Find EDAM ontology terms by definition
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-query]             string     Definition word(s) to search for in ontology
                                  (Any string)
  [-outfile]           outobo     [*.edamdef] Output ontology term file name

   Additional (Optional) qualifiers:
   -namespace          menu       [*] By default all terms are returned.
                                  Searches can be limited to one or a few
                                  namespaces. (Values: data (Data entity);
                                  entity (Biological entity); format (Data
                                  format); identifier (Identifier); operation
                                  (Bioinformatics operation); resource (Data
                                  resource); topic (Field of bioinformatics
                                  study))

   Advanced (Unprompted) qualifiers:
   -subclasses         boolean    [N] Extend the query matches to include all
                                  terms which are specialisations (EDAM
                                  sub-classes) of the matched type.
   -obsolete           boolean    [N] The default behaviour is to not use or
                                  return obsolete terms. This option if set
                                  will include all terms.

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     Ontology term output format

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

[Term]
id: EDAM_data:1354
name: Sequence profile
namespace: data
def: Some type of statistical model representing a (typically multiple) sequence alignment.
subset: data
synonym: "sequence profile" EXACT [http://semanticscience.org/resource/SIO_010531]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs

[Term]
id: EDAM_operation:0467
name: Protein secondary structure prediction (integrated)
namespace: operation
def: Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions.
subset: operations
is_a: EDAM_operation:0267 ! Protein secondary structure prediction

[Term]
id: EDAM_data:1385
name: Sequence alignment (hybrid)
namespace: data
def: Alignment of multiple molecular sequences of different types.
comment: Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA.
subset: data
is_a: EDAM_data:0863 ! Sequence alignment

[Term]
id: EDAM_data:1384
name: Sequence alignment (protein)
namespace: data
def: Alignment of multiple protein sequences.
subset: data
is_a: EDAM_data:0863 ! Sequence alignment
is_a: EDAM_data:3154 ! Protein alignment

[Term]
id: EDAM_data:0863
name: Sequence alignment
namespace: data
def: Alignment of multiple molecular sequences.
subset: data
synonym: "Sequence alignment" EXACT [http://en.wikipedia.org/wiki/Sequence_alignment]
synonym: "sequence alignment" EXACT [http://semanticscience.org/resource/SIO_010066]
is_a: EDAM_data:1916 ! Alignment
relationship: has_topic EDAM_topic:0182 ! Sequence alignment

[Term]
id: EDAM_operation:0520
name: PCR primer design (for conserved primers)


  [Part of this file has been deleted for brevity]

name: Comparative genomics
namespace: topic
def: Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes.
subset: topics
xref: BioCatalogue:Comparative Genomics
is_a: EDAM_topic:0622 ! Genomics

[Term]
id: EDAM_data:0850
name: Sequence set
namespace: data
def: A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.
comment: This concept may be used for arbitrary sequence sets and associated data arising from processing.
subset: data
synonym: "sequence_collection" EXACT [SO:0001260]
is_a: EDAM_data:2955 ! Sequence report

[Term]
id: EDAM_operation:0487
name: Haplotype inference
namespace: operation
def: Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated.
comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).
subset: operations
synonym: "Haplotype mapping" EXACT [http://edamontology.org]
synonym: "Haplotype reconstruction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0283 ! Linkage analysis
relationship: has_output EDAM_data:1863 {min_cardinality=1} ! Haplotype map

[Term]
id: EDAM_format:2001
name: simple
namespace: format
def: EMBOSS simple multiple alignment format.
subset: formats
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_operation:2499
name: Splicing analysis
namespace: operation
def: Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences.
subset: operations
synonym: "Splicing modelling" EXACT [http://edamontology.org]
is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison
is_a: EDAM_operation:2426 ! Modelling and simulation
is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)
relationship: has_output EDAM_data:1307 {min_cardinality=1} ! Nucleic acid features (splice sites)
relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing

[Term]
id: EDAM_data:1354
name: Sequence profile
namespace: data
def: Some type of statistical model representing a (typically multiple) sequence alignment.
subset: data
synonym: "sequence profile" EXACT [http://semanticscience.org/resource/SIO_010531]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs

[Term]
id: EDAM_data:1364
name: Hidden Markov model
namespace: data
def: A hidden Markov model representation of a set or alignment of sequences.
subset: data
synonym: "HMM" EXACT [http://edamontology.org]
is_a: EDAM_data:1354 ! Sequence profile

[Term]
id: EDAM_data:2854
name: Position-specific scoring matrix
namespace: data
def: A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment.
subset: data
is_a: EDAM_data:1354 ! Sequence profile
is_a: EDAM_data:2082 ! Matrix

[Term]
id: EDAM_data:1361
name: Position frequency matrix
namespace: data
def: A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position.
subset: data
synonym: "PFM" EXACT [http://edamontology.org]
is_a: EDAM_data:2854 ! Position-specific scoring matrix

[Term]
id: EDAM_data:1362
name: Position weight matrix
namespace: data
def: A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.
comment: Contributions of individual sequences to the matrix might be uneven (weighted).
subset: data
synonym: "PWM" EXACT [http://edamontology.org]
is_a: EDAM_data:2854 ! Position-specific scoring matrix

[Term]
id: EDAM_data:1363
name: Information content matrix


  [Part of this file has been deleted for brevity]

id: EDAM_data:2245
name: Sequence set (bootstrapped)
namespace: data
def: A collection of sequences output from a bootstrapping (resampling) procedure.
comment: Bootstrapping is often performed in phylogenetic analysis.
subset: data
is_a: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_operation:0487
name: Haplotype inference
namespace: operation
def: Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated.
comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).
subset: operations
synonym: "Haplotype mapping" EXACT [http://edamontology.org]
synonym: "Haplotype reconstruction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0283 ! Linkage analysis
relationship: has_output EDAM_data:1863 {min_cardinality=1} ! Haplotype map

[Term]
id: EDAM_format:2001
name: simple
namespace: format
def: EMBOSS simple multiple alignment format.
subset: formats
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_operation:2499
name: Splicing analysis
namespace: operation
def: Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences.
subset: operations
synonym: "Splicing modelling" EXACT [http://edamontology.org]
is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison
is_a: EDAM_operation:2426 ! Modelling and simulation
is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)
relationship: has_output EDAM_data:1307 {min_cardinality=1} ! Nucleic acid features (splice sites)
relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing

[Term]
id: EDAM_operation:0264
name: Splice transcript prediction
namespace: operation
def: Predict splicing alternatives or transcript isoforms from analysis of sequence data.
subset: operations
is_a: EDAM_operation:2499 ! Splicing analysis
relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing