Find EDAM ontology terms by name
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-query]             string     Name(s) to search for in ontology (Any
                                  string)
  [-outfile]           outobo     [*.edamname] 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:0001064
name: Sequence set ID
namespace: identifier
def: An identifier of a set of molecular sequence(s).
subset: identifier
is_a: EDAM:0000976 ! Identifier (typed)
is_a: EDAM:0002091 ! Accession
relationship: is_identifier_of EDAM:0000850 ! Sequence set

[Term]
id: EDAM:0001234
name: Sequence set (nucleic acid)
namespace: data
def: Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
subset: data
is_a: EDAM:0000850 ! Sequence set
is_a: EDAM:0002977 ! Nucleic acid sequence

[Term]
id: EDAM:0001233
name: Sequence set (protein)
namespace: data
def: Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
subset: data
is_a: EDAM:0000850 ! Sequence set

[Term]
id: EDAM:0002245
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:0000850 ! Sequence set

[Term]
id: EDAM:0002874
name: Sequence set (polymorphic)
namespace: data
def: A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata.
subset: data
is_a: EDAM:0001234 ! Sequence set (nucleic acid)

[Term]
id: EDAM:0000850
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 term may be used for arbitrary sequence sets and associated data arising from processing.
subset: data
is_a: EDAM:0002955 ! Sequence report

[Term]
id: EDAM:0001064
name: Sequence set ID
namespace: identifier
def: An identifier of a set of molecular sequence(s).
subset: identifier
is_a: EDAM:0000976 ! Identifier (typed)
is_a: EDAM:0002091 ! Accession
relationship: is_identifier_of EDAM:0000850 ! Sequence set

[Term]
id: EDAM:0001112
name: Sequence cluster ID
namespace: identifier
def: An identifier of a cluster of molecular sequence(s).
subset: identifier
is_a: EDAM:0001064 ! Sequence set ID
relationship: is_identifier_of EDAM:0001235 ! Sequence cluster

[Term]
id: EDAM:0002612
name: Sequence cluster ID (CluSTr)
namespace: identifier
def: Unique identifier of a sequence cluster from the CluSTr database.
subset: identifier
synonym: "CluSTr cluster ID" EXACT []
synonym: "CluSTr ID" EXACT []
regex: "[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(.[0-9])?"
is_a: EDAM:0001112 ! Sequence cluster ID

[Term]
id: EDAM:0002220
name: Sequence cluster ID (SYSTERS)
namespace: identifier
def: Unique identifier of a sequence cluster from the SYSTERS database.
subset: identifier
synonym: "SYSTERS cluster ID" EXACT []
is_a: EDAM:0001112 ! Sequence cluster ID

[Term]
id: EDAM:0002346
name: Sequence cluster ID (UniRef)
namespace: identifier
def: Unique identifier of an entry from the UniRef database.
subset: identifier
synonym: "UniRef entry accession" EXACT []
synonym: "UniRef cluster id" EXACT []
is_a: EDAM:0001112 ! Sequence cluster ID

[Term]


  [Part of this file has been deleted for brevity]

comment: The sequences are typically related, for example a family of sequences.
subset: data
synonym: "Protein sequence cluster" EXACT []
is_a: EDAM:0001233 ! Sequence set (protein)
is_a: EDAM:0001235 ! Sequence cluster

[Term]
id: EDAM:0001238
name: Proteolytic digest
namespace: data
def: A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses.
subset: data
is_a: EDAM:0001233 ! Sequence set (protein)

[Term]
id: EDAM:0001262
name: Peptide molecular weight hits
namespace: data
def: A report on peptide fragments of certain molecular weight(s) in one or more protein sequences.
subset: data
is_a: EDAM:0001233 ! Sequence set (protein)

[Term]
id: EDAM:0002245
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:0000850 ! Sequence set

[Term]
id: EDAM:0000850
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 term may be used for arbitrary sequence sets and associated data arising from processing.
subset: data
is_a: EDAM:0002955 ! Sequence report

[Term]
id: EDAM:0001235
name: Sequence cluster
namespace: data
def: A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.
comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information.
subset: data
is_a: EDAM:0000850 ! Sequence set
relationship: in_topic EDAM:0000164 ! Sequence clustering
relationship: in_topic EDAM:0000724 ! Protein families