                                   goname



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Function

   Find GO ontology terms by name

Description

   goname searches the names and synonyms 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 goname


% goname glycoprotein
Find GO ontology terms by name
Obo output file [goname.obo]:


   Go to the output files for this example

Command line arguments

Find GO ontology terms by name
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-query]             string     Name(s) to search for in ontology (Any
                                  string)
  [-outfile]           outobo     [*.goname] 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

   goname 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: goname.obo

[Term]
id: GO:0051082
name: unfolded protein binding
namespace: molecular_function
def: Interacting selectively and non-covalently with an unfolded protein.
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_yeast
subset: gosubset_prok
synonym: "binding unfolded ER proteins" NARROW []
synonym: "chaperone activity" RELATED []
synonym: "fimbrium-specific chaperone activity" RELATED []
synonym: "glycoprotein-specific chaperone activity" RELATED []
synonym: "histone-specific chaperone activity" RELATED []
synonym: "ribosomal chaperone activity" RELATED []
synonym: "tubulin-specific chaperone activity" RELATED []
is_a: GO:0005515 ! protein binding

[Term]
id: GO:0030144
name: alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase acti
vity
namespace: molecular_function
def: Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + N-acetyl-beta-D-glu
cosaminyl-1,2-alpha-D-mannosyl-1,3(6)-(N-acetyl-beta-D-glucosaminyl-1,2-alpha-D-
mannosyl,1,6(3))-beta-D-mannosyl-1,4-N-acetyl-beta-D-glucosaminyl-R = UDP + N-ac
etyl-beta-D-glucosaminyl-1,2-(N-acetyl-beta-D-glucosaminyl-1,6)-1,2-alpha-D-mann
osyl-1,3(6)-(N-acetyl-beta-D-glucosaminyl-1,2-alpha-D-mannosyl-1,6(3))-beta-D-ma
nnosyl-1,4-N-acetyl-beta-D-glucosaminyl-R. Only branched mannose glycopeptides w
ith non-reducing N-acetylglucosamine terminal residues act as acceptors.
synonym: "alpha-1,3(6)-mannosylglycoprotein beta-1,6-N-acetylglucosaminyltransfe
rase activity" EXACT []
synonym: "alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase
 activity" EXACT []
synonym: "alpha-mannoside beta-1,6-N-acetylglucosaminyltransferase activity" EXA
CT [EC:2.4.1.155]
synonym: "GnTV activity" EXACT [EC:2.4.1.155]
synonym: "N-acetylglucosaminyltransferase V activity" RELATED [EC:2.4.1.155]
synonym: "UDP-N-acetyl-D-glucosamine:6-[2-(N-acetyl-beta-D-glucosaminyl)-alpha-D
-mannosyl]-glycoprotein 6-beta-N-acetyl-D-glucosaminyltransferase activity" EXAC
T [EC:2.4.1.155]
synonym: "UDP-N-acetylglucosamine:alpha-mannoside-beta-1,6 N-acetylglucosaminylt
ransferase activity" EXACT [EC:2.4.1.155]
synonym: "UDP-N-acetylglucosamine:alpha-mannoside-beta1,6 N-acetylglucosaminyltr
ansferase activity" EXACT [EC:2.4.1.155]
synonym: "uridine diphosphoacetylglucosamine-alpha-mannoside beta-1->6-acetylglu
cosaminyltransferase activity" EXACT [EC:2.4.1.155]
synonym: "uridine diphosphoacetylglucosamine-alpha-mannoside beta1->6-acetylgluc
osaminyltransferase activity" EXACT [EC:2.4.1.155]
xref: EC:2.4.1.155
xref: MetaCyc:2.4.1.155-RXN
xref: Reactome:REACT_25314 "Addition of GlcNAc to position 5 by MGAT5, Homo sapi
ens"
xref: RHEA:16924
is_a: GO:0008375 ! acetylglucosaminyltransferase activity

[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:0006457
name: protein folding


