Enum: EnumEDAMFormats

Data formats from the EDAM ontology.

Enumeration Source

Reachable From: - Source: NONE - Nodes: edam:format_1915 - Via: rdfs:subClassOf

Permissible Values

Value	Meaning	Description	Additional Info
edam:format_1915	edam:format_1915	Format	Title: Format
edam:format_1196	edam:format_1196	Chemical structure specified in Simplified Molecular Input Line Entry System ...	Title: SMILES
edam:format_1197	edam:format_1197	Chemical structure specified in IUPAC International Chemical Identifier (InCh...	Title: InChI
edam:format_1198	edam:format_1198	Chemical structure specified by Molecular Formula (MF), including a count of ...	Title: mf
edam:format_1199	edam:format_1199	An InChIKey identifier is not human- nor machine-readable but is more suitabl...	Title: InChIKey
edam:format_1200	edam:format_1200	SMILES ARbitrary Target Specification (SMARTS) format for chemical structure ...	Title: smarts
edam:format_1206	edam:format_1206	Alphabet for a molecular sequence with possible unknown positions but without...	Title: unambiguous pure
edam:format_1207	edam:format_1207	Alphabet for a nucleotide sequence with possible ambiguity, unknown positions...	Title: nucleotide
edam:format_1208	edam:format_1208	Alphabet for a protein sequence with possible ambiguity, unknown positions an...	Title: protein
edam:format_1209	edam:format_1209	Alphabet for the consensus of two or more molecular sequences	Title: consensus
edam:format_1210	edam:format_1210	Alphabet for a nucleotide sequence with possible ambiguity and unknown positi...	Title: pure nucleotide
edam:format_1211	edam:format_1211	Alphabet for a nucleotide sequence (characters ACGTU only) with possible unkn...	Title: unambiguous pure nucleotide
edam:format_1212	edam:format_1212	Alphabet for a DNA sequence with possible ambiguity, unknown positions and no...	Title: dna
edam:format_1213	edam:format_1213	Alphabet for an RNA sequence with possible ambiguity, unknown positions and n...	Title: rna
edam:format_1214	edam:format_1214	Alphabet for a DNA sequence (characters ACGT only) with possible unknown posi...	Title: unambiguous pure dna
edam:format_1215	edam:format_1215	Alphabet for a DNA sequence with possible ambiguity and unknown positions but...	Title: pure dna
edam:format_1216	edam:format_1216	Alphabet for an RNA sequence (characters ACGU only) with possible unknown pos...	Title: unambiguous pure rna sequence
edam:format_1217	edam:format_1217	Alphabet for an RNA sequence with possible ambiguity and unknown positions bu...	Title: pure rna
edam:format_1218	edam:format_1218	Alphabet for any protein sequence with possible unknown positions but without...	Title: unambiguous pure protein
edam:format_1219	edam:format_1219	Alphabet for any protein sequence with possible ambiguity and unknown positio...	Title: pure protein
edam:format_1248	edam:format_1248	Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank...	Title: EMBL feature location
edam:format_1295	edam:format_1295	Report format for tandem repeats in a nucleotide sequence (format generated b...	Title: quicktandem
edam:format_1296	edam:format_1296	Report format for inverted repeats in a nucleotide sequence (format generated...	Title: Sanger inverted repeats
edam:format_1297	edam:format_1297	Report format for tandem repeats in a sequence (an EMBOSS report format)	Title: EMBOSS repeat
edam:format_1316	edam:format_1316	Format of a report on exon-intron structure generated by EMBOSS est2genome	Title: est2genome format
edam:format_1318	edam:format_1318	Report format for restriction enzyme recognition sites used by EMBOSS restric...	Title: restrict format
edam:format_1319	edam:format_1319	Report format for restriction enzyme recognition sites used by EMBOSS restove...	Title: restover format
edam:format_1320	edam:format_1320	Report format for restriction enzyme recognition sites used by REBASE databas...	Title: REBASE restriction sites
edam:format_1332	edam:format_1332	Format of results of a sequence database search using FASTA	Title: FASTA search results format
edam:format_1333	edam:format_1333	Format of results of a sequence database search using some variant of BLAST	Title: BLAST results
edam:format_1334	edam:format_1334	Format of results of a sequence database search using some variant of MSPCrun...	Title: mspcrunch
edam:format_1335	edam:format_1335	Format of results of a sequence database search using some variant of Smith W...	Title: Smith-Waterman format
edam:format_1336	edam:format_1336	Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain clas...	Title: dhf
edam:format_1337	edam:format_1337	Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with li...	Title: lhf
edam:format_1341	edam:format_1341	Results format for searches of the InterPro database	Title: InterPro hits format
edam:format_1342	edam:format_1342	Format of results of a search of the InterPro database showing matches of que...	Title: InterPro protein view report format
edam:format_1343	edam:format_1343	Format of results of a search of the InterPro database showing matches betwee...	Title: InterPro match table format
edam:format_1349	edam:format_1349	Dirichlet distribution HMMER format	Title: HMMER Dirichlet prior
edam:format_1350	edam:format_1350	Dirichlet distribution MEME format	Title: MEME Dirichlet prior
edam:format_1351	edam:format_1351	Format of a report from the HMMER package on the emission and transition coun...	Title: HMMER emission and transition
edam:format_1356	edam:format_1356	Format of a regular expression pattern from the Prosite database	Title: prosite-pattern
edam:format_1357	edam:format_1357	Format of an EMBOSS sequence pattern	Title: EMBOSS sequence pattern
edam:format_1360	edam:format_1360	A motif in the format generated by the MEME program	Title: meme-motif
edam:format_1366	edam:format_1366	Sequence profile (sequence classifier) format used in the PROSITE database	Title: prosite-profile
edam:format_1367	edam:format_1367	A profile (sequence classifier) in the format used in the JASPAR database	Title: JASPAR format
edam:format_1369	edam:format_1369	Format of the model of random sequences used by MEME	Title: MEME background Markov model
edam:format_1370	edam:format_1370	Format of a hidden Markov model representation used by the HMMER package	Title: HMMER format
edam:format_1391	edam:format_1391	FASTA-style format for multiple sequences aligned by HMMER package to an HMM	Title: HMMER-aln
edam:format_1392	edam:format_1392	Format of multiple sequences aligned by DIALIGN package	Title: DIALIGN format
edam:format_1393	edam:format_1393	EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment...	Title: daf
edam:format_1419	edam:format_1419	Format for alignment of molecular sequences to MEME profiles (position-depend...	Title: Sequence-MEME profile alignment
edam:format_1421	edam:format_1421	Format used by the HMMER package for an alignment of a sequence against a hid...	Title: HMMER profile alignment (sequences versus HMMs)
edam:format_1422	edam:format_1422	Format used by the HMMER package for of an alignment of a hidden Markov model...	Title: HMMER profile alignment (HMM versus sequences)
edam:format_1423	edam:format_1423	Data Type must include the distance matrix, probably as pairs of sequence ide...	Title: Phylip distance matrix
edam:format_1424	edam:format_1424	Dendrogram (tree file) format generated by ClustalW	Title: ClustalW dendrogram
edam:format_1425	edam:format_1425	Raw data file format used by Phylip from which a phylogenetic tree is directl...	Title: Phylip tree raw
edam:format_1430	edam:format_1430	PHYLIP file format for continuous quantitative character data	Title: Phylip continuous quantitative characters
edam:format_1432	edam:format_1432	PHYLIP file format for phylogenetics character frequency data	Title: Phylip character frequencies format
edam:format_1433	edam:format_1433	Format of PHYLIP discrete states data	Title: Phylip discrete states format
edam:format_1434	edam:format_1434	Format of PHYLIP cliques data	Title: Phylip cliques format
edam:format_1435	edam:format_1435	Phylogenetic tree data format used by the PHYLIP program	Title: Phylip tree format
edam:format_1436	edam:format_1436	The format of an entry from the TreeBASE database of phylogenetic data	Title: TreeBASE format
edam:format_1437	edam:format_1437	The format of an entry from the TreeFam database of phylogenetic data	Title: TreeFam format
edam:format_1445	edam:format_1445	Format for distances, such as Branch Score distance, between two or more phyl...	Title: Phylip tree distance format
edam:format_1454	edam:format_1454	Format of an entry from the DSSP database (Dictionary of Secondary Structure ...	Title: dssp
edam:format_1455	edam:format_1455	Entry format of the HSSP database (Homology-derived Secondary Structure in Pr...	Title: hssp
edam:format_1457	edam:format_1457	Format of RNA secondary structure in dot-bracket notation, originally generat...	Title: Dot-bracket format
edam:format_1458	edam:format_1458	Format of local RNA secondary structure components with free energy values, g...	Title: Vienna local RNA secondary structure format
edam:format_1475	edam:format_1475	Format of an entry (or part of an entry) from the PDB database	Title: PDB database entry format
edam:format_1476	edam:format_1476	Entry format of PDB database in PDB format	Title: PDB
edam:format_1477	edam:format_1477	Entry format of PDB database in mmCIF format	Title: mmCIF
edam:format_1478	edam:format_1478	Entry format of PDB database in PDBML (XML) format	Title: PDBML
edam:format_1504	edam:format_1504	Amino acid index format used by the AAindex database	Title: aaindex
edam:format_1551	edam:format_1551	Format of output of the Pcons Model Quality Assessment Program (MQAP)	Title: Pcons report format
edam:format_1552	edam:format_1552	Format of output of the ProQ protein model quality predictor	Title: ProQ report format
edam:format_1582	edam:format_1582	A report format for the kinetics of enzyme-catalysed reaction(s) in a format ...	Title: findkm
edam:format_1627	edam:format_1627	Report format on PCR primers and hybridisation oligos as generated by Whitehe...	Title: Primer3 primer
edam:format_1628	edam:format_1628	A format of raw sequence read data from an Applied Biosystems sequencing mach...	Title: ABI
edam:format_1629	edam:format_1629	Format of MIRA sequence trace information file	Title: mira
edam:format_1630	edam:format_1630	Common Assembly Format (CAF)	Title: CAF
edam:format_1631	edam:format_1631	Sequence assembly project file EXP format	Title: EXP
edam:format_1632	edam:format_1632	Staden Chromatogram Files format (SCF) of base-called sequence reads, qualiti...	Title: SCF
edam:format_1633	edam:format_1633	PHD sequence trace format to store serialised chromatogram data (reads)	Title: PHD
edam:format_1637	edam:format_1637	Format of Affymetrix data file of raw image data	Title: dat
edam:format_1638	edam:format_1638	Format of Affymetrix data file of information about (raw) expression levels o...	Title: cel
edam:format_1639	edam:format_1639	Format of affymetrix gene cluster files (hc-genes	Title: affymetrix
edam:format_1641	edam:format_1641	Affymetrix data file format for information about experimental conditions and...	Title: affymetrix-exp
edam:format_1644	edam:format_1644	Format of Affymetrix data file of information about (normalised) expression l...	Title: CHP
edam:format_1665	edam:format_1665	Format of Taverna workflows	Title: Taverna workflow format
edam:format_1705	edam:format_1705	The format of an entry from the HET group dictionary (HET groups from PDB fil...	Title: HET group dictionary entry format
edam:format_1734	edam:format_1734	Format of bibliographic reference as used by the PubMed database	Title: PubMed citation
edam:format_1735	edam:format_1735	Bibliographic reference information including citation information is include...	Title: Medline Display Format
edam:format_1736	edam:format_1736	CiteXplore 'core' citation format including title, journal, authors and abstr...	Title: CiteXplore-core
edam:format_1737	edam:format_1737	CiteXplore 'all' citation format includes all known details such as Mesh term...	Title: CiteXplore-all
edam:format_1739	edam:format_1739	Article format of the PubMed Central database	Title: pmc
edam:format_1740	edam:format_1740	The format of iHOP (Information Hyperlinked over Proteins) text-mining result	Title: iHOP format
edam:format_1741	edam:format_1741	OSCAR (Open-Source Chemistry Analysis Routines) software performs chemistry-s...	Title: OSCAR format
edam:format_1861	edam:format_1861	Map of a plasmid (circular DNA) in PlasMapper TextMap format	Title: PlasMapper TextMap
edam:format_1910	edam:format_1910	Phylogenetic tree Newick (text) format	Title: newick
edam:format_1911	edam:format_1911	Phylogenetic tree TreeCon (text) format	Title: TreeCon format
edam:format_1912	edam:format_1912	Phylogenetic tree Nexus (text) format	Title: Nexus format
edam:format_1919	edam:format_1919	Data format for a molecular sequence record	Title: Sequence record format
edam:format_1920	edam:format_1920	Data format for molecular sequence feature information	Title: Sequence feature annotation format
edam:format_1921	edam:format_1921	Data format for molecular sequence alignment information	Title: Alignment format
edam:format_1923	edam:format_1923	ACEDB sequence format	Title: acedb
edam:format_1925	edam:format_1925	Codata entry format	Title: codata
edam:format_1926	edam:format_1926	Fasta format variant with database name before ID	Title: dbid
edam:format_1927	edam:format_1927	EMBL entry format	Title: EMBL format
edam:format_1928	edam:format_1928	Staden experiment file format	Title: Staden experiment format
edam:format_1929	edam:format_1929	FASTA format including NCBI-style IDs	Title: FASTA
edam:format_1930	edam:format_1930	FASTQ short read format ignoring quality scores	Title: FASTQ
edam:format_1931	edam:format_1931	FASTQ Illumina 1	Title: FASTQ-illumina
edam:format_1932	edam:format_1932	FASTQ short read format with phred quality	Title: FASTQ-sanger
edam:format_1933	edam:format_1933	FASTQ Solexa/Illumina 1	Title: FASTQ-solexa
edam:format_1934	edam:format_1934	Fitch program format	Title: fitch program
edam:format_1935	edam:format_1935	GCG SSF (single sequence file) file format	Title: GCG
edam:format_1936	edam:format_1936	Genbank entry format	Title: GenBank format
edam:format_1937	edam:format_1937	Currently identical to refseqp format	Title: genpept
edam:format_1938	edam:format_1938	GFF feature file format with sequence in the header	Title: GFF2-seq
edam:format_1939	edam:format_1939	GFF3 feature file format with sequence	Title: GFF3-seq
edam:format_1940	edam:format_1940	FASTA sequence format including NCBI-style GIs	Title: giFASTA format
edam:format_1941	edam:format_1941	Hennig86 output sequence format	Title: hennig86
edam:format_1942	edam:format_1942	Intelligenetics sequence format	Title: ig
edam:format_1943	edam:format_1943	Intelligenetics sequence format (strict version)	Title: igstrict
edam:format_1944	edam:format_1944	Jackknifer interleaved and non-interleaved sequence format	Title: jackknifer
edam:format_1945	edam:format_1945	Mase program sequence format	Title: mase format
edam:format_1946	edam:format_1946	Mega interleaved and non-interleaved sequence format	Title: mega-seq
edam:format_1947	edam:format_1947	GCG MSF (multiple sequence file) file format	Title: GCG MSF
edam:format_1948	edam:format_1948	NBRF/PIR entry sequence format	Title: nbrf/pir
edam:format_1949	edam:format_1949	Nexus/paup interleaved sequence format	Title: nexus-seq
edam:format_1950	edam:format_1950	PDB sequence format (ATOM lines)	Title: pdbatom
edam:format_1951	edam:format_1951	PDB nucleotide sequence format (ATOM lines)	Title: pdbatomnuc
edam:format_1952	edam:format_1952	PDB nucleotide sequence format (SEQRES lines)	Title: pdbseqresnuc
edam:format_1953	edam:format_1953	PDB sequence format (SEQRES lines)	Title: pdbseqres
edam:format_1954	edam:format_1954	Plain old FASTA sequence format (unspecified format for IDs)	Title: Pearson format
edam:format_1957	edam:format_1957	Raw sequence format with no non-sequence characters	Title: raw
edam:format_1958	edam:format_1958	Currently identical to genpept format	Title: refseqp
edam:format_1960	edam:format_1960	Staden suite sequence format	Title: Staden format
edam:format_1961	edam:format_1961	Stockholm multiple sequence alignment format (used by Pfam and Rfam)	Title: Stockholm format
edam:format_1962	edam:format_1962	DNA strider output sequence format	Title: strider format
edam:format_1963	edam:format_1963	UniProtKB entry sequence format	Title: UniProtKB format
edam:format_1964	edam:format_1964	Plain text sequence format (essentially unformatted)	Title: plain text format (unformatted)
edam:format_1966	edam:format_1966	NCBI ASN	Title: ASN.1 sequence format
edam:format_1967	edam:format_1967	DAS sequence (XML) format (any type)	Title: DAS format
edam:format_1968	edam:format_1968	DAS sequence (XML) format (nucleotide-only)	Title: dasdna
edam:format_1969	edam:format_1969	EMBOSS debugging trace sequence format of full internal data content	Title: debug-seq
edam:format_1970	edam:format_1970	Jackknifer output sequence non-interleaved format	Title: jackknifernon
edam:format_1972	edam:format_1972	NCBI FASTA sequence format with NCBI-style IDs	Title: NCBI format
edam:format_1973	edam:format_1973	Nexus/paup non-interleaved sequence format	Title: nexusnon
edam:format_1974	edam:format_1974	General Feature Format (GFF) of sequence features	Title: GFF2
edam:format_1975	edam:format_1975	Generic Feature Format version 3 (GFF3) of sequence features	Title: GFF3
edam:format_1978	edam:format_1978	DAS GFF (XML) feature format	Title: DASGFF
edam:format_1979	edam:format_1979	EMBOSS debugging trace feature format of full internal data content	Title: debug-feat
edam:format_1982	edam:format_1982	ClustalW format for (aligned) sequences	Title: ClustalW format
edam:format_1983	edam:format_1983	EMBOSS alignment format for debugging trace of full internal data content	Title: debug
edam:format_1984	edam:format_1984	Fasta format for (aligned) sequences	Title: FASTA-aln
edam:format_1985	edam:format_1985	Pearson MARKX0 alignment format	Title: markx0
edam:format_1986	edam:format_1986	Pearson MARKX1 alignment format	Title: markx1
edam:format_1987	edam:format_1987	Pearson MARKX10 alignment format	Title: markx10
edam:format_1988	edam:format_1988	Pearson MARKX2 alignment format	Title: markx2
edam:format_1989	edam:format_1989	Pearson MARKX3 alignment format	Title: markx3
edam:format_1990	edam:format_1990	Alignment format for start and end of matches between sequence pairs	Title: match
edam:format_1991	edam:format_1991	Mega format for (typically aligned) sequences	Title: mega
edam:format_1992	edam:format_1992	Mega non-interleaved format for (typically aligned) sequences	Title: meganon
edam:format_1996	edam:format_1996	EMBOSS simple sequence pairwise alignment format	Title: pair
edam:format_1997	edam:format_1997	Phylip format for (aligned) sequences	Title: PHYLIP format
edam:format_1998	edam:format_1998	Phylip non-interleaved format for (aligned) sequences	Title: PHYLIP sequential
edam:format_1999	edam:format_1999	Alignment format for score values for pairs of sequences	Title: scores format
edam:format_2000	edam:format_2000	SELEX format for (aligned) sequences	Title: selex
edam:format_2001	edam:format_2001	EMBOSS simple multiple alignment format	Title: EMBOSS simple format
edam:format_2002	edam:format_2002	Simple multiple sequence (alignment) format for SRS	Title: srs format
edam:format_2003	edam:format_2003	Simple sequence pair (alignment) format for SRS	Title: srspair
edam:format_2004	edam:format_2004	T-Coffee program alignment format	Title: T-Coffee format
edam:format_2005	edam:format_2005	Treecon format for (aligned) sequences	Title: TreeCon-seq
edam:format_2006	edam:format_2006	Data format for a phylogenetic tree	Title: Phylogenetic tree format
edam:format_2013	edam:format_2013	Data format for a biological pathway or network	Title: Biological pathway or network format
edam:format_2014	edam:format_2014	Data format for a sequence-profile alignment	Title: Sequence-profile alignment format
edam:format_2017	edam:format_2017	Data format for an amino acid index	Title: Amino acid index format
edam:format_2020	edam:format_2020	Data format for a full-text scientific article	Title: Article format
edam:format_2021	edam:format_2021	Data format of a report from text mining	Title: Text mining report format
edam:format_2027	edam:format_2027	Data format for reports on enzyme kinetics	Title: Enzyme kinetics report format
edam:format_2030	edam:format_2030	Format of a report on a chemical compound	Title: Chemical data format
edam:format_2031	edam:format_2031	Format of a report on a particular locus, gene, gene system or groups of gene...	Title: Gene annotation format
edam:format_2032	edam:format_2032	Format of a workflow	Title: Workflow format
edam:format_2033	edam:format_2033	Data format for a molecular tertiary structure	Title: Tertiary structure format
edam:format_2035	edam:format_2035	Text format of a chemical formula	Title: Chemical formula format
edam:format_2036	edam:format_2036	Format of raw (unplotted) phylogenetic data	Title: Phylogenetic character data format
edam:format_2037	edam:format_2037	Format of phylogenetic continuous quantitative character data	Title: Phylogenetic continuous quantitative character format
edam:format_2038	edam:format_2038	Format of phylogenetic discrete states data	Title: Phylogenetic discrete states format
edam:format_2039	edam:format_2039	Format of phylogenetic cliques data	Title: Phylogenetic tree report (cliques) format
edam:format_2040	edam:format_2040	Format of phylogenetic invariants data	Title: Phylogenetic tree report (invariants) format
edam:format_2049	edam:format_2049	Format for phylogenetic tree distance data	Title: Phylogenetic tree report (tree distances) format
edam:format_2052	edam:format_2052	Format for reports on a protein family	Title: Protein family report format
edam:format_2054	edam:format_2054	Format for molecular interaction data	Title: Protein interaction format
edam:format_2055	edam:format_2055	Format for sequence assembly data	Title: Sequence assembly format
edam:format_2056	edam:format_2056	Format for information about a microarray experimental per se (not the data g...	Title: Microarray experiment data format
edam:format_2057	edam:format_2057	Format for sequence trace data (i	Title: Sequence trace format
edam:format_2058	edam:format_2058	Format of a file of gene expression data, e	Title: Gene expression report format
edam:format_2060	edam:format_2060	Format of a map of (typically one) molecular sequence annotated with features	Title: Map format
edam:format_2061	edam:format_2061	Format of a report on PCR primers or hybridisation oligos in a nucleic acid s...	Title: Nucleic acid features (primers) format
edam:format_2062	edam:format_2062	Format of a report of general information about a specific protein	Title: Protein report format
edam:format_2064	edam:format_2064	Format of a matrix of 3D-1D scores (amino acid environment probabilities)	Title: 3D-1D scoring matrix format
edam:format_2065	edam:format_2065	Format of a report on the quality of a protein three-dimensional model	Title: Protein structure report (quality evaluation) format
edam:format_2066	edam:format_2066	Format of a report on sequence hits and associated data from searching a sequ...	Title: Database hits (sequence) format
edam:format_2067	edam:format_2067	Format of a matrix of genetic distances between molecular sequences	Title: Sequence distance matrix format
edam:format_2068	edam:format_2068	Format of a sequence motif	Title: Sequence motif format
edam:format_2069	edam:format_2069	Format of a sequence profile	Title: Sequence profile format
edam:format_2072	edam:format_2072	Format of a hidden Markov model	Title: Hidden Markov model format
edam:format_2074	edam:format_2074	Data format of a dirichlet distribution	Title: Dirichlet distribution format
edam:format_2075	edam:format_2075	Data format for the emission and transition counts of a hidden Markov model	Title: HMM emission and transition counts format
edam:format_2076	edam:format_2076	Format for secondary structure (predicted or real) of an RNA molecule	Title: RNA secondary structure format
edam:format_2077	edam:format_2077	Format for secondary structure (predicted or real) of a protein molecule	Title: Protein secondary structure format
edam:format_2078	edam:format_2078	Format used to specify range(s) of sequence positions	Title: Sequence range format
edam:format_2094	edam:format_2094	Alphabet for molecular sequence with possible unknown positions but without n...	Title: pure
edam:format_2095	edam:format_2095	Alphabet for a molecular sequence with possible unknown positions but possibl...	Title: unpure
edam:format_2096	edam:format_2096	Alphabet for a molecular sequence with possible unknown positions but without...	Title: unambiguous sequence
edam:format_2097	edam:format_2097	Alphabet for a molecular sequence with possible unknown positions and possibl...	Title: ambiguous
edam:format_2155	edam:format_2155	Format used for map of repeats in molecular (typically nucleotide) sequences	Title: Sequence features (repeats) format
edam:format_2158	edam:format_2158	Format used for report on restriction enzyme recognition sites in nucleotide ...	Title: Nucleic acid features (restriction sites) format
edam:format_2170	edam:format_2170	Format used for clusters of molecular sequences	Title: Sequence cluster format
edam:format_2171	edam:format_2171	Format used for clusters of protein sequences	Title: Sequence cluster format (protein)
edam:format_2172	edam:format_2172	Format used for clusters of nucleotide sequences	Title: Sequence cluster format (nucleic acid)
edam:format_2181	edam:format_2181	A text format resembling EMBL entry format	Title: EMBL-like (text)
edam:format_2182	edam:format_2182	A text format resembling FASTQ short read format	Title: FASTQ-like format (text)
edam:format_2183	edam:format_2183	XML format for EMBL entries	Title: EMBLXML
edam:format_2184	edam:format_2184	Specific XML format for EMBL entries (only uses certain sections)	Title: cdsxml
edam:format_2185	edam:format_2185	INSDSeq provides the elements of a sequence as presented in the GenBank/EMBL/...	Title: INSDSeq
edam:format_2186	edam:format_2186	Geneseq sequence format	Title: geneseq
edam:format_2187	edam:format_2187	A text sequence format resembling uniprotkb entry format	Title: UniProt-like (text)
edam:format_2194	edam:format_2194	Abstract format used by MedLine database	Title: medline
edam:format_2195	edam:format_2195	Format used for ontologies	Title: Ontology format
edam:format_2196	edam:format_2196	A serialisation format conforming to the Open Biomedical Ontologies (OBO) mod...	Title: OBO format
edam:format_2197	edam:format_2197	A serialisation format conforming to the Web Ontology Language (OWL) model	Title: OWL format
edam:format_2200	edam:format_2200	A text format resembling FASTA format	Title: FASTA-like (text)
edam:format_2204	edam:format_2204	An XML format for EMBL entries	Title: EMBL format (XML)
edam:format_2205	edam:format_2205	A text format resembling GenBank entry (plain text) format	Title: GenBank-like format (text)
edam:format_2206	edam:format_2206	Text format for a sequence feature table	Title: Sequence feature table format (text)
edam:format_2304	edam:format_2304	Entry format (XML) for the STRING database of protein interaction	Title: STRING entry format (XML)
edam:format_2305	edam:format_2305	GFF feature format (of indeterminate version)	Title: GFF
edam:format_2306	edam:format_2306	Gene Transfer Format (GTF), a restricted version of GFF	Title: GTF
edam:format_2310	edam:format_2310	FASTA format wrapped in HTML elements	Title: FASTA-HTML
edam:format_2311	edam:format_2311	EMBL entry format wrapped in HTML elements	Title: EMBL-HTML
edam:format_2330	edam:format_2330	Data in text format can be compressed into binary format, or can be a value o...	Title: Textual format
edam:format_2331	edam:format_2331	HTML format	Title: HTML
edam:format_2332	edam:format_2332	Data in XML format can be serialised into text, or binary format	Title: XML
edam:format_2333	edam:format_2333	Binary format	Title: Binary format
edam:format_2350	edam:format_2350	A placeholder concept for visual navigation by dividing data formats by the c...	Title: Format (by type of data)
edam:format_2352	edam:format_2352	'BioXSD' belongs to the 'BioXSD	GTrack' ecosystem of generic formats
edam:format_2376	edam:format_2376	A serialisation format conforming to the Resource Description Framework (RDF)...	Title: RDF format
edam:format_2532	edam:format_2532	Genbank entry format wrapped in HTML elements	Title: GenBank-HTML
edam:format_2543	edam:format_2543	A format resembling EMBL entry (plain text) format	Title: EMBL-like format
edam:format_2545	edam:format_2545	A format resembling FASTQ short read format	Title: FASTQ-like format
edam:format_2546	edam:format_2546	A format resembling FASTA format	Title: FASTA-like
edam:format_2547	edam:format_2547	A sequence format resembling uniprotkb entry format	Title: uniprotkb-like format
edam:format_2548	edam:format_2548	Format for a sequence feature table	Title: Sequence feature table format
edam:format_2549	edam:format_2549	OBO ontology text format	Title: OBO
edam:format_2550	edam:format_2550	OBO ontology XML format	Title: OBO-XML
edam:format_2551	edam:format_2551	Data format for a molecular sequence record (text)	Title: Sequence record format (text)
edam:format_2552	edam:format_2552	Data format for a molecular sequence record (XML)	Title: Sequence record format (XML)
edam:format_2553	edam:format_2553	XML format for a sequence feature table	Title: Sequence feature table format (XML)
edam:format_2554	edam:format_2554	Text format for molecular sequence alignment information	Title: Alignment format (text)
edam:format_2555	edam:format_2555	XML format for molecular sequence alignment information	Title: Alignment format (XML)
edam:format_2556	edam:format_2556	Text format for a phylogenetic tree	Title: Phylogenetic tree format (text)
edam:format_2557	edam:format_2557	XML format for a phylogenetic tree	Title: Phylogenetic tree format (XML)
edam:format_2558	edam:format_2558	An XML format resembling EMBL entry format	Title: EMBL-like (XML)
edam:format_2559	edam:format_2559	A format resembling GenBank entry (plain text) format	Title: GenBank-like format
edam:format_2561	edam:format_2561	Text format for sequence assembly data	Title: Sequence assembly format (text)
edam:format_2566	edam:format_2566	Alphabet for a molecular sequence without any unknown positions or ambiguity ...	Title: completely unambiguous
edam:format_2567	edam:format_2567	Alphabet for a molecular sequence without unknown positions, ambiguity or non...	Title: completely unambiguous pure
edam:format_2568	edam:format_2568	Alphabet for a nucleotide sequence (characters ACGTU only) without unknown po...	Title: completely unambiguous pure nucleotide
edam:format_2569	edam:format_2569	Alphabet for a DNA sequence (characters ACGT only) without unknown positions,...	Title: completely unambiguous pure dna
edam:format_2570	edam:format_2570	Alphabet for an RNA sequence (characters ACGU only) without unknown positions...	Title: completely unambiguous pure rna sequence
edam:format_2571	edam:format_2571	Format of a raw molecular sequence (i	Title: Raw sequence format
edam:format_2572	edam:format_2572	BAM format, the binary, BGZF-formatted compressed version of SAM format for a...	Title: BAM
edam:format_2573	edam:format_2573	Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e	Title: SAM
edam:format_2585	edam:format_2585	Systems Biology Markup Language (SBML), the standard XML format for models of...	Title: SBML
edam:format_2607	edam:format_2607	Alphabet for any protein sequence without unknown positions, ambiguity or non...	Title: completely unambiguous pure protein
edam:format_2848	edam:format_2848	Format of a bibliographic reference	Title: Bibliographic reference format
edam:format_2919	edam:format_2919	Format of a sequence annotation track	Title: Sequence annotation track format
edam:format_2920	edam:format_2920	Data format for molecular sequence alignment information that can hold sequen...	Title: Alignment format (pair only)
edam:format_2921	edam:format_2921	Format of sequence variation annotation	Title: Sequence variation annotation format
edam:format_2922	edam:format_2922	Some variant of Pearson MARKX alignment format	Title: markx0 variant
edam:format_2923	edam:format_2923	Some variant of Mega format for (typically aligned) sequences	Title: mega variant
edam:format_2924	edam:format_2924	Some variant of Phylip format for (aligned) sequences	Title: Phylip format variant
edam:format_3000	edam:format_3000	AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' se...	Title: AB1
edam:format_3001	edam:format_3001	ACE sequence assembly format including contigs, base-call qualities, and othe...	Title: ACE
edam:format_3003	edam:format_3003	BED detail format includes 2 additional columns (http://genome	Title: BED
edam:format_3004	edam:format_3004	bigBed format for large sequence annotation tracks, similar to textual BED fo...	Title: bigBed
edam:format_3005	edam:format_3005	Wiggle format (WIG) of a sequence annotation track that consists of a value f...	Title: WIG
edam:format_3006	edam:format_3006	bigWig format for large sequence annotation tracks that consist of a value fo...	Title: bigWig
edam:format_3007	edam:format_3007	PSL format of alignments, typically generated by BLAT or psLayout	Title: PSL
edam:format_3008	edam:format_3008	Multiple Alignment Format (MAF) supporting alignments of whole genomes with r...	Title: MAF
edam:format_3009	edam:format_3009	2bit binary format of nucleotide sequences using 2 bits per nucleotide	Title: 2bit
edam:format_3010	edam:format_3010		Title: .nib
edam:format_3011	edam:format_3011	genePred format has 3 main variations (http://genome	Title: genePred
edam:format_3012	edam:format_3012	Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and ...	Title: pgSnp
edam:format_3013	edam:format_3013	axt format of alignments, typically produced from BLASTZ	Title: axt
edam:format_3014	edam:format_3014	LAV format of alignments generated by BLASTZ and LASTZ	Title: LAV
edam:format_3015	edam:format_3015	Pileup format of alignment of sequences (e	Title: Pileup
edam:format_3016	edam:format_3016	1000 Genomes Project has its own specification for encoding structural variat...	Title: VCF
edam:format_3017	edam:format_3017	Sequence Read Format (SRF) of sequence trace data	Title: SRF
edam:format_3018	edam:format_3018	ZTR format for storing chromatogram data from DNA sequencing instruments	Title: ZTR
edam:format_3019	edam:format_3019	Genome Variation Format (GVF)	Title: GVF
edam:format_3020	edam:format_3020	BCF is the binary version of Variant Call Format (VCF) for sequence variation...	Title: BCF
edam:format_3033	edam:format_3033	Format of a matrix (array) of numerical values	Title: Matrix format
edam:format_3097	edam:format_3097	Format of data concerning the classification of the sequences and/or structur...	Title: Protein domain classification format
edam:format_3098	edam:format_3098	Format of raw SCOP domain classification data files	Title: Raw SCOP domain classification format
edam:format_3099	edam:format_3099	Format of raw CATH domain classification data files	Title: Raw CATH domain classification format
edam:format_3100	edam:format_3100	Format of summary of domain classification information for a CATH domain	Title: CATH domain report format
edam:format_3155	edam:format_3155	Systems Biology Result Markup Language (SBRML), the standard XML format for s...	Title: SBRML
edam:format_3156	edam:format_3156	BioPAX is an exchange format for pathway data, with its data model defined in...	Title: BioPAX
edam:format_3157	edam:format_3157	EBI Application Result XML is a format returned by sequence similarity search...	Title: EBI Application Result XML
edam:format_3158	edam:format_3158	XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI	Title: PSI MI XML (MIF)
edam:format_3159	edam:format_3159	phyloXML is a standardised XML format for phylogenetic trees, networks, and a...	Title: phyloXML
edam:format_3160	edam:format_3160	NeXML is a standardised XML format for rich phyloinformatic data	Title: NeXML
edam:format_3161	edam:format_3161	MAGE-ML XML format for microarray expression data, standardised by MGED (now ...	Title: MAGE-ML
edam:format_3162	edam:format_3162	MAGE-TAB textual format for microarray expression data, standardised by MGED ...	Title: MAGE-TAB
edam:format_3163	edam:format_3163	GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MI...	Title: GCDML
edam:format_3164	edam:format_3164	'GTrack' belongs to the 'BioXSD	GTrack' ecosystem of generic formats, and par...
