                                  ontotext



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   Please help by correcting and extending the Wiki pages.

Function

   Get ontology term(s) original full text

Description

   ontotext reads one or more complete ontology term entries from a
   database or a file and writes them to a text file. Optionally, the
   first ontology term from the input stream only can be retrieved. The
   complete entry, including heading annotation, is retrieved and written
   and the data is not altered or reformatted in any way.

Usage

   Here is a sample session with ontotext


% ontotext edam:1234
Get ontology term(s) original full text
Full text output file [1234.ontotext]:


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

   Example 2


% ontotext edam:0850 -subclasses
Get ontology term(s) original full text
Full text output file [0850.ontotext]:


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

Command line arguments

Get ontology term(s) original full text
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-oboterms]          obo        Obo term filename and optional format, or
                                  reference (input query)
  [-outfile]           outfile    [*.ontotext] Full text output file

   Additional (Optional) qualifiers:
   -subclasses         boolean    [N] Extend the query matches to include all
                                  terms which are specialisations
                                  (sub-classes) of the matched terms.
   -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

   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

   The input is a standard EMBOSS ontology query.

   The major ontology sources defined as standard in EMBOSS installations
   are EDAM, GO (gene Ontology) and SO (Sequence Ontology).

   Data can also be read from ontology output in "obo" format written by
   an EMBOSS application.

  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: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence


  Input files for usage example 2

  Database entry: edam:0850

[Term]
id: EDAM_data:0850
name: Sequence set
namespace: data
def: A collection of multiple molecular sequences and associated metadata that d
o not (typically) correspond to molecular sequence database records or entries a
nd which (typically) are derived from some analytical method.
comment: This concept may be used for arbitrary sequence sets and associated dat
a arising from processing.
subset: bioinformatics
subset: data
subset: edam
synonym: "SO:0001260" RELATED []
created_in: "beta12orEarlier"
is_a: EDAM_data:2955 ! Sequence report


Output file format

   ontotext reports the full text of the input ontology terms.

  Output files for usage example

  File: 1234.ontotext

[Term]
id: EDAM_data:1234
name: Sequence set (nucleic acid)
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
def: "Any collection of multiple nucleotide sequences and associated metadata th
at do not (typically) correspond to common sequence database records or database
 entries." [http://edamontology.org]
namespace: data
is_a: EDAM_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence


  Output files for usage example 2

  File: 0850.ontotext

[Term]
id: EDAM_data:0850
name: Sequence set
comment: This concept may be used for arbitrary sequence sets and associated dat
a arising from processing.
subset: bioinformatics
subset: data
subset: edam
synonym: "SO:0001260" RELATED []
created_in: "beta12orEarlier"
def: "A collection of multiple molecular sequences and associated metadata that
do not (typically) correspond to molecular sequence database records or entries
and which (typically) are derived from some analytical method." [http://edamonto
logy.org]
namespace: data
is_a: EDAM_data:2955 ! Sequence report

[Term]
id: EDAM_data:1233
name: Sequence set (protein)
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
def: "Any collection of multiple protein sequences and associated metadata that
do not (typically) correspond to common sequence database records or database en
tries." [http://edamontology.org]
namespace: data
is_a: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1245
name: Sequence cluster (protein)
comment: The sequences are typically related, for example a family of sequences.
subset: bioinformatics
subset: data
subset: edam
synonym: "Protein sequence cluster" EXACT []
created_in: "beta12orEarlier"
def: "A cluster of protein sequences." [http://edamontology.org]
namespace: data
is_a: EDAM_data:1233 ! Sequence set (protein)
is_a: EDAM_data:1235 ! Sequence cluster

[Term]
id: EDAM_data:1262
name: Peptide molecular weight hits
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
def: "A report on peptide fragments of certain molecular weight(s) in one or mor
e protein sequences." [http://edamontology.org]
namespace: data
is_a: EDAM_data:1233 ! Sequence set (protein)

[Term]


  [Part of this file has been deleted for brevity]

id: EDAM_data:1246
name: Sequence cluster (nucleic acid)
comment: The sequences are typically related, for example a family of sequences.
subset: bioinformatics
subset: data
subset: edam
synonym: "Nucleotide sequence cluster" EXACT []
created_in: "beta12orEarlier"
def: "A cluster of nucleotide sequences." [http://edamontology.org]
namespace: data
is_a: EDAM_data:1234 ! Sequence set (nucleic acid)
is_a: EDAM_data:1235 ! Sequence cluster

[Term]
id: EDAM_data:1239
name: Restriction digest
subset: bioinformatics
subset: data
subset: edam
xref: SO:0000412
created_in: "beta12orEarlier"
def: "Restriction digest fragments from digesting a nucleotide sequence with res
triction sites using a restriction endonuclease." [http://edamontology.org]
namespace: data
is_a: EDAM_data:1234 ! Sequence set (nucleic acid)

[Term]
id: EDAM_data:2245
name: Sequence set (bootstrapped)
comment: Bootstrapping is often performed in phylogenetic analysis.
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
def: "A collection of sequences output from a bootstrapping (resampling) procedu
re." [http://edamontology.org]
namespace: data
is_a: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1235
name: Sequence cluster
comment: The cluster might include sequences identifiers, short descriptions, al
ignment and summary information.
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
def: "A set of sequences that have been clustered or otherwise classified as bel
onging to a group including (typically) sequence cluster information." [http://e
damontology.org]
namespace: data
is_a: EDAM_data:0850 ! Sequence set
relationship: has_topic EDAM_topic:0724 ! Protein families
relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification


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
                    drtext          Get data resource entries complete text
                    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
                    entret          Retrieve sequence entries from flatfile databases and files
                    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
                    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
                    textget         Get text data entries
                    textsearch      Search the textual description of sequence(s)
                    xmltext         Get XML document original full text

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
