Enum: EnumEDAMFormats
Data formats from the EDAM ontology.
URI: cam:EnumEDAMFormats
Permissible Values
| Value | Meaning | Description |
|---|---|---|
| edam:format_1196 | edam:format_1196 | Chemical structure specified in Simplified Molecular Input Line Entry System ... |
| edam:format_1197 | edam:format_1197 | Chemical structure specified in IUPAC International Chemical Identifier (InCh... |
| edam:format_1198 | edam:format_1198 | Chemical structure specified by Molecular Formula (MF), including a count of ... |
| edam:format_1199 | edam:format_1199 | The InChIKey (hashed InChI) is a fixed length (25 character) condensed digita... |
| edam:format_1200 | edam:format_1200 | SMILES ARbitrary Target Specification (SMARTS) format for chemical structure ... |
| edam:format_1206 | edam:format_1206 | Alphabet for a molecular sequence with possible unknown positions but without... |
| edam:format_1207 | edam:format_1207 | Alphabet for a nucleotide sequence with possible ambiguity, unknown positions... |
| edam:format_1208 | edam:format_1208 | Alphabet for a protein sequence with possible ambiguity, unknown positions an... |
| edam:format_1209 | edam:format_1209 | Alphabet for the consensus of two or more molecular sequences |
| edam:format_1210 | edam:format_1210 | Alphabet for a nucleotide sequence with possible ambiguity and unknown positi... |
| edam:format_1211 | edam:format_1211 | Alphabet for a nucleotide sequence (characters ACGTU only) with possible unkn... |
| edam:format_1212 | edam:format_1212 | Alphabet for a DNA sequence with possible ambiguity, unknown positions and no... |
| edam:format_1213 | edam:format_1213 | Alphabet for an RNA sequence with possible ambiguity, unknown positions and n... |
| edam:format_1214 | edam:format_1214 | Alphabet for a DNA sequence (characters ACGT only) with possible unknown posi... |
| edam:format_1215 | edam:format_1215 | Alphabet for a DNA sequence with possible ambiguity and unknown positions but... |
| edam:format_1216 | edam:format_1216 | Alphabet for an RNA sequence (characters ACGU only) with possible unknown pos... |
| edam:format_1217 | edam:format_1217 | Alphabet for an RNA sequence with possible ambiguity and unknown positions bu... |
| edam:format_1218 | edam:format_1218 | Alphabet for any protein sequence with possible unknown positions but without... |
| edam:format_1219 | edam:format_1219 | Alphabet for any protein sequence with possible ambiguity and unknown positio... |
| edam:format_1248 | edam:format_1248 | Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank... |
| edam:format_1295 | edam:format_1295 | Report format for tandem repeats in a nucleotide sequence (format generated b... |
| edam:format_1296 | edam:format_1296 | Report format for inverted repeats in a nucleotide sequence (format generated... |
| edam:format_1297 | edam:format_1297 | Report format for tandem repeats in a sequence (an EMBOSS report format) |
| edam:format_1316 | edam:format_1316 | Format of a report on exon-intron structure generated by EMBOSS est2genome |
| edam:format_1318 | edam:format_1318 | Report format for restriction enzyme recognition sites used by EMBOSS restric... |
| edam:format_1319 | edam:format_1319 | Report format for restriction enzyme recognition sites used by EMBOSS restove... |
| edam:format_1320 | edam:format_1320 | Report format for restriction enzyme recognition sites used by REBASE databas... |
| edam:format_1332 | edam:format_1332 | Format of results of a sequence database search using FASTA |
| edam:format_1333 | edam:format_1333 | Format of results of a sequence database search using some variant of BLAST |
| edam:format_1334 | edam:format_1334 | Format of results of a sequence database search using some variant of MSPCrun... |
| edam:format_1335 | edam:format_1335 | Format of results of a sequence database search using some variant of Smith W... |
| edam:format_1336 | edam:format_1336 | Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain clas... |
| edam:format_1337 | edam:format_1337 | Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with li... |
| edam:format_1341 | edam:format_1341 | Results format for searches of the InterPro database |
| edam:format_1342 | edam:format_1342 | Format of results of a search of the InterPro database showing matches of que... |
| edam:format_1343 | edam:format_1343 | Format of results of a search of the InterPro database showing matches betwee... |
| edam:format_1349 | edam:format_1349 | Dirichlet distribution HMMER format |
| edam:format_1350 | edam:format_1350 | Dirichlet distribution MEME format |
| edam:format_1351 | edam:format_1351 | Format of a report from the HMMER package on the emission and transition coun... |
| edam:format_1356 | edam:format_1356 | Format of a regular expression pattern from the Prosite database |
| edam:format_1357 | edam:format_1357 | Format of an EMBOSS sequence pattern |
| edam:format_1360 | edam:format_1360 | A motif in the format generated by the MEME program |
| edam:format_1366 | edam:format_1366 | Sequence profile (sequence classifier) format used in the PROSITE database |
| edam:format_1367 | edam:format_1367 | A profile (sequence classifier) in the format used in the JASPAR database |
| edam:format_1369 | edam:format_1369 | Format of the model of random sequences used by MEME |
| edam:format_1370 | edam:format_1370 | Format of a hidden Markov model representation used by the HMMER package |
| edam:format_1391 | edam:format_1391 | FASTA-style format for multiple sequences aligned by HMMER package to an HMM |
| edam:format_1392 | edam:format_1392 | Format of multiple sequences aligned by DIALIGN package |
| edam:format_1393 | edam:format_1393 | EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment... |
| edam:format_1419 | edam:format_1419 | Format for alignment of molecular sequences to MEME profiles (position-depend... |
| edam:format_1421 | edam:format_1421 | Format used by the HMMER package for an alignment of a sequence against a hid... |
| edam:format_1422 | edam:format_1422 | Format used by the HMMER package for of an alignment of a hidden Markov model... |
| edam:format_1423 | edam:format_1423 | Format of PHYLIP phylogenetic distance matrix data |
| edam:format_1424 | edam:format_1424 | Dendrogram (tree file) format generated by ClustalW |
| edam:format_1425 | edam:format_1425 | Raw data file format used by Phylip from which a phylogenetic tree is directl... |
| edam:format_1430 | edam:format_1430 | PHYLIP file format for continuous quantitative character data |
| edam:format_1432 | edam:format_1432 | PHYLIP file format for phylogenetics character frequency data |
| edam:format_1433 | edam:format_1433 | Format of PHYLIP discrete states data |
| edam:format_1434 | edam:format_1434 | Format of PHYLIP cliques data |
| edam:format_1435 | edam:format_1435 | Phylogenetic tree data format used by the PHYLIP program |
| edam:format_1436 | edam:format_1436 | The format of an entry from the TreeBASE database of phylogenetic data |
| edam:format_1437 | edam:format_1437 | The format of an entry from the TreeFam database of phylogenetic data |
| edam:format_1445 | edam:format_1445 | Format for distances, such as Branch Score distance, between two or more phyl... |
| edam:format_1454 | edam:format_1454 | Format of an entry from the DSSP database (Dictionary of Secondary Structure ... |
| edam:format_1455 | edam:format_1455 | Entry format of the HSSP database (Homology-derived Secondary Structure in Pr... |
| edam:format_1457 | edam:format_1457 | Format of RNA secondary structure in dot-bracket notation, originally generat... |
| edam:format_1458 | edam:format_1458 | Format of local RNA secondary structure components with free energy values, g... |
| edam:format_1475 | edam:format_1475 | Format of an entry (or part of an entry) from the PDB database |
| edam:format_1476 | edam:format_1476 | Entry format of PDB database in PDB format |
| edam:format_1477 | edam:format_1477 | Entry format of PDB database in mmCIF format |
| edam:format_1478 | edam:format_1478 | Entry format of PDB database in PDBML (XML) format |
| edam:format_1504 | edam:format_1504 | Amino acid index format used by the AAindex database |
| edam:format_1551 | edam:format_1551 | Format of output of the Pcons Model Quality Assessment Program (MQAP) |
| edam:format_1552 | edam:format_1552 | Format of output of the ProQ protein model quality predictor |
| edam:format_1582 | edam:format_1582 | A report format for the kinetics of enzyme-catalysed reaction(s) in a format ... |
| edam:format_1627 | edam:format_1627 | Report format on PCR primers and hybridisation oligos as generated by Whitehe... |
| edam:format_1628 | edam:format_1628 | A format of raw sequence read data from an Applied Biosystems sequencing mach... |
| edam:format_1629 | edam:format_1629 | Format of MIRA sequence trace information file |
| edam:format_1630 | edam:format_1630 | Common Assembly Format (CAF) |
| edam:format_1631 | edam:format_1631 | Sequence assembly project file EXP format |
| edam:format_1632 | edam:format_1632 | Staden Chromatogram Files format (SCF) of base-called sequence reads, qualiti... |
| edam:format_1633 | edam:format_1633 | PHD sequence trace format to store serialised chromatogram data (reads) |
| edam:format_1637 | edam:format_1637 | Format of Affymetrix data file of raw image data |
| edam:format_1638 | edam:format_1638 | Format of Affymetrix data file of information about (raw) expression levels o... |
| edam:format_1639 | edam:format_1639 | Format of affymetrix gene cluster files (hc-genes |
| edam:format_1641 | edam:format_1641 | Affymetrix data file format for information about experimental conditions and... |
| edam:format_1644 | edam:format_1644 | Format of Affymetrix data file of information about (normalised) expression l... |
| edam:format_1665 | edam:format_1665 | Format of Taverna workflows |
| edam:format_1705 | edam:format_1705 | The format of an entry from the HET group dictionary (HET groups from PDB fil... |
| edam:format_1734 | edam:format_1734 | Format of bibliographic reference as used by the PubMed database |
| edam:format_1735 | edam:format_1735 | Format for abstracts of scientific articles from the Medline database |
| edam:format_1736 | edam:format_1736 | CiteXplore 'core' citation format including title, journal, authors and abstr... |
| edam:format_1737 | edam:format_1737 | CiteXplore 'all' citation format includes all known details such as Mesh term... |
| edam:format_1739 | edam:format_1739 | Article format of the PubMed Central database |
| edam:format_1740 | edam:format_1740 | The format of iHOP (Information Hyperlinked over Proteins) text-mining result |
| edam:format_1741 | edam:format_1741 | OSCAR format of annotated chemical text |
| edam:format_1861 | edam:format_1861 | Map of a plasmid (circular DNA) in PlasMapper TextMap format |
| edam:format_1910 | edam:format_1910 | Phylogenetic tree Newick (text) format |
| edam:format_1911 | edam:format_1911 | Phylogenetic tree TreeCon (text) format |
| edam:format_1912 | edam:format_1912 | Phylogenetic tree Nexus (text) format |
| edam:format_1919 | edam:format_1919 | Data format for a molecular sequence record |
| edam:format_1920 | edam:format_1920 | Data format for molecular sequence feature information |
| edam:format_1921 | edam:format_1921 | Data format for molecular sequence alignment information |
| edam:format_1923 | edam:format_1923 | ACEDB sequence format |
| edam:format_1925 | edam:format_1925 | Codata entry format |
| edam:format_1926 | edam:format_1926 | Fasta format variant with database name before ID |
| edam:format_1927 | edam:format_1927 | EMBL entry format |
| edam:format_1928 | edam:format_1928 | Staden experiment file format |
| edam:format_1929 | edam:format_1929 | FASTA format including NCBI-style IDs |
| edam:format_1930 | edam:format_1930 | FASTQ short read format ignoring quality scores |
| edam:format_1931 | edam:format_1931 | FASTQ Illumina 1 |
| edam:format_1932 | edam:format_1932 | FASTQ short read format with phred quality |
| edam:format_1933 | edam:format_1933 | FASTQ Solexa/Illumina 1 |
| edam:format_1934 | edam:format_1934 | Fitch program format |
| edam:format_1935 | edam:format_1935 | GCG sequence file format |
| edam:format_1936 | edam:format_1936 | Genbank entry format |
| edam:format_1937 | edam:format_1937 | Genpept protein entry format |
| edam:format_1938 | edam:format_1938 | GFF feature file format with sequence in the header |
| edam:format_1939 | edam:format_1939 | GFF3 feature file format with sequence |
| edam:format_1940 | edam:format_1940 | FASTA sequence format including NCBI-style GIs |
| edam:format_1941 | edam:format_1941 | Hennig86 output sequence format |
| edam:format_1942 | edam:format_1942 | Intelligenetics sequence format |
| edam:format_1943 | edam:format_1943 | Intelligenetics sequence format (strict version) |
| edam:format_1944 | edam:format_1944 | Jackknifer interleaved and non-interleaved sequence format |
| edam:format_1945 | edam:format_1945 | Mase program sequence format |
| edam:format_1946 | edam:format_1946 | Mega interleaved and non-interleaved sequence format |
| edam:format_1947 | edam:format_1947 | GCG MSF (multiple sequence file) file format |
| edam:format_1948 | edam:format_1948 | NBRF/PIR entry sequence format |
| edam:format_1949 | edam:format_1949 | Nexus/paup interleaved sequence format |
| edam:format_1950 | edam:format_1950 | PDB sequence format (ATOM lines) |
| edam:format_1951 | edam:format_1951 | PDB nucleotide sequence format (ATOM lines) |
| edam:format_1952 | edam:format_1952 | PDB nucleotide sequence format (SEQRES lines) |
| edam:format_1953 | edam:format_1953 | PDB sequence format (SEQRES lines) |
| edam:format_1954 | edam:format_1954 | Plain old FASTA sequence format (unspecified format for IDs) |
| edam:format_1957 | edam:format_1957 | Raw sequence format with no non-sequence characters |
| edam:format_1958 | edam:format_1958 | Refseq protein entry sequence format |
| edam:format_1960 | edam:format_1960 | Staden suite sequence format |
| edam:format_1961 | edam:format_1961 | Stockholm multiple sequence alignment format (used by Pfam and Rfam) |
| edam:format_1962 | edam:format_1962 | DNA strider output sequence format |
| edam:format_1963 | edam:format_1963 | UniProtKB entry sequence format |
| edam:format_1964 | edam:format_1964 | Plain text sequence format (essentially unformatted) |
| edam:format_1966 | edam:format_1966 | NCBI ASN |
| edam:format_1967 | edam:format_1967 | DAS sequence (XML) format (any type) |
| edam:format_1968 | edam:format_1968 | DAS sequence (XML) format (nucleotide-only) |
| edam:format_1969 | edam:format_1969 | EMBOSS debugging trace sequence format of full internal data content |
| edam:format_1970 | edam:format_1970 | Jackknifer output sequence non-interleaved format |
| edam:format_1972 | edam:format_1972 | NCBI FASTA sequence format with NCBI-style IDs |
| edam:format_1973 | edam:format_1973 | Nexus/paup non-interleaved sequence format |
| edam:format_1974 | edam:format_1974 | General Feature Format (GFF) of sequence features |
| edam:format_1975 | edam:format_1975 | Generic Feature Format version 3 (GFF3) of sequence features |
| edam:format_1978 | edam:format_1978 | DAS GFF (XML) feature format |
| edam:format_1979 | edam:format_1979 | EMBOSS debugging trace feature format of full internal data content |
| edam:format_1982 | edam:format_1982 | ClustalW format for (aligned) sequences |
| edam:format_1983 | edam:format_1983 | EMBOSS alignment format for debugging trace of full internal data content |
| edam:format_1984 | edam:format_1984 | Fasta format for (aligned) sequences |
| edam:format_1985 | edam:format_1985 | Pearson MARKX0 alignment format |
| edam:format_1986 | edam:format_1986 | Pearson MARKX1 alignment format |
| edam:format_1987 | edam:format_1987 | Pearson MARKX10 alignment format |
| edam:format_1988 | edam:format_1988 | Pearson MARKX2 alignment format |
| edam:format_1989 | edam:format_1989 | Pearson MARKX3 alignment format |
| edam:format_1990 | edam:format_1990 | Alignment format for start and end of matches between sequence pairs |
| edam:format_1991 | edam:format_1991 | Mega format for (typically aligned) sequences |
| edam:format_1992 | edam:format_1992 | Mega non-interleaved format for (typically aligned) sequences |
| edam:format_1996 | edam:format_1996 | EMBOSS simple sequence pairwise alignment format |
| edam:format_1997 | edam:format_1997 | Phylip format for (aligned) sequences |
| edam:format_1998 | edam:format_1998 | Phylip non-interleaved format for (aligned) sequences |
| edam:format_1999 | edam:format_1999 | Alignment format for score values for pairs of sequences |
| edam:format_2000 | edam:format_2000 | SELEX format for (aligned) sequences |
| edam:format_2001 | edam:format_2001 | EMBOSS simple multiple alignment format |
| edam:format_2002 | edam:format_2002 | Simple multiple sequence (alignment) format for SRS |
| edam:format_2003 | edam:format_2003 | Simple sequence pair (alignment) format for SRS |
| edam:format_2004 | edam:format_2004 | T-Coffee program alignment format |
| edam:format_2005 | edam:format_2005 | Treecon format for (aligned) sequences |
| edam:format_2006 | edam:format_2006 | Data format for a phylogenetic tree |
| edam:format_2013 | edam:format_2013 | Data format for a biological pathway or network |
| edam:format_2014 | edam:format_2014 | Data format for a sequence-profile alignment |
| edam:format_2017 | edam:format_2017 | Data format for an amino acid index |
| edam:format_2020 | edam:format_2020 | Data format for a full-text scientific article |
| edam:format_2021 | edam:format_2021 | Data format of a report from text mining |
| edam:format_2027 | edam:format_2027 | Data format for reports on enzyme kinetics |
| edam:format_2030 | edam:format_2030 | Format of a report on a chemical compound |
| edam:format_2031 | edam:format_2031 | Format of a report on a particular locus, gene, gene system or groups of gene... |
| edam:format_2032 | edam:format_2032 | Format of a workflow |
| edam:format_2033 | edam:format_2033 | Data format for a molecular tertiary structure |
| edam:format_2035 | edam:format_2035 | Text format of a chemical formula |
| edam:format_2036 | edam:format_2036 | Format of raw (unplotted) phylogenetic data |
| edam:format_2037 | edam:format_2037 | Format of phylogenetic continuous quantitative character data |
| edam:format_2038 | edam:format_2038 | Format of phylogenetic discrete states data |
| edam:format_2039 | edam:format_2039 | Format of phylogenetic cliques data |
| edam:format_2040 | edam:format_2040 | Format of phylogenetic invariants data |
| edam:format_2049 | edam:format_2049 | Format for phylogenetic tree distance data |
| edam:format_2052 | edam:format_2052 | Format for reports on a protein family |
| edam:format_2054 | edam:format_2054 | Format for molecular interaction data |
