Mapping- brain maps(.sdm))

== Oceanographic, Atmospheric and Meteorological ==

* [[GRIB]] (Grid in Binary)
* [[BUFR]] (Binary Universal Format Representation)
* [[IOAPI]] (netCDF augmented with metadata from the I/O API)
* [[PP]] (UK Met Office format for weather model data)

== Physics ==

* [[CGNS]] (Computational Fluid Dynamics General Notation System)
* [[NeXuS]] (Common data format for neutron, x-ray and muon science)
* [[QCDml]] (Lattice QCD gauge configuration markup language)

== Scientific Signal data ==

* [[ACQ]] (AcqKnowledge File Format for Windows)
* [[BKR]] (EEG data format)
* [[BDF]] (BioSemi data format)
* [[CFWB]] (Chart Data File Format)
* [[EDF]] (European data format)
* [[FEF]] (File Exchange Format for Vital signs)
* [[GDF]] (General data formats for biomedical signals)
* [[GMS]] (Gesture And Motion Signal format)
* [[IROCK]] (intelliRock Sensor Data File Format)
* [[MFER]] (Medical waveform Format Encoding Rules)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SEG Y]] (Reflection seismology data format)
* [[SIGIF]] (SIGnal Interchange Format)

== Social Sciences ==

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

Scientific Data formats

2012-11-03T16:23:37Z

Crusbridge: Listed a bunch more formats, sourced from Wikipedia

{|
|[[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)
* [[SDF]] (Simple Data Format, a platform-independent, precision-preserving binary data I/O format capable of handling large, multi-dimensional arrays)
* [[SDXF]] (Structured Data Exchange Format)
* [[Silo]] (a storage format for visualization developed at Lawrence Livermore National Laboratory)* [[XDF]] (eXtensible Data Format)
* [[XSIL]] (Extensible Scientific Interchange Language)

== Astronomical and Space ==
* [[FITS]] (Flexible Image Transport System)
* [[PDS/ODL]] (Planetary Data System)

== Biological ==

* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
* [[ACE]] (Sequence assembly format)
* [[BAM]] (Binary compressed SAM format)
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
* [[CAF]] (Common Assembly Format for sequence assembly)
* [[EMBL]] (Flatfile format used by the EMBL for nucleotide and peptide sequences)
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality).
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
* [[GTF]] (Gene transfer format holds information about gene structure)
* [[NEXUS]] (Encodes mixed information about genetic sequence data in a block structured format)
* [[PDB]] (Structures of biomolecules deposited in Protein Data Bank)
* [[PHD]] (Output from the basecalling software Phred)
* [[SAM]] (Sequence Alignment/Map format)
* [[SCF]] (Staden chromatogram files used to store data from DNA sequencing)
* [[SBML]] (Systems Biology Markup Language used to store biochemical network computational models)
* [[Stockholm]] (Representing multiple sequence alignments)
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database)
* [[VCF]] (Variant Call Format)

== Biomedical signals (time series) ==

* [[ACQ]] (AcqKnowledge)
* [[BCI2000]] (The BCI2000 project)
* [[BDF]] (BioSemi data format0
* [[BKR]] (EEG data format)
* [[CFWB]] (Chart Data File Format)
* [[ DICOM-Waveform]] (An extension of Dicom for storing waveform data)
* [[ecgML]] (A markup language for electrocardiogram data acquisition and analysis)
* [[EDF/EDF+]] (European Data Format)
* [[FEF]] (File Exchange Format for Vital signs, CEN TS 14271)
* [[GDF v1.x]] (General Data Format for biomedical signals - Version 1.x)
* [[ GDF v2.x]] (The General Data Format for biomedical signals - Version 2.x)
* [[ HL7aECG]] (Health Level 7 v3 annotated ECG)
* [[OpenXDF]] (Open Exchange Data Format)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SIGIF]] (A digital SIGnal Interchange Format)
* [[WFDB]] (Format of Physiobank)

== Chemical ==
* [[CCP4]] (X-ray crystallography voxels (electron density))
* [[Chemical data]]
* [[CTab]] (Chemical table file .mol, .sd, .sdf)
* [[HITRAN]] (spectroscopic data with one optical/infrared transition per line in the ASCII file (.hit))
* [[JCAMP]] (Joint Committee on Atomic and Molecular Physical Data, .dx, .jdx)
* [[MRC]] (voxels in cryo-electron microscopy)
* [[SMILES]] (Simplified molecular input line entry specification, .smi)
* [[SPC]] (spectroscopic data)