edam:format_3166	edam:format_3166	Data format for a report of information derived from a biological pathway or ...	Title: Biological pathway or network report format
edam:format_3167	edam:format_3167	Data format for annotation on a laboratory experiment	Title: Experiment annotation format
edam:format_3235	edam:format_3235	Cytoband format for chromosome cytobands	Title: Cytoband format
edam:format_3239	edam:format_3239	CopasiML, the native format of COPASI	Title: CopasiML
edam:format_3240	edam:format_3240	CellML, the format for mathematical models of biological and other networks	Title: CellML
edam:format_3242	edam:format_3242	Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI	Title: PSI MI TAB (MITAB)
edam:format_3243	edam:format_3243	Protein affinity format (PSI-PAR), standardised by HUPO PSI MI	Title: PSI-PAR
edam:format_3244	edam:format_3244	mzML format for raw spectrometer output data, standardised by HUPO PSI MSS	Title: mzML
edam:format_3245	edam:format_3245	Format for mass pectra and derived data, include peptide sequences etc	Title: Mass spectrometry data format
edam:format_3246	edam:format_3246	TraML (Transition Markup Language) is the format for mass spectrometry transi...	Title: TraML
edam:format_3247	edam:format_3247	mzIdentML is the exchange format for peptides and proteins identified from ma...	Title: mzIdentML
edam:format_3248	edam:format_3248	mzQuantML is the format for quantitation values associated with peptides, pro...	Title: mzQuantML
edam:format_3249	edam:format_3249	GelML is the format for describing the process of gel electrophoresis, standa...	Title: GelML
edam:format_3250	edam:format_3250	spML is the format for describing proteomics sample processing, other than us...	Title: spML
edam:format_3252	edam:format_3252	A human-readable encoding for the Web Ontology Language (OWL)	Title: OWL Functional Syntax
edam:format_3253	edam:format_3253	A syntax for writing OWL class expressions	Title: Manchester OWL Syntax
edam:format_3254	edam:format_3254	A superset of the "Description-Logic Knowledge Representation System Specific...	Title: KRSS2 Syntax
edam:format_3255	edam:format_3255	The SPARQL Query Language incorporates a very similar syntax	Title: Turtle
edam:format_3256	edam:format_3256	A plain text serialisation format for RDF (Resource Description Framework) gr...	Title: N-Triples
edam:format_3257	edam:format_3257	A shorthand non-XML serialisation of Resource Description Framework model, de...	Title: Notation3
edam:format_3261	edam:format_3261	RDF/XML can be used as a standard serialisation syntax for OWL DL, but not fo...	Title: RDF/XML
edam:format_3262	edam:format_3262	OWL ontology XML serialisation format	Title: OWL/XML
edam:format_3281	edam:format_3281	The A2M format is used as the primary format for multiple alignments of prote...	Title: A2M
edam:format_3284	edam:format_3284	Standard flowgram format (SFF) is a binary file format used to encode results...	Title: SFF
edam:format_3285	edam:format_3285	The MAP file describes SNPs and is used by the Plink package	Title: MAP
edam:format_3286	edam:format_3286	The PED file describes individuals and genetic data and is used by the Plink ...	Title: PED
edam:format_3287	edam:format_3287	Data format for a metadata on an individual and their genetic data	Title: Individual genetic data format
edam:format_3288	edam:format_3288	The PED/MAP file describes data used by the Plink package	Title: PED/MAP
edam:format_3309	edam:format_3309	File format of a CT (Connectivity Table) file from the RNAstructure package	Title: CT
edam:format_3310	edam:format_3310	XRNA old input style format	Title: SS
edam:format_3311	edam:format_3311	RNA Markup Language	Title: RNAML
edam:format_3312	edam:format_3312	Format for the Genetic Data Environment (GDE)	Title: GDE
edam:format_3313	edam:format_3313	A multiple alignment in vertical format, as used in the AMPS (Alignment of Mu...	Title: BLC
edam:format_3326	edam:format_3326	Format of a data index of some type	Title: Data index format
edam:format_3327	edam:format_3327	BAM indexing format	Title: BAI
edam:format_3328	edam:format_3328	HMMER profile HMM file for HMMER versions 2	Title: HMMER2
edam:format_3329	edam:format_3329	HMMER profile HMM file for HMMER versions 3	Title: HMMER3
edam:format_3330	edam:format_3330	PO is the output format of Partial Order Alignment program (POA) performing M...	Title: PO
edam:format_3331	edam:format_3331	XML format as produced by the NCBI Blast package	Title: BLAST XML results format
edam:format_3462	edam:format_3462	Reference-based compression of alignment format	Title: CRAM
edam:format_3464	edam:format_3464	JavaScript Object Notation format; a lightweight, text-based format to repres...	Title: JSON
edam:format_3466	edam:format_3466	Encapsulated PostScript format	Title: EPS
edam:format_3467	edam:format_3467	Graphics Interchange Format	Title: GIF
edam:format_3468	edam:format_3468	Microsoft Excel spreadsheet format	Title: xls
edam:format_3475	edam:format_3475	Tabular data represented as tab-separated values in a text file	Title: TSV
edam:format_3477	edam:format_3477	Format of the cytoscape input file of gene expression ratios or values are sp...	Title: Cytoscape input file format
edam:format_3484	edam:format_3484	Bowtie format for indexed reference genome for "small" genomes	Title: ebwt
edam:format_3485	edam:format_3485	RSF-format files contain one or more sequences that may or may not be related	Title: RSF
edam:format_3486	edam:format_3486	Some format based on the GCG format	Title: GCG format variant
edam:format_3487	edam:format_3487	Bioinformatics Sequence Markup Language format	Title: BSML
edam:format_3491	edam:format_3491	Bowtie format for indexed reference genome for "large" genomes	Title: ebwtl
edam:format_3499	edam:format_3499	Ensembl standard format for variation data	Title: Ensembl variation file format
edam:format_3506	edam:format_3506	Microsoft Word format	Title: docx
edam:format_3507	edam:format_3507	Format of documents including word processor, spreadsheet and presentation	Title: Document format
edam:format_3508	edam:format_3508	Portable Document Format	Title: PDF
edam:format_3547	edam:format_3547	Format used for images and image metadata	Title: Image format
edam:format_3548	edam:format_3548	Medical image format corresponding to the Digital Imaging and Communications ...	Title: DICOM format
edam:format_3549	edam:format_3549	An open file format from the Neuroimaging Informatics Technology Initiative (...	Title: nii
edam:format_3550	edam:format_3550	Text-based tagged file format for medical images generated using the MetaImag...	Title: mhd
edam:format_3551	edam:format_3551	Nearly Raw Rasta Data format designed to support scientific visualisation and...	Title: nrrd
edam:format_3554	edam:format_3554	File format used for scripts written in the R programming language for execut...	Title: R file format
edam:format_3555	edam:format_3555	File format used for scripts for the Statistical Package for the Social Scien...	Title: SPSS
edam:format_3556	edam:format_3556	MHTML is not strictly an HTML format, it is encoded as an HTML email message ...	Title: MHTML
edam:format_3578	edam:format_3578	Proprietary file format for (raw) BeadArray data used by genomewide profiling...	Title: IDAT
edam:format_3579	edam:format_3579	Joint Picture Group file format for lossy graphics file	Title: JPG
edam:format_3580	edam:format_3580	Reporter Code Count-A data file (	Title: rcc
edam:format_3581	edam:format_3581	ARFF (Attribute-Relation File Format) is an ASCII text file format that descr...	Title: arff
edam:format_3582	edam:format_3582	AFG is a single text-based file assembly format that holds read and consensus...	Title: afg
edam:format_3583	edam:format_3583	Holds a tab-delimited chromosome /start /end / datavalue dataset	Title: bedgraph
edam:format_3584	edam:format_3584	Browser Extensible Data (BED) format of sequence annotation track that strict...	Title: bedstrict
edam:format_3585	edam:format_3585	BED file format where each feature is described by chromosome, start, end, na...	Title: bed6
edam:format_3586	edam:format_3586	A BED file where each feature is described by all twelve columns	Title: bed12
edam:format_3587	edam:format_3587	Galaxy allows BED files to contain non-standard fields beyond the first 3 col...	Title: chrominfo
edam:format_3588	edam:format_3588	Custom Sequence annotation track format used by Galaxy	Title: customtrack
edam:format_3589	edam:format_3589	Color space FASTA format sequence variant	Title: csfasta
edam:format_3590	edam:format_3590	An HDF5 file appears to the user as a directed graph	Title: HDF5
edam:format_3591	edam:format_3591	A versatile bitmap format	Title: TIFF
edam:format_3592	edam:format_3592	Although it is based on Windows internal bitmap data structures, it is suppor...	Title: BMP
edam:format_3593	edam:format_3593	IFUNC library reads and writes most uncompressed interchange versions of this...	Title: im
edam:format_3594	edam:format_3594	PCD was developed by Kodak	Title: pcd
edam:format_3595	edam:format_3595	PCX is an image file format that uses a simple form of run-length encoding	Title: pcx
edam:format_3596	edam:format_3596	The PPM format is a lowest common denominator color image file format	Title: ppm
edam:format_3597	edam:format_3597	PSD (Photoshop Document) is a proprietary file that allows the user to work w...	Title: psd
edam:format_3598	edam:format_3598	The XBM format was replaced by XPM for X11 in 1989	Title: xbm
edam:format_3599	edam:format_3599	Sequence of segments with markers	Title: xpm
edam:format_3600	edam:format_3600	RGB file format is the native raster graphics file format for Silicon Graphic...	Title: rgb
edam:format_3601	edam:format_3601	The PBM format is a lowest common denominator monochrome file format	Title: pbm
edam:format_3602	edam:format_3602	It is designed to be extremely easy to learn and write programs for	Title: pgm
edam:format_3603	edam:format_3603	It iis expected to replace the Graphics Interchange Format (GIF)	Title: PNG
edam:format_3604	edam:format_3604	Scalable Vector Graphics (SVG) is an XML-based vector image format for two-di...	Title: SVG
edam:format_3605	edam:format_3605	Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems	Title: rast
edam:format_3606	edam:format_3606	Textual report format for sequence quality for reports from sequencing machin...	Title: Sequence quality report format (text)
edam:format_3607	edam:format_3607	FASTQ format subset for Phred sequencing quality score data only (no sequence...	Title: qual
edam:format_3608	edam:format_3608	FASTQ format subset for Phred sequencing quality score data only (no sequence...	Title: qualsolexa
edam:format_3609	edam:format_3609	FASTQ format subset for Phred sequencing quality score data only (no sequence...	Title: qualillumina
edam:format_3610	edam:format_3610	FASTQ format subset for Phred sequencing quality score data only (no sequence...	Title: qualsolid
edam:format_3611	edam:format_3611	FASTQ format subset for Phred sequencing quality score data only (no sequence...	Title: qual454
edam:format_3612	edam:format_3612	Format that covers both the broad peak format and narrow peak format from ENC...	Title: ENCODE peak format
edam:format_3613	edam:format_3613	Format that covers both the broad peak format and narrow peak format from ENC...	Title: ENCODE narrow peak format
edam:format_3614	edam:format_3614	Human ENCODE broad peak format	Title: ENCODE broad peak format
edam:format_3615	edam:format_3615	BAM files are compressed using a variant of GZIP (GNU ZIP), into a format cal...	Title: bgzip
edam:format_3616	edam:format_3616	TAB-delimited genome position file index format	Title: tabix
edam:format_3617	edam:format_3617	Data format for graph data	Title: Graph format
edam:format_3618	edam:format_3618	XML-based format used to store graph descriptions within Galaxy	Title: xgmml
edam:format_3619	edam:format_3619	SIF (simple interaction file) Format - a network/pathway format used for inst...	Title: sif
edam:format_3620	edam:format_3620	MS Excel spreadsheet format consisting of a set of XML documents stored in a ...	Title: xlsx
edam:format_3621	edam:format_3621	Data format used by the SQLite database	Title: SQLite format
edam:format_3622	edam:format_3622	Data format used by the SQLite database conformant to the Gemini schema	Title: Gemini SQLite format
edam:format_3624	edam:format_3624	An index of a genome database, indexed for use by the snpeff tool	Title: snpeffdb
edam:format_3626	edam:format_3626	Binary format used by MATLAB files to store workspace variables	Title: MAT
edam:format_3650	edam:format_3650	Format used by netCDF software library for writing and reading chromatography...	Title: NetCDF
edam:format_3651	edam:format_3651	Files includes m/z, intensity pairs separated by headers; headers can con...	Title: MGF
edam:format_3652	edam:format_3652	Each file contains one header line for the known or assumed charge and the ma...	Title: dta
edam:format_3653	edam:format_3653	Differ from	Title: pkl
edam:format_3654	edam:format_3654	Common file format for proteomics mass spectrometric data developed at the Se...	Title: mzXML
edam:format_3655	edam:format_3655	Open data format for the storage, exchange, and processing of peptide sequenc...	Title: pepXML
edam:format_3657	edam:format_3657	Graphical Pathway Markup Language (GPML) is an XML format used for exchanging...	Title: GPML
edam:format_3665	edam:format_3665	A list of k-mers and their occurrences in a dataset	Title: K-mer countgraph
edam:format_3681	edam:format_3681	For mass spectrometry-based chemical profiling data (including metabolomics),...	Title: mzTab
edam:format_3682	edam:format_3682	imzML data are recorded in 2 files: '	Title: imzML metadata file
edam:format_3683	edam:format_3683	The focus of qcML is towards mass spectrometry based proteomics, but the form...	Title: qcML
edam:format_3684	edam:format_3684	PRIDE XML is an XML format for mass spectra, peptide and protein identificati...	Title: PRIDE XML
edam:format_3685	edam:format_3685	Simulation Experiment Description Markup Language (SED-ML) is an XML format f...	Title: SED-ML
edam:format_3686	edam:format_3686	An OMEX file is a ZIP container that includes a manifest file, listing the co...	Title: COMBINE OMEX
edam:format_3687	edam:format_3687	ISA-TAB is based on MAGE-TAB	Title: ISA-TAB
edam:format_3688	edam:format_3688	SBtab is a tabular format for biochemical network models	Title: SBtab
edam:format_3689	edam:format_3689	Biological Connection Markup Language (BCML) is an XML format for biological ...	Title: BCML
edam:format_3690	edam:format_3690	Biological Dynamics Markup Language (BDML) is an XML format for quantitative ...	Title: BDML
edam:format_3691	edam:format_3691	Biological Expression Language (BEL) is a textual format for representing sci...	Title: BEL
edam:format_3692	edam:format_3692	SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagra...	Title: SBGN-ML
edam:format_3693	edam:format_3693	AGP is a tabular format for a sequence assembly (a contig, a scaffold/superco...	Title: AGP
edam:format_3696	edam:format_3696	PostScript format	Title: PS
edam:format_3698	edam:format_3698	SRA archive format (SRA) is the archive format used for input to the NCBI Seq...	Title: SRA format
edam:format_3699	edam:format_3699	VDB ('vertical database') is the native format used for export from the NCBI ...	Title: VDB
edam:format_3701	edam:format_3701	A five-column, tab-delimited table of feature locations and qualifiers for im...	Title: Sequin format
edam:format_3702	edam:format_3702	Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscovere...	Title: MSF
edam:format_3706	edam:format_3706	Data format for biodiversity data	Title: Biodiversity data format
edam:format_3708	edam:format_3708	Exchange format of the Access to Biological Collections Data (ABCD) Schema; a...	Title: ABCD format
edam:format_3709	edam:format_3709	Tab-delimited text files of GenePattern that contain a column for each sample...	Title: GCT/Res format
edam:format_3710	edam:format_3710	Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex)	Title: WIFF format
edam:format_3711	edam:format_3711	Output format used by X! series search engines that is based on the XML langu...	Title: X!Tandem XML
edam:format_3712	edam:format_3712	Proprietary file format for mass spectrometry data from Thermo Scientific	Title: Thermo RAW
edam:format_3713	edam:format_3713	"Raw" result file from Mascot database search	Title: Mascot .dat file
edam:format_3714	edam:format_3714	Format of peak list files from Andromeda search engine (MaxQuant) that consis...	Title: MaxQuant APL peaklist format
edam:format_3725	edam:format_3725	SBOL introduces a standardised format for the electronic exchange of informat...	Title: SBOL
edam:format_3726	edam:format_3726	One or more mining models can be contained in a PMML document	Title: PMML
edam:format_3727	edam:format_3727	An OME-TIFF dataset consists of one or more files in standard TIFF or BigTIFF...	Title: OME-TIFF
edam:format_3728	edam:format_3728	Format for multiple aligned or single sequences together with the probabilist...	Title: LocARNA PP
edam:format_3729	edam:format_3729	Input format used by the Database of Genotypes and Phenotypes (dbGaP)	Title: dbGaP format
edam:format_3746	edam:format_3746	BIOM is a recognised standard for the Earth Microbiome Project, and is a proj...	Title: BIOM format
edam:format_3747	edam:format_3747	A format for storage, exchange, and processing of protein identifications cre...	Title: protXML
edam:format_3748	edam:format_3748	A linked data format enables publishing structured data as linked data (Linke...	Title: Linked data format
edam:format_3749	edam:format_3749	JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encodi...	Title: JSON-LD
edam:format_3750	edam:format_3750	Data in YAML format can be serialised into text, or binary format	Title: YAML
edam:format_3751	edam:format_3751	Tabular data represented as values in a text file delimited by some character	Title: DSV
edam:format_3752	edam:format_3752	Tabular data represented as comma-separated values in a text file	Title: CSV
edam:format_3758	edam:format_3758	"Raw" result file from SEQUEST database search	Title: SEQUEST .out file
edam:format_3764	edam:format_3764	XML file format for files containing information about peptide identification...	Title: idXML
edam:format_3765	edam:format_3765	Data table formatted such that it can be passed/streamed within the KNIME pla...	Title: KNIME datatable format
edam:format_3770	edam:format_3770	UniProtKB XML sequence features format is an XML format available for downloa...	Title: UniProtKB XML
edam:format_3771	edam:format_3771	UniProtKB RDF sequence features format is an RDF format available for downloa...	Title: UniProtKB RDF
edam:format_3772	edam:format_3772	BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some ...	Title: BioJSON (BioXSD)
edam:format_3773	edam:format_3773	BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some ...	Title: BioYAML
edam:format_3774	edam:format_3774	BioJSON is a JSON format of single multiple sequence alignments, with their a...	Title: BioJSON (Jalview)
edam:format_3775	edam:format_3775	'GSuite' belongs to the 'BioXSD	GTrack' ecosystem of generic formats, and par...
edam:format_3776	edam:format_3776	'BTrack' belongs to the 'BioXSD	GTrack' ecosystem of generic formats, and par...
edam:format_3777	edam:format_3777	Multi-Crop Passport Descriptors is a format available in 2 successive version...	Title: MCPD
edam:format_3780	edam:format_3780	Data format of an annotated text, e	Title: Annotated text format
edam:format_3781	edam:format_3781	JSON format of annotated scientific text used by PubAnnotations and other too...	Title: PubAnnotation format
edam:format_3782	edam:format_3782	BioC is a standardised XML format for sharing and integrating text data and a...	Title: BioC
edam:format_3783	edam:format_3783	Native textual export format of annotated scientific text from PubTator	Title: PubTator format
edam:format_3784	edam:format_3784	A format of text annotation using the linked-data Open Annotation Data Model,...	Title: Open Annotation format
edam:format_3785	edam:format_3785	A family of similar formats of text annotation, used by BRAT and other tools,...	Title: BioNLP Shared Task format
edam:format_3787	edam:format_3787	A query language (format) for structured database queries	Title: Query language
edam:format_3788	edam:format_3788	SQL (Structured Query Language) is the de-facto standard query language (form...	Title: SQL
edam:format_3789	edam:format_3789	XQuery (XML Query) is a query language (format of queries) for querying and m...	Title: XQuery
edam:format_3790	edam:format_3790	SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language ...	Title: SPARQL
edam:format_3804	edam:format_3804	XML format for XML Schema	Title: xsd
edam:format_3811	edam:format_3811	XMFA format stands for eXtended Multi-FastA format and is used to store colli...	Title: XMFA
edam:format_3812	edam:format_3812	The GEN file format contains genetic data and describes SNPs	Title: GEN
edam:format_3813	edam:format_3813	The SAMPLE file format contains information about each individual i	Title: SAMPLE file format
edam:format_3814	edam:format_3814	SDF is one of a family of chemical-data file formats developed by MDL Informa...	Title: SDF
edam:format_3815	edam:format_3815	An MDL Molfile is a file format for holding information about the atoms, bond...	Title: Molfile
edam:format_3816	edam:format_3816	Complete, portable representation of a SYBYL molecule	Title: Mol2
edam:format_3817	edam:format_3817	format for the LaTeX document preparation system	Title: latex
edam:format_3818	edam:format_3818	Tab-delimited text file format used by Eland - the read-mapping program distr...	Title: ELAND format
edam:format_3819	edam:format_3819	It differs from Phylip Format (format_1997) on length of the ID sequence	Title: Relaxed PHYLIP Interleaved
edam:format_3820	edam:format_3820	It differs from Phylip sequential format (format_1997) on length of the ID se...	Title: Relaxed PHYLIP Sequential
edam:format_3821	edam:format_3821	Default XML format of VisANT, containing all the network information	Title: VisML
edam:format_3822	edam:format_3822	GML (Graph Modeling Language) is a text file format supporting network data w...	Title: GML
edam:format_3823	edam:format_3823	FASTG is a format for faithfully representing genome assemblies in the face o...	Title: FASTG
edam:format_3824	edam:format_3824	Data format for raw data from a nuclear magnetic resonance (NMR) spectroscopy...	Title: NMR data format
edam:format_3825	edam:format_3825	nmrML is an MSI supported XML-based open access format for metabolomics NMR r...	Title: nmrML
edam:format_3826	edam:format_3826		Title: proBAM
edam:format_3827	edam:format_3827		Title: proBED
edam:format_3828	edam:format_3828	Data format for raw microarray data	Title: Raw microarray data format
edam:format_3829	edam:format_3829	GenePix Results (GPR) text file format developed by Axon Instruments that is ...	Title: GPR
edam:format_3830	edam:format_3830	Binary format used by the ARB software suite	Title: ARB
edam:format_3832	edam:format_3832	OpenMS format for grouping features in one map or across several maps	Title: consensusXML
edam:format_3833	edam:format_3833	OpenMS format for quantitation results (LC/MS features)	Title: featureXML
edam:format_3834	edam:format_3834	Now deprecated data format of the HUPO Proteomics Standards Initiative	Title: mzData
edam:format_3835	edam:format_3835	Format supported by the Tide tool for identifying peptides from tandem mass s...	Title: TIDE TXT
edam:format_3836	edam:format_3836	XML format as produced by the NCBI Blast package v2	Title: BLAST XML v2 results format
edam:format_3838	edam:format_3838	Microsoft Powerpoint format	Title: pptx
edam:format_3839	edam:format_3839	ibd is a data format for mass spectrometry imaging data	Title: ibd
edam:format_3841	edam:format_3841	Data format used in Natural Language Processing	Title: NLP format
edam:format_3843	edam:format_3843	XML input file format for BEAST Software (Bayesian Evolutionary Analysis Samp...	Title: BEAST
edam:format_3844	edam:format_3844	Chado-XML format is a direct mapping of the Chado relational schema into XML	Title: Chado-XML
edam:format_3845	edam:format_3845	An alignment format generated by PRANK/PRANKSTER consisting of four elements:...	Title: HSAML
edam:format_3846	edam:format_3846	Output xml file from the InterProScan sequence analysis application	Title: InterProScan XML
edam:format_3847	edam:format_3847	The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway map...	Title: KGML
edam:format_3848	edam:format_3848	XML format for collected entries from bibliographic databases MEDLINE and Pub...	Title: PubMed XML
edam:format_3849	edam:format_3849	A set of XML compliant markup components for describing multiple sequence ali...	Title: MSAML
edam:format_3850	edam:format_3850	OrthoXML is designed broadly to allow the storage and comparison of orthology...	Title: OrthoXML
edam:format_3851	edam:format_3851	Tree structure of Protein Sequence Database Markup Language generated using M...	Title: PSDML
edam:format_3852	edam:format_3852	SeqXML is an XML Schema to describe biological sequences, developed by the St...	Title: SeqXML
edam:format_3853	edam:format_3853	XML format for the UniParc database	Title: UniParc XML
edam:format_3854	edam:format_3854	XML format for the UniRef reference clusters	Title: UniRef XML
edam:format_3857	edam:format_3857	Common Workflow Language (CWL) format for description of command-line tools a...	Title: CWL
edam:format_3858	edam:format_3858	Proprietary file format for mass spectrometry data from Waters	Title: Waters RAW
edam:format_3859	edam:format_3859	A standardized file format for data exchange in mass spectrometry, initially ...	Title: JCAMP-DX
edam:format_3862	edam:format_3862	An NLP format used for annotated textual documents	Title: NLP annotation format
edam:format_3863	edam:format_3863	NLP format used by a specific type of corpus (collection of texts)	Title: NLP corpus format
edam:format_3864	edam:format_3864	mirGFF3 is a common format for microRNA data resulting from small-RNA RNA-Seq...	Title: mirGFF3
edam:format_3865	edam:format_3865	A "placeholder" concept for formats of annotated RNA data, including e	Title: RNA annotation format
edam:format_3866	edam:format_3866	File format to store trajectory information for a 3D structure	Title: Trajectory format
edam:format_3867	edam:format_3867	Binary file format to store trajectory information for a 3D structure	Title: Trajectory format (binary)
edam:format_3868	edam:format_3868	Textual file format to store trajectory information for a 3D structure	Title: Trajectory format (text)
edam:format_3873	edam:format_3873	HDF is currently supported by many commercial and non-commercial software pla...	Title: HDF
edam:format_3874	edam:format_3874	PCAZip format is a binary compressed file to store atom coordinates based on ...	Title: PCAzip
edam:format_3875	edam:format_3875	Portable binary format for trajectories produced by GROMACS package	Title: XTC
edam:format_3876	edam:format_3876	Fully architecture-independent format, regarding both endianness and the abil...	Title: TNG
edam:format_3877	edam:format_3877	The XYZ chemical file format is widely supported by many programs, although m...	Title: XYZ
edam:format_3878	edam:format_3878	AMBER trajectory (also called mdcrd), with 10 coordinates per line and format...	Title: mdcrd
edam:format_3879	edam:format_3879	Format of topology files; containing the static information of a structure mo...	Title: Topology format
edam:format_3880	edam:format_3880	GROMACS MD package top textual files define an entire structure system topolo...	Title: GROMACS top
edam:format_3881	edam:format_3881	AMBER Prmtop file (version 7) is a structure topology text file divided in se...	Title: AMBER top
edam:format_3882	edam:format_3882	The high similarity in the functional form of the two potential energy functi...	Title: PSF
edam:format_3883	edam:format_3883	GROMACS itp files (include topology) contain structure topology information, ...	Title: GROMACS itp
edam:format_3884	edam:format_3884	Format of force field parameter files, which store the set of parameters (cha...	Title: FF parameter format
edam:format_3885	edam:format_3885	It is basically a translation of the ASCII atom coordinate format to binary c...	Title: BinPos
edam:format_3886	edam:format_3886	AMBER coordinate/restart file with 6 coordinates per line and decimal format ...	Title: RST
edam:format_3887	edam:format_3887	Format of CHARMM Residue Topology Files (RTF), which define groups by includi...	Title: CHARMM rtf
edam:format_3888	edam:format_3888	AMBER frcmod (Force field Modification) is a file format to store any modific...	Title: AMBER frcmod
edam:format_3889	edam:format_3889	AMBER Object File Format library files (OFF library files) store residue libr...	Title: AMBER off
edam:format_3906	edam:format_3906	MReData is a text based data standard for processed NMR data	Title: NMReDATA
edam:format_3909	edam:format_3909	BpForms is a string format for concretely representing the primary structures...	Title: BpForms
edam:format_3910	edam:format_3910	Format of trr files that contain the trajectory of a simulation experiment us...	Title: trr
edam:format_3911	edam:format_3911	Mash sketch is a format for sequence / sequence checksum information	Title: msh
edam:format_3913	edam:format_3913	The Loom file format is based on HDF5, a standard for storing large numerical...	Title: Loom
edam:format_3915	edam:format_3915	The Zarr format is an implementation of chunked, compressed, N-dimensional ar...	Title: Zarr
edam:format_3916	edam:format_3916	The Matrix Market matrix (MTX) format stores numerical or pattern matrices in...	Title: MTX
edam:format_3951	edam:format_3951	BcForms is a format for abstractly describing the molecular structure (atoms ...	Title: BcForms
edam:format_3956	edam:format_3956	N-Quads is a line-based, plain text format for encoding an RDF dataset	Title: N-Quads
edam:format_3969	edam:format_3969	Vega is a visualization grammar, a declarative language for creating, saving,...	Title: Vega
edam:format_3970	edam:format_3970	Vega-Lite is a high-level grammar of interactive graphics	Title: Vega-lite
edam:format_3971	edam:format_3971	A model description language for computational neuroscience	Title: NeuroML
edam:format_3972	edam:format_3972	BioNetGen is a format for the specification and simulation of rule-based mode...	Title: BNGL
edam:format_3973	edam:format_3973	A Docker image is a file, comprised of multiple layers, that is used to execu...	Title: Docker image
edam:format_3975	edam:format_3975	Graphical Fragment Assembly captures sequence graphs as the product of an ass...	Title: GFA 1
edam:format_3976	edam:format_3976	Graphical Fragment Assembly captures sequence graphs as the product of an ass...	Title: GFA 2
edam:format_3977	edam:format_3977	ObjTables is a toolkit for creating re-usable datasets that are both human an...	Title: ObjTables
edam:format_3978	edam:format_3978	The CONTIG format used for output of the SOAPdenovo alignment program	Title: CONTIG
edam:format_3979	edam:format_3979	WEGO native format used by the Web Gene Ontology Annotation Plot application	Title: WEGO
edam:format_3980	edam:format_3980	For example a 1kb transcript with 1000 alignments in a sample of 10 million r...	Title: RPKM
edam:format_3981	edam:format_3981	For example a 1kb transcript with 1000 alignments in a sample of 10 million r...	Title: TAR format
edam:format_3982	edam:format_3982	The CHAIN format describes a pairwise alignment that allow gaps in both seque...	Title: CHAIN
edam:format_3983	edam:format_3983	The NET file format is used to describe the data that underlie the net alignm...	Title: NET
edam:format_3984	edam:format_3984	Format of QMAP files generated for methylation data from an internal BGI pipe...	Title: QMAP
edam:format_3985	edam:format_3985	An emerging format for high-level Galaxy workflow description	Title: gxformat2
edam:format_3986	edam:format_3986	The proprietary native video format of various Microsoft programs such as Win...	Title: WMV
edam:format_3987	edam:format_3987	A ZIP file may contain one or more files or directories that may have been co...	Title: ZIP format
edam:format_3988	edam:format_3988	LSM files are the default data export for the Zeiss LSM series confocal micro...	Title: LSM
edam:format_3989	edam:format_3989	GNU zip compressed file format common to Unix-based operating systems	Title: GZIP format
edam:format_3990	edam:format_3990	Audio Video Interleaved (AVI) format is a multimedia container format for AVI...	Title: AVI
edam:format_3991	edam:format_3991	A declaration file format for UCSC browsers track dataset display charaterist...	Title: TrackDB
edam:format_3992	edam:format_3992	Compact Idiosyncratic Gapped Alignment Report format is a compressed (run-len...	Title: CIGAR format
edam:format_3993	edam:format_3993	STL is a file format native to the stereolithography CAD software created by ...	Title: Stereolithography format
edam:format_3994	edam:format_3994	U3D (Universal 3D) is a compressed file format and data structure for 3D comp...	Title: U3D
edam:format_3995	edam:format_3995	Bitmap image format used for storing textures	Title: Texture file format
edam:format_3996	edam:format_3996	Format for scripts writtenin Python - a widely used high-level programming la...	Title: Python script
edam:format_3997	edam:format_3997	A digital multimedia container format most commonly used to store video and a...	Title: MPEG-4
edam:format_3998	edam:format_3998	Format for scripts written in Perl - a family of high-level, general-purpose,...	Title: Perl script
edam:format_3999	edam:format_3999	Format for scripts written in the R language - an open source programming lan...	Title: R script
edam:format_4000	edam:format_4000	A file format for making dynamic documents (R Markdown scripts) with the R la...	Title: R markdown
edam:format_4002	edam:format_4002	Format used by Python pickle module for serializing and de-serializing a Pyth...	Title: pickle
edam:format_4003	edam:format_4003	The standard binary file format used by NumPy - a fundamental package for sci...	Title: NumPy format
edam:format_4004	edam:format_4004	Format of repertoire (archive) files that can be read by SimToolbox (a MATLAB...	Title: SimTools repertoire file format
edam:format_4005	edam:format_4005	A configuration file used by various programs to store settings that are spec...	Title: Configuration file format
edam:format_4006	edam:format_4006	Format used by the Zstandard real-time compression algorithm	Title: Zstandard format
edam:format_4007	edam:format_4007	The file format for MATLAB scripts or functions	Title: MATLAB script
edam:format_4015	edam:format_4015	A data format for specifying parameter estimation problems in systems biology	Title: PEtab
edam:format_4018	edam:format_4018	Genomic Variant Call Format (gVCF) is a version of VCF that includes not only...	Title: gVCF
edam:format_4023	edam:format_4023	Chemical Markup Language (CML) is an XML-based format for encoding detailed i...	Title: cml
edam:format_4024	edam:format_4024	Crystallographic Information File (CIF) is a data exchange standard file form...	Title: cif
edam:format_4025	edam:format_4025	Format for describing the capabilities of a biosimulation tool including the ...	Title: BioSimulators format for the specifications of biosimulation tools
edam:format_4026	edam:format_4026	Outlines the syntax and semantics of the input and output arguments for comma...	Title: BioSimulators standard for command-line interfaces for biosimulation tools
edam:format_4035	edam:format_4035	Data format derived from the standard PDB format, which enables user to incor...	Title: PQR
edam:format_4036	edam:format_4036	Data format used in AutoDock 4 for storing atomic coordinates, partial atomic...	Title: PDBQT
edam:format_4039	edam:format_4039	MSP is a data format for mass spectrometry data	Title: MSP
edam:format_4041	edam:format_4041	A standard for DMPs developed by the Research Data Alliance	Title: maDMP
edam:format_4048	edam:format_4048	Nextflow is a workflow system for creating scalable, portable, and reproducib...	Title: Nextflow
edam:format_4049	edam:format_4049	The Snakemake workflow management system is a tool to create reproducible and...	Title: Snakemake
edam:format_4050	edam:format_4050	Sample and Data Relationship File for a proteomics experiment	Title: SDRF
edam:format_4058	edam:format_4058	The reference implementation of mzTab-M in Java is https://github	Title: mzTab-M
edam:format_4059	edam:format_4059	mzTab-L is a light-weight, tab-delimited format for mass spectrometry-based l...	Title: mzTab-L

