Editing List of file formats (section)

== Scientific data (data exchange) ==
* [[FITS]] – Flexible Image Transport System, a standard data format for astronomy
* [[Silo (library)|Silo]] – a storage format for visualization developed at [[Lawrence Livermore National Laboratory]]
* SPC – [[SPC file format|SPC]], spectroscopic data
* [[EAS3]] – binary format for structured data
* [[EOSSA]] – Electro-Optic Space Situational Awareness format
* OST – (Open Spatio-Temporal) extensible, mainly images with related data, or just pure data; meant as an open alternative for microscope images
* CCP4 – [[CCP4 (file format)|CCP4]], X-ray crystallography voxels (electron density)
* MRC – [[MRC (file format)|MRC]], voxels in cryo-electron microscopy
* [[HITRAN]] – spectroscopic data with one optical/infrared transition per line in the ASCII file (.hit)
* ROOT – hierarchical platform-independent compressed binary format used by [[ROOT]]
* SDF – [[Simple Data Format|Simple Data Format (SDF)]], a platform-independent, precision-preserving binary data I/O format capable of handling large, multi-dimensional arrays.
* MYD – Everfine LEDSpec software file for LED measurements
* CSDM – (Core Scientific Dataset Model) model for multi-dimensional and correlated datasets from various spectroscopies, diffraction, microscopy, and imaging techniques (.csdf, .csdfe).<ref>
{{cite journal |last1= Srivastava |first1= Deepansh |last2= Vosegaard|first2=Thomas | last3 = Massiot | first3 = Dominique | last4 = Grandinetti | first4 = Philip | author-link4=Philip Grandinetti |date=January 2020 |title=Core Scientific Dataset Model: A lightweight and portable model and file format for multi- dimensional scientific data 
 |journal= PLOS ONE |volume= 15 
 |issue=1 |pages= e0225953 
|doi=10.1371/journal.pone.0225953 |pmid= 31895936 |pmc= 6940021 |bibcode= 2020PLoSO..1525953S |doi-access= free }}
</ref>

=== Multi-domain ===
* [[NetCDF]] – Network common data format
* HDR, HDF, h4, h5 – [[Hierarchical Data Format]]
* SDXF – [[SDXF]], (Structured Data Exchange Format)
* CDF – [[Common Data Format]]
* CGNS – [[CGNS]], CFD General Notation System
* [https://dx.doi.org/10.1016/j.cpc.2009.11.014 FMF] – Full-Metadata Format

=== Meteorology ===
* [[GRIB]] – Grid in Binary, WMO format for weather model data
* [[BUFR]] – WMO format for weather observation data
* [[PP-format|PP]] – UK Met Office format for weather model data
* NASA-Ames – Simple text format for observation data. First used in aircraft studies of the atmosphere.

=== Chemistry ===
{{Main|chemical file format}}
* CML – [[Chemical Markup Language]] (CML) (.cml)
* MOL, SD, SDF – [[Chemical table file]] (CTab)
* DX, JDX – [[Joint Committee on Atomic and Molecular Physical Data]] (JCAMP)
* SMI – [[Simplified molecular input line entry specification]] (SMILES)

=== Mathematics ===
* G6, S6 – graph6, sparse6, ASCII encoding of [[Adjacency matrix|Adjacency matrices]]

