                                    godef



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Find GO ontology terms by definition

Description

   godef searches the definition of gene ontology terms and returns
   matching terms. The input is read from the installed GO 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 GO namespaces.

Usage

   Here is a sample session with godef


% godef glycoprotein
Find GO ontology terms by definition
Obo output file [godef.obo]:


   Go to the output files for this example

Command line arguments

Find GO ontology terms by definition
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-query]             string     Definition word(s) to search for in ontology
                                  (Any string)
  [-outfile]           outobo     [*.godef] 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: biological_process
                                  (Biological process); cellular_component
                                  (Cellular component); molecular_function
                                  (Molecular function))

   Advanced (Unprompted) qualifiers:
   -subclasses         boolean    [N] Extend the query matches to include all
                                  terms which are specialisations (GO
                                  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

   godef queries the gene 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: godef.obo

[Term]
id: GO:0004579
name: dolichyl-diphosphooligosaccharide-protein glycotransferase activity
namespace: molecular_function
def: Catalysis of the reaction: dolichyl diphosphooligosaccharide + protein L-as
paragine = dolichyl diphosphate + a glycoprotein with the oligosaccharide chain
attached by glycosylamine linkage to protein L-asparagine.
synonym: "asparagine N-glycosyltransferase activity" EXACT [EC:2.4.1.119]
synonym: "dolichyl-diphosphooligosaccharide-protein glycosyltransferase activity
" EXACT []
synonym: "dolichyl-diphosphooligosaccharide:protein-L-asparagine oligopolysaccha
ridotransferase activity" EXACT [EC:2.4.1.119]
synonym: "dolichyldiphosphooligosaccharide-protein glycosyltransferase activity"
 EXACT [EC:2.4.1.119]
synonym: "dolichyldiphosphooligosaccharide-protein oligosaccharyltransferase act
ivity" EXACT [EC:2.4.1.119]
synonym: "dolichyldiphosphoryloligosaccharide-protein oligosaccharyltransferase
activity" EXACT [EC:2.4.1.119]
synonym: "dolichylpyrophosphodiacetylchitobiose-protein glycosyltransferase acti
vity" EXACT [EC:2.4.1.119]
synonym: "oligomannosyltransferase activity" RELATED [EC:2.4.1.119]
xref: EC:2.4.1.119
xref: MetaCyc:2.4.1.119-RXN
xref: Reactome:12500 "dolichyl-diphosphooligosaccharide-protein glycotransferase
 activity"
is_a: GO:0004576 ! oligosaccharyl transferase activity

[Term]
id: GO:0015572
name: N-acetylglucosamine transmembrane transporter activity
namespace: molecular_function
def: Catalysis of the transfer of N-acetylglucosamine from one side of the membr
ane to the other. The D isomer of N-acetylglucosamine is a common structural uni
t of glycoproteins in plants, bacteria and animals; it is often the terminal sug
ar of an oligosaccharide group of a glycoprotein.
alt_id: GO:0015580
subset: gosubset_prok
synonym: "D-GlcNAc transmembrane transporter activity" EXACT []
synonym: "N-Acetyl-D-glucosamine permease" RELATED []
synonym: "N-acetyl-D-glucosamine transmembrane transporter activity" EXACT []
synonym: "N-acetylchitosamine transmembrane transporter activity" EXACT []
synonym: "N-acetylglucosamine permease activity" RELATED []
is_a: GO:0015149 ! hexose transmembrane transporter activity

[Term]
id: GO:0002162
name: dystroglycan binding
namespace: molecular_function
def: Interacting selectively and non-covalently with dystroglycan. Dystroglycan
is glycoprotein found in non-muscle tissues as well as in muscle tissues, often
in association with dystrophin. The native dystroglycan cleaved into two non-cov
alently associated subunits, alpha (N-terminal) and beta (C-terminal).
is_a: GO:0001948 ! glycoprotein binding

[Term]
id: GO:0031150
name: sorocarp stalk development
namespace: biological_process
def: The process whose specific outcome is the progression of the sorocarp stalk
 over time, from its formation to the mature structure. The sorocarp stalk is a
tubular structure that consists of cellulose-covered cells stacked on top of eac
h other and surrounded by an acellular stalk tube composed of cellulose and glyc
oprotein. An example of this process is found in Dictyostelium discoideum.
synonym: "sorophore development" EXACT []
synonym: "stalk development" BROAD []
synonym: "stalk formation" BROAD []
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048856 ! anatomical structure development
relationship: part_of GO:0031154 ! culmination involved in sorocarp development


  [Part of this file has been deleted for brevity]

synonym: "positive regulation of glycoprotein biosynthetic process of formation
of immunological synapse" EXACT [GOC:obol]
synonym: "positive regulation of glycoprotein biosynthetic process of immunologi
cal synapse formation" EXACT [GOC:obol]
is_a: GO:0010560 ! positive regulation of glycoprotein biosynthetic process
relationship: part_of GO:0001771 ! immunological synapse formation

[Term]
id: GO:0016914
name: follicle-stimulating hormone complex
namespace: cellular_component
def: A gonadotrophic glycoprotein hormone secreted, in mammals, by the anterior
pituitary gland; consists of alpha and beta subunits, the latter of which confer
s hormonal specificity.
synonym: "follicle stimulating hormone complex" EXACT []
synonym: "FSH complex" EXACT []
is_a: GO:0043234 ! protein complex
is_a: GO:0044421 ! extracellular region part

[Term]
id: GO:0043256
name: laminin complex
namespace: cellular_component
def: A large, extracellular glycoprotein complex composed of three different pol
ypeptide chains, alpha, beta and gamma. Provides an integral part of the structu
ral scaffolding of basement membranes.
subset: goslim_pir
is_a: GO:0043234 ! protein complex
is_a: GO:0044420 ! extracellular matrix part
relationship: part_of GO:0005605 ! basal lamina

[Term]
id: GO:0048829
name: root cap development
namespace: biological_process
def: The process whose specific outcome is the progression of the root cap over
time, from its formation to the mature structure. The root cap protects the root
 meristem from friction as the root grows through the soil. The cap is made up o
f a group of parenchyma cells which secrete a glycoprotein mucilage as a lubrica
nt.
is_a: GO:0048856 ! anatomical structure development
relationship: part_of GO:0048364 ! root development

[Term]
id: GO:0051541
name: elastin metabolic process
namespace: biological_process
def: The chemical reactions and pathways involving elastin, a glycoprotein which
 is randomly coiled and crosslinked to form elastic fibers that are found in con
nective tissue.
synonym: "elastin metabolism" EXACT []
is_a: GO:0009100 ! glycoprotein metabolic process

[Term]
id: GO:0033947
name: mannosylglycoprotein endo-beta-mannosidase activity
namespace: molecular_function
def: Catalysis of the hydrolysis of the alpha-D-mannosyl-(1->6)-beta-D-mannosyl-
(1->4)-beta-D-N-acetylglucosaminyl-(1->4)-beta-D-N-acetylglucosaminyl sequence o
f glycoprotein to alpha-D-mannosyl-(1->6)-D-mannose and beta-D-N-acetylglucosami
nyl-(1->4)-beta-D-N-acetylglucosaminyl sequences.
synonym: "endo-beta-mannosidase activity" EXACT [EC:3.2.1.152]
xref: EC:3.2.1.152
xref: MetaCyc:3.2.1.152-RXN
is_a: GO:0015923 ! mannosidase activity


Data files

   The gene Ontology is included in EMBOSS as local database go.

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
                    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
                    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

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