Identifier and Mapping Information

Schema Source

from schema: https://includedcc.org/cam-expanded-enums

LinkML Source

name: EnumEDAMFormats
description: Data formats from the EDAM ontology.
from_schema: https://includedcc.org/cam-expanded-enums
rank: 1000
permissible_values:
  edam:format_1915:
    text: edam:format_1915
    description: Format
    meaning: edam:format_1915
    title: Format
  edam:format_1196:
    text: edam:format_1196
    description: Chemical structure specified in Simplified Molecular Input Line Entry
      System (SMILES) line notation.
    meaning: edam:format_1196
    title: SMILES
  edam:format_1197:
    text: edam:format_1197
    description: Chemical structure specified in IUPAC International Chemical Identifier
      (InChI) line notation.
    meaning: edam:format_1197
    title: InChI
  edam:format_1198:
    text: edam:format_1198
    description: 'Chemical structure specified by Molecular Formula (MF), including
      a count of each element in a compound.

      The general MF query format consists of a series of valid atomic symbols, with
      an optional number or range.'
    meaning: edam:format_1198
    title: mf
  edam:format_1199:
    text: edam:format_1199
    description: 'An InChIKey identifier is not human- nor machine-readable but is
      more suitable for web searches than an InChI chemical structure specification.

      The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital
      representation of an InChI chemical structure specification. It uniquely identifies
      a chemical compound.'
    meaning: edam:format_1199
    title: InChIKey
  edam:format_1200:
    text: edam:format_1200
    description: SMILES ARbitrary Target Specification (SMARTS) format for chemical
      structure specification, which is a subset of the SMILES line notation.
    meaning: edam:format_1200
    title: smarts
  edam:format_1206:
    text: edam:format_1206
    description: Alphabet for a molecular sequence with possible unknown positions
      but without ambiguity or non-sequence characters.
    meaning: edam:format_1206
    title: unambiguous pure
  edam:format_1207:
    text: edam:format_1207
    description: 'Alphabet for a nucleotide sequence with possible ambiguity, unknown
      positions and non-sequence characters.

      Non-sequence characters may be used for example for gaps.'
    meaning: edam:format_1207
    title: nucleotide
  edam:format_1208:
    text: edam:format_1208
    description: 'Alphabet for a protein sequence with possible ambiguity, unknown
      positions and non-sequence characters.

      Non-sequence characters may be used for gaps and translation stop.'
    meaning: edam:format_1208
    title: protein
  edam:format_1209:
    text: edam:format_1209
    description: Alphabet for the consensus of two or more molecular sequences.
    meaning: edam:format_1209
    title: consensus
  edam:format_1210:
    text: edam:format_1210
    description: Alphabet for a nucleotide sequence with possible ambiguity and unknown
      positions but without non-sequence characters.
    meaning: edam:format_1210
    title: pure nucleotide
  edam:format_1211:
    text: edam:format_1211
    description: Alphabet for a nucleotide sequence (characters ACGTU only) with possible
      unknown positions but without ambiguity or non-sequence characters .
    meaning: edam:format_1211
    title: unambiguous pure nucleotide
  edam:format_1212:
    text: edam:format_1212
    description: Alphabet for a DNA sequence with possible ambiguity, unknown positions
      and non-sequence characters.
    meaning: edam:format_1212
    title: dna
  edam:format_1213:
    text: edam:format_1213
    description: Alphabet for an RNA sequence with possible ambiguity, unknown positions
      and non-sequence characters.
    meaning: edam:format_1213
    title: rna
  edam:format_1214:
    text: edam:format_1214
    description: Alphabet for a DNA sequence (characters ACGT only) with possible
      unknown positions but without ambiguity or non-sequence characters.
    meaning: edam:format_1214
    title: unambiguous pure dna
  edam:format_1215:
    text: edam:format_1215
    description: Alphabet for a DNA sequence with possible ambiguity and unknown positions
      but without non-sequence characters.
    meaning: edam:format_1215
    title: pure dna
  edam:format_1216:
    text: edam:format_1216
    description: Alphabet for an RNA sequence (characters ACGU only) with possible
      unknown positions but without ambiguity or non-sequence characters.
    meaning: edam:format_1216
    title: unambiguous pure rna sequence
  edam:format_1217:
    text: edam:format_1217
    description: Alphabet for an RNA sequence with possible ambiguity and unknown
      positions but without non-sequence characters.
    meaning: edam:format_1217
    title: pure rna
  edam:format_1218:
    text: edam:format_1218
    description: Alphabet for any protein sequence with possible unknown positions
      but without ambiguity or non-sequence characters.
    meaning: edam:format_1218
    title: unambiguous pure protein
  edam:format_1219:
    text: edam:format_1219
    description: Alphabet for any protein sequence with possible ambiguity and unknown
      positions but without non-sequence characters.
    meaning: edam:format_1219
    title: pure protein
  edam:format_1248:
    text: edam:format_1248
    description: Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank
      database.
    meaning: edam:format_1248
    title: EMBL feature location
  edam:format_1295:
    text: edam:format_1295
    description: Report format for tandem repeats in a nucleotide sequence (format
      generated by the Sanger Centre quicktandem program).
    meaning: edam:format_1295
    title: quicktandem
  edam:format_1296:
    text: edam:format_1296
    description: Report format for inverted repeats in a nucleotide sequence (format
      generated by the Sanger Centre inverted program).
    meaning: edam:format_1296
    title: Sanger inverted repeats
  edam:format_1297:
    text: edam:format_1297
    description: Report format for tandem repeats in a sequence (an EMBOSS report
      format).
    meaning: edam:format_1297
    title: EMBOSS repeat
  edam:format_1316:
    text: edam:format_1316
    description: Format of a report on exon-intron structure generated by EMBOSS est2genome.
    meaning: edam:format_1316
    title: est2genome format
  edam:format_1318:
    text: edam:format_1318
    description: Report format for restriction enzyme recognition sites used by EMBOSS
      restrict program.
    meaning: edam:format_1318
    title: restrict format
  edam:format_1319:
    text: edam:format_1319
    description: Report format for restriction enzyme recognition sites used by EMBOSS
      restover program.
    meaning: edam:format_1319
    title: restover format
  edam:format_1320:
    text: edam:format_1320
    description: Report format for restriction enzyme recognition sites used by REBASE
      database.
    meaning: edam:format_1320
    title: REBASE restriction sites
  edam:format_1332:
    text: edam:format_1332
    description: 'Format of results of a sequence database search using FASTA.

      This includes (typically) score data, alignment data and a histogram (of observed
      and expected distribution of E values.)'
    meaning: edam:format_1332
    title: FASTA search results format
  edam:format_1333:
    text: edam:format_1333
    description: 'Format of results of a sequence database search using some variant
      of BLAST.

      This includes score data, alignment data and summary table.'
    meaning: edam:format_1333
    title: BLAST results
  edam:format_1334:
    text: edam:format_1334
    description: Format of results of a sequence database search using some variant
      of MSPCrunch.
    meaning: edam:format_1334
    title: mspcrunch
  edam:format_1335:
    text: edam:format_1335
    description: Format of results of a sequence database search using some variant
      of Smith Waterman.
    meaning: edam:format_1335
    title: Smith-Waterman format
  edam:format_1336:
    text: edam:format_1336
    description: 'Format of EMBASSY domain hits file (DHF) of hits (sequences) with
      domain classification information.

      The hits are relatives to a SCOP or CATH family and are found from a search
      of a sequence database.'
    meaning: edam:format_1336
    title: dhf
  edam:format_1337:
    text: edam:format_1337
    description: 'Format of EMBASSY ligand hits file (LHF) of database hits (sequences)
      with ligand classification information.

      The hits are putative ligand-binding sequences and are found from a search of
      a sequence database.'
    meaning: edam:format_1337
    title: lhf
  edam:format_1341:
    text: edam:format_1341
    description: Results format for searches of the InterPro database.
    meaning: edam:format_1341
    title: InterPro hits format
  edam:format_1342:
    text: edam:format_1342
    description: 'Format of results of a search of the InterPro database showing matches
      of query protein sequence(s) to InterPro entries.

      The report includes a classification of regions in a query protein sequence
      which are assigned to a known InterPro protein family or group.'
    meaning: edam:format_1342
    title: InterPro protein view report format
  edam:format_1343:
    text: edam:format_1343
    description: 'Format of results of a search of the InterPro database showing matches
      between protein sequence(s) and signatures for an InterPro entry.

