edamisformat

 

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Function

Find EDAM ontology terms by is_format_of relation

Description

edamisformat searches the is_format_of 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 edamisformat


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

Go to the output files for this example

Command line arguments

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

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

edamisformat 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: edamisformat.obo

[Term]
id: EDAM_format:2352
name: BioXSD
namespace: format
def: BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more).
subset: formats
synonym: "BioXSD XML format" EXACT [http://edamontology.org]
xref: http://bioxsd.org {documentation=true}
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:1919 ! Sequence record format
is_a: EDAM_format:1920 ! Sequence feature annotation format
is_a: EDAM_format:2555 ! Alignment format (XML)
is_a: EDAM_format:2332 ! XML
relationship: is_format_of EDAM_data:2044 ! Sequence
relationship: is_format_of EDAM_data:1255 ! Feature record
relationship: is_format_of EDAM_data:0863 ! Sequence alignment

[Term]
id: EDAM_format:2202
name: Sequence record full format
namespace: format
def: Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database.
subset: formats
is_a: EDAM_format:1919 ! Sequence record format
relationship: is_format_of EDAM_data:2201 ! Sequence record full

[Term]
id: EDAM_format:2068
name: Sequence motif format
namespace: format
def: Format of a sequence motif.
subset: formats
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1353 ! Sequence motif

[Term]
id: EDAM_format:2067
name: Sequence distance matrix format
namespace: format
def: Format of a matrix of genetic distances between molecular sequences.
subset: formats
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0870 ! Sequence distance matrix

[Term]
id: EDAM_format:2203
name: Sequence record lite format
namespace: format
def: Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment.
subset: formats


  [Part of this file has been deleted for brevity]

namespace: format
def: Format of a sequence annotation track.
subset: formats
is_a: EDAM_format:1920 ! Sequence feature annotation format
relationship: is_format_of EDAM_data:3002 ! Sequence annotation track

[Term]
id: EDAM_format:2920
name: Alignment format (pair only)
namespace: format
def: Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.
subset: formats
is_a: EDAM_format:1921 ! Alignment format
relationship: is_format_of EDAM_data:1381 ! Sequence alignment (pair)

[Term]
id: EDAM_format:2155
name: Sequence features (repeats) format
namespace: format
def: Format used for map of repeats in molecular (typically nucleotide) sequences.
subset: formats
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1299 ! Sequence features (repeats)

[Term]
id: EDAM_format:2921
name: Sequence variation annotation format
namespace: format
def: Format of sequence variation annotation.
subset: formats
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0918 ! Nucleic acid features (variation)

[Term]
id: EDAM_format:2055
name: Sequence assembly format
namespace: format
def: Format for sequence assembly data.
subset: formats
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0925 ! Sequence assembly

[Term]
id: EDAM_format:2057
name: Sequence trace format
namespace: format
def: Format for sequence trace data (i.e. including base call information).
subset: formats
is_a: EDAM_format:1919 ! Sequence record format
relationship: is_format_of EDAM_data:0924 ! Sequence trace

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
edamhasoutput Find EDAM ontology terms by has_output 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