| edam:format_2055 | edam:format_2055 | Format for sequence assembly data |
| edam:format_2056 | edam:format_2056 | Format for information about a microarray experimental per se (not the data g... |
| edam:format_2057 | edam:format_2057 | Format for sequence trace data (i |
| edam:format_2058 | edam:format_2058 | Format of a file of gene expression data, e |
| edam:format_2060 | edam:format_2060 | Format of a map of (typically one) molecular sequence annotated with features |
| edam:format_2061 | edam:format_2061 | Format of a report on PCR primers or hybridisation oligos in a nucleic acid s... |
| edam:format_2062 | edam:format_2062 | Format of a report of general information about a specific protein |
| edam:format_2064 | edam:format_2064 | Format of a matrix of 3D-1D scores (amino acid environment probabilities) |
| edam:format_2065 | edam:format_2065 | Format of a report on the quality of a protein three-dimensional model |
| edam:format_2066 | edam:format_2066 | Format of a report on sequence hits and associated data from searching a sequ... |
| edam:format_2067 | edam:format_2067 | Format of a matrix of genetic distances between molecular sequences |
| edam:format_2068 | edam:format_2068 | Format of a sequence motif |
| edam:format_2069 | edam:format_2069 | Format of a sequence profile |
| edam:format_2072 | edam:format_2072 | Format of a hidden Markov model |
| edam:format_2074 | edam:format_2074 | Data format of a dirichlet distribution |
| edam:format_2075 | edam:format_2075 | Data format for the emission and transition counts of a hidden Markov model |
| edam:format_2076 | edam:format_2076 | Format for secondary structure (predicted or real) of an RNA molecule |
| edam:format_2077 | edam:format_2077 | Format for secondary structure (predicted or real) of a protein molecule |
| edam:format_2078 | edam:format_2078 | Format used to specify range(s) of sequence positions |
| edam:format_2094 | edam:format_2094 | Alphabet for molecular sequence with possible unknown positions but without n... |
| edam:format_2095 | edam:format_2095 | Alphabet for a molecular sequence with possible unknown positions but possibl... |
| edam:format_2096 | edam:format_2096 | Alphabet for a molecular sequence with possible unknown positions but without... |
| edam:format_2097 | edam:format_2097 | Alphabet for a molecular sequence with possible unknown positions and possibl... |
| edam:format_2155 | edam:format_2155 | Format used for map of repeats in molecular (typically nucleotide) sequences |
| edam:format_2158 | edam:format_2158 | Format used for report on restriction enzyme recognition sites in nucleotide ... |
| edam:format_2170 | edam:format_2170 | Format used for clusters of molecular sequences |
| edam:format_2171 | edam:format_2171 | Format used for clusters of protein sequences |
| edam:format_2172 | edam:format_2172 | Format used for clusters of nucleotide sequences |
| edam:format_2181 | edam:format_2181 | A text format resembling EMBL entry format |
| edam:format_2182 | edam:format_2182 | A text format resembling FASTQ short read format |
| edam:format_2183 | edam:format_2183 | XML format for EMBL entries |
| edam:format_2184 | edam:format_2184 | Specific XML format for EMBL entries (only uses certain sections) |
| edam:format_2185 | edam:format_2185 | INSDSeq provides the elements of a sequence as presented in the GenBank/EMBL/... |
| edam:format_2186 | edam:format_2186 | Geneseq sequence format |
| edam:format_2187 | edam:format_2187 | A text sequence format resembling uniprotkb entry format |
| edam:format_2194 | edam:format_2194 | Abstract format used by MedLine database |
| edam:format_2195 | edam:format_2195 | Format used for ontologies |
| edam:format_2196 | edam:format_2196 | A serialisation format conforming to the Open Biomedical Ontologies (OBO) mod... |
| edam:format_2197 | edam:format_2197 | A serialisation format conforming to the Web Ontology Language (OWL) model |
| edam:format_2200 | edam:format_2200 | A text format resembling FASTA format |
| edam:format_2204 | edam:format_2204 | An XML format for EMBL entries |
| edam:format_2205 | edam:format_2205 | A text format resembling GenBank entry (plain text) format |
| edam:format_2206 | edam:format_2206 | Text format for a sequence feature table |
| edam:format_2304 | edam:format_2304 | Entry format (XML) for the STRING database of protein interaction |
| edam:format_2305 | edam:format_2305 | GFF feature format (of indeterminate version) |
| edam:format_2306 | edam:format_2306 | Gene Transfer Format (GTF), a restricted version of GFF |
| edam:format_2310 | edam:format_2310 | FASTA format wrapped in HTML elements |
| edam:format_2311 | edam:format_2311 | EMBL entry format wrapped in HTML elements |
| edam:format_2330 | edam:format_2330 | Textual format |
| edam:format_2331 | edam:format_2331 | HTML format |
| edam:format_2332 | edam:format_2332 | eXtensible Markup Language (XML) format |
| edam:format_2333 | edam:format_2333 | Binary format |
| edam:format_2350 | edam:format_2350 | A placeholder concept for visual navigation by dividing data formats by the c... |
| edam:format_2352 | edam:format_2352 | BioXSD-schema-based XML format of sequence-based data and some other common d... |
| edam:format_2376 | edam:format_2376 | A serialisation format conforming to the Resource Description Framework (RDF)... |
| edam:format_2532 | edam:format_2532 | Genbank entry format wrapped in HTML elements |
| edam:format_2543 | edam:format_2543 | A format resembling EMBL entry (plain text) format |
| edam:format_2545 | edam:format_2545 | A format resembling FASTQ short read format |
| edam:format_2546 | edam:format_2546 | A format resembling FASTA format |
| edam:format_2547 | edam:format_2547 | A sequence format resembling uniprotkb entry format |
| edam:format_2548 | edam:format_2548 | Format for a sequence feature table |
| edam:format_2549 | edam:format_2549 | OBO ontology text format |
| edam:format_2550 | edam:format_2550 | OBO ontology XML format |
| edam:format_2551 | edam:format_2551 | Data format for a molecular sequence record (text) |
| edam:format_2552 | edam:format_2552 | Data format for a molecular sequence record (XML) |
| edam:format_2553 | edam:format_2553 | XML format for a sequence feature table |
| edam:format_2554 | edam:format_2554 | Text format for molecular sequence alignment information |
| edam:format_2555 | edam:format_2555 | XML format for molecular sequence alignment information |
| edam:format_2556 | edam:format_2556 | Text format for a phylogenetic tree |
| edam:format_2557 | edam:format_2557 | XML format for a phylogenetic tree |
| edam:format_2558 | edam:format_2558 | An XML format resembling EMBL entry format |
| edam:format_2559 | edam:format_2559 | A format resembling GenBank entry (plain text) format |
| edam:format_2561 | edam:format_2561 | Text format for sequence assembly data |
| edam:format_2566 | edam:format_2566 | Alphabet for a molecular sequence without any unknown positions or ambiguity ... |
| edam:format_2567 | edam:format_2567 | Alphabet for a molecular sequence without unknown positions, ambiguity or non... |
| edam:format_2568 | edam:format_2568 | Alphabet for a nucleotide sequence (characters ACGTU only) without unknown po... |
| edam:format_2569 | edam:format_2569 | Alphabet for a DNA sequence (characters ACGT only) without unknown positions,... |
| edam:format_2570 | edam:format_2570 | Alphabet for an RNA sequence (characters ACGU only) without unknown positions... |
| edam:format_2571 | edam:format_2571 | Format of a raw molecular sequence (i |
| edam:format_2572 | edam:format_2572 | BAM format, the binary, BGZF-formatted compressed version of SAM format for a... |
| edam:format_2573 | edam:format_2573 | Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e |
| edam:format_2585 | edam:format_2585 | Systems Biology Markup Language (SBML), the standard XML format for models of... |
| edam:format_2607 | edam:format_2607 | Alphabet for any protein sequence without unknown positions, ambiguity or non... |
| edam:format_2848 | edam:format_2848 | Format of a bibliographic reference |
| edam:format_2919 | edam:format_2919 | Format of a sequence annotation track |
| edam:format_2920 | edam:format_2920 | Data format for molecular sequence alignment information that can hold sequen... |
| edam:format_2921 | edam:format_2921 | Format of sequence variation annotation |
| edam:format_2922 | edam:format_2922 | Some variant of Pearson MARKX alignment format |
| edam:format_2923 | edam:format_2923 | Some variant of Mega format for (typically aligned) sequences |
| edam:format_2924 | edam:format_2924 | Some variant of Phylip format for (aligned) sequences |
| edam:format_3000 | edam:format_3000 | AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' se... |
| edam:format_3001 | edam:format_3001 | ACE sequence assembly format including contigs, base-call qualities, and othe... |
| edam:format_3003 | edam:format_3003 | Browser Extensible Data (BED) format of sequence annotation track, typically ... |
| edam:format_3004 | edam:format_3004 | bigBed format for large sequence annotation tracks, similar to textual BED fo... |
| edam:format_3005 | edam:format_3005 | Wiggle format (WIG) of a sequence annotation track that consists of a value f... |
| edam:format_3006 | edam:format_3006 | bigWig format for large sequence annotation tracks that consist of a value fo... |