      The table presents matches between query proteins (rows) and signature methods
      (columns) for this entry. Alternatively the sequence(s) might be from from the
      InterPro entry itself. The match position in the protein sequence and match
      status (true positive, false positive etc) are indicated.'
    meaning: edam:format_1343
    title: InterPro match table format
  edam:format_1349:
    text: edam:format_1349
    description: Dirichlet distribution HMMER format.
    meaning: edam:format_1349
    title: HMMER Dirichlet prior
  edam:format_1350:
    text: edam:format_1350
    description: Dirichlet distribution MEME format.
    meaning: edam:format_1350
    title: MEME Dirichlet prior
  edam:format_1351:
    text: edam:format_1351
    description: Format of a report from the HMMER package on the emission and transition
      counts of a hidden Markov model.
    meaning: edam:format_1351
    title: HMMER emission and transition
  edam:format_1356:
    text: edam:format_1356
    description: Format of a regular expression pattern from the Prosite database.
    meaning: edam:format_1356
    title: prosite-pattern
  edam:format_1357:
    text: edam:format_1357
    description: Format of an EMBOSS sequence pattern.
    meaning: edam:format_1357
    title: EMBOSS sequence pattern
  edam:format_1360:
    text: edam:format_1360
    description: A motif in the format generated by the MEME program.
    meaning: edam:format_1360
    title: meme-motif
  edam:format_1366:
    text: edam:format_1366
    description: Sequence profile (sequence classifier) format used in the PROSITE
      database.
    meaning: edam:format_1366
    title: prosite-profile
  edam:format_1367:
    text: edam:format_1367
    description: A profile (sequence classifier) in the format used in the JASPAR
      database.
    meaning: edam:format_1367
    title: JASPAR format
  edam:format_1369:
    text: edam:format_1369
    description: Format of the model of random sequences used by MEME.
    meaning: edam:format_1369
    title: MEME background Markov model
  edam:format_1370:
    text: edam:format_1370
    description: Format of a hidden Markov model representation used by the HMMER
      package.
    meaning: edam:format_1370
    title: HMMER format
  edam:format_1391:
    text: edam:format_1391
    description: FASTA-style format for multiple sequences aligned by HMMER package
      to an HMM.
    meaning: edam:format_1391
    title: HMMER-aln
  edam:format_1392:
    text: edam:format_1392
    description: Format of multiple sequences aligned by DIALIGN package.
    meaning: edam:format_1392
    title: DIALIGN format
  edam:format_1393:
    text: edam:format_1393
    description: 'EMBASSY ''domain alignment file'' (DAF) format, containing a sequence
      alignment of protein domains belonging to the same SCOP or CATH family.

      The format is clustal-like and includes annotation of domain family classification
      information.'
    meaning: edam:format_1393
    title: daf
  edam:format_1419:
    text: edam:format_1419
    description: Format for alignment of molecular sequences to MEME profiles (position-dependent
      scoring matrices) as generated by the MAST tool from the MEME package.
    meaning: edam:format_1419
    title: Sequence-MEME profile alignment
  edam:format_1421:
    text: edam:format_1421
    description: Format used by the HMMER package for an alignment of a sequence against
      a hidden Markov model database.
    meaning: edam:format_1421
    title: HMMER profile alignment (sequences versus HMMs)
  edam:format_1422:
    text: edam:format_1422
    description: Format used by the HMMER package for of an alignment of a hidden
      Markov model against a sequence database.
    meaning: edam:format_1422
    title: HMMER profile alignment (HMM versus sequences)
  edam:format_1423:
    text: edam:format_1423
    description: 'Data Type must include the distance matrix, probably as pairs of
      sequence identifiers with a distance (integer or float).

      Format of PHYLIP phylogenetic distance matrix data.'
    meaning: edam:format_1423
    title: Phylip distance matrix
  edam:format_1424:
    text: edam:format_1424
    description: Dendrogram (tree file) format generated by ClustalW.
    meaning: edam:format_1424
    title: ClustalW dendrogram
  edam:format_1425:
    text: edam:format_1425
    description: Raw data file format used by Phylip from which a phylogenetic tree
      is directly generated or plotted.
    meaning: edam:format_1425
    title: Phylip tree raw
  edam:format_1430:
    text: edam:format_1430
    description: PHYLIP file format for continuous quantitative character data.
    meaning: edam:format_1430
    title: Phylip continuous quantitative characters
  edam:format_1432:
    text: edam:format_1432
    description: PHYLIP file format for phylogenetics character frequency data.
    meaning: edam:format_1432
    title: Phylip character frequencies format
  edam:format_1433:
    text: edam:format_1433
    description: Format of PHYLIP discrete states data.
    meaning: edam:format_1433
    title: Phylip discrete states format
  edam:format_1434:
    text: edam:format_1434
    description: Format of PHYLIP cliques data.
    meaning: edam:format_1434
    title: Phylip cliques format
  edam:format_1435:
    text: edam:format_1435
    description: Phylogenetic tree data format used by the PHYLIP program.
    meaning: edam:format_1435
    title: Phylip tree format
  edam:format_1436:
    text: edam:format_1436
    description: The format of an entry from the TreeBASE database of phylogenetic
      data.
    meaning: edam:format_1436
    title: TreeBASE format
  edam:format_1437:
    text: edam:format_1437
    description: The format of an entry from the TreeFam database of phylogenetic
      data.
    meaning: edam:format_1437
    title: TreeFam format
  edam:format_1445:
    text: edam:format_1445
    description: Format for distances, such as Branch Score distance, between two
      or more phylogenetic trees as used by the Phylip package.
    meaning: edam:format_1445
    title: Phylip tree distance format
  edam:format_1454:
    text: edam:format_1454
    description: 'Format of an entry from the DSSP database (Dictionary of Secondary
      Structure in Proteins).

      The DSSP database is built using the DSSP application which defines secondary
      structure, geometrical features and solvent exposure of proteins, given atomic
      coordinates in PDB format.'
    meaning: edam:format_1454
    title: dssp
  edam:format_1455:
    text: edam:format_1455
    description: Entry format of the HSSP database (Homology-derived Secondary Structure
      in Proteins).
    meaning: edam:format_1455
    title: hssp
  edam:format_1457:
    text: edam:format_1457
    description: Format of RNA secondary structure in dot-bracket notation, originally
      generated by the Vienna RNA package/server.
    meaning: edam:format_1457
    title: Dot-bracket format
  edam:format_1458:
    text: edam:format_1458
    description: Format of local RNA secondary structure components with free energy
      values, generated by the Vienna RNA package/server.
    meaning: edam:format_1458
    title: Vienna local RNA secondary structure format
  edam:format_1475:
    text: edam:format_1475
    description: Format of an entry (or part of an entry) from the PDB database.
    meaning: edam:format_1475
    title: PDB database entry format
  edam:format_1476:
    text: edam:format_1476
    description: Entry format of PDB database in PDB format.
    meaning: edam:format_1476
    title: PDB
  edam:format_1477:
    text: edam:format_1477
    description: Entry format of PDB database in mmCIF format.
    meaning: edam:format_1477
    title: mmCIF
  edam:format_1478:
    text: edam:format_1478
    description: Entry format of PDB database in PDBML (XML) format.
    meaning: edam:format_1478
    title: PDBML
  edam:format_1504:
    text: edam:format_1504
    description: Amino acid index format used by the AAindex database.
    meaning: edam:format_1504
    title: aaindex
  edam:format_1551:
    text: edam:format_1551
    description: 'Format of output of the Pcons Model Quality Assessment Program (MQAP).

      Pcons ranks protein models by assessing their quality based on the occurrence
      of recurring common three-dimensional structural patterns. Pcons returns a score
      reflecting the overall global quality and a score for each individual residue
      in the protein reflecting the local residue quality.'
    meaning: edam:format_1551
    title: Pcons report format
  edam:format_1552:
    text: edam:format_1552
    description: 'Format of output of the ProQ protein model quality predictor.

      ProQ is a neural network-based predictor that predicts the quality of a protein
      model based on the number of structural features.'
    meaning: edam:format_1552
    title: ProQ report format
  edam:format_1582:
    text: edam:format_1582
    description: A report format for the kinetics of enzyme-catalysed reaction(s)
      in a format generated by EMBOSS findkm. This includes Michaelis Menten plot,
      Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax).
    meaning: edam:format_1582
    title: findkm
  edam:format_1627:
    text: edam:format_1627
    description: Report format on PCR primers and hybridisation oligos as generated
      by Whitehead primer3 program.
    meaning: edam:format_1627
    title: Primer3 primer
  edam:format_1628:
    text: edam:format_1628
    description: A format of raw sequence read data from an Applied Biosystems sequencing
      machine.
    meaning: edam:format_1628
    title: ABI
  edam:format_1629:
    text: edam:format_1629
    description: Format of MIRA sequence trace information file.
    meaning: edam:format_1629
    title: mira
  edam:format_1630:
    text: edam:format_1630
    description: Common Assembly Format (CAF). A sequence assembly format including
      contigs, base-call qualities, and other metadata.
    meaning: edam:format_1630
    title: CAF
  edam:format_1631:
    text: edam:format_1631
    description: Sequence assembly project file EXP format.
    meaning: edam:format_1631
    title: EXP
  edam:format_1632:
    text: edam:format_1632
    description: Staden Chromatogram Files format (SCF) of base-called sequence reads,
      qualities, and other metadata.
    meaning: edam:format_1632
    title: SCF
  edam:format_1633:
    text: edam:format_1633
    description: PHD sequence trace format to store serialised chromatogram data (reads).
    meaning: edam:format_1633
    title: PHD
  edam:format_1637:
    text: edam:format_1637
    description: Format of Affymetrix data file of raw image data.
    meaning: edam:format_1637
    title: dat
  edam:format_1638:
    text: edam:format_1638
    description: Format of Affymetrix data file of information about (raw) expression
      levels of the individual probes.
    meaning: edam:format_1638
    title: cel
  edam:format_1639:
    text: edam:format_1639
    description: Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt)
      from hierarchical clustering.
    meaning: edam:format_1639
    title: affymetrix
  edam:format_1641:
    text: edam:format_1641
    description: Affymetrix data file format for information about experimental conditions
      and protocols.
    meaning: edam:format_1641
    title: affymetrix-exp
  edam:format_1644:
    text: edam:format_1644
    description: Format of Affymetrix data file of information about (normalised)
      expression levels of the individual probes.
    meaning: edam:format_1644
    title: CHP
  edam:format_1665:
    text: edam:format_1665
    description: Format of Taverna workflows.
    meaning: edam:format_1665
    title: Taverna workflow format
  edam:format_1705:
    text: edam:format_1705
    description: The format of an entry from the HET group dictionary (HET groups
      from PDB files).
    meaning: edam:format_1705
    title: HET group dictionary entry format
  edam:format_1734:
    text: edam:format_1734
    description: Format of bibliographic reference as used by the PubMed database.
    meaning: edam:format_1734
    title: PubMed citation
  edam:format_1735:
    text: edam:format_1735
    description: 'Bibliographic reference information including citation information
      is included

      Format for abstracts of scientific articles from the Medline database.'
    meaning: edam:format_1735
    title: Medline Display Format
  edam:format_1736:
    text: edam:format_1736
    description: CiteXplore 'core' citation format including title, journal, authors
      and abstract.
    meaning: edam:format_1736
    title: CiteXplore-core
  edam:format_1737:
    text: edam:format_1737
    description: CiteXplore 'all' citation format includes all known details such
      as Mesh terms and cross-references.
    meaning: edam:format_1737
    title: CiteXplore-all
  edam:format_1739:
    text: edam:format_1739
    description: Article format of the PubMed Central database.
    meaning: edam:format_1739
    title: pmc
  edam:format_1740:
    text: edam:format_1740
    description: The format of iHOP (Information Hyperlinked over Proteins) text-mining
      result.
    meaning: edam:format_1740
    title: iHOP format
  edam:format_1741:
    text: edam:format_1741
    description: 'OSCAR (Open-Source Chemistry Analysis Routines) software performs
      chemistry-specific parsing of chemical documents. It attempts to identify chemical
      names, ontology concepts, and chemical data from a document.

      OSCAR format of annotated chemical text.'
    meaning: edam:format_1741
    title: OSCAR format
  edam:format_1861:
    text: edam:format_1861
    description: Map of a plasmid (circular DNA) in PlasMapper TextMap format.
    meaning: edam:format_1861
    title: PlasMapper TextMap
  edam:format_1910:
    text: edam:format_1910
    description: Phylogenetic tree Newick (text) format.
    meaning: edam:format_1910
    title: newick
  edam:format_1911:
    text: edam:format_1911
    description: Phylogenetic tree TreeCon (text) format.
    meaning: edam:format_1911
    title: TreeCon format
  edam:format_1912:
    text: edam:format_1912
    description: Phylogenetic tree Nexus (text) format.
    meaning: edam:format_1912
    title: Nexus format
  edam:format_1919:
    text: edam:format_1919
    description: Data format for a molecular sequence record.
    meaning: edam:format_1919
    title: Sequence record format
  edam:format_1920:
    text: edam:format_1920
    description: Data format for molecular sequence feature information.
    meaning: edam:format_1920
    title: Sequence feature annotation format
  edam:format_1921:
    text: edam:format_1921
    description: Data format for molecular sequence alignment information.
    meaning: edam:format_1921
    title: Alignment format
  edam:format_1923:
    text: edam:format_1923
    description: ACEDB sequence format.
    meaning: edam:format_1923
    title: acedb
  edam:format_1925:
    text: edam:format_1925
    description: Codata entry format.
    meaning: edam:format_1925
    title: codata
  edam:format_1926:
    text: edam:format_1926
    description: Fasta format variant with database name before ID.
    meaning: edam:format_1926
    title: dbid
  edam:format_1927:
    text: edam:format_1927
    description: EMBL entry format.
    meaning: edam:format_1927
    title: EMBL format
  edam:format_1928:
    text: edam:format_1928
    description: Staden experiment file format.
    meaning: edam:format_1928
    title: Staden experiment format
  edam:format_1929:
    text: edam:format_1929
    description: FASTA format including NCBI-style IDs.
    meaning: edam:format_1929
    title: FASTA
  edam:format_1930:
    text: edam:format_1930
    description: FASTQ short read format ignoring quality scores.
    meaning: edam:format_1930
    title: FASTQ
  edam:format_1931:
    text: edam:format_1931
    description: FASTQ Illumina 1.3 short read format.
    meaning: edam:format_1931
    title: FASTQ-illumina
  edam:format_1932:
    text: edam:format_1932
    description: FASTQ short read format with phred quality.
    meaning: edam:format_1932
    title: FASTQ-sanger
  edam:format_1933:
    text: edam:format_1933
    description: FASTQ Solexa/Illumina 1.0 short read format.
    meaning: edam:format_1933
    title: FASTQ-solexa
  edam:format_1934:
    text: edam:format_1934
    description: Fitch program format.
    meaning: edam:format_1934
    title: fitch program
  edam:format_1935:
    text: edam:format_1935
    description: 'GCG SSF (single sequence file) file format.

      GCG sequence file format.'
    meaning: edam:format_1935
    title: GCG
  edam:format_1936:
    text: edam:format_1936
    description: Genbank entry format.
    meaning: edam:format_1936
    title: GenBank format
  edam:format_1937:
    text: edam:format_1937
    description: 'Currently identical to refseqp format

      Genpept protein entry format.'
    meaning: edam:format_1937
    title: genpept
  edam:format_1938:
    text: edam:format_1938
    description: GFF feature file format with sequence in the header.
    meaning: edam:format_1938
    title: GFF2-seq
  edam:format_1939:
    text: edam:format_1939
    description: GFF3 feature file format with sequence.
    meaning: edam:format_1939
    title: GFF3-seq
  edam:format_1940:
    text: edam:format_1940
    description: FASTA sequence format including NCBI-style GIs.
    meaning: edam:format_1940
    title: giFASTA format
  edam:format_1941:
    text: edam:format_1941
    description: Hennig86 output sequence format.
    meaning: edam:format_1941
    title: hennig86
  edam:format_1942:
    text: edam:format_1942
    description: Intelligenetics sequence format.
    meaning: edam:format_1942
    title: ig
  edam:format_1943:
    text: edam:format_1943
    description: Intelligenetics sequence format (strict version).
    meaning: edam:format_1943
    title: igstrict
  edam:format_1944:
    text: edam:format_1944
    description: Jackknifer interleaved and non-interleaved sequence format.
    meaning: edam:format_1944
    title: jackknifer
  edam:format_1945:
    text: edam:format_1945
    description: Mase program sequence format.
    meaning: edam:format_1945
    title: mase format
  edam:format_1946:
    text: edam:format_1946
    description: Mega interleaved and non-interleaved sequence format.
    meaning: edam:format_1946
    title: mega-seq
  edam:format_1947:
    text: edam:format_1947
    description: GCG MSF (multiple sequence file) file format.
    meaning: edam:format_1947
    title: GCG MSF
  edam:format_1948:
    text: edam:format_1948
    description: NBRF/PIR entry sequence format.
    meaning: edam:format_1948
    title: nbrf/pir
  edam:format_1949:
    text: edam:format_1949
    description: Nexus/paup interleaved sequence format.
    meaning: edam:format_1949
    title: nexus-seq
  edam:format_1950:
    text: edam:format_1950
    description: 'PDB sequence format (ATOM lines).

      pdb format in EMBOSS.'
    meaning: edam:format_1950
    title: pdbatom
  edam:format_1951:
    text: edam:format_1951
    description: 'PDB nucleotide sequence format (ATOM lines).

      pdbnuc format in EMBOSS.'
    meaning: edam:format_1951
    title: pdbatomnuc
  edam:format_1952:
    text: edam:format_1952
    description: 'PDB nucleotide sequence format (SEQRES lines).

      pdbnucseq format in EMBOSS.'
    meaning: edam:format_1952
    title: pdbseqresnuc
  edam:format_1953:
    text: edam:format_1953
    description: 'PDB sequence format (SEQRES lines).

      pdbseq format in EMBOSS.'
    meaning: edam:format_1953
    title: pdbseqres
  edam:format_1954:
    text: edam:format_1954
    description: Plain old FASTA sequence format (unspecified format for IDs).
    meaning: edam:format_1954
    title: Pearson format
  edam:format_1957:
    text: edam:format_1957
    description: Raw sequence format with no non-sequence characters.
    meaning: edam:format_1957
    title: raw
  edam:format_1958:
    text: edam:format_1958
    description: 'Currently identical to genpept format

      Refseq protein entry sequence format.'
    meaning: edam:format_1958
    title: refseqp
  edam:format_1960:
    text: edam:format_1960
    description: Staden suite sequence format.
    meaning: edam:format_1960
    title: Staden format
  edam:format_1961:
    text: edam:format_1961
    description: Stockholm multiple sequence alignment format (used by Pfam and Rfam).
    meaning: edam:format_1961
    title: Stockholm format
  edam:format_1962:
    text: edam:format_1962
    description: DNA strider output sequence format.
    meaning: edam:format_1962
    title: strider format
  edam:format_1963:
    text: edam:format_1963
    description: UniProtKB entry sequence format.
    meaning: edam:format_1963
    title: UniProtKB format
  edam:format_1964:
    text: edam:format_1964
    description: Plain text sequence format (essentially unformatted).
    meaning: edam:format_1964
    title: plain text format (unformatted)
  edam:format_1966:
    text: edam:format_1966
    description: NCBI ASN.1-based sequence format.
    meaning: edam:format_1966
    title: ASN.1 sequence format
  edam:format_1967:
    text: edam:format_1967
    description: DAS sequence (XML) format (any type).
    meaning: edam:format_1967
    title: DAS format
  edam:format_1968:
    text: edam:format_1968
    description: 'DAS sequence (XML) format (nucleotide-only).

      The use of this format is deprecated.'
    meaning: edam:format_1968
    title: dasdna
  edam:format_1969:
    text: edam:format_1969
    description: EMBOSS debugging trace sequence format of full internal data content.
    meaning: edam:format_1969
    title: debug-seq
  edam:format_1970:
    text: edam:format_1970
    description: Jackknifer output sequence non-interleaved format.
    meaning: edam:format_1970
    title: jackknifernon
  edam:format_1972:
    text: edam:format_1972
    description: 'NCBI FASTA sequence format with NCBI-style IDs.

      There are several variants of this.'
    meaning: edam:format_1972
    title: NCBI format
  edam:format_1973:
    text: edam:format_1973
    description: Nexus/paup non-interleaved sequence format.
    meaning: edam:format_1973
    title: nexusnon
  edam:format_1974:
    text: edam:format_1974
    description: General Feature Format (GFF) of sequence features.
    meaning: edam:format_1974
    title: GFF2
  edam:format_1975:
    text: edam:format_1975
    description: Generic Feature Format version 3 (GFF3) of sequence features.
    meaning: edam:format_1975
    title: GFF3
  edam:format_1978:
    text: edam:format_1978
    description: DAS GFF (XML) feature format.
    meaning: edam:format_1978
    title: DASGFF
  edam:format_1979:
    text: edam:format_1979
    description: EMBOSS debugging trace feature format of full internal data content.
    meaning: edam:format_1979
    title: debug-feat
  edam:format_1982:
    text: edam:format_1982
    description: ClustalW format for (aligned) sequences.
    meaning: edam:format_1982
    title: ClustalW format
  edam:format_1983:
    text: edam:format_1983
    description: EMBOSS alignment format for debugging trace of full internal data
      content.
    meaning: edam:format_1983
    title: debug
  edam:format_1984:
    text: edam:format_1984
    description: Fasta format for (aligned) sequences.
    meaning: edam:format_1984
    title: FASTA-aln
  edam:format_1985:
    text: edam:format_1985
    description: Pearson MARKX0 alignment format.
    meaning: edam:format_1985
    title: markx0
  edam:format_1986:
    text: edam:format_1986
    description: Pearson MARKX1 alignment format.
    meaning: edam:format_1986
    title: markx1
  edam:format_1987:
    text: edam:format_1987
    description: Pearson MARKX10 alignment format.
    meaning: edam:format_1987
    title: markx10
  edam:format_1988:
    text: edam:format_1988
    description: Pearson MARKX2 alignment format.
    meaning: edam:format_1988
    title: markx2
  edam:format_1989:
    text: edam:format_1989
    description: Pearson MARKX3 alignment format.
    meaning: edam:format_1989
    title: markx3
  edam:format_1990:
    text: edam:format_1990
    description: Alignment format for start and end of matches between sequence pairs.
    meaning: edam:format_1990
    title: match
  edam:format_1991:
    text: edam:format_1991
    description: Mega format for (typically aligned) sequences.
    meaning: edam:format_1991
    title: mega
  edam:format_1992:
    text: edam:format_1992
    description: Mega non-interleaved format for (typically aligned) sequences.
    meaning: edam:format_1992
    title: meganon
  edam:format_1996:
    text: edam:format_1996
    description: EMBOSS simple sequence pairwise alignment format.
    meaning: edam:format_1996
    title: pair
  edam:format_1997:
    text: edam:format_1997
    description: Phylip format for (aligned) sequences.
    meaning: edam:format_1997
    title: PHYLIP format
  edam:format_1998:
    text: edam:format_1998
    description: Phylip non-interleaved format for (aligned) sequences.
    meaning: edam:format_1998
    title: PHYLIP sequential
  edam:format_1999:
    text: edam:format_1999
    description: Alignment format for score values for pairs of sequences.
    meaning: edam:format_1999
    title: scores format
  edam:format_2000:
    text: edam:format_2000
    description: SELEX format for (aligned) sequences.
    meaning: edam:format_2000
    title: selex
  edam:format_2001:
    text: edam:format_2001
    description: EMBOSS simple multiple alignment format.
    meaning: edam:format_2001
    title: EMBOSS simple format
  edam:format_2002:
    text: edam:format_2002
    description: Simple multiple sequence (alignment) format for SRS.
    meaning: edam:format_2002
    title: srs format
  edam:format_2003:
    text: edam:format_2003
    description: Simple sequence pair (alignment) format for SRS.
    meaning: edam:format_2003
    title: srspair
  edam:format_2004:
    text: edam:format_2004
    description: T-Coffee program alignment format.
    meaning: edam:format_2004
    title: T-Coffee format
  edam:format_2005:
    text: edam:format_2005
    description: Treecon format for (aligned) sequences.
    meaning: edam:format_2005
    title: TreeCon-seq
  edam:format_2006:
    text: edam:format_2006
    description: Data format for a phylogenetic tree.
    meaning: edam:format_2006
    title: Phylogenetic tree format
  edam:format_2013:
    text: edam:format_2013
    description: Data format for a biological pathway or network.
    meaning: edam:format_2013
    title: Biological pathway or network format
  edam:format_2014:
    text: edam:format_2014
    description: Data format for a sequence-profile alignment.
    meaning: edam:format_2014
    title: Sequence-profile alignment format
  edam:format_2017:
    text: edam:format_2017
    description: Data format for an amino acid index.
    meaning: edam:format_2017
    title: Amino acid index format
  edam:format_2020:
    text: edam:format_2020
    description: Data format for a full-text scientific article.
    meaning: edam:format_2020
    title: Article format
  edam:format_2021:
    text: edam:format_2021
    description: Data format of a report from text mining.
    meaning: edam:format_2021
    title: Text mining report format
  edam:format_2027:
    text: edam:format_2027
    description: Data format for reports on enzyme kinetics.
    meaning: edam:format_2027
    title: Enzyme kinetics report format
  edam:format_2030:
    text: edam:format_2030
    description: Format of a report on a chemical compound.
    meaning: edam:format_2030
    title: Chemical data format
  edam:format_2031:
    text: edam:format_2031
    description: Format of a report on a particular locus, gene, gene system or groups
      of genes.
    meaning: edam:format_2031
    title: Gene annotation format
  edam:format_2032:
    text: edam:format_2032
    description: Format of a workflow.
    meaning: edam:format_2032
    title: Workflow format
  edam:format_2033:
    text: edam:format_2033
    description: Data format for a molecular tertiary structure.
    meaning: edam:format_2033
    title: Tertiary structure format
  edam:format_2035:
    text: edam:format_2035
    description: Text format of a chemical formula.
    meaning: edam:format_2035
    title: Chemical formula format
  edam:format_2036:
    text: edam:format_2036
    description: Format of raw (unplotted) phylogenetic data.
    meaning: edam:format_2036
    title: Phylogenetic character data format
  edam:format_2037:
    text: edam:format_2037
    description: Format of phylogenetic continuous quantitative character data.
    meaning: edam:format_2037
    title: Phylogenetic continuous quantitative character format
  edam:format_2038:
    text: edam:format_2038
    description: Format of phylogenetic discrete states data.
    meaning: edam:format_2038
    title: Phylogenetic discrete states format
  edam:format_2039:
    text: edam:format_2039
    description: Format of phylogenetic cliques data.
    meaning: edam:format_2039
    title: Phylogenetic tree report (cliques) format
  edam:format_2040:
    text: edam:format_2040
    description: Format of phylogenetic invariants data.
    meaning: edam:format_2040
    title: Phylogenetic tree report (invariants) format
  edam:format_2049:
    text: edam:format_2049
    description: Format for phylogenetic tree distance data.
    meaning: edam:format_2049
    title: Phylogenetic tree report (tree distances) format
  edam:format_2052:
    text: edam:format_2052
    description: Format for reports on a protein family.
    meaning: edam:format_2052
    title: Protein family report format
  edam:format_2054:
    text: edam:format_2054
    description: Format for molecular interaction data.
    meaning: edam:format_2054
    title: Protein interaction format
  edam:format_2055:
    text: edam:format_2055
    description: Format for sequence assembly data.
    meaning: edam:format_2055
    title: Sequence assembly format
  edam:format_2056:
    text: edam:format_2056
    description: Format for information about a microarray experimental per se (not
      the data generated from that experiment).
    meaning: edam:format_2056
    title: Microarray experiment data format
  edam:format_2057:
    text: edam:format_2057
    description: Format for sequence trace data (i.e. including base call information).
    meaning: edam:format_2057
    title: Sequence trace format
  edam:format_2058:
    text: edam:format_2058
    description: Format of a file of gene expression data, e.g. a gene expression
      matrix or profile.
    meaning: edam:format_2058
    title: Gene expression report format
  edam:format_2060:
    text: edam:format_2060
    description: Format of a map of (typically one) molecular sequence annotated with
      features.
    meaning: edam:format_2060
    title: Map format
  edam:format_2061:
    text: edam:format_2061
    description: Format of a report on PCR primers or hybridisation oligos in a nucleic
      acid sequence.
    meaning: edam:format_2061
    title: Nucleic acid features (primers) format
  edam:format_2062:
    text: edam:format_2062
    description: Format of a report of general information about a specific protein.
    meaning: edam:format_2062
    title: Protein report format
  edam:format_2064:
    text: edam:format_2064
    description: Format of a matrix of 3D-1D scores (amino acid environment probabilities).
    meaning: edam:format_2064
    title: 3D-1D scoring matrix format
  edam:format_2065:
    text: edam:format_2065
    description: Format of a report on the quality of a protein three-dimensional
      model.
    meaning: edam:format_2065
    title: Protein structure report (quality evaluation) format
  edam:format_2066:
    text: edam:format_2066
    description: Format of a report on sequence hits and associated data from searching
      a sequence database.
    meaning: edam:format_2066
    title: Database hits (sequence) format
  edam:format_2067:
    text: edam:format_2067
    description: Format of a matrix of genetic distances between molecular sequences.
    meaning: edam:format_2067
    title: Sequence distance matrix format
  edam:format_2068:
    text: edam:format_2068
    description: Format of a sequence motif.
    meaning: edam:format_2068
    title: Sequence motif format
  edam:format_2069:
    text: edam:format_2069
    description: Format of a sequence profile.
    meaning: edam:format_2069
    title: Sequence profile format
  edam:format_2072:
    text: edam:format_2072
    description: Format of a hidden Markov model.
    meaning: edam:format_2072
    title: Hidden Markov model format
  edam:format_2074:
    text: edam:format_2074
    description: Data format of a dirichlet distribution.
    meaning: edam:format_2074
    title: Dirichlet distribution format
  edam:format_2075:
    text: edam:format_2075
    description: Data format for the emission and transition counts of a hidden Markov
      model.
    meaning: edam:format_2075
    title: HMM emission and transition counts format
  edam:format_2076:
    text: edam:format_2076
    description: Format for secondary structure (predicted or real) of an RNA molecule.
    meaning: edam:format_2076
    title: RNA secondary structure format
  edam:format_2077:
    text: edam:format_2077
    description: Format for secondary structure (predicted or real) of a protein molecule.
    meaning: edam:format_2077
    title: Protein secondary structure format
  edam:format_2078:
    text: edam:format_2078
    description: Format used to specify range(s) of sequence positions.
    meaning: edam:format_2078
    title: Sequence range format
  edam:format_2094:
    text: edam:format_2094
    description: Alphabet for molecular sequence with possible unknown positions but
      without non-sequence characters.
    meaning: edam:format_2094
    title: pure
  edam:format_2095:
    text: edam:format_2095
    description: Alphabet for a molecular sequence with possible unknown positions
      but possibly with non-sequence characters.
    meaning: edam:format_2095
    title: unpure
  edam:format_2096:
    text: edam:format_2096
    description: Alphabet for a molecular sequence with possible unknown positions
      but without ambiguity characters.
    meaning: edam:format_2096
    title: unambiguous sequence
  edam:format_2097:
    text: edam:format_2097
    description: Alphabet for a molecular sequence with possible unknown positions
      and possible ambiguity characters.
    meaning: edam:format_2097
    title: ambiguous
  edam:format_2155:
    text: edam:format_2155
    description: Format used for map of repeats in molecular (typically nucleotide)
      sequences.
    meaning: edam:format_2155
    title: Sequence features (repeats) format
  edam:format_2158:
    text: edam:format_2158
    description: Format used for report on restriction enzyme recognition sites in
      nucleotide sequences.
    meaning: edam:format_2158
    title: Nucleic acid features (restriction sites) format
  edam:format_2170:
    text: edam:format_2170
    description: Format used for clusters of molecular sequences.
    meaning: edam:format_2170
    title: Sequence cluster format
  edam:format_2171:
    text: edam:format_2171
    description: Format used for clusters of protein sequences.
    meaning: edam:format_2171
    title: Sequence cluster format (protein)
  edam:format_2172:
    text: edam:format_2172
    description: Format used for clusters of nucleotide sequences.
    meaning: edam:format_2172
    title: Sequence cluster format (nucleic acid)
  edam:format_2181:
    text: edam:format_2181
    description: 'A text format resembling EMBL entry format.

