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:6.5.0.0

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-identifier]
(Parameter 1)
string Identifier(s) to search for in ontology Any string  
[-outfile]
(Parameter 2)
outobo Output ontology term file name OBO ontology term(s) <*>.edamhasoutput
Additional (Optional) qualifiers
-namespace list By default all terms are returned. Searches can be limited to one or a few namespaces.
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 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. Boolean value Yes/No No
-subclasses boolean Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type. Boolean value Yes/No No
-obsolete boolean The default behaviour is to not use or return obsolete terms. This option if set will include all terms. Boolean value Yes/No No
Associated qualifiers
"-outfile" associated outobo qualifiers
-odirectory2
-odirectory_outfile
string Output directory Any string  
-oformat2
-oformat_outfile
string Ontology term output format Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 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

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 © 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