== Ecological ==
* [[Darwin Core]] (Standard for sharing information about biological diversity)
* [[EML]] (Ecological Metadata Language)

== Geographic and Geospatial ==

See also [[Geospatial]]

* [[DEM]] (Digital Elevation Model)
* [[DOQ]] (Digital Orthophotos)
* [[e00]] (ESRI ArcInfo Interchange File)
* [[FGDC]] (Content Standard for Digital Geospatial Metadata??)
* [[GeoTIFF]] (Geospatial extensions to TIFF)
* [[GML]] (Geography Markup Language)
* [[HDFEOS, HD2, HD4]] (Hierarchical Data Format-Earth Observing System)
* [[KML]] (KML (formerly Keyhole Markup Language), Version 2.2)
* [[NDF]] (National Landsat Archive Production System (NLAPS) Data Format)
* [[SAIF]] (Spatial Archive and Interchange Format, Canadian)
* [[SDTS]] (Spatial Data Transfer Standard)
* [[shp and shx]] (ESRI Shaepfile must have components; other optional components as well, see entry)
* [[SID]] (MrSID- Multi-resolution Seamless Image Database)
* [[TAB]] (MapInfo dataset format, must have component)

== Mathematical ==
* [[graph6, sparse6]] (ASCII encoding of Adjacency matrices (.g6, .s6))
* [[M]] (Mathematica package file)
* [[MathML]]

== Medical Imaging ==
* [[AFNI]] (data, meta-data (.BRIK,.HEAD))
* [[.MGH]] (uncompressed)
* [[.MGZ]] (zip-compressed)
* [[Analyze data, meta-data]] (.img,.hdr)
* [[DICOM]] (Digital Imaging and Communications in Medicine (.dcm))
* [[MINC]] (Medical Imaging NetCDF format; since version 2.0, based on HDF5 (.mnc))
* [[OME-TIFF]] (Open Microscopy Imaging format)
* [[OST (Open Spatio-Temporal)]] (extensible, open alternative for microscope images)
* [[nii]] (Neuroimaging Informatics Technology Initiative (NIfTI) single-file (combined data and meta-data))
* [[gii]] (NIfTI offspring for brain surface data, single-file (combined data and meta-data) style)
* [[.img,.hdr]] (NIfTI offspring for brain surface data, dual-file (separate data and meta-data, respectively) style)
* [[SDM]] (Signed Differential Mapping- brain maps(.sdm))

== Oceanographic, Atmospheric and Meteorological ==

* [[GRIB]] (Grid in Binary)
* [[BUFR]] (Binary Universal Format Representation)
* [[IOAPI]] (netCDF augmented with metadata from the I/O API)
* [[PP]] (UK Met Office format for weather model data)

== Physics ==

* [[CGNS]] (Computational Fluid Dynamics General Notation System)
* [[NeXuS]] (Common data format for neutron, x-ray and muon science)
* [[QCDml]] (Lattice QCD gauge configuration markup language)

== Scientific Signal data ==

* [[ACQ]] (AcqKnowledge File Format for Windows)
* [[BKR]] (EEG data format)
* [[BDF]] (BioSemi data format)
* [[CFWB]] (Chart Data File Format)
* [[EDF]] (European data format)
* [[FEF]] (File Exchange Format for Vital signs)
* [[GDF]] (General data formats for biomedical signals)
* [[GMS]] (Gesture And Motion Signal format)
* [[IROCK]] (intelliRock Sensor Data File Format)
* [[MFER]] (Medical waveform Format Encoding Rules)
* [[SCP-ECG]] (Standard Communication Protocol for Computer assisted electrocardiography)
* [[SEG Y]] (Reflection seismology data format)
* [[SIGIF]] (SIGnal Interchange Format)

== Social Sciences ==

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

Scientific Data formats

2012-11-03T02:55:08Z

Crusbridge: /* Medical Imaging */

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

== General ==
* [[cdf]] (Common Data Format)
* [[hdf]] (Hierarchical Data Format, from NASA)
* [[NetCDF]] (Network Common Data Format)
* [[SDXF]] (Structured Data Exchange Format)
* [[XDF]] (eXtensible Data Format)
* [[XSIL]] (Extensible Scientific Interchange Language)

== Astronomical and Space ==
* [[FITS]] (Flexible Image Transport System)
* [[PDS/ODL]] (Planetary Data System)