      This concept may be used for the many non-standard EMBL-like text formats.'
    meaning: edam:format_2181
    title: EMBL-like (text)
  edam:format_2182:
    text: edam:format_2182
    description: 'A text format resembling FASTQ short read format.

      This concept may be used for non-standard FASTQ short read-like formats.'
    meaning: edam:format_2182
    title: FASTQ-like format (text)
  edam:format_2183:
    text: edam:format_2183
    description: XML format for EMBL entries.
    meaning: edam:format_2183
    title: EMBLXML
  edam:format_2184:
    text: edam:format_2184
    description: Specific XML format for EMBL entries (only uses certain sections).
    meaning: edam:format_2184
    title: cdsxml
  edam:format_2185:
    text: edam:format_2185
    description: INSDSeq provides the elements of a sequence as presented in the GenBank/EMBL/DDBJ-style
      flatfile formats, with a small amount of additional structure.
    meaning: edam:format_2185
    title: INSDSeq
  edam:format_2186:
    text: edam:format_2186
    description: Geneseq sequence format.
    meaning: edam:format_2186
    title: geneseq
  edam:format_2187:
    text: edam:format_2187
    description: A text sequence format resembling uniprotkb entry format.
    meaning: edam:format_2187
    title: UniProt-like (text)
  edam:format_2194:
    text: edam:format_2194
    description: Abstract format used by MedLine database.
    meaning: edam:format_2194
    title: medline
  edam:format_2195:
    text: edam:format_2195
    description: Format used for ontologies.
    meaning: edam:format_2195
    title: Ontology format
  edam:format_2196:
    text: edam:format_2196
    description: A serialisation format conforming to the Open Biomedical Ontologies
      (OBO) model.
    meaning: edam:format_2196
    title: OBO format
  edam:format_2197:
    text: edam:format_2197
    description: A serialisation format conforming to the Web Ontology Language (OWL)
      model.
    meaning: edam:format_2197
    title: OWL format
  edam:format_2200:
    text: edam:format_2200
    description: 'A text format resembling FASTA format.

      This concept may also be used for the many non-standard FASTA-like formats.'
    meaning: edam:format_2200
    title: FASTA-like (text)
  edam:format_2204:
    text: edam:format_2204
    description: 'An XML format for EMBL entries.

      This is a placeholder for other more specific concepts. It should not normally
      be used for annotation.'
    meaning: edam:format_2204
    title: EMBL format (XML)
  edam:format_2205:
    text: edam:format_2205
    description: 'A text format resembling GenBank entry (plain text) format.

      This concept may be used for the non-standard GenBank-like text formats.'
    meaning: edam:format_2205
    title: GenBank-like format (text)
  edam:format_2206:
    text: edam:format_2206
    description: Text format for a sequence feature table.
    meaning: edam:format_2206
    title: Sequence feature table format (text)
  edam:format_2304:
    text: edam:format_2304
    description: Entry format (XML) for the STRING database of protein interaction.
    meaning: edam:format_2304
    title: STRING entry format (XML)
  edam:format_2305:
    text: edam:format_2305
    description: GFF feature format (of indeterminate version).
    meaning: edam:format_2305
    title: GFF
  edam:format_2306:
    text: edam:format_2306
    description: Gene Transfer Format (GTF), a restricted version of GFF.
    meaning: edam:format_2306
    title: GTF
  edam:format_2310:
    text: edam:format_2310
    description: FASTA format wrapped in HTML elements.
    meaning: edam:format_2310
    title: FASTA-HTML
  edam:format_2311:
    text: edam:format_2311
    description: EMBL entry format wrapped in HTML elements.
    meaning: edam:format_2311
    title: EMBL-HTML
  edam:format_2330:
    text: edam:format_2330
    description: 'Data in text format can be compressed into binary format, or can
      be a value of an XML element or attribute. Markup formats are not considered
      textual (or more precisely, not plain-textual).

      Textual format.'
    meaning: edam:format_2330
    title: Textual format
  edam:format_2331:
    text: edam:format_2331
    description: HTML format.
    meaning: edam:format_2331
    title: HTML
  edam:format_2332:
    text: edam:format_2332
    description: 'Data in XML format can be serialised into text, or binary format.

      eXtensible Markup Language (XML) format.'
    meaning: edam:format_2332
    title: XML
  edam:format_2333:
    text: edam:format_2333
    description: 'Binary format.

      Only specific native binary formats are listed under ''Binary format'' in EDAM.
      Generic binary formats - such as any data being zipped, or any XML data being
      serialised into the Efficient XML Interchange (EXI) format - are not modelled
      in EDAM. Refer to http://wsio.org/compression_004.'
    meaning: edam:format_2333
    title: Binary format
  edam:format_2350:
    text: edam:format_2350
    description: 'A placeholder concept for visual navigation by dividing data formats
      by the content of the data that is represented.

      This concept exists only to assist EDAM maintenance and navigation in graphical
      browsers. It does not add semantic information. The concept branch under ''Format
      (typed)'' provides an alternative organisation of the concepts nested under
      the other top-level branches (''Binary'', ''HTML'', ''RDF'', ''Text'' and ''XML''.
      All concepts under here are already included under those branches.'
    meaning: edam:format_2350
    title: Format (by type of data)
  edam:format_2352:
    text: edam:format_2352
    description: '''BioXSD'' belongs to the ''BioXSD|GTrack'' ecosystem of generic
      formats. ''BioXSD in XML'' is the XML format based on the common, unified ''BioXSD
      data model'', a.k.a. ''BioXSD|BioJSON|BioYAML''.

      BioXSD-schema-based XML format of sequence-based data and some other common
      data - sequence records, alignments, feature records, references to resources,
      and more - optimised for integrative bioinformatics, Web services, and object-oriented
      programming.'
    meaning: edam:format_2352
    title: BioXSD (XML)
  edam:format_2376:
    text: edam:format_2376
    description: A serialisation format conforming to the Resource Description Framework
      (RDF) model.
    meaning: edam:format_2376
    title: RDF format
  edam:format_2532:
    text: edam:format_2532
    description: Genbank entry format wrapped in HTML elements.
    meaning: edam:format_2532
    title: GenBank-HTML
  edam:format_2543:
    text: edam:format_2543
    description: 'A format resembling EMBL entry (plain text) format.

      This concept may be used for the many non-standard EMBL-like formats.'
    meaning: edam:format_2543
    title: EMBL-like format
  edam:format_2545:
    text: edam:format_2545
    description: 'A format resembling FASTQ short read format.

      This concept may be used for non-standard FASTQ short read-like formats.'
    meaning: edam:format_2545
    title: FASTQ-like format
  edam:format_2546:
    text: edam:format_2546
    description: 'A format resembling FASTA format.

      This concept may be used for the many non-standard FASTA-like formats.'
    meaning: edam:format_2546
    title: FASTA-like
  edam:format_2547:
    text: edam:format_2547
    description: A sequence format resembling uniprotkb entry format.
    meaning: edam:format_2547
    title: uniprotkb-like format
  edam:format_2548:
    text: edam:format_2548
    description: Format for a sequence feature table.
    meaning: edam:format_2548
    title: Sequence feature table format
  edam:format_2549:
    text: edam:format_2549
    description: OBO ontology text format.
    meaning: edam:format_2549
    title: OBO
  edam:format_2550:
    text: edam:format_2550
    description: OBO ontology XML format.
    meaning: edam:format_2550
    title: OBO-XML
  edam:format_2551:
    text: edam:format_2551
    description: Data format for a molecular sequence record (text).
    meaning: edam:format_2551
    title: Sequence record format (text)
  edam:format_2552:
    text: edam:format_2552
    description: Data format for a molecular sequence record (XML).
    meaning: edam:format_2552
    title: Sequence record format (XML)
  edam:format_2553:
    text: edam:format_2553
    description: XML format for a sequence feature table.
    meaning: edam:format_2553
    title: Sequence feature table format (XML)
  edam:format_2554:
    text: edam:format_2554
    description: Text format for molecular sequence alignment information.
    meaning: edam:format_2554
    title: Alignment format (text)
  edam:format_2555:
    text: edam:format_2555
    description: XML format for molecular sequence alignment information.
    meaning: edam:format_2555
    title: Alignment format (XML)
  edam:format_2556:
    text: edam:format_2556
    description: Text format for a phylogenetic tree.
    meaning: edam:format_2556
    title: Phylogenetic tree format (text)
  edam:format_2557:
    text: edam:format_2557
    description: XML format for a phylogenetic tree.
    meaning: edam:format_2557
    title: Phylogenetic tree format (XML)
  edam:format_2558:
    text: edam:format_2558
    description: 'An XML format resembling EMBL entry format.

      This concept may be used for the any non-standard EMBL-like XML formats.'
    meaning: edam:format_2558
    title: EMBL-like (XML)
  edam:format_2559:
    text: edam:format_2559
    description: 'A format resembling GenBank entry (plain text) format.

      This concept may be used for the non-standard GenBank-like formats.'
    meaning: edam:format_2559
    title: GenBank-like format
  edam:format_2561:
    text: edam:format_2561
    description: Text format for sequence assembly data.
    meaning: edam:format_2561
    title: Sequence assembly format (text)
  edam:format_2566:
    text: edam:format_2566
    description: Alphabet for a molecular sequence without any unknown positions or
      ambiguity characters.
    meaning: edam:format_2566
    title: completely unambiguous
  edam:format_2567:
    text: edam:format_2567
    description: Alphabet for a molecular sequence without unknown positions, ambiguity
      or non-sequence characters.
    meaning: edam:format_2567
    title: completely unambiguous pure
  edam:format_2568:
    text: edam:format_2568
    description: Alphabet for a nucleotide sequence (characters ACGTU only) without
      unknown positions, ambiguity or non-sequence characters .
    meaning: edam:format_2568
    title: completely unambiguous pure nucleotide
  edam:format_2569:
    text: edam:format_2569
    description: Alphabet for a DNA sequence (characters ACGT only) without unknown
      positions, ambiguity or non-sequence characters.
    meaning: edam:format_2569
    title: completely unambiguous pure dna
  edam:format_2570:
    text: edam:format_2570
    description: Alphabet for an RNA sequence (characters ACGU only) without unknown
      positions, ambiguity or non-sequence characters.
    meaning: edam:format_2570
    title: completely unambiguous pure rna sequence
  edam:format_2571:
    text: edam:format_2571
    description: Format of a raw molecular sequence (i.e. the alphabet used).
    meaning: edam:format_2571
    title: Raw sequence format
  edam:format_2572:
    text: edam:format_2572
    description: BAM format, the binary, BGZF-formatted compressed version of SAM
      format for alignment of nucleotide sequences (e.g. sequencing reads) to (a)
      reference sequence(s). May contain base-call and alignment qualities and other
      data.
    meaning: edam:format_2572
    title: BAM
  edam:format_2573:
    text: edam:format_2573
    description: 'Sequence Alignment/Map (SAM) format for alignment of nucleotide
      sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain
      base-call and alignment qualities and other data.

      The format supports short and long reads (up to 128Mbp) produced by different
      sequencing platforms and is used to hold mapped data within the GATK and across
      the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project.'
    meaning: edam:format_2573
    title: SAM
  edam:format_2585:
    text: edam:format_2585
    description: Systems Biology Markup Language (SBML), the standard XML format for
      models of biological processes such as for example metabolism, cell signaling,
      and gene regulation.
    meaning: edam:format_2585
    title: SBML
  edam:format_2607:
    text: edam:format_2607
    description: Alphabet for any protein sequence without unknown positions, ambiguity
      or non-sequence characters.
    meaning: edam:format_2607
    title: completely unambiguous pure protein
  edam:format_2848:
    text: edam:format_2848
    description: Format of a bibliographic reference.
    meaning: edam:format_2848
    title: Bibliographic reference format
  edam:format_2919:
    text: edam:format_2919
    description: Format of a sequence annotation track.
    meaning: edam:format_2919
    title: Sequence annotation track format
  edam:format_2920:
    text: edam:format_2920
    description: Data format for molecular sequence alignment information that can
      hold sequence alignment(s) of only 2 sequences.
    meaning: edam:format_2920
    title: Alignment format (pair only)
  edam:format_2921:
    text: edam:format_2921
    description: Format of sequence variation annotation.
    meaning: edam:format_2921
    title: Sequence variation annotation format
  edam:format_2922:
    text: edam:format_2922
    description: Some variant of Pearson MARKX alignment format.
    meaning: edam:format_2922
    title: markx0 variant
  edam:format_2923:
    text: edam:format_2923
    description: Some variant of Mega format for (typically aligned) sequences.
    meaning: edam:format_2923
    title: mega variant
  edam:format_2924:
    text: edam:format_2924
    description: Some variant of Phylip format for (aligned) sequences.
    meaning: edam:format_2924
    title: Phylip format variant
  edam:format_3000:
    text: edam:format_3000
    description: 'AB1 binary format of raw DNA sequence reads (output of Applied Biosystems''
      sequencing analysis software). Contains an electropherogram and the DNA base
      sequence.

      AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF).'
    meaning: edam:format_3000
    title: AB1
  edam:format_3001:
    text: edam:format_3001
    description: ACE sequence assembly format including contigs, base-call qualities,
      and other metadata (version Aug 1998 and onwards).
    meaning: edam:format_3001
    title: ACE
  edam:format_3003:
    text: edam:format_3003
    description: 'BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7)
      and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track).

      Browser Extensible Data (BED) format of sequence annotation track, typically
      to be displayed in a genome browser.'
    meaning: edam:format_3003
    title: BED
  edam:format_3004:
    text: edam:format_3004
    description: bigBed format for large sequence annotation tracks, similar to textual
      BED format.
    meaning: edam:format_3004
    title: bigBed
  edam:format_3005:
    text: edam:format_3005
    description: Wiggle format (WIG) of a sequence annotation track that consists
      of a value for each sequence position. Typically to be displayed in a genome
      browser.
    meaning: edam:format_3005
    title: WIG
  edam:format_3006:
    text: edam:format_3006
    description: bigWig format for large sequence annotation tracks that consist of
      a value for each sequence position. Similar to textual WIG format.
    meaning: edam:format_3006
    title: bigWig
  edam:format_3007:
    text: edam:format_3007
    description: PSL format of alignments, typically generated by BLAT or psLayout.
      Can be displayed in a genome browser like a sequence annotation track.
    meaning: edam:format_3007
    title: PSL
  edam:format_3008:
    text: edam:format_3008
    description: 'Multiple Alignment Format (MAF) supporting alignments of whole genomes
      with rearrangements, directions, multiple pieces to the alignment, and so forth.

      Typically generated by Multiz and TBA aligners; can be displayed in a genome
      browser like a sequence annotation track. This should not be confused with MIRA
      Assembly Format or Mutation Annotation Format.'
    meaning: edam:format_3008
    title: MAF
  edam:format_3009:
    text: edam:format_3009
    description: 2bit binary format of nucleotide sequences using 2 bits per nucleotide.
      In addition encodes unknown nucleotides and lower-case 'masking'.
    meaning: edam:format_3009
    title: 2bit
  edam:format_3010:
    text: edam:format_3010
    description: .nib (nibble) binary format of a nucleotide sequence using 4 bits
      per nucleotide (including unknown) and its lower-case 'masking'.
    meaning: edam:format_3010
    title: .nib
  edam:format_3011:
    text: edam:format_3011
    description: 'genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9
      http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser
      DB tables.

      genePred table format for gene prediction tracks.'
    meaning: edam:format_3011
    title: genePred
  edam:format_3012:
    text: edam:format_3012
    description: Personal Genome SNP (pgSnp) format for sequence variation tracks
      (indels and polymorphisms), supported by the UCSC Genome Browser.
    meaning: edam:format_3012
    title: pgSnp
  edam:format_3013:
    text: edam:format_3013
    description: axt format of alignments, typically produced from BLASTZ.
    meaning: edam:format_3013
    title: axt
  edam:format_3014:
    text: edam:format_3014
    description: LAV format of alignments generated by BLASTZ and LASTZ.
    meaning: edam:format_3014
    title: LAV
  edam:format_3015:
    text: edam:format_3015
    description: Pileup format of alignment of sequences (e.g. sequencing reads) to
      (a) reference sequence(s). Contains aligned bases per base of the reference
      sequence(s).
    meaning: edam:format_3015
    title: Pileup
  edam:format_3016:
    text: edam:format_3016
    description: '1000 Genomes Project has its own specification for encoding structural
      variations in VCF (https://www.internationalgenome.org/wiki/Analysis/Variant%20Call%20Format/VCF%20(Variant%20Call%20Format)%20version%204.0/encoding-structural-variants).
      This is based on VCF version 4.0 and not directly compatible with VCF version
      4.3.

      Variant Call Format (VCF) is tabular format for storing genomic sequence variations.'
    meaning: edam:format_3016
    title: VCF
  edam:format_3017:
    text: edam:format_3017
    description: Sequence Read Format (SRF) of sequence trace data. Supports submission
      to the NCBI Short Read Archive.
    meaning: edam:format_3017
    title: SRF
  edam:format_3018:
    text: edam:format_3018
    description: ZTR format for storing chromatogram data from DNA sequencing instruments.
    meaning: edam:format_3018
    title: ZTR
  edam:format_3019:
    text: edam:format_3019
    description: Genome Variation Format (GVF). A GFF3-compatible format with defined
      header and attribute tags for sequence variation.
    meaning: edam:format_3019
    title: GVF
  edam:format_3020:
    text: edam:format_3020
    description: BCF is the binary version of Variant Call Format (VCF) for sequence
      variation (indels, polymorphisms, structural variation).
    meaning: edam:format_3020
    title: BCF
  edam:format_3033:
    text: edam:format_3033
    description: Format of a matrix (array) of numerical values.
    meaning: edam:format_3033
    title: Matrix format
  edam:format_3097:
    text: edam:format_3097
    description: Format of data concerning the classification of the sequences and/or
      structures of protein structural domain(s).
    meaning: edam:format_3097
    title: Protein domain classification format
  edam:format_3098:
    text: edam:format_3098
    description: 'Format of raw SCOP domain classification data files.

      These are the parsable data files provided by SCOP.'
    meaning: edam:format_3098
    title: Raw SCOP domain classification format
  edam:format_3099:
    text: edam:format_3099
    description: 'Format of raw CATH domain classification data files.

      These are the parsable data files provided by CATH.'
    meaning: edam:format_3099
    title: Raw CATH domain classification format
  edam:format_3100:
    text: edam:format_3100
    description: 'Format of summary of domain classification information for a CATH
      domain.

      The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH
      codes for levels in the hierarchy for the domain, level descriptions and relevant
      data and links.'
    meaning: edam:format_3100
    title: CATH domain report format
  edam:format_3155:
    text: edam:format_3155
    description: Systems Biology Result Markup Language (SBRML), the standard XML
      format for simulated or calculated results (e.g. trajectories) of systems biology
      models.
    meaning: edam:format_3155
    title: SBRML
  edam:format_3156:
    text: edam:format_3156
    description: BioPAX is an exchange format for pathway data, with its data model
      defined in OWL.
    meaning: edam:format_3156
    title: BioPAX
  edam:format_3157:
    text: edam:format_3157
    description: EBI Application Result XML is a format returned by sequence similarity
      search Web services at EBI.
    meaning: edam:format_3157
    title: EBI Application Result XML
  edam:format_3158:
    text: edam:format_3158
    description: XML Molecular Interaction Format (MIF), standardised by HUPO PSI
      MI.
    meaning: edam:format_3158
    title: PSI MI XML (MIF)
  edam:format_3159:
    text: edam:format_3159
    description: phyloXML is a standardised XML format for phylogenetic trees, networks,
      and associated data.
    meaning: edam:format_3159
    title: phyloXML
  edam:format_3160:
    text: edam:format_3160
    description: NeXML is a standardised XML format for rich phyloinformatic data.
    meaning: edam:format_3160
    title: NeXML
  edam:format_3161:
    text: edam:format_3161
    description: MAGE-ML XML format for microarray expression data, standardised by
      MGED (now FGED).
    meaning: edam:format_3161
    title: MAGE-ML
  edam:format_3162:
    text: edam:format_3162
    description: MAGE-TAB textual format for microarray expression data, standardised
      by MGED (now FGED).
    meaning: edam:format_3162
    title: MAGE-TAB
  edam:format_3163:
    text: edam:format_3163
    description: GCDML XML format for genome and metagenome metadata according to
      MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards
      Consortium (GSC).
    meaning: edam:format_3163
    title: GCDML
  edam:format_3164:
    text: edam:format_3164
    description: '''GTrack'' belongs to the ''BioXSD|GTrack'' ecosystem of generic
      formats, and particular to its subset, the ''GTrack ecosystem'' (GTrack, GSuite,
      BTrack). ''GTrack'' is the tabular format for representing features of sequences
      and genomes.

      GTrack is a generic and optimised tabular format for genome or sequence feature
      tracks. GTrack unifies the power of other track formats (e.g. GFF3, BED, WIG),
      and while optimised in size, adds more flexibility, customisation, and automation
      ("machine understandability").'
    meaning: edam:format_3164
    title: GTrack
  edam:format_3166:
    text: edam:format_3166
    description: Data format for a report of information derived from a biological
      pathway or network.
    meaning: edam:format_3166
    title: Biological pathway or network report format
  edam:format_3167:
    text: edam:format_3167
    description: Data format for annotation on a laboratory experiment.
    meaning: edam:format_3167
    title: Experiment annotation format
  edam:format_3235:
    text: edam:format_3235
    description: 'Cytoband format for chromosome cytobands.

      Reflects a UCSC Browser DB table.'
    meaning: edam:format_3235
    title: Cytoband format
  edam:format_3239:
    text: edam:format_3239
    description: CopasiML, the native format of COPASI.
    meaning: edam:format_3239
    title: CopasiML
  edam:format_3240:
    text: edam:format_3240
    description: CellML, the format for mathematical models of biological and other
      networks.
    meaning: edam:format_3240
    title: CellML
  edam:format_3242:
    text: edam:format_3242
    description: Tabular Molecular Interaction format (MITAB), standardised by HUPO
      PSI MI.
    meaning: edam:format_3242
    title: PSI MI TAB (MITAB)
  edam:format_3243:
    text: edam:format_3243
    description: Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It
      is compatible with PSI MI XML (MIF) and uses the same XML Schema.
    meaning: edam:format_3243
    title: PSI-PAR
  edam:format_3244:
    text: edam:format_3244
    description: 'mzML format for raw spectrometer output data, standardised by HUPO
      PSI MSS.

      mzML is the successor and unifier of the mzData format developed by PSI and
      mzXML developed at the Seattle Proteome Center.'
    meaning: edam:format_3244
    title: mzML
  edam:format_3245:
    text: edam:format_3245
    description: Format for mass pectra and derived data, include peptide sequences
      etc.
    meaning: edam:format_3245
    title: Mass spectrometry data format
  edam:format_3246:
    text: edam:format_3246
    description: TraML (Transition Markup Language) is the format for mass spectrometry
      transitions, standardised by HUPO PSI MSS.
    meaning: edam:format_3246
    title: TraML
  edam:format_3247:
    text: edam:format_3247
    description: mzIdentML is the exchange format for peptides and proteins identified
      from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of
      proteomics search engines.
    meaning: edam:format_3247
    title: mzIdentML
  edam:format_3248:
    text: edam:format_3248
    description: mzQuantML is the format for quantitation values associated with peptides,
      proteins and small molecules from mass spectra, standardised by HUPO PSI PI.
      It can be used for outputs of quantitation software for proteomics.
    meaning: edam:format_3248
    title: mzQuantML
  edam:format_3249:
    text: edam:format_3249
    description: GelML is the format for describing the process of gel electrophoresis,
      standardised by HUPO PSI PS.
    meaning: edam:format_3249
    title: GelML
  edam:format_3250:
    text: edam:format_3250
    description: spML is the format for describing proteomics sample processing, other
      than using gels, prior to mass spectrometric protein identification, standardised
      by HUPO PSI PS. It may also be applicable for metabolomics.
    meaning: edam:format_3250
    title: spML
  edam:format_3252:
    text: edam:format_3252
    description: A human-readable encoding for the Web Ontology Language (OWL).
    meaning: edam:format_3252
    title: OWL Functional Syntax
  edam:format_3253:
    text: edam:format_3253
    description: 'A syntax for writing OWL class expressions.

      This format was influenced by the OWL Abstract Syntax and the DL style syntax.'
    meaning: edam:format_3253
    title: Manchester OWL Syntax
  edam:format_3254:
    text: edam:format_3254
    description: 'A superset of the "Description-Logic Knowledge Representation System
      Specification from the KRSS Group of the ARPA Knowledge Sharing Effort".

      This format is used in Protege 4.'
    meaning: edam:format_3254
    title: KRSS2 Syntax
  edam:format_3255:
    text: edam:format_3255
    description: 'The SPARQL Query Language incorporates a very similar syntax.

      The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format
      for RDF (Resource Description Framework) graphs.'
    meaning: edam:format_3255
    title: Turtle
  edam:format_3256:
    text: edam:format_3256
    description: 'A plain text serialisation format for RDF (Resource Description
      Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format.

      N-Triples should not be confused with Notation 3 which is a superset of Turtle.'
    meaning: edam:format_3256
    title: N-Triples
  edam:format_3257:
    text: edam:format_3257
    description: A shorthand non-XML serialisation of Resource Description Framework
      model, designed with human-readability in mind.
    meaning: edam:format_3257
    title: Notation3
  edam:format_3261:
    text: edam:format_3261
    description: 'RDF/XML can be used as a standard serialisation syntax for OWL DL,
      but not for OWL Full.

      Resource Description Framework (RDF) XML format.'
    meaning: edam:format_3261
    title: RDF/XML
  edam:format_3262:
    text: edam:format_3262
    description: OWL ontology XML serialisation format.
    meaning: edam:format_3262
    title: OWL/XML
  edam:format_3281:
    text: edam:format_3281
    description: The A2M format is used as the primary format for multiple alignments
      of protein or nucleic-acid sequences in the SAM suite of tools. It is a small
      modification of FASTA format for sequences and is compatible with most tools
      that read FASTA.
    meaning: edam:format_3281
    title: A2M
  edam:format_3284:
    text: edam:format_3284
    description: Standard flowgram format (SFF) is a binary file format used to encode
      results of pyrosequencing from the 454 Life Sciences platform for high-throughput
      sequencing.
    meaning: edam:format_3284
    title: SFF
  edam:format_3285:
    text: edam:format_3285
    description: The MAP file describes SNPs and is used by the Plink package.
    meaning: edam:format_3285
    title: MAP
  edam:format_3286:
    text: edam:format_3286
    description: The PED file describes individuals and genetic data and is used by
      the Plink package.
    meaning: edam:format_3286
    title: PED
  edam:format_3287:
    text: edam:format_3287
    description: Data format for a metadata on an individual and their genetic data.
    meaning: edam:format_3287
    title: Individual genetic data format
  edam:format_3288:
    text: edam:format_3288
    description: The PED/MAP file describes data used by the Plink package.
    meaning: edam:format_3288
    title: PED/MAP
  edam:format_3309:
    text: edam:format_3309
    description: File format of a CT (Connectivity Table) file from the RNAstructure
      package.
    meaning: edam:format_3309
    title: CT
  edam:format_3310:
    text: edam:format_3310
    description: XRNA old input style format.
    meaning: edam:format_3310
    title: SS
  edam:format_3311:
    text: edam:format_3311
    description: RNA Markup Language.
    meaning: edam:format_3311
    title: RNAML
  edam:format_3312:
    text: edam:format_3312
    description: Format for the Genetic Data Environment (GDE).
    meaning: edam:format_3312
    title: GDE
  edam:format_3313:
    text: edam:format_3313
    description: A multiple alignment in vertical format, as used in the AMPS (Alignment
      of Multiple Protein Sequences) package.
    meaning: edam:format_3313
    title: BLC
  edam:format_3326:
    text: edam:format_3326
    description: Format of a data index of some type.
    meaning: edam:format_3326
    title: Data index format
  edam:format_3327:
    text: edam:format_3327
    description: BAM indexing format.
    meaning: edam:format_3327
    title: BAI
  edam:format_3328:
    text: edam:format_3328
    description: HMMER profile HMM file for HMMER versions 2.x.
    meaning: edam:format_3328
    title: HMMER2
  edam:format_3329:
    text: edam:format_3329
    description: HMMER profile HMM file for HMMER versions 3.x.
    meaning: edam:format_3329
    title: HMMER3
  edam:format_3330:
    text: edam:format_3330
    description: PO is the output format of Partial Order Alignment program (POA)
      performing Multiple Sequence Alignment (MSA).
    meaning: edam:format_3330
    title: PO
  edam:format_3331:
    text: edam:format_3331
    description: XML format as produced by the NCBI Blast package.
    meaning: edam:format_3331
    title: BLAST XML results format
  edam:format_3462:
    text: edam:format_3462
    description: Reference-based compression of alignment format.
    meaning: edam:format_3462
    title: CRAM
  edam:format_3464:
    text: edam:format_3464
    description: JavaScript Object Notation format; a lightweight, text-based format
      to represent tree-structured data using key-value pairs.
    meaning: edam:format_3464
    title: JSON
  edam:format_3466:
    text: edam:format_3466
    description: Encapsulated PostScript format.
    meaning: edam:format_3466
    title: EPS
  edam:format_3467:
    text: edam:format_3467
    description: Graphics Interchange Format.
    meaning: edam:format_3467
    title: GIF
  edam:format_3468:
    text: edam:format_3468
    description: Microsoft Excel spreadsheet format.
    meaning: edam:format_3468
    title: xls
  edam:format_3475:
    text: edam:format_3475
    description: Tabular data represented as tab-separated values in a text file.
    meaning: edam:format_3475
    title: TSV
  edam:format_3477:
    text: edam:format_3477
    description: Format of the cytoscape input file of gene expression ratios or values
      are specified over one or more experiments.
    meaning: edam:format_3477
    title: Cytoscape input file format
  edam:format_3484:
    text: edam:format_3484
    description: Bowtie format for indexed reference genome for "small" genomes.
    meaning: edam:format_3484
    title: ebwt
  edam:format_3485:
    text: edam:format_3485
    description: 'RSF-format files contain one or more sequences that may or may not
      be related. In addition to the sequence data, each sequence can be annotated
      with descriptive sequence information (from the GCG manual).

      Rich sequence format.'
    meaning: edam:format_3485
    title: RSF
  edam:format_3486:
    text: edam:format_3486
    description: Some format based on the GCG format.
    meaning: edam:format_3486
    title: GCG format variant
  edam:format_3487:
    text: edam:format_3487
    description: Bioinformatics Sequence Markup Language format.
    meaning: edam:format_3487
    title: BSML
  edam:format_3491:
    text: edam:format_3491
    description: Bowtie format for indexed reference genome for "large" genomes.
    meaning: edam:format_3491
    title: ebwtl
  edam:format_3499:
    text: edam:format_3499
    description: Ensembl standard format for variation data.
    meaning: edam:format_3499
    title: Ensembl variation file format
  edam:format_3506:
    text: edam:format_3506
    description: Microsoft Word format.
    meaning: edam:format_3506
    title: docx
  edam:format_3507:
    text: edam:format_3507
    description: Format of documents including word processor, spreadsheet and presentation.
    meaning: edam:format_3507
    title: Document format
  edam:format_3508:
    text: edam:format_3508
    description: Portable Document Format.
    meaning: edam:format_3508
    title: PDF
  edam:format_3547:
    text: edam:format_3547
    description: Format used for images and image metadata.
    meaning: edam:format_3547
    title: Image format
  edam:format_3548:
    text: edam:format_3548
    description: Medical image format corresponding to the Digital Imaging and Communications
      in Medicine (DICOM) standard.
    meaning: edam:format_3548
    title: DICOM format
  edam:format_3549:
    text: edam:format_3549
    description: An open file format from the Neuroimaging Informatics Technology
      Initiative (NIfTI) commonly used to store brain imaging data obtained using
      Magnetic Resonance Imaging (MRI) methods.
    meaning: edam:format_3549
    title: nii
  edam:format_3550:
    text: edam:format_3550
    description: Text-based tagged file format for medical images generated using
      the MetaImage software package.
    meaning: edam:format_3550
    title: mhd
  edam:format_3551:
    text: edam:format_3551
    description: Nearly Raw Rasta Data format designed to support scientific visualisation
      and image processing involving N-dimensional raster data.
    meaning: edam:format_3551
    title: nrrd
  edam:format_3554:
    text: edam:format_3554
    description: File format used for scripts written in the R programming language
      for execution within the R software environment, typically for statistical computation
      and graphics.
    meaning: edam:format_3554
    title: R file format
  edam:format_3555:
    text: edam:format_3555
    description: File format used for scripts for the Statistical Package for the
      Social Sciences.
    meaning: edam:format_3555
    title: SPSS
  edam:format_3556:
    text: edam:format_3556
    description: 'MHTML is not strictly an HTML format, it is encoded as an HTML email
      message (although with multipart/related instead of multipart/alternative).
      It, however, contains the main HTML block as its core, and thus it is for practical
      reasons included in EDAM as a specialisation of ''HTML''.

      MIME HTML format for Web pages, which can include external resources, including
      images, Flash animations and so on.'
    meaning: edam:format_3556
    title: MHTML
  edam:format_3578:
    text: edam:format_3578
    description: Proprietary file format for (raw) BeadArray data used by genomewide
      profiling platforms from Illumina Inc. This format is output directly from the
      scanner and stores summary intensities for each probe-type on an array.
    meaning: edam:format_3578
    title: IDAT
  edam:format_3579:
    text: edam:format_3579
    description: 'Joint Picture Group file format for lossy graphics file.

      Sequence of segments with markers. Begins with byte of 0xFF and follows by marker
      type.'
    meaning: edam:format_3579
    title: JPG
  edam:format_3580:
    text: edam:format_3580
    description: Reporter Code Count-A data file (.csv) output by the Nanostring nCounter
      Digital Analyzer, which contains gene sample information, probe information
      and probe counts.
    meaning: edam:format_3580
    title: rcc
  edam:format_3581:
    text: edam:format_3581
    description: 'ARFF (Attribute-Relation File Format) is an ASCII text file format
      that describes a list of instances sharing a set of attributes.

      This file format is for machine learning.'
    meaning: edam:format_3581
    title: arff
  edam:format_3582:
    text: edam:format_3582
    description: AFG is a single text-based file assembly format that holds read and
      consensus information together.
    meaning: edam:format_3582
    title: afg
  edam:format_3583:
    text: edam:format_3583
    description: 'Holds a tab-delimited chromosome /start /end / datavalue dataset.

      The bedGraph format allows display of continuous-valued data in track format.
      This display type is useful for probability scores and transcriptome data.'
    meaning: edam:format_3583
    title: bedgraph
  edam:format_3584:
    text: edam:format_3584
    description: 'Browser Extensible Data (BED) format of sequence annotation track
      that strictly does not contain non-standard fields beyond the first 3 columns.

      Galaxy allows BED files to contain non-standard fields beyond the first 3 columns,
      some other implementations do not.'
    meaning: edam:format_3584
    title: bedstrict
  edam:format_3585:
    text: edam:format_3585
    description: 'BED file format where each feature is described by chromosome, start,
      end, name, score, and strand.

      Tab delimited data in strict BED format - no non-standard columns allowed; column
      count forced to 6'
    meaning: edam:format_3585
    title: bed6
  edam:format_3586:
    text: edam:format_3586
    description: 'A BED file where each feature is described by all twelve columns.

      Tab delimited data in strict BED format - no non-standard columns allowed; column
      count forced to 12'
    meaning: edam:format_3586
    title: bed12
  edam:format_3587:
    text: edam:format_3587
    description: 'Galaxy allows BED files to contain non-standard fields beyond the
      first 3 columns, some other implementations do not.

      Tabular format of chromosome names and sizes used by Galaxy.'
    meaning: edam:format_3587
    title: chrominfo
  edam:format_3588:
    text: edam:format_3588
    description: 'Custom Sequence annotation track format used by Galaxy.

      Used for tracks/track views within galaxy.'
    meaning: edam:format_3588
    title: customtrack
  edam:format_3589:
    text: edam:format_3589
    description: 'Color space FASTA format sequence variant.

      FASTA format extended for color space information.'
    meaning: edam:format_3589
    title: csfasta
  edam:format_3590:
    text: edam:format_3590
    description: 'An HDF5 file appears to the user as a directed graph. The nodes
      of this graph are the higher-level HDF5 objects that are exposed by the HDF5
      APIs: Groups, Datasets, Named datatypes. Currently supported by the Python MDTraj
      package.

      HDF5 is a data model, library, and file format for storing and managing data,
      based on Hierarchical Data Format (HDF).

      HDF5 is the new version, according to the HDF group, a completely different
      technology (https://support.hdfgroup.org/products/hdf4/ compared to HDF.'
    meaning: edam:format_3590
    title: HDF5
  edam:format_3591:
    text: edam:format_3591
    description: 'A versatile bitmap format.

      The TIFF format is perhaps the most versatile and diverse bitmap format in existence.
      Its extensible nature and support for numerous data compression schemes allow
      developers to customize the TIFF format to fit any peculiar data storage needs.'
    meaning: edam:format_3591
    title: TIFF
  edam:format_3592:
    text: edam:format_3592
    description: 'Although it is based on Windows internal bitmap data structures,
      it is supported by many non-Windows and non-PC applications.

      Standard bitmap storage format in the Microsoft Windows environment.'
    meaning: edam:format_3592
    title: BMP
  edam:format_3593:
    text: edam:format_3593
    description: 'IFUNC library reads and writes most uncompressed interchange versions
      of this format.

      IM is a format used by LabEye and other applications based on the IFUNC image
      processing library.'
    meaning: edam:format_3593
    title: im
  edam:format_3594:
    text: edam:format_3594
    description: 'PCD was developed by Kodak. A PCD file contains five different resolution
      (ranging from low to high) of a slide or film negative. Due to it PCD is often
      used by many photographers and graphics professionals for high-end printed applications.

      Photo CD format, which is the highest resolution format for images on a CD.'
    meaning: edam:format_3594
    title: pcd
  edam:format_3595:
    text: edam:format_3595
    description: PCX is an image file format that uses a simple form of run-length
      encoding. It is lossless.
    meaning: edam:format_3595
    title: pcx
  edam:format_3596:
    text: edam:format_3596
    description: The PPM format is a lowest common denominator color image file format.
    meaning: edam:format_3596
    title: ppm
  edam:format_3597:
    text: edam:format_3597
    description: PSD (Photoshop Document) is a proprietary file that allows the user
      to work with the images' individual layers even after the file has been saved.
    meaning: edam:format_3597
    title: psd
  edam:format_3598:
    text: edam:format_3598
    description: 'The XBM format was replaced by XPM for X11 in 1989.

      X BitMap is a plain text binary image format used by the X Window System used
      for storing cursor and icon bitmaps used in the X GUI.'
    meaning: edam:format_3598
    title: xbm
  edam:format_3599:
    text: edam:format_3599
    description: 'Sequence of segments with markers. Begins with byte of 0xFF and
      follows by marker type.

      X PixMap (XPM) is an image file format used by the X Window System, it is intended
      primarily for creating icon pixmaps, and supports transparent pixels.'
    meaning: edam:format_3599
    title: xpm
  edam:format_3600:
    text: edam:format_3600
    description: RGB file format is the native raster graphics file format for Silicon
      Graphics workstations.
    meaning: edam:format_3600
    title: rgb
  edam:format_3601:
    text: edam:format_3601
    description: The PBM format is a lowest common denominator monochrome file format.
      It serves as the common language of a large family of bitmap image conversion
      filters.
    meaning: edam:format_3601
    title: pbm
  edam:format_3602:
    text: edam:format_3602
    description: 'It is designed to be extremely easy to learn and write programs
      for.

      The PGM format is a lowest common denominator grayscale file format.'
    meaning: edam:format_3602
    title: pgm
  edam:format_3603:
    text: edam:format_3603
    description: 'It iis expected to replace the Graphics Interchange Format (GIF).

      PNG is a file format for image compression.'
    meaning: edam:format_3603
    title: PNG
  edam:format_3604:
    text: edam:format_3604
    description: 'Scalable Vector Graphics (SVG) is an XML-based vector image format
      for two-dimensional graphics with support for interactivity and animation.

      The SVG specification is an open standard developed by the World Wide Web Consortium
      (W3C) since 1999.'
    meaning: edam:format_3604
    title: SVG
  edam:format_3605:
    text: edam:format_3605
    description: 'Sun Raster is a raster graphics file format used on SunOS by Sun
      Microsystems.

      The SVG specification is an open standard developed by the World Wide Web Consortium
      (W3C) since 1999.'
    meaning: edam:format_3605
    title: rast
  edam:format_3606:
    text: edam:format_3606
    description: Textual report format for sequence quality for reports from sequencing
      machines.
    meaning: edam:format_3606
    title: Sequence quality report format (text)
  edam:format_3607:
    text: edam:format_3607
    description: 'FASTQ format subset for Phred sequencing quality score data only
      (no sequences).

      Phred quality scores are defined as a property which is logarithmically related
      to the base-calling error probabilities.'
    meaning: edam:format_3607
    title: qual
  edam:format_3608:
    text: edam:format_3608
    description: 'FASTQ format subset for Phred sequencing quality score data only
      (no sequences) for Solexa/Illumina 1.0 format.

      Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5
      to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5
      to 40 only are expected)'
    meaning: edam:format_3608
    title: qualsolexa
  edam:format_3609:
    text: edam:format_3609
    description: 'FASTQ format subset for Phred sequencing quality score data only
      (no sequences) from Illumina 1.5 and before Illumina 1.8.

      Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have
      a slightly different meaning. The values 0 and 1 are no longer used and the
      value 2, encoded by ASCII 66 "B", is used also at the end of reads as a Read
      Segment Quality Control Indicator.'
    meaning: edam:format_3609
    title: qualillumina
  edam:format_3610:
    text: edam:format_3610
    description: 'FASTQ format subset for Phred sequencing quality score data only
      (no sequences) for SOLiD data.

      For SOLiD data, the sequence is in color space, except the first position. The
      quality values are those of the Sanger format.'
    meaning: edam:format_3610
    title: qualsolid
  edam:format_3611:
    text: edam:format_3611
    description: FASTQ format subset for Phred sequencing quality score data only
      (no sequences) from 454 sequencers.
    meaning: edam:format_3611
    title: qual454
  edam:format_3612:
    text: edam:format_3612
    description: 'Format that covers both the broad peak format and narrow peak format
      from ENCODE.

      Human ENCODE peak format.'
    meaning: edam:format_3612
    title: ENCODE peak format
  edam:format_3613:
    text: edam:format_3613
    description: 'Format that covers both the broad peak format and narrow peak format
      from ENCODE.

      Human ENCODE narrow peak format.'
    meaning: edam:format_3613
    title: ENCODE narrow peak format
  edam:format_3614:
    text: edam:format_3614
    description: Human ENCODE broad peak format.
    meaning: edam:format_3614
    title: ENCODE broad peak format
  edam:format_3615:
    text: edam:format_3615
    description: 'BAM files are compressed using a variant of GZIP (GNU ZIP), into
      a format called BGZF (Blocked GNU Zip Format).

      Blocked GNU Zip format.'
    meaning: edam:format_3615
    title: bgzip
  edam:format_3616:
    text: edam:format_3616
    description: TAB-delimited genome position file index format.
    meaning: edam:format_3616
    title: tabix
  edam:format_3617:
    text: edam:format_3617
    description: Data format for graph data.
    meaning: edam:format_3617
    title: Graph format
  edam:format_3618:
    text: edam:format_3618
    description: XML-based format used to store graph descriptions within Galaxy.
    meaning: edam:format_3618
    title: xgmml
  edam:format_3619:
    text: edam:format_3619
    description: SIF (simple interaction file) Format - a network/pathway format used
      for instance in cytoscape.
    meaning: edam:format_3619
    title: sif
  edam:format_3620:
    text: edam:format_3620
    description: MS Excel spreadsheet format consisting of a set of XML documents
      stored in a ZIP-compressed file.
    meaning: edam:format_3620
    title: xlsx
  edam:format_3621:
    text: edam:format_3621
    description: Data format used by the SQLite database.
    meaning: edam:format_3621
    title: SQLite format
  edam:format_3622:
    text: edam:format_3622
    description: Data format used by the SQLite database conformant to the Gemini
      schema.
    meaning: edam:format_3622
    title: Gemini SQLite format
  edam:format_3624:
    text: edam:format_3624
    description: An index of a genome database, indexed for use by the snpeff tool.
    meaning: edam:format_3624
    title: snpeffdb
  edam:format_3626:
    text: edam:format_3626
    description: Binary format used by MATLAB files to store workspace variables.
    meaning: edam:format_3626
    title: MAT
  edam:format_3650:
    text: edam:format_3650
    description: 'Format used by netCDF software library for writing and reading chromatography-MS
      data files. Also used to store trajectory atom coordinates information, such
      as the ones obtained by Molecular Dynamics simulations.

      Network Common Data Form (NetCDF) library is supported by AMBER MD package from
      version 9.'
    meaning: edam:format_3650
    title: NetCDF
  edam:format_3651:
    text: edam:format_3651
    description: 'Files includes *m*/*z*, intensity pairs separated by headers; headers
      can contain a bit more information, including search engine instructions.

      Mascot Generic Format. Encodes multiple MS/MS spectra in a single file.'
    meaning: edam:format_3651
    title: MGF
  edam:format_3652:
    text: edam:format_3652
    description: 'Each file contains one header line for the known or assumed charge
      and the mass of the precursor peptide ion, calculated from the measured *m*/*z*
      and the charge. This one line was then followed by all the *m*/*z*, intensity
      pairs that represent the spectrum.

      Spectral data format file where each spectrum is written to a separate file.'
    meaning: edam:format_3652
    title: dta
  edam:format_3653:
    text: edam:format_3653
    description: 'Differ from .dta only in subtleties of the header line format and
      content and support the added feature of being able to.

      Spectral data file similar to dta.'
    meaning: edam:format_3653
    title: pkl
  edam:format_3654:
    text: edam:format_3654
    description: Common file format for proteomics mass spectrometric data developed
      at the Seattle Proteome Center/Institute for Systems Biology.
    meaning: edam:format_3654
    title: mzXML
  edam:format_3655:
    text: edam:format_3655
    description: Open data format for the storage, exchange, and processing of peptide
      sequence assignments of MS/MS scans, intended to provide a common data output
      format for many different MS/MS search engines and subsequent peptide-level
      analyses.
    meaning: edam:format_3655
    title: pepXML
  edam:format_3657:
    text: edam:format_3657
    description: Graphical Pathway Markup Language (GPML) is an XML format used for
      exchanging biological pathways.
    meaning: edam:format_3657
    title: GPML
  edam:format_3665:
    text: edam:format_3665
    description: A list of k-mers and their occurrences in a dataset. Can also be
      used as an implicit De Bruijn graph.
    meaning: edam:format_3665
    title: K-mer countgraph
  edam:format_3681:
    text: edam:format_3681
    description: 'For mass spectrometry-based chemical profiling data (including metabolomics),
      there is a derived (but incompatible) format mzTab-M (also named mzTab 2.0,
      http://edamontology.org/format_4058), and its lipidomics version mzTab-L (http://edamontology.org/format_4059).

      For more detailed metadata, there are formats such as mzIdentML (http://edamontology.org/format_3247)
      and mzQuantML (http://edamontology.org/format_3248).

      The reference implementation of mzTab in Java is https://github.com/PRIDE-Archive/jmzTab
      (maintenance stopped in 2022).

      mzTab is a light-weight, tab-delimited format for mass spectrometry-based proteomics
      data.

      mzTab is alternatively named mzTab 1.0, as opposed to mzTab 2.0 (and 2.1), which
      is the incompatible mzTab-M format for chemical profiling e.g. metabolomics.'
    meaning: edam:format_3681
    title: mzTab
  edam:format_3682:
    text: edam:format_3682
    description: 'imzML data are recorded in 2 files: ''.imzXML'' (this concept) is
      a metadata XML file based on mzML by HUPO-PSI, and ''.ibd'' (http://edamontology.org/format_3839)
      is a binary file containing the mass spectra. This entry is for the metadata
      XML file.

      imzML metadata is a data format for mass spectrometry imaging metadata.'
    meaning: edam:format_3682
    title: imzML metadata file
  edam:format_3683:
    text: edam:format_3683
    description: 'The focus of qcML is towards mass spectrometry based proteomics,
      but the format is suitable for metabolomics and sequencing as well.

      qcML is an XML format for quality-related data of mass spectrometry and other
      high-throughput measurements.'
    meaning: edam:format_3683
    title: qcML
  edam:format_3684:
    text: edam:format_3684
    description: PRIDE XML is an XML format for mass spectra, peptide and protein
      identifications, and metadata about a corresponding measurement, sample, experiment.
    meaning: edam:format_3684
    title: PRIDE XML
  edam:format_3685:
    text: edam:format_3685
    description: Simulation Experiment Description Markup Language (SED-ML) is an
      XML format for encoding simulation setups, according to the MIASE (Minimum Information
      About a Simulation Experiment) requirements.
    meaning: edam:format_3685
    title: SED-ML
  edam:format_3686:
    text: edam:format_3686
    description: 'An OMEX file is a ZIP container that includes a manifest file, listing
      the content of the archive, an optional metadata file adding information about
      the archive and its content, and the files describing the model. OMEX is one
      of the standardised formats within COMBINE (Computational Modeling in Biology
      Network).

      Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all
      information necessary for a modeling and simulation project in systems biology.'
    meaning: edam:format_3686
    title: COMBINE OMEX
  edam:format_3687:
    text: edam:format_3687
    description: 'ISA-TAB is based on MAGE-TAB. Other than tabular, the ISA model
      can also be represented in RDF, and in JSON (compliable with a set of defined
      JSON Schemata).

      The Investigation / Study / Assay (ISA) tab-delimited (TAB) format incorporates
      metadata from experiments employing a combination of technologies.'
    meaning: edam:format_3687
    title: ISA-TAB
  edam:format_3688:
    text: edam:format_3688
    description: SBtab is a tabular format for biochemical network models.
    meaning: edam:format_3688
    title: SBtab
  edam:format_3689:
    text: edam:format_3689
    description: Biological Connection Markup Language (BCML) is an XML format for
      biological pathways.
    meaning: edam:format_3689
    title: BCML
  edam:format_3690:
    text: edam:format_3690
    description: Biological Dynamics Markup Language (BDML) is an XML format for quantitative
      data describing biological dynamics.
    meaning: edam:format_3690
    title: BDML
  edam:format_3691:
    text: edam:format_3691
    description: Biological Expression Language (BEL) is a textual format for representing
      scientific findings in life sciences in a computable form.
    meaning: edam:format_3691
    title: BEL
  edam:format_3692:
    text: edam:format_3692
    description: SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN)
      diagrams of biological pathways or networks.
    meaning: edam:format_3692
    title: SBGN-ML
  edam:format_3693:
    text: edam:format_3693
    description: AGP is a tabular format for a sequence assembly (a contig, a scaffold/supercontig,
      or a chromosome).
    meaning: edam:format_3693
    title: AGP
  edam:format_3696:
    text: edam:format_3696
    description: PostScript format.
    meaning: edam:format_3696
    title: PS
  edam:format_3698:
    text: edam:format_3698
    description: SRA archive format (SRA) is the archive format used for input to
      the NCBI Sequence Read Archive.
    meaning: edam:format_3698
    title: SRA format
  edam:format_3699:
    text: edam:format_3699
    description: VDB ('vertical database') is the native format used for export from
      the NCBI Sequence Read Archive.
    meaning: edam:format_3699
    title: VDB
  edam:format_3701:
    text: edam:format_3701
    description: A five-column, tab-delimited table of feature locations and qualifiers
      for importing annotation into an existing Sequin submission (an NCBI tool for
      submitting and updating GenBank entries).
    meaning: edam:format_3701
    title: Sequin format
  edam:format_3702:
    text: edam:format_3702
    description: 'Proprietary mass-spectrometry format of Thermo Scientific''s ProteomeDiscoverer
      software.

      This format corresponds to an SQLite database, and you can look into the files
      with e.g. SQLiteStudio3. There are also some readers (http://doi.org/10.1021/pr2005154)
      and converters (http://doi.org/10.1016/j.jprot.2015.06.015) for this format
      available, which re-engineered the database schema, but there is no official
      DB schema specification of Thermo Scientific for the format.'
    meaning: edam:format_3702
    title: MSF
  edam:format_3706:
    text: edam:format_3706
    description: Data format for biodiversity data.
    meaning: edam:format_3706
    title: Biodiversity data format
  edam:format_3708:
    text: edam:format_3708
    description: Exchange format of the Access to Biological Collections Data (ABCD)
      Schema; a standard for the access to and exchange of data about specimens and
      observations (primary biodiversity data).
    meaning: edam:format_3708
    title: ABCD format
  edam:format_3709:
    text: edam:format_3709
    description: Tab-delimited text files of GenePattern that contain a column for
      each sample, a row for each gene, and an expression value for each gene in each
      sample.
    meaning: edam:format_3709
    title: GCT/Res format
  edam:format_3710:
    text: edam:format_3710
    description: Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex).
    meaning: edam:format_3710
    title: WIFF format
  edam:format_3711:
    text: edam:format_3711
    description: Output format used by X! series search engines that is based on the
      XML language BIOML.
    meaning: edam:format_3711
    title: X!Tandem XML
  edam:format_3712:
    text: edam:format_3712
    description: 'Proprietary file format for mass spectrometry data from Thermo Scientific.

      Proprietary format for which documentation is not available.'
    meaning: edam:format_3712
    title: Thermo RAW
  edam:format_3713:
    text: edam:format_3713
    description: '"Raw" result file from Mascot database search.'
    meaning: edam:format_3713
    title: Mascot .dat file
  edam:format_3714:
    text: edam:format_3714
    description: Format of peak list files from Andromeda search engine (MaxQuant)
      that consist of arbitrarily many spectra.
    meaning: edam:format_3714
    title: MaxQuant APL peaklist format
  edam:format_3725:
    text: edam:format_3725
    description: 'SBOL introduces a standardised format for the electronic exchange
      of information on the structural and functional aspects of biological designs.

      Synthetic Biology Open Language (SBOL) is an XML format for the specification
      and exchange of biological design information in synthetic biology.'
    meaning: edam:format_3725
    title: SBOL
  edam:format_3726:
    text: edam:format_3726
    description: 'One or more mining models can be contained in a PMML document.

      PMML uses XML to represent mining models. The structure of the models is described
      by an XML Schema.'
    meaning: edam:format_3726
    title: PMML
  edam:format_3727:
    text: edam:format_3727
    description: 'An OME-TIFF dataset consists of one or more files in standard TIFF
      or BigTIFF format, with the file extension .ome.tif or .ome.tiff, and an identical
      (or in the case of multiple files, nearly identical) string of OME-XML metadata
      embedded in the ImageDescription tag of each file''s first IFD (Image File Directory).
      BigTIFF file extensions are also permitted, with the file extension .ome.tf2,
      .ome.tf8 or .ome.btf, but note these file extensions are an addition to the
      original specification, and software using an older version of the specification
      may not be able to handle these file extensions.

      Image file format used by the Open Microscopy Environment (OME).

      OME develops open-source software and data format standards for the storage
      and manipulation of biological microscopy data. It is a joint project between
      universities, research establishments, industry and the software development
      community.'
    meaning: edam:format_3727
    title: OME-TIFF
  edam:format_3728:
    text: edam:format_3728
    description: 'Format for multiple aligned or single sequences together with the
      probabilistic description of the (consensus) RNA secondary structure ensemble
      by probabilities of base pairs, base pair stackings, and base pairs and unpaired
      bases in the loop of base pairs.

      The LocARNA PP format combines sequence or alignment information and (respectively,
      single or consensus) ensemble probabilities into an PP 2.0 record.'
    meaning: edam:format_3728
    title: LocARNA PP
  edam:format_3729:
    text: edam:format_3729
    description: 'Input format used by the Database of Genotypes and Phenotypes (dbGaP).

      The Database of Genotypes and Phenotypes (dbGaP) is a National Institutes of
      Health (NIH) sponsored repository charged to archive, curate and distribute
      information produced by studies investigating the interaction of genotype and
      phenotype.'
    meaning: edam:format_3729
    title: dbGaP format
  edam:format_3746:
    text: edam:format_3746
    description: 'BIOM is a recognised standard for the Earth Microbiome Project,
      and is a project supported by Genomics Standards Consortium. Supported in QIIME,
      Mothur, MEGAN, etc.

      The BIological Observation Matrix (BIOM) is a format for representing biological
      sample by observation contingency tables in broad areas of comparative omics.
      The primary use of this format is to represent OTU tables and metagenome tables.'
    meaning: edam:format_3746
    title: BIOM format
  edam:format_3747:
    text: edam:format_3747
    description: 'A format for storage, exchange, and processing of protein identifications
      created from ms/ms-derived peptide sequence data.

      No human-consumable information about this format is available (see http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML).'
    meaning: edam:format_3747
    title: protXML
  edam:format_3748:
    text: edam:format_3748
    description: A linked data format enables publishing structured data as linked
      data (Linked Data), so that the data can be interlinked and become more useful
      through semantic queries.
    meaning: edam:format_3748
    title: Linked data format
  edam:format_3749:
    text: edam:format_3749
    description: JSON-LD, or JavaScript Object Notation for Linked Data, is a method
      of encoding Linked Data using JSON.
    meaning: edam:format_3749
    title: JSON-LD
  edam:format_3750:
    text: edam:format_3750
    description: 'Data in YAML format can be serialised into text, or binary format.

      YAML (YAML Ain''t Markup Language) is a human-readable tree-structured data
      serialisation language.

      YAML version 1.2 is a superset of JSON; prior versions were "not strictly compatible".'
    meaning: edam:format_3750
    title: YAML
  edam:format_3751:
    text: edam:format_3751
    description: Tabular data represented as values in a text file delimited by some
      character.
    meaning: edam:format_3751
    title: DSV
  edam:format_3752:
    text: edam:format_3752
    description: Tabular data represented as comma-separated values in a text file.
    meaning: edam:format_3752
    title: CSV
  edam:format_3758:
    text: edam:format_3758
    description: '"Raw" result file from SEQUEST database search.'
    meaning: edam:format_3758
    title: SEQUEST .out file
  edam:format_3764:
    text: edam:format_3764
    description: XML file format for files containing information about peptide identifications
      from mass spectrometry data analysis carried out with OpenMS.
    meaning: edam:format_3764
    title: idXML
  edam:format_3765:
    text: edam:format_3765
    description: Data table formatted such that it can be passed/streamed within the
      KNIME platform.
    meaning: edam:format_3765
    title: KNIME datatable format
  edam:format_3770:
    text: edam:format_3770
    description: UniProtKB XML sequence features format is an XML format available
      for downloading UniProt entries.
    meaning: edam:format_3770
    title: UniProtKB XML
  edam:format_3771:
    text: edam:format_3771
    description: UniProtKB RDF sequence features format is an RDF format available
      for downloading UniProt entries (in RDF/XML).
    meaning: edam:format_3771
    title: UniProtKB RDF
  edam:format_3772:
    text: edam:format_3772
    description: 'BioJSON is a BioXSD-schema-based JSON format of sequence-based data
      and some other common data - sequence records, alignments, feature records,
      references to resources, and more - optimised for integrative bioinformatics,
      web applications and APIs, and object-oriented programming.

      Work in progress. ''BioXSD'' belongs to the ''BioXSD|GTrack'' ecosystem of generic
      formats. ''BioJSON'' is the JSON format based on the common, unified ''BioXSD
      data model'', a.k.a. ''BioXSD|BioJSON|BioYAML''.'
    meaning: edam:format_3772
    title: BioJSON (BioXSD)
  edam:format_3773:
    text: edam:format_3773
    description: 'BioYAML is a BioXSD-schema-based YAML format of sequence-based data
      and some other common data - sequence records, alignments, feature records,
      references to resources, and more - optimised for integrative bioinformatics,
      web APIs, human readability and editing, and object-oriented programming.

      Work in progress. ''BioXSD'' belongs to the ''BioXSD|GTrack'' ecosystem of generic
      formats. ''BioYAML'' is the YAML format based on the common, unified ''BioXSD
      data model'', a.k.a. ''BioXSD|BioJSON|BioYAML''.'
    meaning: edam:format_3773
    title: BioYAML
  edam:format_3774:
    text: edam:format_3774
    description: BioJSON is a JSON format of single multiple sequence alignments,
      with their annotations, features, and custom visualisation and application settings
      for the Jalview workbench.
    meaning: edam:format_3774
    title: BioJSON (Jalview)
  edam:format_3775:
    text: edam:format_3775
    description: '''GSuite'' belongs to the ''BioXSD|GTrack'' ecosystem of generic
      formats, and particular to its subset, the ''GTrack ecosystem'' (GTrack, GSuite,
      BTrack). ''GSuite'' is the tabular format for an annotated collection of individual
      GTrack files.

      GSuite is a tabular format for collections of genome or sequence feature tracks,
      suitable for integrative multi-track analysis. GSuite contains links to genome/sequence
      tracks, with additional metadata.'
    meaning: edam:format_3775
    title: GSuite
  edam:format_3776:
    text: edam:format_3776
    description: '''BTrack'' belongs to the ''BioXSD|GTrack'' ecosystem of generic
      formats, and particular to its subset, the ''GTrack ecosystem'' (GTrack, GSuite,
      BTrack). ''BTrack'' is the binary, optionally compressed HDF5-based version
      of the GTrack and GSuite formats.

      BTrack is an HDF5-based binary format for genome or sequence feature tracks
      and their collections, suitable for integrative multi-track analysis. BTrack
      is a binary, compressed alternative to the GTrack and GSuite formats.'
    meaning: edam:format_3776
    title: BTrack
  edam:format_3777:
    text: edam:format_3777
    description: 'Multi-Crop Passport Descriptors is a format available in 2 successive
      versions, V.1 (FAO/IPGRI 2001) and V.2 (FAO/Bioversity 2012).

      The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an international
      standard format for exchange of germplasm information.'
    meaning: edam:format_3777
    title: MCPD
  edam:format_3780:
    text: edam:format_3780
    description: Data format of an annotated text, e.g. with recognised entities,
      concepts, and relations.
    meaning: edam:format_3780
    title: Annotated text format
  edam:format_3781:
    text: edam:format_3781
    description: JSON format of annotated scientific text used by PubAnnotations and
      other tools.
    meaning: edam:format_3781
    title: PubAnnotation format
  edam:format_3782:
    text: edam:format_3782
    description: BioC is a standardised XML format for sharing and integrating text
      data and annotations.
    meaning: edam:format_3782
    title: BioC
  edam:format_3783:
    text: edam:format_3783
    description: Native textual export format of annotated scientific text from PubTator.
    meaning: edam:format_3783
    title: PubTator format
  edam:format_3784:
    text: edam:format_3784
    description: A format of text annotation using the linked-data Open Annotation
      Data Model, serialised typically in RDF or JSON-LD.
    meaning: edam:format_3784
    title: Open Annotation format
  edam:format_3785:
    text: edam:format_3785
    description: A family of similar formats of text annotation, used by BRAT and
      other tools, known as BioNLP Shared Task format (BioNLP 2009 Shared Task on
      Event Extraction, BioNLP Shared Task 2011, BioNLP Shared Task 2013), BRAT format,
      BRAT standoff format, and similar.
    meaning: edam:format_3785
    title: BioNLP Shared Task format
  edam:format_3787:
    text: edam:format_3787
    description: A query language (format) for structured database queries.
    meaning: edam:format_3787
    title: Query language
  edam:format_3788:
    text: edam:format_3788
    description: SQL (Structured Query Language) is the de-facto standard query language
      (format of queries) for querying and manipulating data in relational databases.
    meaning: edam:format_3788
    title: SQL
  edam:format_3789:
    text: edam:format_3789
    description: XQuery (XML Query) is a query language (format of queries) for querying
      and manipulating structured and unstructured data, usually in the form of XML,
      text, and with vendor-specific extensions for other data formats (JSON, binary,
      etc.).
    meaning: edam:format_3789
    title: XQuery
  edam:format_3790:
    text: edam:format_3790
    description: SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query
      language for querying and manipulating data stored in Resource Description Framework
      (RDF) format.
    meaning: edam:format_3790
    title: SPARQL
  edam:format_3804:
    text: edam:format_3804
    description: XML format for XML Schema.
    meaning: edam:format_3804
    title: xsd
  edam:format_3811:
    text: edam:format_3811
    description: XMFA format stands for eXtended Multi-FastA format and is used to
      store collinear sub-alignments that constitute a single genome alignment.
    meaning: edam:format_3811
    title: XMFA
  edam:format_3812:
    text: edam:format_3812
    description: The GEN file format contains genetic data and describes SNPs.
    meaning: edam:format_3812
    title: GEN
  edam:format_3813:
    text: edam:format_3813
    description: The SAMPLE file format contains information about each individual
      i.e. individual IDs, covariates, phenotypes and missing data proportions, from
      a GWAS study.
    meaning: edam:format_3813
    title: SAMPLE file format
  edam:format_3814:
    text: edam:format_3814
    description: SDF is one of a family of chemical-data file formats developed by
      MDL Information Systems; it is intended especially for structural information.
    meaning: edam:format_3814
    title: SDF
  edam:format_3815:
    text: edam:format_3815
    description: An MDL Molfile is a file format for holding information about the
      atoms, bonds, connectivity and coordinates of a molecule.
    meaning: edam:format_3815
    title: Molfile
  edam:format_3816:
    text: edam:format_3816
    description: Complete, portable representation of a SYBYL molecule. ASCII file
      which contains all the information needed to reconstruct a SYBYL molecule.
    meaning: edam:format_3816
    title: Mol2
  edam:format_3817:
    text: edam:format_3817
    description: 'format for the LaTeX document preparation system.

      uses the TeX typesetting program format'
    meaning: edam:format_3817
    title: latex
  edam:format_3818:
    text: edam:format_3818
    description: Tab-delimited text file format used by Eland - the read-mapping program
      distributed by Illumina with its sequencing analysis pipeline - which maps short
      Solexa sequence reads to the human reference genome.
    meaning: edam:format_3818
    title: ELAND format
  edam:format_3819:
    text: edam:format_3819
    description: 'It differs from Phylip Format (format_1997) on length of the ID
      sequence. There no length restrictions on the ID, but whitespaces aren''t allowed
      in the sequence ID/Name because one space separates the longest ID and the beginning
      of the sequence. Sequences IDs must be padded to the longest ID length.

      Phylip multiple alignment sequence format, less stringent than PHYLIP format.'
    meaning: edam:format_3819
    title: Relaxed PHYLIP Interleaved
  edam:format_3820:
    text: edam:format_3820
    description: 'It differs from Phylip sequential format (format_1997) on length
      of the ID sequence. There no length restrictions on the ID, but whitespaces
      aren''t allowed in the sequence ID/Name because one space separates the longest
      ID and the beginning of the sequence. Sequences IDs must be padded to the longest
      ID length.

      Phylip multiple alignment sequence format, less stringent than PHYLIP sequential
      format (format_1998).'
    meaning: edam:format_3820
    title: Relaxed PHYLIP Sequential
  edam:format_3821:
    text: edam:format_3821
    description: Default XML format of VisANT, containing all the network information.
    meaning: edam:format_3821
    title: VisML
  edam:format_3822:
    text: edam:format_3822
    description: GML (Graph Modeling Language) is a text file format supporting network
      data with a very easy syntax. It is used by Graphlet, Pajek, yEd, LEDA and NetworkX.
    meaning: edam:format_3822
    title: GML
  edam:format_3823:
    text: edam:format_3823
    description: 'FASTG is a format for faithfully representing genome assemblies
      in the face of allelic polymorphism and assembly uncertainty.

      It is called FASTG, like FASTA, but the G stands for "graph".'
    meaning: edam:format_3823
    title: FASTG
  edam:format_3824:
    text: edam:format_3824
    description: Data format for raw data from a nuclear magnetic resonance (NMR)
      spectroscopy experiment.
    meaning: edam:format_3824
    title: NMR data format
  edam:format_3825:
    text: edam:format_3825
    description: nmrML is an MSI supported XML-based open access format for metabolomics
      NMR raw and processed spectral data. It is accompanies by an nmrCV (controlled
      vocabulary) to allow ontology-based annotations.
    meaning: edam:format_3825
    title: nmrML
  edam:format_3826:
    text: edam:format_3826
    description: . proBAM is an adaptation of BAM (format_2572), which was extended
      to meet specific requirements entailed by proteomics data.
    meaning: edam:format_3826
    title: proBAM
  edam:format_3827:
    text: edam:format_3827
    description: . proBED is an adaptation of BED (format_3003), which was extended
      to meet specific requirements entailed by proteomics data.
    meaning: edam:format_3827
    title: proBED
  edam:format_3828:
    text: edam:format_3828
    description: Data format for raw microarray data.
    meaning: edam:format_3828
    title: Raw microarray data format
  edam:format_3829:
    text: edam:format_3829
    description: GenePix Results (GPR) text file format developed by Axon Instruments
      that is used to save GenePix Results data.
    meaning: edam:format_3829
    title: GPR
  edam:format_3830:
    text: edam:format_3830
    description: Binary format used by the ARB software suite.
    meaning: edam:format_3830
    title: ARB
  edam:format_3832:
    text: edam:format_3832
    description: OpenMS format for grouping features in one map or across several
      maps.
    meaning: edam:format_3832
    title: consensusXML
  edam:format_3833:
    text: edam:format_3833
    description: OpenMS format for quantitation results (LC/MS features).
    meaning: edam:format_3833
    title: featureXML
  edam:format_3834:
    text: edam:format_3834
    description: Now deprecated data format of the HUPO Proteomics Standards Initiative.
      Replaced by mzML (format_3244).
    meaning: edam:format_3834
    title: mzData
  edam:format_3835:
    text: edam:format_3835
    description: Format supported by the Tide tool for identifying peptides from tandem
      mass spectra.
    meaning: edam:format_3835
    title: TIDE TXT
  edam:format_3836:
    text: edam:format_3836
    description: XML format as produced by the NCBI Blast package v2.
    meaning: edam:format_3836
    title: BLAST XML v2 results format
  edam:format_3838:
    text: edam:format_3838
    description: Microsoft Powerpoint format.
    meaning: edam:format_3838
    title: pptx
  edam:format_3839:
    text: edam:format_3839
    description: 'ibd is a data format for mass spectrometry imaging data.

      imzML data is recorded in 2 files: ''.imzXML'' (http://edamontology.org/format_3682)
      is a metadata XML file based on mzML by HUPO-PSI, and ''.ibd'' (this concept)
      is a binary file containing the mass spectra.'
    meaning: edam:format_3839
    title: ibd
  edam:format_3841:
    text: edam:format_3841
    description: Data format used in Natural Language Processing.
    meaning: edam:format_3841
    title: NLP format
  edam:format_3843:
    text: edam:format_3843
    description: XML input file format for BEAST Software (Bayesian Evolutionary Analysis
      Sampling Trees).
    meaning: edam:format_3843
    title: BEAST
  edam:format_3844:
    text: edam:format_3844
    description: Chado-XML format is a direct mapping of the Chado relational schema
      into XML.
    meaning: edam:format_3844
    title: Chado-XML
  edam:format_3845:
    text: edam:format_3845
    description: 'An alignment format generated by PRANK/PRANKSTER consisting of four
      elements: newick, nodes, selection and model.'
    meaning: edam:format_3845
    title: HSAML
  edam:format_3846:
    text: edam:format_3846
    description: Output xml file from the InterProScan sequence analysis application.
    meaning: edam:format_3846
    title: InterProScan XML
  edam:format_3847:
    text: edam:format_3847
    description: The KEGG Markup Language (KGML) is an exchange format of the KEGG
      pathway maps, which is converted from internally used KGML+ (KGML+SVG) format.
    meaning: edam:format_3847
    title: KGML
  edam:format_3848:
    text: edam:format_3848
    description: XML format for collected entries from bibliographic databases MEDLINE
      and PubMed.
    meaning: edam:format_3848
    title: PubMed XML
  edam:format_3849:
    text: edam:format_3849
    description: A set of XML compliant markup components for describing multiple
      sequence alignments.
    meaning: edam:format_3849
    title: MSAML
  edam:format_3850:
    text: edam:format_3850
    description: OrthoXML is designed broadly to allow the storage and comparison
      of orthology data from any ortholog database. It establishes a structure for
      describing orthology relationships while still allowing flexibility for database-specific
      information to be encapsulated in the same format.
    meaning: edam:format_3850
    title: OrthoXML
  edam:format_3851:
    text: edam:format_3851
    description: Tree structure of Protein Sequence Database Markup Language generated
      using Matra software.
    meaning: edam:format_3851
    title: PSDML
  edam:format_3852:
    text: edam:format_3852
    description: SeqXML is an XML Schema to describe biological sequences, developed
      by the Stockholm Bioinformatics Centre.
    meaning: edam:format_3852
    title: SeqXML
  edam:format_3853:
    text: edam:format_3853
    description: XML format for the UniParc database.
    meaning: edam:format_3853
    title: UniParc XML
  edam:format_3854:
    text: edam:format_3854
    description: XML format for the UniRef reference clusters.
    meaning: edam:format_3854
    title: UniRef XML
  edam:format_3857:
    text: edam:format_3857
    description: Common Workflow Language (CWL) format for description of command-line
      tools and workflows.
    meaning: edam:format_3857
    title: CWL
  edam:format_3858:
    text: edam:format_3858
    description: 'Proprietary file format for mass spectrometry data from Waters.

      Proprietary format for which documentation is not available, but used by multiple
      tools.'
    meaning: edam:format_3858
    title: Waters RAW
  edam:format_3859:
    text: edam:format_3859
    description: 'A standardized file format for data exchange in mass spectrometry,
      initially developed for infrared spectrometry.

      JCAMP-DX is an ASCII based format and therefore not very compact even though
      it includes standards for file compression.'
    meaning: edam:format_3859
    title: JCAMP-DX
  edam:format_3862:
    text: edam:format_3862
    description: An NLP format used for annotated textual documents.
    meaning: edam:format_3862
    title: NLP annotation format
  edam:format_3863:
    text: edam:format_3863
    description: NLP format used by a specific type of corpus (collection of texts).
    meaning: edam:format_3863
    title: NLP corpus format
  edam:format_3864:
    text: edam:format_3864
    description: 'mirGFF3 is a common format for microRNA data resulting from small-RNA
      RNA-Seq workflows.

      mirGFF3 is a specialisation of GFF3; produced by small-RNA-Seq analysis workflows,
      usable and convertible with the miRTop API (https://mirtop.readthedocs.io/en/latest/),
      and consumable by tools for downstream analysis.'
    meaning: edam:format_3864
    title: mirGFF3
  edam:format_3865:
    text: edam:format_3865
    description: A "placeholder" concept for formats of annotated RNA data, including
      e.g. microRNA and RNA-Seq data.
    meaning: edam:format_3865
    title: RNA annotation format
  edam:format_3866:
    text: edam:format_3866
    description: 'File format to store trajectory information for a 3D structure .