| edam:format_3007 | edam:format_3007 | PSL format of alignments, typically generated by BLAT or psLayout |
| edam:format_3008 | edam:format_3008 | Multiple Alignment Format (MAF) supporting alignments of whole genomes with r... |
| edam:format_3009 | edam:format_3009 | 2bit binary format of nucleotide sequences using 2 bits per nucleotide |
| edam:format_3010 | edam:format_3010 | |
| edam:format_3011 | edam:format_3011 | genePred table format for gene prediction tracks |
| edam:format_3012 | edam:format_3012 | Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and ... |
| edam:format_3013 | edam:format_3013 | axt format of alignments, typically produced from BLASTZ |
| edam:format_3014 | edam:format_3014 | LAV format of alignments generated by BLASTZ and LASTZ |
| edam:format_3015 | edam:format_3015 | Pileup format of alignment of sequences (e |
| edam:format_3016 | edam:format_3016 | Variant Call Format (VCF) is tabular format for storing genomic sequence vari... |
| edam:format_3017 | edam:format_3017 | Sequence Read Format (SRF) of sequence trace data |
| edam:format_3018 | edam:format_3018 | ZTR format for storing chromatogram data from DNA sequencing instruments |
| edam:format_3019 | edam:format_3019 | Genome Variation Format (GVF) |
| edam:format_3020 | edam:format_3020 | BCF is the binary version of Variant Call Format (VCF) for sequence variation... |
| edam:format_3033 | edam:format_3033 | Format of a matrix (array) of numerical values |
| edam:format_3097 | edam:format_3097 | Format of data concerning the classification of the sequences and/or structur... |
| edam:format_3098 | edam:format_3098 | Format of raw SCOP domain classification data files |
| edam:format_3099 | edam:format_3099 | Format of raw CATH domain classification data files |
| edam:format_3100 | edam:format_3100 | Format of summary of domain classification information for a CATH domain |
| edam:format_3155 | edam:format_3155 | Systems Biology Result Markup Language (SBRML), the standard XML format for s... |
| edam:format_3156 | edam:format_3156 | BioPAX is an exchange format for pathway data, with its data model defined in... |
| edam:format_3157 | edam:format_3157 | EBI Application Result XML is a format returned by sequence similarity search... |
| edam:format_3158 | edam:format_3158 | XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI |
| edam:format_3159 | edam:format_3159 | phyloXML is a standardised XML format for phylogenetic trees, networks, and a... |
| edam:format_3160 | edam:format_3160 | NeXML is a standardised XML format for rich phyloinformatic data |
| edam:format_3161 | edam:format_3161 | MAGE-ML XML format for microarray expression data, standardised by MGED (now ... |
| edam:format_3162 | edam:format_3162 | MAGE-TAB textual format for microarray expression data, standardised by MGED ... |
| edam:format_3163 | edam:format_3163 | GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MI... |
| edam:format_3164 | edam:format_3164 | GTrack is a generic and optimised tabular format for genome or sequence featu... |
| edam:format_3166 | edam:format_3166 | Data format for a report of information derived from a biological pathway or ... |
| edam:format_3167 | edam:format_3167 | Data format for annotation on a laboratory experiment |
| edam:format_3235 | edam:format_3235 | Cytoband format for chromosome cytobands |
| edam:format_3239 | edam:format_3239 | CopasiML, the native format of COPASI |
| edam:format_3240 | edam:format_3240 | CellML, the format for mathematical models of biological and other networks |
| edam:format_3242 | edam:format_3242 | Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI |
| edam:format_3243 | edam:format_3243 | Protein affinity format (PSI-PAR), standardised by HUPO PSI MI |
| edam:format_3244 | edam:format_3244 | mzML format for raw spectrometer output data, standardised by HUPO PSI MSS |
| edam:format_3245 | edam:format_3245 | Format for mass pectra and derived data, include peptide sequences etc |
| edam:format_3246 | edam:format_3246 | TraML (Transition Markup Language) is the format for mass spectrometry transi... |
| edam:format_3247 | edam:format_3247 | mzIdentML is the exchange format for peptides and proteins identified from ma... |
| edam:format_3248 | edam:format_3248 | mzQuantML is the format for quantitation values associated with peptides, pro... |
| edam:format_3249 | edam:format_3249 | GelML is the format for describing the process of gel electrophoresis, standa... |
| edam:format_3250 | edam:format_3250 | spML is the format for describing proteomics sample processing, other than us... |
| edam:format_3252 | edam:format_3252 | A human-readable encoding for the Web Ontology Language (OWL) |
| edam:format_3253 | edam:format_3253 | A syntax for writing OWL class expressions |
| edam:format_3254 | edam:format_3254 | A superset of the "Description-Logic Knowledge Representation System Specific... |
| edam:format_3255 | edam:format_3255 | The Terse RDF Triple Language (Turtle) is a human-friendly serialisation form... |
| edam:format_3256 | edam:format_3256 | A plain text serialisation format for RDF (Resource Description Framework) gr... |
| edam:format_3257 | edam:format_3257 | A shorthand non-XML serialisation of Resource Description Framework model, de... |
| edam:format_3261 | edam:format_3261 | Resource Description Framework (RDF) XML format |
| edam:format_3262 | edam:format_3262 | OWL ontology XML serialisation format |
| edam:format_3281 | edam:format_3281 | The A2M format is used as the primary format for multiple alignments of prote... |
| edam:format_3284 | edam:format_3284 | Standard flowgram format (SFF) is a binary file format used to encode results... |
| edam:format_3285 | edam:format_3285 | The MAP file describes SNPs and is used by the Plink package |
| edam:format_3286 | edam:format_3286 | The PED file describes individuals and genetic data and is used by the Plink ... |
| edam:format_3287 | edam:format_3287 | Data format for a metadata on an individual and their genetic data |
| edam:format_3288 | edam:format_3288 | The PED/MAP file describes data used by the Plink package |
| edam:format_3309 | edam:format_3309 | File format of a CT (Connectivity Table) file from the RNAstructure package |
| edam:format_3310 | edam:format_3310 | XRNA old input style format |
| edam:format_3311 | edam:format_3311 | RNA Markup Language |
| edam:format_3312 | edam:format_3312 | Format for the Genetic Data Environment (GDE) |
| edam:format_3313 | edam:format_3313 | A multiple alignment in vertical format, as used in the AMPS (Alignment of Mu... |
| edam:format_3326 | edam:format_3326 | Format of a data index of some type |
| edam:format_3327 | edam:format_3327 | BAM indexing format |
| edam:format_3328 | edam:format_3328 | HMMER profile HMM file for HMMER versions 2 |
| edam:format_3329 | edam:format_3329 | HMMER profile HMM file for HMMER versions 3 |
| edam:format_3330 | edam:format_3330 | PO is the output format of Partial Order Alignment program (POA) performing M... |
| edam:format_3331 | edam:format_3331 | XML format as produced by the NCBI Blast package |
| edam:format_3462 | edam:format_3462 | Reference-based compression of alignment format |
| edam:format_3464 | edam:format_3464 | JavaScript Object Notation format; a lightweight, text-based format to repres... |
| edam:format_3466 | edam:format_3466 | Encapsulated PostScript format |
| edam:format_3467 | edam:format_3467 | Graphics Interchange Format |
| edam:format_3468 | edam:format_3468 | Microsoft Excel spreadsheet format |
| edam:format_3475 | edam:format_3475 | Tabular data represented as tab-separated values in a text file |
| edam:format_3477 | edam:format_3477 | Format of the cytoscape input file of gene expression ratios or values are sp... |
| edam:format_3484 | edam:format_3484 | Bowtie format for indexed reference genome for "small" genomes |
| edam:format_3485 | edam:format_3485 | Rich sequence format |
| edam:format_3486 | edam:format_3486 | Some format based on the GCG format |
| edam:format_3487 | edam:format_3487 | Bioinformatics Sequence Markup Language format |
| edam:format_3491 | edam:format_3491 | Bowtie format for indexed reference genome for "large" genomes |
| edam:format_3499 | edam:format_3499 | Ensembl standard format for variation data |
| edam:format_3506 | edam:format_3506 | Microsoft Word format |
| edam:format_3507 | edam:format_3507 | Format of documents including word processor, spreadsheet and presentation |
| edam:format_3508 | edam:format_3508 | Portable Document Format |
| edam:format_3547 | edam:format_3547 | Format used for images and image metadata |
| edam:format_3548 | edam:format_3548 | Medical image format corresponding to the Digital Imaging and Communications ... |
| edam:format_3549 | edam:format_3549 | An open file format from the Neuroimaging Informatics Technology Initiative (... |
| edam:format_3550 | edam:format_3550 | Text-based tagged file format for medical images generated using the MetaImag... |
| edam:format_3551 | edam:format_3551 | Nearly Raw Rasta Data format designed to support scientific visualisation and... |
| edam:format_3554 | edam:format_3554 | File format used for scripts written in the R programming language for execut... |
| edam:format_3555 | edam:format_3555 | File format used for scripts for the Statistical Package for the Social Scien... |
| edam:format_3556 | edam:format_3556 | MIME HTML format for Web pages, which can include external resources, includi... |
