EMBOSS: ontotext manual

ontotext

Wiki

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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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-oboterms] (Parameter 1)	obo	Obo term filename and optional format, or reference (input query)	OBO bio-ontology term(s)
[-outfile] (Parameter 2)	outfile	Full text output file	Output file	<>*.ontotext
Additional (Optional) qualifiers
-subclasses	boolean	Extend the query matches to include all terms which are specialisations (sub-classes) of the matched terms.	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
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-oboterms" associated obo qualifiers
-iformat1 -iformat_oboterms	string	Input obo format	Any string
-iquery1 -iquery_oboterms	string	Input query fields or ID list	Any string
-ioffset1 -ioffset_oboterms	integer	Input start position offset	Any integer value	0
-idbname1 -idbname_oboterms	string	User-provided database name	Any string
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile	string	Output directory	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

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 that 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 do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.
comment: This concept may be used for arbitrary sequence sets and associated data 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 that 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 data 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://edamontology.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 entries." [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 more 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 restriction 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) procedure." [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, alignment 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 belonging to a group including (typically) sequence cluster information." [http://edamontology.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.

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

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: edam:1234

Input files for usage example 2

Database entry: edam:0850

Output file format

Output files for usage example

File: 1234.ontotext

Output files for usage example 2

File: 0850.ontotext

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments