EMBOSS: edamhasinput

| edamhasinput

## Wiki

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## Function

Find EDAM ontology terms by has_input relation

## Description

edamhasinput searches the has_input relations of EDAM terms and returns matching terms. The input is read from the installed EDAM databas. 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 edamhasinput

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

Go to the output files for this example

## Command line arguments

    Find EDAM ontology terms by has_input relation
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-identifier]        string     Identifier(s) to search for in ontology (Any
                                      string)
      [-outfile]           outobo     [*.edamhasinput] 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) | <*>.edamhasinput
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

edamhasinput 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: edamhasinput.obo

    [Term]
    id: EDAM_operation:2403
    name: Sequence analysis
    namespace: operation
    def: Analyse one or more known molecular sequences.
    subset: operations
    synonym: "Sequence analysis (general)" EXACT [http://edamontology.org]
    is_a: EDAM_operation:2446 ! Sequence processing
    relationship: has_input EDAM_data:2044 {min_cardinality=1} ! Sequence
    relationship: has_output EDAM_data:2955 {min_cardinality=1} ! Sequence report
    relationship: has_topic EDAM_topic:0080 ! Sequence analysis

    [Term]
    id: EDAM_operation:0292
    name: Sequence alignment construction
    namespace: operation
    def: Align (identify equivalent sites within) molecular sequences.
    subset: operations
    synonym: "Sequence alignment" EXACT [http://edamontology.org]
    synonym: "Sequence alignment computation" EXACT [http://edamontology.org]
    synonym: "Sequence alignment generation" EXACT [http://edamontology.org]
    is_a: EDAM_operation:2463 ! Sequence alignment processing !(?)
    is_a: EDAM_operation:2451 ! Sequence comparison
    is_a: EDAM_operation:2928 ! Alignment construction
    relationship: has_input EDAM_data:2044 {minCardinality=2, note="Applies to both pure/raw sequences and sequence records. Indirectly also to sequence sets or IDs (?)"} ! Sequence
    relationship: has_output EDAM_data:0863 {min_cardinality=1} ! Sequence alignment
    relationship: has_topic EDAM_topic:0182 ! Sequence alignment

    [Term]
    id: EDAM_operation:1780
    name: Sequence submission
    namespace: operation
    def: Submit a molecular sequence to a database.
    subset: operations
    is_a: EDAM_operation:2446 ! Sequence processing
    relationship: has_input EDAM_data:2044 {min_cardinality=1} ! Sequence
    relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition

    [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

      [Part of this file has been deleted for brevity]

    synonym: "PCR primer prediction" EXACT [http://edamontology.org]
    is_a: EDAM_operation:2419 ! Primer and probe design
    relationship: has_input EDAM_data:2977 ! Nucleic acid sequence
    relationship: has_output EDAM_data:1240 {min_cardinality=0} ! PCR primers
    relationship: has_topic EDAM_topic:3032 ! Primer or probe design

    [Term]
    id: EDAM_operation:2506
    name: Sequence alignment analysis (protein)
    namespace: operation
    def: Analyse a protein sequence alignment, typically to detect features or make predictions.
    subset: operations
    is_a: EDAM_operation:0258 ! Sequence alignment analysis
    is_a: EDAM_operation:2502 ! Protein data processing
    is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
    relationship: has_input EDAM_data:1384 {min_cardinality=1} ! Sequence alignment (protein)
    relationship: has_topic EDAM_topic:0741 ! Protein sequence alignment

    [Term]
    id: EDAM_operation:0361
    name: Sequence annotation
    namespace: operation
    def: Annotate a molecular sequence record with terms from a controlled vocabulary.
    subset: operations
    is_a: EDAM_operation:0226 ! Annotation
    relationship: has_input EDAM_data:0849 {min_cardinality=1} ! Sequence record
    relationship: has_output EDAM_data:0849 {min_cardinality=1} ! Sequence record

    [Term]
    id: EDAM_operation:0368
    name: Sequence masking
    namespace: operation
    def: Mask characters in a molecular sequence (replacing those characters with a mask character).
    comment: For example, SNPs or repeats in a DNA sequence might be masked.
    subset: operations
    is_a: EDAM_operation:0231 ! Sequence editing
    relationship: has_input EDAM_data:0851 {min_cardinality=1} ! Sequence mask character

    [Term]
    id: EDAM_operation:3180
    name: Sequence assembly evaluation
    namespace: operation
    def: Evaluate a DNA sequence assembly, typically for purposes of quality control.
    subset: operations
    is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
    is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
    is_a: EDAM_operation:2425 ! Optimisation and refinement
    relationship: has_input EDAM_data:0925 ! Sequence assembly
    relationship: has_output EDAM_data:3181 ! Sequence assembly report
    relationship: has_topic EDAM_topic:0196 ! Sequence assembly

## 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
edamhasoutput | Find EDAM ontology terms by has_output 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