| edam:format_3578 | edam:format_3578 | Proprietary file format for (raw) BeadArray data used by genomewide profiling... |
| edam:format_3579 | edam:format_3579 | Joint Picture Group file format for lossy graphics file |
| edam:format_3580 | edam:format_3580 | Reporter Code Count-A data file ( |
| edam:format_3581 | edam:format_3581 | ARFF (Attribute-Relation File Format) is an ASCII text file format that descr... |
| edam:format_3582 | edam:format_3582 | AFG is a single text-based file assembly format that holds read and consensus... |
| edam:format_3583 | edam:format_3583 | The bedGraph format allows display of continuous-valued data in track format |
| edam:format_3584 | edam:format_3584 | Browser Extensible Data (BED) format of sequence annotation track that strict... |
| edam:format_3585 | edam:format_3585 | BED file format where each feature is described by chromosome, start, end, na... |
| edam:format_3586 | edam:format_3586 | A BED file where each feature is described by all twelve columns |
| edam:format_3587 | edam:format_3587 | Tabular format of chromosome names and sizes used by Galaxy |
| edam:format_3588 | edam:format_3588 | Custom Sequence annotation track format used by Galaxy |
| edam:format_3589 | edam:format_3589 | Color space FASTA format sequence variant |
| edam:format_3590 | edam:format_3590 | HDF5 is a data model, library, and file format for storing and managing data,... |
| edam:format_3591 | edam:format_3591 | A versatile bitmap format |
| edam:format_3592 | edam:format_3592 | Standard bitmap storage format in the Microsoft Windows environment |
| edam:format_3593 | edam:format_3593 | IM is a format used by LabEye and other applications based on the IFUNC image... |
| edam:format_3594 | edam:format_3594 | Photo CD format, which is the highest resolution format for images on a CD |
| edam:format_3595 | edam:format_3595 | PCX is an image file format that uses a simple form of run-length encoding |
| edam:format_3596 | edam:format_3596 | The PPM format is a lowest common denominator color image file format |
| edam:format_3597 | edam:format_3597 | PSD (Photoshop Document) is a proprietary file that allows the user to work w... |
| edam:format_3598 | edam:format_3598 | X BitMap is a plain text binary image format used by the X Window System used... |
| edam:format_3599 | edam:format_3599 | X PixMap (XPM) is an image file format used by the X Window System, it is int... |
| edam:format_3600 | edam:format_3600 | RGB file format is the native raster graphics file format for Silicon Graphic... |
| edam:format_3601 | edam:format_3601 | The PBM format is a lowest common denominator monochrome file format |
| edam:format_3602 | edam:format_3602 | The PGM format is a lowest common denominator grayscale file format |
| edam:format_3603 | edam:format_3603 | PNG is a file format for image compression |
| edam:format_3604 | edam:format_3604 | Scalable Vector Graphics (SVG) is an XML-based vector image format for two-di... |
| edam:format_3605 | edam:format_3605 | Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems |
| edam:format_3606 | edam:format_3606 | Textual report format for sequence quality for reports from sequencing machin... |
| edam:format_3607 | edam:format_3607 | FASTQ format subset for Phred sequencing quality score data only (no sequence... |
| edam:format_3608 | edam:format_3608 | FASTQ format subset for Phred sequencing quality score data only (no sequence... |
| edam:format_3609 | edam:format_3609 | FASTQ format subset for Phred sequencing quality score data only (no sequence... |
| edam:format_3610 | edam:format_3610 | FASTQ format subset for Phred sequencing quality score data only (no sequence... |
| edam:format_3611 | edam:format_3611 | FASTQ format subset for Phred sequencing quality score data only (no sequence... |
| edam:format_3612 | edam:format_3612 | Human ENCODE peak format |
| edam:format_3613 | edam:format_3613 | Human ENCODE narrow peak format |
| edam:format_3614 | edam:format_3614 | Human ENCODE broad peak format |
| edam:format_3615 | edam:format_3615 | Blocked GNU Zip format |
| edam:format_3616 | edam:format_3616 | TAB-delimited genome position file index format |
| edam:format_3617 | edam:format_3617 | Data format for graph data |
| edam:format_3618 | edam:format_3618 | XML-based format used to store graph descriptions within Galaxy |
| edam:format_3619 | edam:format_3619 | SIF (simple interaction file) Format - a network/pathway format used for inst... |
| edam:format_3620 | edam:format_3620 | MS Excel spreadsheet format consisting of a set of XML documents stored in a ... |
| edam:format_3621 | edam:format_3621 | Data format used by the SQLite database |
| edam:format_3622 | edam:format_3622 | Data format used by the SQLite database conformant to the Gemini schema |
| edam:format_3624 | edam:format_3624 | An index of a genome database, indexed for use by the snpeff tool |
| edam:format_3626 | edam:format_3626 | Binary format used by MATLAB files to store workspace variables |
| edam:format_3650 | edam:format_3650 | Format used by netCDF software library for writing and reading chromatography... |
| edam:format_3651 | edam:format_3651 | Mascot Generic Format |
| edam:format_3652 | edam:format_3652 | Spectral data format file where each spectrum is written to a separate file |
| edam:format_3653 | edam:format_3653 | Spectral data file similar to dta |
| edam:format_3654 | edam:format_3654 | Common file format for proteomics mass spectrometric data developed at the Se... |
| edam:format_3655 | edam:format_3655 | Open data format for the storage, exchange, and processing of peptide sequenc... |
| edam:format_3657 | edam:format_3657 | Graphical Pathway Markup Language (GPML) is an XML format used for exchanging... |
| edam:format_3665 | edam:format_3665 | A list of k-mers and their occurrences in a dataset |
| edam:format_3681 | edam:format_3681 | mzTab is a light-weight, tab-delimited format for mass spectrometry-based pro... |
| edam:format_3682 | edam:format_3682 | imzML metadata is a data format for mass spectrometry imaging metadata |
| edam:format_3683 | edam:format_3683 | qcML is an XML format for quality-related data of mass spectrometry and other... |
| edam:format_3684 | edam:format_3684 | PRIDE XML is an XML format for mass spectra, peptide and protein identificati... |
| edam:format_3685 | edam:format_3685 | Simulation Experiment Description Markup Language (SED-ML) is an XML format f... |
| edam:format_3686 | edam:format_3686 | Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all... |
| edam:format_3687 | edam:format_3687 | ISA-Tab stands for Investigation / Study / Assay (ISA) tab-delimited (Tab) fo... |
| edam:format_3688 | edam:format_3688 | SBtab is a tabular format for biochemical network models |
| edam:format_3689 | edam:format_3689 | Biological Connection Markup Language (BCML) is an XML format for biological ... |
| edam:format_3690 | edam:format_3690 | Biological Dynamics Markup Language (BDML) is an XML format for quantitative ... |
| edam:format_3691 | edam:format_3691 | Biological Expression Language (BEL) is a textual format for representing sci... |
| edam:format_3692 | edam:format_3692 | SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagra... |
| edam:format_3693 | edam:format_3693 | AGP is a tabular format for a sequence assembly (a contig, a scaffold/superco... |
| edam:format_3696 | edam:format_3696 | PostScript format |
| edam:format_3698 | edam:format_3698 | SRA archive format (SRA) is the archive format used for input to the NCBI Seq... |
| edam:format_3699 | edam:format_3699 | VDB ('vertical database') is the native format used for export from the NCBI ... |
| edam:format_3701 | edam:format_3701 | A five-column, tab-delimited table of feature locations and qualifiers for im... |
| edam:format_3702 | edam:format_3702 | Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscovere... |
| edam:format_3706 | edam:format_3706 | Data format for biodiversity data |
| edam:format_3708 | edam:format_3708 | Exchange format of the Access to Biological Collections Data (ABCD) Schema; a... |
| edam:format_3709 | edam:format_3709 | Tab-delimited text files of GenePattern that contain a column for each sample... |
| edam:format_3710 | edam:format_3710 | Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex) |
| edam:format_3711 | edam:format_3711 | Output format used by X! series search engines that is based on the XML langu... |
| edam:format_3712 | edam:format_3712 | Proprietary file format for mass spectrometry data from Thermo Scientific |
| edam:format_3713 | edam:format_3713 | "Raw" result file from Mascot database search |
| edam:format_3714 | edam:format_3714 | Format of peak list files from Andromeda search engine (MaxQuant) that consis... |
| edam:format_3725 | edam:format_3725 | Synthetic Biology Open Language (SBOL) is an XML format for the specification... |
| edam:format_3726 | edam:format_3726 | PMML uses XML to represent mining models |
| edam:format_3727 | edam:format_3727 | Image file format used by the Open Microscopy Environment (OME) |
| edam:format_3728 | edam:format_3728 | The LocARNA PP format combines sequence or alignment information and (respect... |
| edam:format_3729 | edam:format_3729 | Input format used by the Database of Genotypes and Phenotypes (dbGaP) |
| edam:format_3746 | edam:format_3746 | The BIological Observation Matrix (BIOM) is a format for representing biologi... |