== Biological ==

* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
* [[ACE]] (Sequence assembly format)
* [[BAM]] (Binary compressed SAM format)
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
* [[CAF]] (Common Assembly Format for sequence assembly)
* [[EMBL]] (Flatfile format used by the EMBL for nucleotide and peptide sequences)
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality).
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
* [[GTF]] (Gene transfer format holds information about gene structure)
* [[NEXUS]] (Encodes mixed information about genetic sequence data in a block structured format)
* [[PDB]] (Structures of biomolecules deposited in Protein Data Bank)
* [[PHD]] (Output from the basecalling software Phred)
* [[SAM]] (Sequence Alignment/Map format)
* [[SCF]] (Staden chromatogram files used to store data from DNA sequencing)
* [[SBML]] (Systems Biology Markup Language used to store biochemical network computational models)
* [[Stockholm]] (Representing multiple sequence alignments)
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database)
* [[VCF]] (Variant Call Format)

== Chemical ==
* [[Chemical data]]

== Ecological ==
* [[Darwin Core]] (Standard for sharing information about biological diversity)
* [[EML]] (Ecological Metadata Language)

== Geographic and Geospatial ==

See also [[Geospatial]]

* [[DEM]] (Digital Elevation Model)
* [[DOQ]] (Digital Orthophotos)
* [[e00]] (ESRI ArcInfo Interchange File)
* [[FGDC]] (Content Standard for Digital Geospatial Metadata??)
* [[GeoTIFF]] (Geospatial extensions to TIFF)
* [[GML]] (Geography Markup Language)
* [[HDFEOS, HD2, HD4]] (Hierarchical Data Format-Earth Observing System)
* [[KML]] (KML (formerly Keyhole Markup Language), Version 2.2)
* [[NDF]] (National Landsat Archive Production System (NLAPS) Data Format)
* [[SAIF]] (Spatial Archive and Interchange Format, Canadian)
* [[SDTS]] (Spatial Data Transfer Standard)
* [[shp and shx]] (ESRI Shaepfile must have components; other optional components as well, see entry)
* [[SID]] (MrSID- Multi-resolution Seamless Image Database)
* [[TAB]] (MapInfo dataset format, must have component)

== Mathematical ==

* [[MathML]]

== Medical Imaging ==
* [[DICOM]]
* [[OME-TIFF]] (Open Microscopy Imaging format)

== 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)

== Social Sciences ==

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

Scientific Data formats

2012-11-03T02:54:49Z

Crusbridge: /* Medical Imaging */ added OME-TIFF

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

== General ==
* [[cdf]] (Common Data Format)
* [[hdf]] (Hierarchical Data Format, from NASA)
* [[NetCDF]] (Network Common Data Format)
* [[SDXF]] (Structured Data Exchange Format)
* [[XDF]] (eXtensible Data Format)
* [[XSIL]] (Extensible Scientific Interchange Language)

== Astronomical and Space ==
* [[FITS]] (Flexible Image Transport System)
* [[PDS/ODL]] (Planetary Data System)

== Biological ==

* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
* [[ACE]] (Sequence assembly format)
* [[BAM]] (Binary compressed SAM format)
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
* [[CAF]] (Common Assembly Format for sequence assembly)
* [[EMBL]] (Flatfile format used by the EMBL for nucleotide and peptide sequences)
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality).
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
* [[GTF]] (Gene transfer format holds information about gene structure)
* [[NEXUS]] (Encodes mixed information about genetic sequence data in a block structured format)
* [[PDB]] (Structures of biomolecules deposited in Protein Data Bank)
* [[PHD]] (Output from the basecalling software Phred)
* [[SAM]] (Sequence Alignment/Map format)
* [[SCF]] (Staden chromatogram files used to store data from DNA sequencing)
* [[SBML]] (Systems Biology Markup Language used to store biochemical network computational models)
* [[Stockholm]] (Representing multiple sequence alignments)
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database)
* [[VCF]] (Variant Call Format)

== Chemical ==
* [[Chemical data]]

== Ecological ==
* [[Darwin Core]] (Standard for sharing information about biological diversity)
* [[EML]] (Ecological Metadata Language)

== Geographic and Geospatial ==

See also [[Geospatial]]