  [Part of this file has been deleted for brevity]

xref: MetaCyc:2.4.1.146-RXN
xref: RHEA:12227
is_a: GO:0008375 ! acetylglucosaminyltransferase activity

[Term]
id: GO:0047186
name: N-acetylneuraminate 7-O(or 9-O)-acetyltransferase activity
namespace: molecular_function
def: Catalysis of the reaction: N-acetylneuraminate + acetyl-CoA = N-acetyl-7-O(
or 9-O)-acetylneuraminate + CoA.
synonym: "acetyl-CoA:N-acetylneuraminate 7-O(or 9-O)-acetyltransferase activity"
 EXACT [EC:2.3.1.45]
synonym: "acetyl-CoA:N-acetylneuraminate-7- and/or 8-O-acetyltransferase activit
y" EXACT [EC:2.3.1.45]
synonym: "acetyl-CoA:N-acetylneuraminate-7- or 8-O-acetyltransferase activity" E
XACT [EC:2.3.1.45]
synonym: "acetyl-CoA:N-acetylneuraminate-9(7)-O-acetyltransferase activity" EXAC
T [EC:2.3.1.45]
synonym: "acetyl-CoA:N-acetylneuraminate-9(or 7)-O-acetyltransferase activity" E
XACT [EC:2.3.1.45]
synonym: "glycoprotein 7(9)-O-acetyltransferase activity" EXACT [EC:2.3.1.45]
synonym: "N-acetylneuraminate 7(8)-O-acetyltransferase activity" EXACT [EC:2.3.1
.45]
synonym: "N-acetylneuraminate 7,8-O-acetyltransferase activity" EXACT [EC:2.3.1.
45]
synonym: "N-acetylneuraminate O7-(or O9-)acetyltransferase activity" EXACT [EC:2
.3.1.45]
synonym: "sialate O-acetyltransferase" BROAD [EC:2.3.1.45]
xref: EC:2.3.1.45
xref: MetaCyc:2.3.1.45-RXN
is_a: GO:0016413 ! O-acetyltransferase activity

[Term]
id: GO:0016263
name: glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity
namespace: molecular_function
def: Catalysis of the addition of a galactosyl residue to a non-reducing O-linke
d N-acetylgalactosamine residue in an O-glycan.
synonym: "Core 1 GalT" RELATED []
synonym: "UDP-galactose:glycoprotein-N-acetyl-D-galactosamine 3-beta-D-galactosy
ltransferase activity" EXACT [EC:2.4.1.122]
synonym: "UDPgalactose:glycoprotein-N-acetyl-D-galactosamine 3-beta-D-galactosyl
transferase activity" EXACT [EC:2.4.1.122]
synonym: "uridine diphosphogalactose-mucin beta-(1->3)-galactosyltransferase act
ivity" EXACT [EC:2.4.1.122]
xref: EC:2.4.1.122
xref: MetaCyc:2.4.1.122-RXN
xref: Reactome:REACT_116072 "C1GALT1 transfers galactose to the Tn antigen formi
ng Core 1 glycoproteins (T antigens), Homo sapiens"
is_a: GO:0048531 ! beta-1,3-galactosyltransferase activity

[Term]
id: GO:0009101
name: glycoprotein biosynthetic process
namespace: biological_process
def: The chemical reactions and pathways resulting in the formation of glycoprot
eins, any protein that contains covalently bound glycose (i.e. monosaccharide) r
esidues; the glycose occurs most commonly as oligosaccharide or fairly small pol
ysaccharide but occasionally as monosaccharide.
subset: gosubset_prok
synonym: "glycoprotein anabolism" EXACT []
synonym: "glycoprotein biosynthesis" EXACT []
synonym: "glycoprotein formation" EXACT []
synonym: "glycoprotein synthesis" EXACT []
is_a: GO:0009100 ! glycoprotein metabolic process
is_a: GO:0034645 ! cellular macromolecule biosynthetic process
is_a: GO:1901137 ! carbohydrate derivative 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
                    godef           Find GO ontology terms by definition
                    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