| edam:format_3747 | edam:format_3747 | A format for storage, exchange, and processing of protein identifications cre... |
| edam:format_3748 | edam:format_3748 | A linked data format enables publishing structured data as linked data (Linke... |
| edam:format_3749 | edam:format_3749 | JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encodi... |
| edam:format_3750 | edam:format_3750 | YAML (YAML Ain't Markup Language) is a human-readable tree-structured data se... |
| edam:format_3751 | edam:format_3751 | Tabular data represented as values in a text file delimited by some character |
| edam:format_3752 | edam:format_3752 | Tabular data represented as comma-separated values in a text file |
| edam:format_3758 | edam:format_3758 | "Raw" result file from SEQUEST database search |
| edam:format_3764 | edam:format_3764 | XML file format for files containing information about peptide identification... |
| edam:format_3765 | edam:format_3765 | Data table formatted such that it can be passed/streamed within the KNIME pla... |
| edam:format_3770 | edam:format_3770 | UniProtKB XML sequence features format is an XML format available for downloa... |
| edam:format_3771 | edam:format_3771 | UniProtKB RDF sequence features format is an RDF format available for downloa... |
| edam:format_3772 | edam:format_3772 | BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some ... |
| edam:format_3773 | edam:format_3773 | BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some ... |
| edam:format_3774 | edam:format_3774 | BioJSON is a JSON format of single multiple sequence alignments, with their a... |
| edam:format_3775 | edam:format_3775 | GSuite is a tabular format for collections of genome or sequence feature trac... |
| edam:format_3776 | edam:format_3776 | BTrack is an HDF5-based binary format for genome or sequence feature tracks a... |
| edam:format_3777 | edam:format_3777 | The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an interna... |
| edam:format_3780 | edam:format_3780 | Data format of an annotated text, e |
| edam:format_3781 | edam:format_3781 | JSON format of annotated scientific text used by PubAnnotations and other too... |
| edam:format_3782 | edam:format_3782 | BioC is a standardised XML format for sharing and integrating text data and a... |
| edam:format_3783 | edam:format_3783 | Native textual export format of annotated scientific text from PubTator |
| edam:format_3784 | edam:format_3784 | A format of text annotation using the linked-data Open Annotation Data Model,... |
| edam:format_3785 | edam:format_3785 | A family of similar formats of text annotation, used by BRAT and other tools,... |
| edam:format_3787 | edam:format_3787 | A query language (format) for structured database queries |
| edam:format_3788 | edam:format_3788 | SQL (Structured Query Language) is the de-facto standard query language (form... |
| edam:format_3789 | edam:format_3789 | XQuery (XML Query) is a query language (format of queries) for querying and m... |
| edam:format_3790 | edam:format_3790 | SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language ... |
| edam:format_3804 | edam:format_3804 | XML format for XML Schema |
| edam:format_3811 | edam:format_3811 | XMFA format stands for eXtended Multi-FastA format and is used to store colli... |
| edam:format_3812 | edam:format_3812 | The GEN file format contains genetic data and describes SNPs |
| edam:format_3813 | edam:format_3813 | The SAMPLE file format contains information about each individual i |
| edam:format_3814 | edam:format_3814 | SDF is one of a family of chemical-data file formats developed by MDL Informa... |
| edam:format_3815 | edam:format_3815 | An MDL Molfile is a file format for holding information about the atoms, bond... |
| edam:format_3816 | edam:format_3816 | Complete, portable representation of a SYBYL molecule |
| edam:format_3817 | edam:format_3817 | format for the LaTeX document preparation system |
| edam:format_3818 | edam:format_3818 | Tab-delimited text file format used by Eland - the read-mapping program distr... |
| edam:format_3819 | edam:format_3819 | Phylip multiple alignment sequence format, less stringent than PHYLIP format |
| edam:format_3820 | edam:format_3820 | Phylip multiple alignment sequence format, less stringent than PHYLIP sequent... |
| edam:format_3821 | edam:format_3821 | Default XML format of VisANT, containing all the network information |
| edam:format_3822 | edam:format_3822 | GML (Graph Modeling Language) is a text file format supporting network data w... |
| edam:format_3823 | edam:format_3823 | FASTG is a format for faithfully representing genome assemblies in the face o... |
| edam:format_3824 | edam:format_3824 | Data format for raw data from a nuclear magnetic resonance (NMR) spectroscopy... |
| edam:format_3825 | edam:format_3825 | nmrML is an MSI supported XML-based open access format for metabolomics NMR r... |
| edam:format_3826 | edam:format_3826 | |
| edam:format_3827 | edam:format_3827 | |
| edam:format_3828 | edam:format_3828 | Data format for raw microarray data |
| edam:format_3829 | edam:format_3829 | GenePix Results (GPR) text file format developed by Axon Instruments that is ... |
| edam:format_3830 | edam:format_3830 | Binary format used by the ARB software suite |
| edam:format_3832 | edam:format_3832 | OpenMS format for grouping features in one map or across several maps |
| edam:format_3833 | edam:format_3833 | OpenMS format for quantitation results (LC/MS features) |
| edam:format_3834 | edam:format_3834 | Now deprecated data format of the HUPO Proteomics Standards Initiative |
| edam:format_3835 | edam:format_3835 | Format supported by the Tide tool for identifying peptides from tandem mass s... |
| edam:format_3836 | edam:format_3836 | XML format as produced by the NCBI Blast package v2 |
| edam:format_3838 | edam:format_3838 | Microsoft Powerpoint format |
| edam:format_3839 | edam:format_3839 | ibd is a data format for mass spectrometry imaging data |
| edam:format_3841 | edam:format_3841 | Data format used in Natural Language Processing |
| edam:format_3843 | edam:format_3843 | XML input file format for BEAST Software (Bayesian Evolutionary Analysis Samp... |
| edam:format_3844 | edam:format_3844 | Chado-XML format is a direct mapping of the Chado relational schema into XML |
| edam:format_3845 | edam:format_3845 | An alignment format generated by PRANK/PRANKSTER consisting of four elements:... |
| edam:format_3846 | edam:format_3846 | Output xml file from the InterProScan sequence analysis application |
| edam:format_3847 | edam:format_3847 | The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway map... |
| edam:format_3848 | edam:format_3848 | XML format for collected entries from bibliographic databases MEDLINE and Pub... |
| edam:format_3849 | edam:format_3849 | A set of XML compliant markup components for describing multiple sequence ali... |
| edam:format_3850 | edam:format_3850 | OrthoXML is designed broadly to allow the storage and comparison of orthology... |
| edam:format_3851 | edam:format_3851 | Tree structure of Protein Sequence Database Markup Language generated using M... |
| edam:format_3852 | edam:format_3852 | SeqXML is an XML Schema to describe biological sequences, developed by the St... |
| edam:format_3853 | edam:format_3853 | XML format for the UniParc database |
| edam:format_3854 | edam:format_3854 | XML format for the UniRef reference clusters |
| edam:format_3857 | edam:format_3857 | Common Workflow Language (CWL) format for description of command-line tools a... |
| edam:format_3858 | edam:format_3858 | Proprietary file format for mass spectrometry data from Waters |
| edam:format_3859 | edam:format_3859 | A standardized file format for data exchange in mass spectrometry, initially ... |
| edam:format_3862 | edam:format_3862 | An NLP format used for annotated textual documents |
| edam:format_3863 | edam:format_3863 | NLP format used by a specific type of corpus (collection of texts) |
| edam:format_3864 | edam:format_3864 | mirGFF3 is a common format for microRNA data resulting from small-RNA RNA-Seq... |
| edam:format_3865 | edam:format_3865 | A "placeholder" concept for formats of annotated RNA data, including e |
| edam:format_3866 | edam:format_3866 | File format to store trajectory information for a 3D structure |
| edam:format_3867 | edam:format_3867 | Binary file format to store trajectory information for a 3D structure |
| edam:format_3868 | edam:format_3868 | Textual file format to store trajectory information for a 3D structure |
| edam:format_3873 | edam:format_3873 | HDF is the name of a set of file formats and libraries designed to store and ... |
| edam:format_3874 | edam:format_3874 | PCAZip format is a binary compressed file to store atom coordinates based on ... |
| edam:format_3875 | edam:format_3875 | Portable binary format for trajectories produced by GROMACS package |
| edam:format_3876 | edam:format_3876 | Trajectory Next Generation (TNG) is a format for storage of molecular simulat... |
| edam:format_3877 | edam:format_3877 | The XYZ chemical file format is widely supported by many programs, although m... |
| edam:format_3878 | edam:format_3878 | AMBER trajectory (also called mdcrd), with 10 coordinates per line and format... |
| edam:format_3879 | edam:format_3879 | Format of topology files; containing the static information of a structure mo... |
| edam:format_3880 | edam:format_3880 | GROMACS MD package top textual files define an entire structure system topolo... |
| edam:format_3881 | edam:format_3881 | AMBER Prmtop file (version 7) is a structure topology text file divided in se... |
| edam:format_3882 | edam:format_3882 | X-Plor Protein Structure Files (PSF) are structure topology files used by NAM... |
| edam:format_3883 | edam:format_3883 | GROMACS itp files (include topology) contain structure topology information, ... |
| edam:format_3884 | edam:format_3884 | Format of force field parameter files, which store the set of parameters (cha... |
| edam:format_3885 | edam:format_3885 | Scripps Research Institute BinPos format is a binary formatted file to store ... |
| edam:format_3886 | edam:format_3886 | AMBER coordinate/restart file with 6 coordinates per line and decimal format ... |
| edam:format_3887 | edam:format_3887 | Format of CHARMM Residue Topology Files (RTF), which define groups by includi... |
| edam:format_3888 | edam:format_3888 | AMBER frcmod (Force field Modification) is a file format to store any modific... |
| edam:format_3889 | edam:format_3889 | AMBER Object File Format library files (OFF library files) store residue libr... |
| edam:format_3906 | edam:format_3906 | MReData is a text based data standard for processed NMR data |
| edam:format_3909 | edam:format_3909 | BpForms is a string format for concretely representing the primary structures... |
| edam:format_3910 | edam:format_3910 | Format of trr files that contain the trajectory of a simulation experiment us... |
| edam:format_3911 | edam:format_3911 | Mash sketch is a format for sequence / sequence checksum information |
| edam:format_3913 | edam:format_3913 | The Loom file format is based on HDF5, a standard for storing large numerical... |
| edam:format_3915 | edam:format_3915 | The Zarr format is an implementation of chunked, compressed, N-dimensional ar... |
| edam:format_3916 | edam:format_3916 | The Matrix Market matrix (MTX) format stores numerical or pattern matrices in... |
| edam:format_3951 | edam:format_3951 | BcForms is a format for abstractly describing the molecular structure (atoms ... |
| edam:format_3956 | edam:format_3956 | N-Quads is a line-based, plain text format for encoding an RDF dataset |
| edam:format_3969 | edam:format_3969 | Vega is a visualization grammar, a declarative language for creating, saving,... |
| edam:format_3970 | edam:format_3970 | Vega-Lite is a high-level grammar of interactive graphics |
| edam:format_3971 | edam:format_3971 | A model description language for computational neuroscience |
| edam:format_3972 | edam:format_3972 | BioNetGen is a format for the specification and simulation of rule-based mode... |
| edam:format_3973 | edam:format_3973 | A Docker image is a file, comprised of multiple layers, that is used to execu... |
| edam:format_3975 | edam:format_3975 | Graphical Fragment Assembly captures sequence graphs as the product of an ass... |
| edam:format_3976 | edam:format_3976 | Graphical Fragment Assembly captures sequence graphs as the product of an ass... |
| edam:format_3977 | edam:format_3977 | ObjTables is a toolkit for creating reusable datasets that are both human and... |
| edam:format_3978 | edam:format_3978 | The CONTIG format used for output of the SOAPdenovo alignment program |
| edam:format_3979 | edam:format_3979 | WEGO native format used by the Web Gene Ontology Annotation Plot application |
| edam:format_3980 | edam:format_3980 | Tab-delimited format for gene expression levels table, calculated as Reads Pe... |
| edam:format_3981 | edam:format_3981 | TAR archive file format generated by the Unix-based utility tar |
| edam:format_3982 | edam:format_3982 | The CHAIN format describes a pairwise alignment that allow gaps in both seque... |
| edam:format_3983 | edam:format_3983 | The NET file format is used to describe the data that underlie the net alignm... |
| edam:format_3984 | edam:format_3984 | Format of QMAP files generated for methylation data from an internal BGI pipe... |
| edam:format_3985 | edam:format_3985 | An emerging format for high-level Galaxy workflow description |
| edam:format_3986 | edam:format_3986 | The proprietary native video format of various Microsoft programs such as Win... |
| edam:format_3987 | edam:format_3987 | ZIP is an archive file format that supports lossless data compression |
| edam:format_3988 | edam:format_3988 | Zeiss' proprietary image format based on TIFF |
| edam:format_3989 | edam:format_3989 | GNU zip compressed file format common to Unix-based operating systems |
| edam:format_3990 | edam:format_3990 | Audio Video Interleaved (AVI) format is a multimedia container format for AVI... |
| edam:format_3991 | edam:format_3991 | A declaration file format for UCSC browsers track dataset display characteris... |
| edam:format_3992 | edam:format_3992 | Compact Idiosyncratic Gapped Alignment Report format is a compressed (run-len... |
| edam:format_3993 | edam:format_3993 | STL is a file format native to the stereolithography CAD software created by ... |
| edam:format_3994 | edam:format_3994 | U3D (Universal 3D) is a compressed file format and data structure for 3D comp... |
| edam:format_3995 | edam:format_3995 | Bitmap image format used for storing textures |
| edam:format_3996 | edam:format_3996 | Format for scripts writtenin Python - a widely used high-level programming la... |
| edam:format_3997 | edam:format_3997 | A digital multimedia container format most commonly used to store video and a... |
| edam:format_3998 | edam:format_3998 | Format for scripts written in Perl - a family of high-level, general-purpose,... |
| edam:format_3999 | edam:format_3999 | Format for scripts written in the R language - an open source programming lan... |
| edam:format_4000 | edam:format_4000 | A file format for making dynamic documents (R Markdown scripts) with the R la... |
| edam:format_4002 | edam:format_4002 | Format used by Python pickle module for serializing and de-serializing a Pyth... |
| edam:format_4003 | edam:format_4003 | The standard binary file format used by NumPy - a fundamental package for sci... |
| edam:format_4004 | edam:format_4004 | Format of repertoire (archive) files that can be read by SimToolbox (a MATLAB... |
| edam:format_4005 | edam:format_4005 | A configuration file used by various programs to store settings that are spec... |
| edam:format_4006 | edam:format_4006 | Format used by the Zstandard real-time compression algorithm |
| edam:format_4007 | edam:format_4007 | The file format for MATLAB scripts or functions |
| edam:format_4015 | edam:format_4015 | A data format for specifying parameter estimation problems in systems biology |
| edam:format_4018 | edam:format_4018 | Genomic Variant Call Format (gVCF) is a version of VCF that includes not only... |
| edam:format_4023 | edam:format_4023 | Chemical Markup Language (CML) is an XML-based format for encoding detailed i... |
| edam:format_4024 | edam:format_4024 | Crystallographic Information File (CIF) is a data exchange standard file form... |
| edam:format_4025 | edam:format_4025 | Format for describing the capabilities of a biosimulation tool including the ... |
| edam:format_4026 | edam:format_4026 | Outlines the syntax and semantics of the input and output arguments for comma... |
| edam:format_4035 | edam:format_4035 | Data format derived from the standard PDB format, which enables user to incor... |
| edam:format_4036 | edam:format_4036 | Data format used in AutoDock 4 for storing atomic coordinates, partial atomic... |
| edam:format_4039 | edam:format_4039 | MSP is a data format for mass spectrometry data |
| edam:format_4041 | edam:format_4041 | maDMP stands for machine-actionable data management plan, a standard for DMPs... |
| edam:format_4048 | edam:format_4048 | Nextflow is a workflow system for creating scalable, portable, and reproducib... |
| edam:format_4049 | edam:format_4049 | The Snakemake workflow management system is a tool to create reproducible and... |
| edam:format_4050 | edam:format_4050 | Sample and Data Relationship File for a proteomics experiment |
| edam:format_4058 | edam:format_4058 | mzTab-M is a light-weight, tab-delimited format for mass spectrometry-based c... |
| edam:format_4059 | edam:format_4059 | mzTab-L is a light-weight, tab-delimited format for mass spectrometry-based l... |
| edam:format_4066 | edam:format_4066 | ISA-Tab Investigation file (i_Investigation |
| edam:format_4067 | edam:format_4067 | ISA-Tab Study file (s_* |
| edam:format_4068 | edam:format_4068 | ISA-Tab Assay file (a_* |
| edam:format_4069 | edam:format_4069 | ISA-JSON stands for Investigation / Study / Assay (ISA) JavaScript Object Not... |
| edam:format_4070 | edam:format_4070 | mwTab is a tab-delimited text format developed by the Metabolomics Workbench ... |
| edam:format_4071 | edam:format_4071 | MHD (MetabolomicsHub Common Data Model) is a JSON-based format providing a st... |
| edam:format_4072 | edam:format_4072 | The MHD announcement file is a JSON-based format used to notify MetabolomicsH... |
| edam:format_4073 | edam:format_4073 | MetaboLights MAF (Metabolite Annotation File) is a tab-separated file format ... |
Slots
| Name | Description |
|---|---|
| format | The format of the file |
Identifier and Mapping Information
Schema Source
- from schema: https://includedcc.org/common-access-model
LinkML Source
name: EnumEDAMFormats
description: Data formats from the EDAM ontology.