* [[DEM]] (Digital Elevation Model)
* [[DOQ]] (Digital Orthophotos)
* [[e00]] (ESRI ArcInfo Interchange File)
* [[FGDC]] (Content Standard for Digital Geospatial Metadata??)
* [[GeoTIFF]] (Geospatial extensions to TIFF)
* [[GML]] (Geography Markup Language)
* [[HDFEOS, HD2, HD4]] (Hierarchical Data Format-Earth Observing System)
* [[KML]] (KML (formerly Keyhole Markup Language), Version 2.2)
* [[NDF]] (National Landsat Archive Production System (NLAPS) Data Format)
* [[SAIF]] (Spatial Archive and Interchange Format, Canadian)
* [[SDTS]] (Spatial Data Transfer Standard)
* [[shp and shx]] (ESRI Shaepfile must have components; other optional components as well, see entry)
* [[SID]] (MrSID- Multi-resolution Seamless Image Database)
* [[TAB]] (MapInfo dataset format, must have component)

== Mathematical ==

* [[MathML]]

== Medical Imaging ==
* [[DICOM]]
* [[OME-TIFF] (Open Microscopy Imaging format)

== 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)

== Social Sciences ==

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

Scientific Data formats

2012-11-03T02:50:46Z

Crusbridge: Added a swag of Biological formats

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

== General ==
* [[cdf]] (Common Data Format)
* [[hdf]] (Hierarchical Data Format, from NASA)
* [[NetCDF]] (Network Common Data Format)
* [[SDXF]] (Structured Data Exchange Format)
* [[XDF]] (eXtensible Data Format)
* [[XSIL]] (Extensible Scientific Interchange Language)

== Astronomical and Space ==
* [[FITS]] (Flexible Image Transport System)
* [[PDS/ODL]] (Planetary Data System)

== Biological ==

* [[AB1]] (Chromatogram files used by DNA sequencing instruments from Applied Biosystems)
* [[ACE]] (Sequence assembly format)
* [[BAM]] (Binary compressed SAM format)
* [[BED]] (Browser extensible display format describing genes and other features of DNA sequences)
* [[CAF]] (Common Assembly Format for sequence assembly)
* [[EMBL]] (Flatfile format used by the EMBL for nucleotide and peptide sequences)
* [[FASTA and FASTQ]] (File format for sequence data, FASTQ with quality).
* [[GenBank]] (Flatfile format used by NCBI for nucleotide and peptide sequences)
* [[GFF]] (General feature format for describing genes and other features of DNA, RNA and protein sequences)
* [[GTF]] (Gene transfer format holds information about gene structure)
* [[NEXUS]] (Encodes mixed information about genetic sequence data in a block structured format)
* [[PDB]] (Structures of biomolecules deposited in Protein Data Bank)
* [[PHD]] (Output from the basecalling software Phred)
* [[SAM]] (Sequence Alignment/Map format)
* [[SCF]] (Staden chromatogram files used to store data from DNA sequencing)
* [[SBML]] (Systems Biology Markup Language used to store biochemical network computational models)
* [[Stockholm]] (Representing multiple sequence alignments)
* [[Swiss-Prot]] (Flatfile format used for protein sequences from the Swiss-Prot database)
* [[VCF]] (Variant Call Format)

== Chemical ==
* [[Chemical data]]

== Ecological ==
* [[Darwin Core]] (Standard for sharing information about biological diversity)
* [[EML]] (Ecological Metadata Language)

== Geographic and Geospatial ==

See also [[Geospatial]]

* [[DEM]] (Digital Elevation Model)
* [[DOQ]] (Digital Orthophotos)
* [[e00]] (ESRI ArcInfo Interchange File)
* [[FGDC]] (Content Standard for Digital Geospatial Metadata??)
* [[GeoTIFF]] (Geospatial extensions to TIFF)
* [[GML]] (Geography Markup Language)
* [[HDFEOS, HD2, HD4]] (Hierarchical Data Format-Earth Observing System)
* [[KML]] (KML (formerly Keyhole Markup Language), Version 2.2)
* [[NDF]] (National Landsat Archive Production System (NLAPS) Data Format)
* [[SAIF]] (Spatial Archive and Interchange Format, Canadian)
* [[SDTS]] (Spatial Data Transfer Standard)
* [[shp and shx]] (ESRI Shaepfile must have components; other optional components as well, see entry)
* [[SID]] (MrSID- Multi-resolution Seamless Image Database)
* [[TAB]] (MapInfo dataset format, must have component)

== Mathematical ==

* [[MathML]]

== Medical Imaging ==
* [[DICOM]]

== 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)

== Social Sciences ==

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