Find EDAM ontology terms by has_output relation
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-identifier]        string     Identifier(s) to search for in ontology (Any
                                  string)
  [-outfile]           outobo     [*.edamhasoutput] 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:
   -sensitive          boolean    [N] By default, the query keywords are
                                  matched against the EDAM term names (and
                                  synonyms) only. This option also matches the
                                  keywords against the EDAM term definitions
                                  and will therefore (typically) report more
                                  matches.
   -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:0001813
name: Sequence retrieval
namespace: operation
def: Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.
comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.
subset: operation
synonym: "Data retrieval (sequences)" EXACT []
is_a: EDAM:0002422 ! Data retrieval
is_a: EDAM:0002446 ! Sequence processing
relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0}

[Term]
id: EDAM:0000290
name: Sequence redundancy removal
namespace: operation
def: Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.
subset: operation
is_a: EDAM:0000291 ! Sequence clustering
relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0}
relationship: in_topic EDAM:0000164 ! Sequence clustering

[Term]
id: EDAM:0002446
name: Sequence processing
namespace: operation
def: Process (read and / or write) one or more molecular sequences and associated annotation.
subset: operation
is_a: EDAM:0002503 ! Sequence data processing
relationship: has_input EDAM:0002044 ! Sequence {minCardinality=0}
relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0}

[Term]
id: EDAM:0000288
name: Sequence word comparison
namespace: operation
def: Find exact character or word matches between molecular sequences without full sequence alignment.
subset: operation
is_a: EDAM:0002451 ! Sequence comparison
relationship: has_output EDAM:0000861 ! Sequence word alignment {minCardinality=1}

[Term]
id: EDAM:0000292
name: Sequence alignment
namespace: operation
def: Align (identify equivalent sites within) molecular sequences.
subset: operation
synonym: "Sequence alignment generation" EXACT []
is_a: EDAM:0002463 ! Sequence alignment processing
is_a: EDAM:0002451 ! Sequence comparison


  [Part of this file has been deleted for brevity]

is_a: EDAM:0002421 ! Database search
is_a: EDAM:0000239 ! Sequence motif recognition
is_a: EDAM:0002995 ! Sequence classification
relationship: has_output EDAM:0001298 ! Sequence features (motifs) {minCardinality=0}
relationship: in_topic EDAM:0000158 ! Sequence motifs

[Term]
id: EDAM:0000234
name: Sequence complexity calculation
namespace: operation
def: Calculate sequence complexity, for example to find low-complexity regions in sequences.
subset: operation
is_a: EDAM:0000236 ! Sequence composition calculation
relationship: has_output EDAM:0001259 ! Sequence property (complexity) {minCardinality=1}
relationship: in_topic EDAM:0000642 ! Low complexity sequence

[Term]
id: EDAM:0000253
name: Sequence feature detection
namespace: operation
def: Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions.
subset: operation
is_a: EDAM:0002403 ! Sequence analysis
is_a: EDAM:0002423 ! Prediction, detection and recognition
relationship: has_output EDAM:0001255 ! Sequence features {minCardinality=1}
relationship: in_topic EDAM:0000160 ! Sequence features

[Term]
id: EDAM:0000301
name: Sequence-3D profile alignment
namespace: operation
def: Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment).
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
subset: operation
is_a: EDAM:0000303 ! Protein fold recognition
is_a: EDAM:0002928 ! Alignment
is_a: EDAM:0002403 ! Sequence analysis
relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=2}
relationship: has_output EDAM:0000891 ! Sequence-3D profile alignment {minCardinality=1}
relationship: in_topic EDAM:0000184 ! Threading

[Term]
id: EDAM:0000235
name: Sequence ambiguity calculation
namespace: operation
def: Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes.
subset: operation
is_a: EDAM:0000236 ! Sequence composition calculation
relationship: has_output EDAM:0001260 ! Sequence property (ambiguity) {minCardinality=1}
relationship: in_topic EDAM:0000157 ! Sequence composition