EMBOSS: edamhasoutput

| edamhasoutput

## Wiki

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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:6.5.6.0

       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