Find EDAM ontology terms by has_output relation
Version: EMBOSS:6.5.0.0

   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_operation:0290
name: Sequence redundancy removal
namespace: operation
def: Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.
subset: operations
is_a: EDAM_operation:0291 ! Sequence clustering
relationship: has_output EDAM_data:2044 {min_cardinality=0} ! Sequence
relationship: has_topic EDAM_topic:0164 ! Sequence clustering

[Term]
id: EDAM_operation:2446
name: Sequence processing
namespace: operation
def: Process (read and / or write) one or more molecular sequences and associated annotation.
subset: operations
synonym: "Sequence processing (general)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:2044 {min_cardinality=0} ! Sequence
relationship: has_output EDAM_data:2044 {min_cardinality=0} ! Sequence
relationship: has_topic EDAM_topic:0080 ! Sequence analysis

[Term]
id: EDAM_operation:1813
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: operations
synonym: "Data retrieval (sequences)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2422 ! Data retrieval
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_output EDAM_data:2044 {min_cardinality=0} ! Sequence

[Term]
id: EDAM_operation:2404
name: Sequence motif processing
namespace: operation
def: Process (read and / or write) molecular sequence motifs.
subset: operations
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:1353 {min_cardinality=0} ! Sequence motif
relationship: has_output EDAM_data:1353 {min_cardinality=0} ! Sequence motif
relationship: has_topic EDAM_topic:0158 ! Sequence motifs

[Term]
id: EDAM_operation:0239
name: Sequence motif recognition
namespace: operation
def: Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s).


  [Part of this file has been deleted for brevity]

relationship: has_topic EDAM_topic:0080 ! Sequence analysis

[Term]
id: EDAM_operation:2451
name: Sequence comparison
namespace: operation
def: Compare two or more molecular sequences.
subset: operations
is_a: EDAM_operation:2403 ! Sequence analysis
is_a: EDAM_operation:2424 ! Comparison
relationship: has_input EDAM_data:2044 {min_cardinality=2} ! Sequence
relationship: has_output EDAM_data:2955 ! Sequence report
relationship: has_topic EDAM_topic:0159 ! Sequence comparison

[Term]
id: EDAM_operation:3197
name: Genetic variation analysis
namespace: operation
def: Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.
comment: Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.
subset: operations
synonym: "Sequence variation analysis" EXACT [http://edamontology.org]
synonym: "Genetic variation annotation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison
relationship: has_output EDAM_data:0918 ! Nucleic acid features (variation)

[Term]
id: EDAM_operation:0310
name: Sequence assembly
namespace: operation
def: Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.
comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.
subset: operations
is_a: EDAM_operation:2429 ! Mapping and assembly
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
relationship: has_output EDAM_data:0925 ! Sequence assembly
relationship: has_topic EDAM_topic:0196 ! Sequence assembly

[Term]
id: EDAM_operation:0258
name: Sequence alignment analysis
namespace: operation
def: Analyse a molecular sequence alignment.
subset: operations
is_a: EDAM_operation:2463 ! Sequence alignment processing
is_a: EDAM_operation:2946 ! Alignment analysis
relationship: has_input EDAM_data:0863 {min_cardinality=1} ! Sequence alignment ! Extends cardinality constraint on parent.
relationship: has_output EDAM_data:0867 {min_cardinality=1} ! Sequence alignment report
relationship: has_topic EDAM_topic:0182 ! Sequence alignment