=== Biology ===
Molecular biology and bioinformatics:
* AB1 – In [[DNA sequencing]], [[chromatogram]] files used by instruments from [[Applied Biosystems]]
* ACE – A [[sequence assembly]] format
* ASN.1 – [[Abstract Syntax Notation One]], is an International Standards Organization ([[International Organization for Standardization|ISO]]) data representation format used to achieve interoperability between platforms. [[National Center for Biotechnology Information|NCBI]] uses ASN.1 for the storage and retrieval of data such as nucleotide and protein sequences, structures, genomes, and PubMed records.
* BAM – [[Binary Alignment/Map]] format (compressed SAM format)
* BCF – Binary compressed VCF format
* BED – The [[BED file format|browser extensible display format]] is used for describing [[gene]]s and other features of [[DNA]] sequences
* CAF – Common Assembly Format for [[sequence assembly]]
* [[CRAM (file format)|CRAM]] – compressed file format for storing biological sequences aligned to a reference sequence
* DDBJ – The flatfile format used by the [[DNA Data Bank of Japan|DDBJ]] to represent database records for [[nucleotide sequence|nucleotide]] and [[peptide sequence]]s from [[DDBJ]] databases.
* EMBL – The flatfile format used by the [[European Molecular Biology Laboratory|EMBL]] to represent database records for [[nucleotide sequence|nucleotide]] and [[peptide sequence]]s from [[EMBL]] databases.
* FASTA – The [[FASTA format]], for sequence data. Sometimes also given as FNA or FAA (Fasta Nucleic Acid or Fasta Amino Acid).
* FASTQ – The [[FASTQ format]], for sequence data with quality. Sometimes also given as QUAL.
* GCPROJ – The [[Genome Compiler]] project. Advanced format for genetic data to be designed, shared and visualized.
* GenBank – The flatfile format used by the [[National Center for Biotechnology Information|NCBI]] to represent database records for [[nucleotide sequence|nucleotide]] and [[peptide sequence]]s from the [[GenBank]] and [[RefSeq]] databases
* GFF – The [[General feature format]] is used to describe [[gene]]s and other features of [[DNA]], [[RNA]], and [[protein]] sequences
* GTF – The [[Gene transfer format]] is used to hold information about [[gene]] structure
* MAF – The [[Multiple Alignment Format]] stores multiple alignments for whole-genome to whole-genome comparisons [https://biopython.org/wiki/Multiple_Alignment_Format]
* NCBI – Structured [[ASN.1]] format used at [[National Center for Biotechnology Information]] for DNA and protein data
* NEXUS – The [[Nexus file]] encodes mixed information about genetic sequence data in a block structured format
* NeXML – XML format for [[phylogenetic tree]]s
* NWK – The [[Newick format|Newick tree format]] is a way of representing graph-theoretical trees with edge lengths using parentheses and commas and useful to hold [[phylogenetic tree]]s.
* PDB – structures of biomolecules deposited in [[Protein Data Bank]], also used to exchange protein and nucleic acid structures
* PHD – Phred output, from the base-calling software [[Phred (software)|Phred]]
* PLN – Protein Line Notation used in [http://www.biochemfusion.com/products/ proteax software] [http://www.biochemfusion.com/doc/Biochemfusion_PLN_1.4_spec.pdf specification]
* SAM – [[SAM (file format)|SAM]], Sequence Alignment Map format, in which the results of the [[1000 Genomes Project]] will be released
* SBML – [[SBML|The Systems Biology Markup Language]] is used to store biochemical network computational models
* SCF – Staden chromatogram files used to store data from [[DNA sequencing]]
* SFF – [[Standard Flowgram Format]]
* SRA – format used by the [[National Center for Biotechnology Information]] Short Read Archive to store high-throughput DNA sequence data
* Stockholm – The [[Stockholm format]] for representing [[multiple sequence alignment]]s
* Swiss-Prot – The flatfile format used to represent database records for [[peptide sequence|protein]] sequences from the [[Swiss-Prot]] database
* VCF – [[Variant Call Format]], a standard created by the [[1000 Genomes Project]] that lists and annotates the entire collection of human variants (with the exception of approximately 1.6 million variants).

=== Biomedical imaging ===
* DCM – [[Digital Imaging and Communications in Medicine]] (DICOM) 
* NIfTI – [[Neuroimaging Informatics Technology Initiative]]
* NII – single-file (combined data and meta-data) style
* NII.GZ – [[gzip]]-compressed, used transparently by some software, notably the [[FMRIB Software Library]] (FSL)
* GII – single-file (combined data and meta-data) style; NIfTI offspring for brain surface data
* IMG, HDR – dual-file (separate data and meta-data, respectively) style
* IMG, HDR – [[Analyze (imaging software)|Analyze]] data, meta-data
* BRIK, HEAD – [[Afni|AFNI]] data, meta-data
* MGH – uncompressed, [[Massachusetts General Hospital]] imaging format, used by the [[FreeSurfer]] brain analysis package
* MGZ – [[ZIP (file format)|zip]]-compressed, [[Massachusetts General Hospital]] imaging format, used by the [[FreeSurfer]] brain analysis package
* MINC – [[Medical Imaging NetCDF]] format
* MNC – previously based on NetCDF; since version 2.0, based on HDF5

=== Biomedical signals (time series) ===
* ACQ – AcqKnowledge format for Windows/PC from Biopac Systems Inc., Goleta, CA, USA
* ADICHT – LabChart format from ADInstruments Pty Ltd, Bella Vista NSW, Australia
* [[BCI2000]] – The [[BCI2000]] project, Albany, NY, USA
* BDF – BioSemi data format from BioSemi B.V. Amsterdam, Netherlands
* BKR – The EEG data format developed at the University of Technology Graz, Austria
* CFWB – Chart Data Format from ADInstruments Pty Ltd, Bella Vista NSW, Australia
* [[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
* [https://arxiv.org/abs/cs/0608052 GDF] – The General Data Format for biomedical signals
* HL7aECG – Health Level 7 v3 annotated ECG
* MFER – Medical waveform Format Encoding Rules
* OpenXDF – Open Exchange Data Format from Neurotronics, Inc., Gainesville, FL, USA
* [[SCP-ECG]] – Standard Communication Protocol for Computer assisted electrocardiography EN1064:2007
* SIGIF – A digital SIGnal Interchange Format with application in neurophysiology
* WFDB – Format of Physiobank
* [https://code.google.com/p/xdf/ XDF] – eXtensible Data Format

=== Other biomedical formats ===
* HL7 – [[Health Level 7]], a framework for exchange, integration, sharing, and retrieval of health information electronically
* [[xDT]] – a family of data exchange formats for medical records

=== Biometric formats ===
* [[CBF (file format)|CBF]] – Common Biometric Format, based on CBEFF 2.0 (Common Biometric ExFramework).
* [[EBF (file format)|EBF]] – Extended Biometric Format, based on CBF but with [[S/MIME]] encryption support and semantic extensions 
* [[CBFX (file format)|CBFX]] – XML Common Biometric Format, based upon XCBF 1.1 (OASIS XML Common Biometric Format) 
* [[EBFX]] – XML Extended Biometric Format, based on CBFX but with W3C XML Encryption support and semantic extensions