      Formats differ on what they are able to store (coordinates, velocities, topologies)
      and how they are storing it (raw, compressed, textual, binary).'
    meaning: edam:format_3866
    title: Trajectory format
  edam:format_3867:
    text: edam:format_3867
    description: Binary file format to store trajectory information for a 3D structure
      .
    meaning: edam:format_3867
    title: Trajectory format (binary)
  edam:format_3868:
    text: edam:format_3868
    description: Textual file format to store trajectory information for a 3D structure
      .
    meaning: edam:format_3868
    title: Trajectory format (text)
  edam:format_3873:
    text: edam:format_3873
    description: 'HDF is currently supported by many commercial and non-commercial
      software platforms such as Java, MATLAB/Scilab, Octave, Python and R.

      HDF is the name of a set of file formats and libraries designed to store and
      organize large amounts of numerical data, originally developed at the National
      Center for Supercomputing Applications at the University of Illinois.'
    meaning: edam:format_3873
    title: HDF
  edam:format_3874:
    text: edam:format_3874
    description: 'PCAZip format is a binary compressed file to store atom coordinates
      based on Essential Dynamics (ED) and Principal Component Analysis (PCA).

      The compression is made projecting the Cartesian snapshots collected along the
      trajectory into an orthogonal space defined by the most relevant eigenvectors
      obtained by diagonalization of the covariance matrix (PCA). In the compression/decompression
      process, part of the original information is lost, depending on the final number
      of eigenvectors chosen. However, with a reasonable choice of the set of eigenvectors
      the compression typically reduces the trajectory file to less than one tenth
      of their original size with very acceptable loss of information. Compression
      with PCAZip can only be applied to unsolvated structures.'
    meaning: edam:format_3874
    title: PCAzip
  edam:format_3875:
    text: edam:format_3875
    description: 'Portable binary format for trajectories produced by GROMACS package.

      XTC uses the External Data Representation (xdr) routines for writing and reading
      data which were created for the Unix Network File System (NFS). XTC files use
      a reduced precision (lossy) algorithm which works multiplying the coordinates
      by a scaling factor (typically 1000), so converting them to pm (GROMACS standard
      distance unit is nm). This allows an integer rounding of the values. Several
      other tricks are performed, such as making use of atom proximity information:
      atoms close in sequence are usually close in space (e.g. water molecules). That
      makes XTC format the most efficient in terms of disk usage, in most cases reducing
      by a factor of 2 the size of any other binary trajectory format.'
    meaning: edam:format_3875
    title: XTC
  edam:format_3876:
    text: edam:format_3876
    description: 'Fully architecture-independent format, regarding both endianness
      and the ability to mix single/double precision trajectories and I/O libraries.
      Self-sufficient, it should not require any other files for reading, and all
      the data should be contained in a single file for easy transport. Temporal compression
      of data, improving the compression rate of the previous XTC format. Possibility
      to store meta-data with information about the simulation. Direct access to a
      particular frame. Efficient parallel I/O.

      Trajectory Next Generation (TNG) is a format for storage of molecular simulation
      data. It is designed and implemented by the GROMACS development group, and it
      is called to be the substitute of the XTC format.'
    meaning: edam:format_3876
    title: TNG
  edam:format_3877:
    text: edam:format_3877
    description: 'The XYZ chemical file format is widely supported by many programs,
      although many slightly different XYZ file formats coexist (Tinker XYZ, UniChem
      XYZ, etc.). Basic information stored for each atom in the system are x, y and
      z coordinates and atom element/atomic number.

      XYZ files are structured in this way: First line contains the number of atoms
      in the file. Second line contains a title, comment, or filename. Remaining lines
      contain atom information. Each line starts with the element symbol, followed
      by x, y and z coordinates in angstroms separated by whitespace. Multiple molecules
      or frames can be contained within one file, so it supports trajectory storage.
      XYZ files can be directly represented by a molecular viewer, as they contain
      all the basic information needed to build the 3D model.'
    meaning: edam:format_3877
    title: XYZ
  edam:format_3878:
    text: edam:format_3878
    description: AMBER trajectory (also called mdcrd), with 10 coordinates per line
      and format F8.3 (fixed point notation with field width 8 and 3 decimal places).
    meaning: edam:format_3878
    title: mdcrd
  edam:format_3879:
    text: edam:format_3879
    description: 'Format of topology files; containing the static information of a
      structure molecular system that is needed for a molecular simulation.

      Many different file formats exist describing structural molecular topology.
      Typically, each MD package or simulation software works with their own implementation
      (e.g. GROMACS top, CHARMM psf, AMBER prmtop).'
    meaning: edam:format_3879
    title: Topology format
  edam:format_3880:
    text: edam:format_3880
    description: 'GROMACS MD package top textual files define an entire structure
      system topology, either directly, or by including itp files.

      There is currently no tool available for conversion between GROMACS topology
      format and other formats, due to the internal differences in both approaches.
      There is, however, a method to convert small molecules parameterized with AMBER
      force-field into GROMACS format, allowing simulations of these systems with
      GROMACS MD package.'
    meaning: edam:format_3880
    title: GROMACS top
  edam:format_3881:
    text: edam:format_3881
    description: 'AMBER Prmtop file (version 7) is a structure topology text file
      divided in several sections designed to be parsed easily using simple Fortran
      code. Each section contains particular topology information, such as atom name,
      charge, mass, angles, dihedrals, etc.

      It can be modified manually, but as the size of the system increases, the hand-editing
      becomes increasingly complex. AMBER Parameter-Topology file format is used extensively
      by the AMBER software suite and is referred to as the Prmtop file for short.

      version 7 is written to distinguish it from old versions of AMBER Prmtop. Similarly
      to HDF5, it is a completely different format, according to AMBER group: a drastic
      change to the file format occurred with the 2004 release of Amber 7 (http://ambermd.org/prmtop.pdf)'
    meaning: edam:format_3881
    title: AMBER top
  edam:format_3882:
    text: edam:format_3882
    description: 'The high similarity in the functional form of the two potential
      energy functions used by AMBER and CHARMM force-fields gives rise to the possible
      use of one force-field within the other MD engine. Therefore, the conversion
      of PSF files to AMBER Prmtop format is possible with the use of AMBER chamber
      (CHARMM - AMBER) program.

      X-Plor Protein Structure Files (PSF) are structure topology files used by NAMD
      and CHARMM molecular simulations programs. PSF files contain six main sections
      of interest: atoms, bonds, angles, dihedrals, improper dihedrals (force terms
      used to maintain planarity) and cross-terms.'
    meaning: edam:format_3882
    title: PSF
  edam:format_3883:
    text: edam:format_3883
    description: 'GROMACS itp files (include topology) contain structure topology
      information, and are typically included in GROMACS topology files (GROMACS top).
      Itp files are used to define individual (or multiple) components of a topology
      as a separate file. This is particularly useful if there is a molecule that
      is used frequently, and also reduces the size of the system topology file, splitting
      it in different parts.

      GROMACS itp files are used also to define position restrictions on the molecule,
      or to define the force field parameters for a particular ligand.'
    meaning: edam:format_3883
    title: GROMACS itp
  edam:format_3884:
    text: edam:format_3884
    description: 'Format of force field parameter files, which store the set of parameters
      (charges, masses, radii, bond lengths, bond dihedrals, etc.) that are essential
      for the proper description and simulation of a molecular system.

      Many different file formats exist describing force field parameters. Typically,
      each MD package or simulation software works with their own implementation (e.g.
      GROMACS itp, CHARMM rtf, AMBER off / frcmod).'
    meaning: edam:format_3884
    title: FF parameter format
  edam:format_3885:
    text: edam:format_3885
    description: 'It is basically a translation of the ASCII atom coordinate format
      to binary code. The only additional information stored is a magic number that
      identifies the BinPos format and the number of atoms per snapshot. The remainder
      is the chain of coordinates binary encoded. A drawback of this format is its
      architecture dependency. Integers and floats codification depends on the architecture,
      thus it needs to be converted if working in different platforms (little endian,
      big endian).

      Scripps Research Institute BinPos format is a binary formatted file to store
      atom coordinates.'
    meaning: edam:format_3885
    title: BinPos
  edam:format_3886:
    text: edam:format_3886
    description: AMBER coordinate/restart file with 6 coordinates per line and decimal
      format F12.7 (fixed point notation with field width 12 and 7 decimal places).
    meaning: edam:format_3886
    title: RST
  edam:format_3887:
    text: edam:format_3887
    description: 'Format of CHARMM Residue Topology Files (RTF), which define groups
      by including the atoms, the properties of the group, and bond and charge information.

      There is currently no tool available for conversion between GROMACS topology
      format and other formats, due to the internal differences in both approaches.
      There is, however, a method to convert small molecules parameterized with AMBER
      force-field into GROMACS format, allowing simulations of these systems with
      GROMACS MD package.'
    meaning: edam:format_3887
    title: CHARMM rtf
  edam:format_3888:
    text: edam:format_3888
    description: AMBER frcmod (Force field Modification) is a file format to store
      any modification to the standard force field needed for a particular molecule
      to be properly represented in the simulation.
    meaning: edam:format_3888
    title: AMBER frcmod
  edam:format_3889:
    text: edam:format_3889
    description: AMBER Object File Format library files (OFF library files) store
      residue libraries (forcefield residue parameters).
    meaning: edam:format_3889
    title: AMBER off
  edam:format_3906:
    text: edam:format_3906
    description: 'MReData is a text based data standard for processed NMR data. It
      is relying on SDF molecule data and allows to store assignments of NMR peaks
      to molecule features. The NMR-extracted data (or "NMReDATA") includes: Chemical
      shift,scalar coupling, 2D correlation, assignment, etc.

      NMReData is a text based data standard for processed NMR data. It is relying
      on SDF molecule data and allows to store assignments of NMR peaks to molecule
      features. The NMR-extracted data (or "NMReDATA") includes: Chemical shift,scalar
      coupling, 2D correlation, assignment, etc. Find more in the paper at https://doi.org/10.1002/mrc.4527.'
    meaning: edam:format_3906
    title: NMReDATA
  edam:format_3909:
    text: edam:format_3909
    description: BpForms is a string format for concretely representing the primary
      structures of biopolymers, including DNA, RNA, and proteins that include non-canonical
      nucleic and amino acids. See https://www.bpforms.org for more information.
    meaning: edam:format_3909
    title: BpForms
  edam:format_3910:
    text: edam:format_3910
    description: 'Format of trr files that contain the trajectory of a simulation
      experiment used by GROMACS.

      The first 4 bytes of any trr file containing 1993. See https://github.com/galaxyproject/galaxy/pull/6597/files#diff-409951594551183dbf886e24de6cb129R760'
    meaning: edam:format_3910
    title: trr
  edam:format_3911:
    text: edam:format_3911
    description: Mash sketch is a format for sequence / sequence checksum information.
      To make a sketch, each k-mer in a sequence is hashed, which creates a pseudo-random
      identifier. By sorting these hashes, a small subset from the top of the sorted
      list can represent the entire sequence.
    meaning: edam:format_3911
    title: msh
  edam:format_3913:
    text: edam:format_3913
    description: The Loom file format is based on HDF5, a standard for storing large
      numerical datasets. The Loom format is designed to efficiently hold large omics
      datasets. Typically, such data takes the form of a large matrix of numbers,
      along with metadata for the rows and columns.
    meaning: edam:format_3913
    title: Loom
  edam:format_3915:
    text: edam:format_3915
    description: The Zarr format is an implementation of chunked, compressed, N-dimensional
      arrays for storing data.
    meaning: edam:format_3915
    title: Zarr
  edam:format_3916:
    text: edam:format_3916
    description: The Matrix Market matrix (MTX) format stores numerical or pattern
      matrices in a dense (array format) or sparse (coordinate format) representation.
    meaning: edam:format_3916
    title: MTX
  edam:format_3951:
    text: edam:format_3951
    description: 'BcForms is a format for abstractly describing the molecular structure
      (atoms and bonds) of macromolecular complexes as a collection of subunits and
      crosslinks. Each subunit can be described with BpForms (http://edamontology.org/format_3909)
      or SMILES (http://edamontology.org/data_2301). BcForms uses an ontology of crosslinks
      to abstract the chemical details of crosslinks from the descriptions of complexes
      (see https://bpforms.org/crosslink.html).

      BcForms is related to http://edamontology.org/format_3909. (BcForms uses BpForms
      to describe subunits which are DNA, RNA, or protein polymers.) However, that
      format isn''t the parent of BcForms. BcForms is similarly related to SMILES
      (http://edamontology.org/data_2301).'
    meaning: edam:format_3951
    title: BcForms
  edam:format_3956:
    text: edam:format_3956
    description: 'N-Quads is a line-based, plain text format for encoding an RDF dataset.
      It includes information about the graph each triple belongs to.

      N-Quads should not be confused with N-Triples which does not contain graph information.'
    meaning: edam:format_3956
    title: N-Quads
  edam:format_3969:
    text: edam:format_3969
    description: Vega is a visualization grammar, a declarative language for creating,
      saving, and sharing interactive visualization designs. With Vega, you can describe
      the visual appearance and interactive behavior of a visualization in a JSON
      format, and generate web-based views using Canvas or SVG.
    meaning: edam:format_3969
    title: Vega
  edam:format_3970:
    text: edam:format_3970
    description: Vega-Lite is a high-level grammar of interactive graphics. It provides
      a concise JSON syntax for rapidly generating visualizations to support analysis.
      Vega-Lite specifications can be compiled to Vega specifications.
    meaning: edam:format_3970
    title: Vega-lite
  edam:format_3971:
    text: edam:format_3971
    description: A model description language for computational neuroscience.
    meaning: edam:format_3971
    title: NeuroML
  edam:format_3972:
    text: edam:format_3972
    description: BioNetGen is a format for the specification and simulation of rule-based
      models of biochemical systems, including signal transduction, metabolic, and
      genetic regulatory networks.
    meaning: edam:format_3972
    title: BNGL
  edam:format_3973:
    text: edam:format_3973
    description: A Docker image is a file, comprised of multiple layers, that is used
      to execute code in a Docker container. An image is essentially built from the
      instructions for a complete and executable version of an application, which
      relies on the host OS kernel.
    meaning: edam:format_3973
    title: Docker image
  edam:format_3975:
    text: edam:format_3975
    description: Graphical Fragment Assembly captures sequence graphs as the product
      of an assembly, a representation of variation in genomes, splice graphs in genes,
      or even overlap between reads from long-read sequencing technology.
    meaning: edam:format_3975
    title: GFA 1
  edam:format_3976:
    text: edam:format_3976
    description: Graphical Fragment Assembly captures sequence graphs as the product
      of an assembly, a representation of variation in genomes, splice graphs in genes,
      or even overlap between reads from long-read sequencing technology. GFA2 is
      an update of GFA1 which is not compatible with GFA1.
    meaning: edam:format_3976
    title: GFA 2
  edam:format_3977:
    text: edam:format_3977
    description: ObjTables is a toolkit for creating re-usable datasets that are both
      human and machine-readable, combining the ease of spreadsheets (e.g., Excel
      workbooks) with the rigor of schemas (classes, their attributes, the type of
      each attribute, and the possible relationships between instances of classes).
      ObjTables consists of a format for describing schemas for spreadsheets, numerous
      data types for science, a syntax for indicating the class and attribute represented
      by each table and column in a workbook, and software for using schemas to rigorously
      validate, merge, split, compare, and revision datasets.
    meaning: edam:format_3977
    title: ObjTables
  edam:format_3978:
    text: edam:format_3978
    description: The CONTIG format used for output of the SOAPdenovo alignment program.
      It contains contig sequences generated without using mate pair information.
    meaning: edam:format_3978
    title: CONTIG
  edam:format_3979:
    text: edam:format_3979
    description: WEGO native format used by the Web Gene Ontology Annotation Plot
      application.   Tab-delimited format with gene names and others GO IDs (columns)
      with one annotation record per line.
    meaning: edam:format_3979
    title: WEGO
  edam:format_3980:
    text: edam:format_3980
    description: 'For example a 1kb transcript with 1000 alignments in a sample of
      10 million reads (out of which 8 million reads can be mapped) will have RPKM
      = 1000/(1 * 8) = 125

      Tab-delimited format for gene expression levels table, calculated as Reads Per
      Kilobase per Million (RPKM) mapped reads.'
    meaning: edam:format_3980
    title: RPKM
  edam:format_3981:
    text: edam:format_3981
    description: 'For example a 1kb transcript with 1000 alignments in a sample of
      10 million reads (out of which 8 million reads can be mapped) will have RPKM
      = 1000/(1 * 8) = 125

      TAR archive file format generated by the Unix-based utility tar.'
    meaning: edam:format_3981
    title: TAR format
  edam:format_3982:
    text: edam:format_3982
    description: The CHAIN format describes a pairwise alignment that allow gaps in
      both sequences simultaneously and is used by the UCSC Genome Browser.
    meaning: edam:format_3982
    title: CHAIN
  edam:format_3983:
    text: edam:format_3983
    description: The NET file format is used to describe the data that underlie the
      net alignment annotations in the UCSC Genome Browser.
    meaning: edam:format_3983
    title: NET
  edam:format_3984:
    text: edam:format_3984
    description: Format of QMAP files generated for methylation data from an internal
      BGI pipeline.
    meaning: edam:format_3984
    title: QMAP
  edam:format_3985:
    text: edam:format_3985
    description: An emerging format for high-level Galaxy workflow description.
    meaning: edam:format_3985
    title: gxformat2
  edam:format_3986:
    text: edam:format_3986
    description: The proprietary native video format of various Microsoft programs
      such as Windows Media Player.
    meaning: edam:format_3986
    title: WMV
  edam:format_3987:
    text: edam:format_3987
    description: 'A ZIP file may contain one or more files or directories that may
      have been compressed.

      ZIP is an archive file format that supports lossless data compression.'
    meaning: edam:format_3987
    title: ZIP format
  edam:format_3988:
    text: edam:format_3988
    description: 'LSM files are the default data export for the Zeiss LSM series confocal
      microscopes (e.g. LSM 510, LSM 710). In addition to the image data, LSM files
      contain most imaging settings.

      Zeiss'' proprietary image format based on TIFF.'
    meaning: edam:format_3988
    title: LSM
  edam:format_3989:
    text: edam:format_3989
    description: GNU zip compressed file format common to Unix-based operating systems.
    meaning: edam:format_3989
    title: GZIP format
  edam:format_3990:
    text: edam:format_3990
    description: Audio Video Interleaved (AVI) format is a multimedia container format
      for AVI files, that allows synchronous audio-with-video playback.
    meaning: edam:format_3990
    title: AVI
  edam:format_3991:
    text: edam:format_3991
    description: A declaration file format for UCSC browsers track dataset display
      charateristics.
    meaning: edam:format_3991
    title: TrackDB
  edam:format_3992:
    text: edam:format_3992
    description: Compact Idiosyncratic Gapped Alignment Report format is a compressed
      (run-length encoded) pairwise alignment format. It is useful for representing
      long (e.g. genomic) pairwise alignments.
    meaning: edam:format_3992
    title: CIGAR format
  edam:format_3993:
    text: edam:format_3993
    description: STL is a file format native to the stereolithography CAD software
      created by 3D Systems. The format is used to save and share surface-rendered
      3D images and also for 3D printing.
    meaning: edam:format_3993
    title: Stereolithography format
  edam:format_3994:
    text: edam:format_3994
    description: U3D (Universal 3D) is a compressed file format and data structure
      for 3D computer graphics. It contains 3D model information such as triangle
      meshes, lighting, shading, motion data, lines and points with color and structure.
    meaning: edam:format_3994
    title: U3D
  edam:format_3995:
    text: edam:format_3995
    description: 'Bitmap image format used for storing textures.

      Texture files can create the appearance of different surfaces and can be applied
      to both 2D and 3D objects. Note the file extension .tex is also used for LaTex
      documents which are a completely different format and they are NOT interchangeable.'
    meaning: edam:format_3995
    title: Texture file format
  edam:format_3996:
    text: edam:format_3996
    description: Format for scripts writtenin Python - a widely used high-level programming
      language for general-purpose programming.
    meaning: edam:format_3996
    title: Python script
  edam:format_3997:
    text: edam:format_3997
    description: A digital multimedia container format most commonly used to store
      video and audio.
    meaning: edam:format_3997
    title: MPEG-4
  edam:format_3998:
    text: edam:format_3998
    description: Format for scripts written in Perl - a family of high-level, general-purpose,
      interpreted, dynamic programming languages.
    meaning: edam:format_3998
    title: Perl script
  edam:format_3999:
    text: edam:format_3999
    description: Format for scripts written in the R language - an open source programming
      language and software environment for statistical computing and graphics that
      is supported by the R Foundation for Statistical Computing.
    meaning: edam:format_3999
    title: R script
  edam:format_4000:
    text: edam:format_4000
    description: A file format for making dynamic documents (R Markdown scripts) with
      the R language.
    meaning: edam:format_4000
    title: R markdown
  edam:format_4002:
    text: edam:format_4002
    description: Format used by Python pickle module for serializing and de-serializing
      a Python object structure.
    meaning: edam:format_4002
    title: pickle
  edam:format_4003:
    text: edam:format_4003
    description: The standard binary file format used by NumPy - a fundamental package
      for scientific computing with Python - for persisting a single arbitrary NumPy
      array on disk. The format stores all of the shape and dtype information necessary
      to reconstruct the array correctly.
    meaning: edam:format_4003
    title: NumPy format
  edam:format_4004:
    text: edam:format_4004
    description: Format of repertoire (archive) files that can be read by SimToolbox
      (a MATLAB toolbox for structured illumination fluorescence microscopy) or alternatively
      extracted with zip file archiver software.
    meaning: edam:format_4004
    title: SimTools repertoire file format
  edam:format_4005:
    text: edam:format_4005
    description: A configuration file used by various programs to store settings that
      are specific to their respective software.
    meaning: edam:format_4005
    title: Configuration file format
  edam:format_4006:
    text: edam:format_4006
    description: Format used by the Zstandard real-time compression algorithm.
    meaning: edam:format_4006
    title: Zstandard format
  edam:format_4007:
    text: edam:format_4007
    description: The file format for MATLAB scripts or functions.
    meaning: edam:format_4007
    title: MATLAB script
  edam:format_4015:
    text: edam:format_4015
    description: A data format for specifying parameter estimation problems in systems
      biology.
    meaning: edam:format_4015
    title: PEtab
  edam:format_4018:
    text: edam:format_4018
    description: Genomic Variant Call Format (gVCF) is a version of VCF that includes
      not only the positions that are variant when compared to a reference genome,
      but also the non-variant positions as ranges, including metrics of confidence
      that the positions in the range are actually non-variant e.g. minimum read-depth
      and genotype quality.
    meaning: edam:format_4018
    title: gVCF
  edam:format_4023:
    text: edam:format_4023
    description: Chemical Markup Language (CML) is an XML-based format for encoding
      detailed information about a wide range of chemical concepts.
    meaning: edam:format_4023
    title: cml
  edam:format_4024:
    text: edam:format_4024
    description: Crystallographic Information File (CIF) is a data exchange standard
      file format for Crystallographic Information and related Structural Science
      data.
    meaning: edam:format_4024
    title: cif
  edam:format_4025:
    text: edam:format_4025
    description: Format for describing the capabilities of a biosimulation tool including
      the modeling frameworks, simulation algorithms, and modeling formats that it
      supports, as well as metadata such as a list of the interfaces, programming
      languages, and operating systems supported by the tool; a link to download the
      tool; a list of the authors of the tool; and the license to the tool.
    meaning: edam:format_4025
    title: BioSimulators format for the specifications of biosimulation tools
  edam:format_4026:
    text: edam:format_4026
    description: Outlines the syntax and semantics of the input and output arguments
      for command-line interfaces for biosimulation tools.
    meaning: edam:format_4026
    title: BioSimulators standard for command-line interfaces for biosimulation tools
  edam:format_4035:
    text: edam:format_4035
    description: Data format derived from the standard PDB format, which enables user
      to incorporate parameters for charge and radius to the existing PDB data file.
    meaning: edam:format_4035
    title: PQR
  edam:format_4036:
    text: edam:format_4036
    description: Data format used in AutoDock 4 for storing atomic coordinates, partial
      atomic charges and AutoDock atom types for both receptors and ligands.
    meaning: edam:format_4036
    title: PDBQT
  edam:format_4039:
    text: edam:format_4039
    description: 'MSP is a data format for mass spectrometry data.

      NIST Text file format for storing MS∕MS spectra (m∕z and intensity of mass peaks)
      along with additional annotations for each spectrum. A single MSP file can thus
      contain single or multiple spectra. This format is frequently used to share
      spectra libraries.'
    meaning: edam:format_4039
    title: MSP
  edam:format_4041:
    text: edam:format_4041
    description: A standard for DMPs developed by the Research Data Alliance
    meaning: edam:format_4041
    title: maDMP
  edam:format_4048:
    text: edam:format_4048
    description: 'Nextflow is a workflow system for creating scalable, portable, and
      reproducible workflows.

      This term covers all versions of Nextflow language specifications.'
    meaning: edam:format_4048
    title: Nextflow
  edam:format_4049:
    text: edam:format_4049
    description: The Snakemake workflow management system is a tool to create reproducible
      and scalable data analyses.
    meaning: edam:format_4049
    title: Snakemake
  edam:format_4050:
    text: edam:format_4050
    description: Sample and Data Relationship File for a proteomics experiment.
    meaning: edam:format_4050
    title: SDRF
  edam:format_4058:
    text: edam:format_4058
    description: 'The reference implementation of mzTab-M in Java is https://github.com/lifs-tools/jmzTab-m.

      mzTab-M is a light-weight, tab-delimited format for mass spectrometry-based
      chemical profiling data, including metabolomics.

      mzTab-M is alternatively named mzTab 2.0, but in 2025 there is a draft version
      2.1 of mzTab-M.

      mzTab-M is not compatible with mzTab (also named mzTab 1.0, for proteomics,
      http://edamontology.org/format_3681). Note: the repository, website, and file
      extension are the same for both formats.'
    meaning: edam:format_4058
    title: mzTab-M
  edam:format_4059:
    text: edam:format_4059
    description: mzTab-L is a light-weight, tab-delimited format for mass spectrometry-based
      lipidomics data. It is a compatible version of mzTab-M, with additional rules
      and information standard (reporting guidelines).
    meaning: edam:format_4059
    title: mzTab-L
reachable_from:
  source_ontology: bioregistry:edam
  source_nodes:
  - edam:format_1915
  relationship_types:
  - rdfs:subClassOf
  is_direct: false
  include_self: true
  traverse_up: false