                                    godef



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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:6.6.0.0

   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: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
is_a: GO:0044421 ! extracellular region part
relationship: part_of GO:0005605 ! basal lamina

[Term]
id: GO:0038026
name: reelin-mediated signaling pathway
namespace: biological_process
def: A series of molecular signals initiated by the binding of reelin (a secrete
d glycoprotein) to a receptor on the surface of a target cell, and ending with r
egulation of a downstream cellular process, e.g. transcription.
synonym: "reeler-mediated signaling pathway" EXACT [GOC:bf, PR:000013879]
synonym: "reelin-mediated signal transduction pathway" EXACT [GOC:bf]
synonym: "reelin-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0007166 ! cell surface receptor signaling pathway
created_by: rfoulger
creation_date: 2011-08-02T02:06:18Z

[Term]
id: GO:0016011
name: dystroglycan complex
namespace: cellular_component
def: A protein complex that includes alpha- and beta-dystroglycan, which are alt
ernative products of the same gene; the laminin-binding component of the dystrop
hin-associated glycoprotein complex, providing a link between the subsarcolemmal
 cytoskeleton (in muscle cells) and the extracellular matrix. Alpha-dystroglycan
 is an extracellular protein binding to alpha-laminin and to beta-dystroglycan;
beta-dystroglycan is a transmembrane protein which binds alpha-dystroglycan and
dystrophin.
is_a: GO:0043234 ! protein complex
is_a: GO:0044459 ! plasma membrane part
relationship: part_of GO:0016010 ! dystrophin-associated glycoprotein complex

[Term]
id: GO:0010405
name: arabinogalactan protein metabolic process
namespace: biological_process
def: The chemical reactions and pathways involving a cell wall arabinogalactan I
I glycoprotein, which is composed of a group of core protein of highly varying l
ength and domain complexity. These are O-glycosylated at one or more hydroxyprol
ine residues by arabinogalactan (AG) type II groups, which consist of (1->3)-bet
a-galactan and (1->6)-beta-linked galactan chains connected to each other by (1-
>3,1->6)-linked branch points, O-3 and O-6 positions substituted with terminal a
rabinosyl residues. Also, rhamnose, fucose, glucuronic and galacturonic acid can
 be present in the glycan structures.
synonym: "arabinogalactan protein metabolism" EXACT []
is_a: GO:0010404 ! cell wall hydroxyproline-rich glycoprotein metabolic process

[Term]
id: GO:0010404
name: cell wall hydroxyproline-rich glycoprotein metabolic process
namespace: biological_process
def: The chemical reactions and pathways involving a cell wall hydroxyproline-ri
ch glycoprotein that consist of a core-protein backbone O-glycosylated by one or
 more complex carbohydrates.
synonym: "cell wall hydroxyproline-rich glycoprotein metabolism" EXACT []
is_a: GO:0010384 ! cell wall proteoglycan metabolic process

[Term]
id: GO:0004569


  [Part of this file has been deleted for brevity]

def: The chemical reactions and pathways involving chondroitin sulfate proteogly
can, any glycoprotein whose glycosaminoglycan units are chondroitin sulfate. Cho
ndroitin sulfates are a group of 10-60 kDa glycosaminoglycans, widely distribute
d in cartilage and other mammalian connective tissues; the repeat units consist
of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate.
subset: gosubset_prok
synonym: "chondroitin sulfate proteoglycan metabolism" EXACT []
synonym: "chondroitin sulphate proteoglycan metabolic process" EXACT []
synonym: "chondroitin sulphate proteoglycan metabolism" EXACT []
is_a: GO:0006029 ! proteoglycan metabolic process
is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0030203 ! glycosaminoglycan metabolic process
is_a: GO:0043436 ! oxoacid metabolic process

[Term]
id: GO:0046884
name: follicle-stimulating hormone secretion
namespace: biological_process
def: The regulated release of follicle-stimulating hormone, a gonadotropic glyco
protein hormone secreted by the anterior pituitary.
synonym: "follicle stimulating hormone secretion" EXACT []
synonym: "follitropin secretion" EXACT []
synonym: "FSH secretion" EXACT []
is_a: GO:0032274 ! gonadotropin secretion

[Term]
id: GO:0018405
name: protein-keratan sulfate linkage via keratan sulfate D-glucuronyl-D-galacto
syl-D-galactosyl-D-xylosyl-L-threonine
namespace: biological_process
def: Keratan sulfate components are covalently linked to a core glycoprotein via
 O-glycosidic linkages between xylose and threonine residues.
subset: gosubset_prok
synonym: "protein-keratan sulphate linkage via keratan sulphate D-glucuronyl-D-g
alactosyl-D-galactosyl-D-xylosyl-L-threonine" EXACT []
xref: RESID:AA0247
is_a: GO:0018210 ! peptidyl-threonine modification

[Term]
id: GO:0010408
name: fasciclin-like arabinogalactan protein metabolic process
namespace: biological_process
def: The chemical reactions and pathways involving the cell wall arabinogalactan
 II glycoprotein variant which contains both an arabinogalactan protein (AGP) mo
tif and a fasciclin domain.
synonym: "fasciclin-like arabinogalactan protein metabolism" EXACT []
is_a: GO:0010405 ! arabinogalactan protein metabolic process

[Term]
id: GO:0006045
name: N-acetylglucosamine biosynthetic process
namespace: biological_process
def: The chemical reactions and pathways resulting in the formation of N-acetylg
lucosamine. The D isomer is a common structural unit of glycoproteins in plants,
 bacteria and animals; it is often the terminal sugar of an oligosaccharide grou
p of a glycoprotein.
subset: gosubset_prok
synonym: "N-acetylglucosamine anabolism" EXACT []
synonym: "N-acetylglucosamine biosynthesis" EXACT []
synonym: "N-acetylglucosamine formation" EXACT []
synonym: "N-acetylglucosamine synthesis" EXACT []
is_a: GO:0006044 ! N-acetylglucosamine metabolic process
is_a: GO:1901073 ! glucosamine-containing compound biosynthetic process


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