from_schema: https://includedcc.org/common-access-model
rank: 1000
permissible_values:
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.
meaning: edam:format_1198
title: mf
edam:format_1199:
text: edam:format_1199
description: 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.
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.
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.
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.
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.
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.
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.
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.
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.
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: 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).
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).
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.
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: 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 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 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: 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).
meaning: edam:format_1950
title: pdbatom
edam:format_1951:
text: edam:format_1951
description: PDB nucleotide sequence format (ATOM lines).
meaning: edam:format_1951
title: pdbatomnuc
edam:format_1952:
text: edam:format_1952
description: PDB nucleotide sequence format (SEQRES lines).
meaning: edam:format_1952
title: pdbseqresnuc
edam:format_1953:
text: edam:format_1953
description: PDB sequence format (SEQRES lines).
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: 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).
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.
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.
meaning: edam:format_2181
title: EMBL-like (text)
edam:format_2182:
text: edam:format_2182
description: A text format resembling FASTQ short read format.
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.
meaning: edam:format_2200
title: FASTA-like (text)
edam:format_2204:
text: edam:format_2204
description: An XML format for EMBL entries.
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.
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: 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: eXtensible Markup Language (XML) format.
meaning: edam:format_2332
title: XML
edam:format_2333:
text: edam:format_2333
description: Binary format.
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.
meaning: edam:format_2350
title: Format (by type of data)
edam:format_2352:
text: edam:format_2352
description: 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.
meaning: edam:format_2543
title: EMBL-like format
edam:format_2545:
text: edam:format_2545
description: A format resembling FASTQ short read format.
meaning: edam:format_2545
title: FASTQ-like format
edam:format_2546:
text: edam:format_2546
description: A format resembling FASTA format.
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.
meaning: edam:format_2558
title: EMBL-like (XML)
edam:format_2559:
text: edam:format_2559
description: A format resembling GenBank entry (plain text) format.
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.
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.
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: 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.
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 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: 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.
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.
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.
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 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.
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.
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.
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".
meaning: edam:format_3254
title: KRSS2 Syntax
edam:format_3255:
text: edam:format_3255
description: 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.
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: 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: 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: 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.
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.
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: 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.
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.
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.
meaning: edam:format_3586
title: bed12
edam:format_3587:
text: edam:format_3587
description: 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.
meaning: edam:format_3588
title: customtrack
edam:format_3589:
text: edam:format_3589
description: Color space FASTA format sequence variant.
meaning: edam:format_3589
title: csfasta
edam:format_3590:
text: edam:format_3590
description: HDF5 is a data model, library, and file format for storing and managing
data, based on Hierarchical Data Format (HDF).
meaning: edam:format_3590
title: HDF5
edam:format_3591:
text: edam:format_3591
description: A versatile bitmap format.
meaning: edam:format_3591
title: TIFF
edam:format_3592:
text: edam:format_3592
description: Standard bitmap storage format in the Microsoft Windows environment.
meaning: edam:format_3592
title: BMP
edam:format_3593:
text: edam:format_3593
description: 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: 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: 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: 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: 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: 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.
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.
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).
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.
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.
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.
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: Human ENCODE peak format.
meaning: edam:format_3612
title: ENCODE peak format
edam:format_3613:
text: edam:format_3613
description: 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: 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.
meaning: edam:format_3650
title: NetCDF
edam:format_3651:
text: edam:format_3651
description: 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: 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: 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: mzTab is a light-weight, tab-delimited format for mass spectrometry-based
proteomics data.
meaning: edam:format_3681
title: mzTab
edam:format_3682:
text: edam:format_3682
description: 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: 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: 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 stands for Investigation / Study / Assay (ISA) tab-delimited
(Tab) format, and it is comprised of metadata describing observational or experimental
scientific studies.
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.
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.
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: 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: 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: Image file format used by the Open Microscopy Environment (OME).
meaning: edam:format_3727
title: OME-TIFF
edam:format_3728:
text: edam:format_3728
description: 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).
meaning: edam:format_3729
title: dbGaP format
edam:format_3746:
text: edam:format_3746
description: 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.
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: YAML (YAML Ain't Markup Language) is a human-readable tree-structured
data serialisation language.
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.
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.
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 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 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: 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.
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: 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: 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.
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.
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.
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.
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.
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 .
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 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).
meaning: edam:format_3874
title: PCAzip
edam:format_3875:
text: edam:format_3875
description: Portable binary format for trajectories produced by GROMACS package.
meaning: edam:format_3875
title: XTC
edam:format_3876:
text: edam:format_3876
description: 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.
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.
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.
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.
meaning: edam:format_3881
title: AMBER top
edam:format_3882:
text: edam:format_3882
description: '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.
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.
meaning: edam:format_3884
title: FF parameter format
edam:format_3885:
text: edam:format_3885
description: 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.
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.'
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.
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).
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.
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 reusable 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: 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: 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: 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: 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
characteristics.
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.
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.
meaning: edam:format_4039
title: MSP
edam:format_4041:
text: edam:format_4041
description: maDMP stands for machine-actionable data management plan, a standard
for DMPs developed by the Research Data Alliance (RDA).
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.
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: mzTab-M is a light-weight, tab-delimited format for mass spectrometry-based
chemical profiling data, including metabolomics.
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
edam:format_4066:
text: edam:format_4066
description: ISA-Tab Investigation file (i_Investigation.txt) contains metadata
describing the overall goals, means, and context of an investigation/experiment,
including references to associated Study and Assay files.
meaning: edam:format_4066
title: ISA-Tab Investigation file
edam:format_4067:
text: edam:format_4067
description: ISA-Tab Study file (s_*.txt) contains sample metadata describing
the subjects under study, their sources, characteristics, sampling methodology,
and any treatments or manipulations applied.
meaning: edam:format_4067
title: ISA-Tab Study file
edam:format_4068:
text: edam:format_4068
description: ISA-Tab Assay file (a_*.txt) contains assay metadata describing test
steps and analytical measurements performed on the sample material, including
measurement types, technology used, and references to raw and derived data files.
meaning: edam:format_4068
title: ISA-Tab Assay file
edam:format_4069:
text: edam:format_4069
description: ISA-JSON stands for Investigation / Study / Assay (ISA) JavaScript
Object Notation (JSON) format, and it is comprised of metadata describing observational
or experimental scientific studies.
meaning: edam:format_4069
title: ISA-JSON
edam:format_4070:
text: edam:format_4070
description: mwTab is a tab-delimited text format developed by the Metabolomics
Workbench to facilitate programmatic processing of metabolomics data and metadata
suitable for submission to the repository.
meaning: edam:format_4070
title: mwTab
edam:format_4071:
text: edam:format_4071
description: MHD (MetabolomicsHub Common Data Model) is a JSON-based format providing
a standardised, FAIR-compliant data model for the exchange, discovery, and reuse
of metabolomics dataset metadata across international repositories.
meaning: edam:format_4071
title: MHD
edam:format_4072:
text: edam:format_4072
description: The MHD announcement file is a JSON-based format used to notify MetabolomicsHub
of new or updated dataset submissions, serving as a manifest or notification
file within the MHD data flow.
meaning: edam:format_4072
title: MHD announcement
edam:format_4073:
text: edam:format_4073
description: MetaboLights MAF (Metabolite Annotation File) is a tab-separated
file format used to report metabolites identified or annotated in a metabolomics
study, including compound identifiers, chemical structure representations, mass-to-charge
ratios, retention times, and per-sample quantitative measurements.
meaning: edam:format_4073
title: MetaboLights MAF
reachable_from:
source_ontology: bioregistry:edam
source_nodes:
- edam:format_1915
relationship_types:
- rdfs:subClassOf
is_direct: false
include_self: false