Table 3. Overview of common standard data formats for ‘omics data.

Data type	Format name	Description	Reference or URL for format specification	URLs for repositories accepting data in this format
Raw DNA/RNA sequence	FASTA FASTQ HDF5 SAM/BAM/ CRAM	FASTA is a common text format to store DNA/RNA/Protein sequence and FASTQ combines base quality information with the nucleotide sequence. HDF5 is a newer sequence read formats used by long read sequencers e.g. PacBio and Oxford Nanopore. Raw sequence can also be stored in unaligned SAM/BAM/CRAM format	41 42 https://support.hdfgroup.org/HDF5/ https://samtools.github.io/hts-specs/ https://www.ncbi.nlm.nih.gov/ sra/docs/submitformats/ http://www.ebi.ac.uk/ena/ submit/data-formats
Assembled DNA sequence	FASTA Flat file AGP	Assemblies without annotation are generally stored in FASTA format. Annotation can be integrated with assemblies in contig, scaffold or chromosome flat file format. AGP files are used to describe how smaller fragments are placed in an assembly but do not contain the sequence information themselves	41 http://www.ebi.ac.uk/ena/submit/contig-flat-file http://www.ebi.ac.uk/ena/submit/scaffold-flat-file https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_ Specification/	http://www.ebi.ac.uk/ena /submit/genomes-sequence- submission
Aligned DNA sequence	SAM/BAM CRAM	Sequences aligned to a reference are represented in sequence alignment and mapping format (SAM). Its binary version is called BAM and further compression can be done using the CRAM format	https://samtools.github.io/hts-specs/	https://www.ncbi.nlm.nih.gov/ sra/docs/submitformats/#bam
Gene model or genomic feature annotation	GTF/GFF/GFF3 BED GB/GBK	General feature format or general transfer format are commonly used to store genomic features in tab-delimited flat text format. GFF3 is a more advanced version of the basic GFF that allows description of more complex features. BED format is a tab-delimited text format that also allows definition of how a feature should be displayed (e.g. on a genome browser). GenBank flat file Format (GB/GBK) is also commonly used but not well standardised	https://github.com/The-Sequence-Ontology/ Specifications/blob/master/gff3.md https://genome.ucsc.edu/FAQ/FAQformat.html https://genome.ucsc.edu/FAQ/FAQformat.html https://www.ncbi.nlm.nih.gov/Sitemap/ samplerecord.html	http://www.ensembl.org/info/ website/upload/gff.html http://www.ensembl.org/info/ website/upload/gff3.html
Gene functional annotation	GAF (GPAD and RDF will also be available in 2018)	A GAF file is a GO Annotation File containing annotations made to the GO by a contributing resource such as FlyBase or Pombase. However, the GAF standard is applicable outside of GO, e.g. using other ontologies such as PO. GAF (v2) is a simple tab-delimited file format with 17 columns to describe an entity (e.g. a protein), its annotation and some annotation metadata	http://geneontology.org/page/go-annotation-file- format-20	http://geneontology.org/page/ submitting-go-annotations
Genetic/genomic variants	VCF	A tab-delimited text format to store meta-information as header lines followed by information about variants position in the genome. The current version is VCF4.2	https://samtools.github.io/hts-specs/VCFv4.2.pdf	http://www.ensembl.org/info/ website/upload/var.html
Interaction data	PSI-MI XML MITAB	Data formats developed to exchange molecular interaction data, related metadata and fully describe molecule constructs	http://psidev.info/groups/molecular-interactions	http://www.ebi.ac.uk/intact
Raw metabolite profile	mzML nmrML	XML based data formats that define mass spectrometry and nuclear magnetic resonance raw data in Metabolomics	http://www.psidev.info/mzml http://nmrml.org/
Protein sequence	FASTA	A text-based format for representing nucleotide sequences or protein sequences, in which nucleotides or amino acids are represented using single-letter codes	[41]	www.uniprot.org
Raw proteome profile	mzML	A formally defined XML format for representing mass spectrometry data. Files typically contain sequences of mass spectra, plus metadata about the experiment	http://www.psidev.info/mzml	www.ebi.ac.uk/pride
Organisms and specimens	Darwin Core	The Darwin Core (DwC) standard facilitates the exchange of information about the geographic location of organisms and associated collection specimens	http://rs.tdwg.org/dwc/