                                edamhasoutput



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Function

   Find EDAM ontology terms by has_output relation

Description

   edamhasoutput searches the has_output relations of EDAM terms and
   returns matching terms. The input is read from the installed EDAM
   database. The ontology term output can be written to screen, to file,
   or passed to another program. A wide range of standard ontology term
   formats may be specified for input and output.

   Optionally the search can be restricted to specified EDAM namespaces.

Usage

   Here is a sample session with edamhasoutput


% edamhasoutput sequence
Find EDAM ontology terms by has_output relation
Obo output file [edamhasoutput.obo]:


   Go to the output files for this example

Command line arguments

Find EDAM ontology terms by has_output relation
Version: EMBOSS:6.6.0.0

   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


Input file format

   edamhasoutput queries the EDAM ontology.

Output file format

   The output is a standard EMBOSS ontology term file.

   The results can be output in one of several styles by using the
   command-line qualifier -oformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: obo,
   brief, list, html, xml, json, excel.

   See: http://emboss.sf.net/docs/themes/OntologyFormats.html for further
   information on ontology formats.

  Output files for usage example

  File: edamhasoutput.obo

[Term]
id: EDAM_operation:0290
name: Sequence redundancy removal
namespace: operation
def: Compare two or more molecular sequences, identify and remove redundant sequ
ences based on some criteria.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0291 ! Sequence clustering
relationship: has_output EDAM_data:2044 ! Sequence
relationship: has_topic EDAM_topic:0164 ! Sequence clustering

[Term]
id: EDAM_operation:1813
name: Sequence retrieval
namespace: operation
def: Query a sequence data resource (typically a database) and retrieve sequence
s and / or annotation.
comment: This includes direct retrieval methods (e.g. the dbfetch program) but n
ot those that perform calculations on the sequence.
subset: bioinformatics
subset: edam
subset: operations
synonym: "Data retrieval (sequences)" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:2422 ! Data retrieval
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_output EDAM_data:2044 ! Sequence

[Term]
id: EDAM_operation:2871
name: Sequence tagged site (STS) mapping
namespace: operation
def: Generate a physical DNA map (sequence map) from analysis of sequence tagged
 sites (STS).
comment: An STS is a short subsequence of known sequence and location that occur
s only once in the chromosome or genome that is being mapped. Sources of STSs in
clude 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (S
SLPs), and random genomic sequences from cloned genomic DNA or database sequence
s.
subset: bioinformatics
subset: edam
subset: operations
synonym: "Sequence mapping" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:2944 ! Physical mapping
relationship: has_output EDAM_data:1279 ! Sequence map

[Term]
id: EDAM_operation:0310
name: Sequence assembly
namespace: operation
def: Combine (align and merge) overlapping fragments of a DNA sequence to recons
truct the original sequence.
comment: For example, assemble overlapping reads from paired-end sequencers into
 contigs (a contiguous sequence corresponding to read overlaps). Or assemble con
tigs, for example ESTs and genomic DNA fragments, depending on the detected frag
ment overlaps.
subset: bioinformatics
subset: edam


  [Part of this file has been deleted for brevity]

subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2463 ! Sequence alignment processing
relationship: has_input EDAM_data:0863 ! Sequence alignment
relationship: has_output EDAM_data:1711 ! Sequence alignment image

[Term]
id: EDAM_operation:0491
name: Pairwise sequence alignment construction
namespace: operation
def: Align exactly two molecular sequences.
comment: Methods might perform one-to-one, one-to-many or many-to-many compariso
ns.
subset: bioinformatics
subset: edam
subset: operations
synonym: "Pairwise sequence alignment" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:0292 ! Sequence alignment construction
relationship: has_output EDAM_data:1381 ! Sequence alignment (pair)

[Term]
id: EDAM_operation:0483
name: Structured RNA prediction and optimisation
namespace: operation
def: Predict or optimise RNA sequences (sequence pools) with likely secondary an
d tertiary structure for in vitro selection.
subset: bioinformatics
subset: edam
subset: operations
synonym: "Nucleic acid folding family identification" EXACT []
synonym: "RNA inverse folding" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:2425 ! Optimisation and refinement
is_a: EDAM_operation:3095 ! Nucleic acid design
relationship: has_output EDAM_data:1234 ! Sequence set (nucleic acid)
relationship: has_topic EDAM_topic:2953 ! Nucleic acid design

[Term]
id: EDAM_operation:0449
name: Sequence alignment analysis (site correlation)
namespace: operation
def: Analyse correlations between sites in a molecular sequence alignment.
comment: This is typically done to identify possible covarying positions and pre
dict contacts or structural constraints in protein structures.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0258 ! Sequence alignment analysis
relationship: has_output EDAM_data:1416 ! Sequence alignment report (site correl
ation)


Data files

   The EDAM Ontology is included in EMBOSS as local database edam.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

                     Program name                        Description
                    drfinddata      Find public databases by data type
                    drfindformat    Find public databases by format
                    drfindid        Find public databases by identifier
                    drfindresource  Find public databases by resource
                    edamdef         Find EDAM ontology terms by definition
                    edamhasinput    Find EDAM ontology terms by has_input relation
                    edamisformat    Find EDAM ontology terms by is_format_of relation
                    edamisid        Find EDAM ontology terms by is_identifier_of relation
                    edamname        Find EDAM ontology terms by name
                    godef           Find GO ontology terms by definition
                    goname          Find GO ontology terms by name
                    ontoget         Get ontology term(s)
                    ontogetcommon   Get common ancestor for terms
                    ontogetdown     Get ontology term(s) by parent id
   ontogetobsolete  Get ontology ontology terms
                    ontogetroot     Get ontology root terms by child identifier
                    ontogetsibs     Get ontology term(s) by id with common parent
                    ontogetup       Get ontology term(s) by id of child
                    ontoisobsolete  Report whether an ontology term id is obsolete
                    ontotext        Get ontology term(s) original full text
                    wossdata        Find programs by EDAM data
                    wossinput       Find programs by EDAM input data
                    wossoperation   Find programs by EDAM operation
                    wossoutput      Find programs by EDAM output data
                    wossparam       Find programs by EDAM parameter
                    wosstopic       Find programs by EDAM topic

Author(s)

   Peter            Rice
   European         Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton,         Cambridge CB10 1SD, UK

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

                    This program is intended to be used by everyone and everything, from
                    naive users to embedded scripts.

Comments

                    None
