                                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:6.6.0.0

   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


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: bioinformatics
subset: edam
subset: formats
synonym: "BioXSD XML format" EXACT []
xref: http://bioxsd.org
created_in: "beta12orEarlier"
documentation: http://bioxsd.org
is_a: EDAM_format:1919 ! Sequence record format
is_a: EDAM_format:1920 ! Sequence feature annotation format
is_a: EDAM_format:2332 ! XML
is_a: EDAM_format:2555 ! Alignment format (XML)
is_a: EDAM_format:2571 ! Raw sequence format
relationship: is_format_of EDAM_data:0863 ! Sequence alignment
relationship: is_format_of EDAM_data:1255 ! Feature record
relationship: is_format_of EDAM_data:2044 ! Sequence

[Term]
id: EDAM_format:2055
name: Sequence assembly format
namespace: format
def: Format for sequence assembly data.
subset: bioinformatics
subset: edam
subset: formats
created_in: "beta12orEarlier"
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0925 ! Sequence assembly

[Term]
id: EDAM_format:2014
name: Sequence-profile alignment format
namespace: format
def: Data format for a sequence-profile alignment.
subset: bioinformatics
subset: edam
subset: formats
created_in: "beta12orEarlier"
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0869 ! Sequence-profile alignment

[Term]
id: EDAM_format:2068
name: Sequence motif format
namespace: format
def: Format of a sequence motif.


  [Part of this file has been deleted for brevity]

relationship: is_format_of EDAM_data:1255 ! Feature record

[Term]
id: EDAM_format:2057
name: Sequence trace format
namespace: format
def: Format for sequence trace data (i.e. including base call information).
subset: bioinformatics
subset: edam
subset: formats
created_in: "beta12orEarlier"
is_a: EDAM_format:1919 ! Sequence record format
relationship: is_format_of EDAM_data:0924 ! Sequence trace

[Term]
id: EDAM_format:2159
name: Gene features (coding region) format
namespace: format
def: Format used for report on coding regions in nucleotide sequences.
subset: bioinformatics
subset: edam
subset: formats
created_in: "beta12orEarlier"
is_a: EDAM_format:2031 ! Gene annotation format
relationship: is_format_of EDAM_data:1313 ! Nucleic acid features (coding sequen
ce)

[Term]
id: EDAM_format:2571
name: Raw sequence format
namespace: format
def: Format of a raw molecular sequence (i.e. the alphabet used).
subset: bioinformatics
subset: edam
subset: formats
synonym: "Symbol_sequence" RELATED []
created_in: "beta12orEarlier"
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0848 ! Raw sequence

[Term]
id: EDAM_format:2920
name: Alignment format (pair only)
namespace: format
def: Data format for molecular sequence alignment information that can hold sequ
ence alignment(s) of only 2 sequences.
subset: bioinformatics
subset: edam
subset: formats
created_in: "beta12orEarlier"
is_a: EDAM_format:1921 ! Alignment format
relationship: is_format_of EDAM_data:1381 ! Sequence alignment (pair)


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 (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
