ontotext

 

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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:6.5.0.0

   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: data
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: data
synonym: "sequence_collection" EXACT [SO:0001260]
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)
namespace: data
subset: data
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]
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
namespace: data
subset: 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." [http://edamontology.org]
comment: This concept may be used for arbitrary sequence sets and associated data arising from processing.
synonym: "sequence_collection" EXACT [SO:0001260]
is_a: EDAM_data:2955 ! Sequence report

[Term]
id: EDAM_data:1234
name: Sequence set (nucleic acid)
namespace: data
subset: data
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]
is_a: EDAM_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence

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

[Term]
id: EDAM_data:1240
name: PCR primers
namespace: data
subset: data
def: "Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set." [http://edamontology.org]
is_a: EDAM_data:1234 ! Sequence set (nucleic acid)

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

[Term]
id: EDAM_data:0925
name: Sequence assembly


  [Part of this file has been deleted for brevity]

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]
comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information.
is_a: EDAM_data:0850 ! Sequence set
relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification
relationship: has_topic EDAM_topic:0724 ! Protein families

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

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

[Term]
id: EDAM_data:1233
name: Sequence set (protein)
namespace: data
subset: data
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]
is_a: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1238
name: Proteolytic digest
namespace: data
subset: data
def: "A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses." [http://edamontology.org]
is_a: EDAM_data:1233 ! Sequence set (protein)
relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification

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

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)

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