                                 ontogetroot



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Function

   Get ontology root terms by child identifier

Description

   ontogetroot displays on-screen for a named ontology the root term
   statement(s). The information may be written to an output file in
   various formats.

   Ontologies from the EMBOSS data directory are used.

Usage

   Here is a sample session with ontogetroot


% ontogetroot edam:1234
Get ontology root terms by child identifier
Obo output file [1234.obo]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Get ontology root terms by child identifier
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-oboterms]          obo        Obo term filename and optional format, or
                                  reference (input query)
  [-outfile]           outobo     [*.ontogetroot] Output ontology term file
                                  name

   Additional (Optional) qualifiers:
   -obsolete           boolean    [N] The default behaviour is to not use or
                                  return obsolete terms. This option if set
                                  will include all terms.

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-oboterms" associated qualifiers
   -iformat1           string     Input obo format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -idbname1           string     User-provided database name

   "-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

  Input files for usage example

  Database entry: edam:1234

[Term]
id: EDAM_data:1234
name: Sequence set (nucleic acid)
namespace: data
def: Any collection of multiple nucleotide sequences and associated metadata tha
t do not (typically) correspond to common sequence database records or database
entries.
subset: data
is_a: EDAM_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence


Output file format

   The default behaviour is to report the entire OBO term statement from
   the ontology. Optionally, then only the the term id, name and
   namespace, or just the term id will be reported.

   The output file by default is in OBO plain text format as used by the
   ontologies in the EMBOSS data directory and explained at
   http://www.geneontology.org/GO.format.obo-1_2.shtml.

   Optionally, the output can be in HTML, OBO-XML or JSON format.

  Output files for usage example

  File: 1234.obo

[Term]
id: EDAM_data:0006
name: Data
namespace: data
def: Information, represented in an information artefact (data record) that is '
understandable' by dedicated computational tools that can use the data as input
or produce it as output.
subset: data
synonym: "Datum" EXACT [http://edamontology.org] {note="The multiplicity is not
taken into account."}
synonym: "Data record" EXACT [http://edamontology.org] {note="Currently we are f
or practical purposes not distinguishing a data record (a tool-understandable in
formation artefact) from data or datum (its content, the tool-understandable inf
ormation)."}
synonym: "Data set" EXACT [http://edamontology.org] {note="The multiplicity is n
ot taken into account."}
synonym: "Data" EXACT [http://wsio.org/data_002]
synonym: "continuant" BROAD [snap:Continuant]
synonym: "digital entity" RELATED [http://purl.org/biotop/biotop.owl#DigitalEnti
ty]
synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetu
ant] {note="GFO 'Perpetuant' is in general broader than data, but it may be seen
 narrower in the sense of being a concrete individual."}
synonym: "data item" RELATED [http://semanticscience.org/resource/SIO_000069] {n
ote="Data does theoretically not need to have a purpose, but in all regular case
s it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472
), in particular the bioinformatics (SIO_010065) and biological (SIO_010019)."}
synonym: "data item" RELATED [http://purl.obolibrary.org/obo/IAO_0000027] {note=
"IAO 'data item' is a closely related ontological category (concept) broader in
the sense of being any type of data in any role, and narrower in the sense of be
ing limited to a 'generically_dependent_continuant' (snap:GenericallyDependentCo
ntinuant), standing in relation of aboutness to some entity (http://purl.obolibr
ary.org/obo/IAO_0000030), and to data that is intended to be a truthful statemen
t about something."}
synonym: "information content entity" RELATED [http://purl.obolibrary.org/obo/IA
O_0000030] {note="IAO 'information content entity' is a closely related ontologi
cal category (concept) broader in the sense of covering any type of data in any
role, and narrower in the sense of being limited to a 'generically_dependent_con
tinuant' (snap:GenericallyDependentContinuant) and standing in relation of about
ness to some entity."}
synonym: "record" RELATED [http://semanticscience.org/resource/SIO_000088] {note
="Data does however not necessarily contain statements and not necessarily about
 an entity."}
relationship: has_topic EDAM_topic:0003 ! Topic ! Unfortunately, OBO-Edit2 doesn
't show the subject concept at the top level when browsed with the 'f' option.


Data files

   OBO-format ontologies must be installed in the EMBOSS data directory
   and indexed. This is done automatically for typical installations.

Notes

References

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It exits with a status of 0.

Known bugs

   None.

See also

                     Program name                        Description
                    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
                    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
                    ontocount       Count ontology term(s)
                    ontoget         Get ontology term(s)
                    ontogetcommon   Get common ancestor for terms
                    ontogetdown     Get ontology term(s) by parent id
   ontogetobsolete  Get ontology ontology terms
                    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

Author(s)

   Jon              Ison
   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.

                    This application was modified by Jon Ison
   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
