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EMBOSS: goname
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:6.4.0.0

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-query]
(Parameter 1)		 string Name(s) to search for in ontology Any string  
[-outfile]
(Parameter 2)		 outobo Output ontology term file name OBO ontology term(s) <*>.goname
Additional (Optional) qualifiers
-namespace list By default all terms are returned. Searches can be limited to one or a few namespaces.
biological_process (Biological process)
cellular_component (Cellular component)
molecular_function (Molecular function)
 *
Advanced (Unprompted) qualifiers
-subclasses boolean Extend the query matches to include all terms which are specialisations (GO sub-classes) of the matched type. 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
Associated qualifiers
"-outfile" associated outobo qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
-oformat2
-oformat_outfile		 string Ontology term output format 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

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:0003980
name: UDP-glucose:glycoprotein glucosyltransferase activity
namespace: molecular_function
def: Catalysis of the addition of UDP-glucose on to asparagine-linked (N-linked) oligosaccharides of the form Man7-9GlcNAc2 on incorrectly folded glycoproteins.
synonym: "UGGT activity" EXACT []
xref: EC:2.4.1.-
xref: Reactome:12706 "UDP-glucose:glycoprotein glucosyltransferase activity"
is_a: GO:0035251 ! UDP-glucosyltransferase activity

[Term]
id: GO:0005201
name: extracellular matrix structural constituent
namespace: molecular_function
def: The action of a molecule that contributes to the structural integrity of the extracellular matrix.
subset: gosubset_prok
synonym: "extracellular matrix glycoprotein" NARROW []
is_a: GO:0005198 ! structural molecule activity

[Term]
id: GO:0009306
name: protein secretion
namespace: biological_process
def: The controlled release of proteins from a cell or group of cells.
alt_id: GO:0045166
alt_id: GO:0045731
subset: gosubset_prok
synonym: "glycoprotein secretion" NARROW []
synonym: "protein secretion during cell fate commitment" NARROW []
synonym: "protein secretion resulting in cell fate commitment" NARROW []
is_a: GO:0015031 ! protein transport
is_a: GO:0032940 ! secretion by cell

[Term]
id: GO:0017060
name: 3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity
namespace: molecular_function
def: Catalysis of the reaction: GDP-L-fucose + beta-D-galactosyl-(1,3)-N-acetyl-D-glucosaminyl-R = GDP + beta-D-galactosyl-(1,3)-[alpha-L-fucosyl-(1,4)]-N-acetyl-D-glucosaminyl-R.
synonym: "(Le(a))-dependent (alpha-3/4)-fucosyltransferase activity" NARROW [EC:2.4.1.65]
synonym: "(Lea)-dependent (alpha-3/4)-fucosyltransferase activity" EXACT [EC:2.4.1.65]
synonym: "3-alpha-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity" EXACT [EC:2.4.1.65]
synonym: "alpha(1,3/1,4) fucosyltransferase III" RELATED [EC:2.4.1.65]
synonym: "alpha(1,4)-L-fucosyltransferase activity" EXACT []
synonym: "alpha-(1,3/1,4) fucosyltransferase III activity" EXACT [EC:2.4.1.65]
synonym: "alpha-(1->4)-L-fucosyltransferase activity" EXACT [EC:2.4.1.65]
synonym: "alpha-4-L-fucosyltransferase activity" EXACT [EC:2.4.1.65]
synonym: "beta-acetylglucosaminylsaccharide fucosyltransferase activity" EXACT [EC:2.4.1.65]
synonym: "blood group Lewis alpha-4-fucosyltransferase" NARROW [EC:2.4.1.65]
synonym: "blood group Lewis alpha-4-fucosyltransferase activity" NARROW [EC:2.4.1.65]
synonym: "blood-group substance Le(a)-dependent fucosyltransferase activity" NARROW [EC:2.4.1.65]


  [Part of this file has been deleted for brevity]

synonym: "GNTI activity" EXACT [EC:2.4.1.101]
synonym: "N-acetylglucosaminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "N-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetyl-D-glucosamine:3-(alpha-D-mannosyl)-beta-D-mannosyl-glycoprotein 2-beta-N-acetyl-D-glucosaminyltransferase activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetylglucosaminyl:alpha-1,3-D-mannoside-beta-1,2-N-acetylglucosaminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetylglucosaminyl:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "uridine diphosphoacetylglucosamine-alpha-1,3-mannosylglycoprotein beta-1,2-N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.101]
xref: EC:2.4.1.101
xref: KEGG:R05983
xref: MetaCyc:2.4.1.101-RXN
xref: Reactome:11577 "alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity"
xref: RHEA:11459
is_a: GO:0008375 ! acetylglucosaminyltransferase activity

[Term]
id: GO:0047253
name: alpha-1,6-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase activity
namespace: molecular_function
def: Catalysis of the reaction: N-acetyl-beta-D-glucosaminyl-1,6-beta-D-(N-acetyl-B-glucosaminyl-1,2)-beta-D-mannosyl-R + UDP-N-acetyl-D-glucosamine = N-acetyl-beta-D-glucosaminyl-1,6-beta-D-(N-acetyl-D-glucosaminyl-1,2-beta)-(N-acetyl-D-glucosaminyl-1,4-beta)-D-mannosyl-R + UDP.
synonym: "mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyl-transferase activity" EXACT []
synonym: "mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.201]
synonym: "N-acetylglucosaminyltransferase VI activity" RELATED [EC:2.4.1.201]
synonym: "N-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase VI activity" EXACT [EC:2.4.1.201]
synonym: "UDP-N-acetyl-D-glucosamine:2,6-bis(N-acetyl-beta-D-glucosaminyl)-alpha-D-mannosyl-glycoprotein 4-beta-N-acetyl-D-glucosaminyltransferase activity" EXACT [EC:2.4.1.201]
synonym: "uridine diphosphoacetylglucosamine-glycopeptide beta-1->4-acetylglucosaminyltransferase VI" RELATED [EC:2.4.1.201]
synonym: "uridine diphosphoacetylglucosamine-glycopeptide beta-1->4-acetylglucosaminyltransferase VI activity" EXACT [EC:2.4.1.201]
xref: EC:2.4.1.201
xref: MetaCyc:2.4.1.201-RXN
is_a: GO:0008375 ! acetylglucosaminyltransferase activity

[Term]
id: GO:0047396
name: glycosylphosphatidylinositol diacylglycerol-lyase activity
namespace: molecular_function
def: Catalysis of the reaction: 6-(alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol = 1,2-diacyl-sn-glycerol + 6-(alpha-D-glucosaminyl)-1D-myo-inositol 1,2-cyclic phosphate.
subset: gosubset_prok
synonym: "(glycosyl)phosphatidylinositol-specific phospholipase C activity" EXACT [EC:4.6.1.14]
synonym: "6-(alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol diacyl-sn-glycerol-lyase [6-(alpha-D-glucosaminyl)-1D-myo-inositol 1,2-cyclic phosphate-forming]" RELATED [EC:4.6.1.14]
synonym: "6-(alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol diacylglycerol-lyase (1,2-cyclic-phosphate-forming) activity" EXACT [EC:4.6.1.14]
synonym: "glycosyl inositol phospholipid anchor-hydrolyzing enzyme activity" EXACT [EC:4.6.1.14]
synonym: "glycosylphosphatidylinositol-phospholipase C activity" NARROW [EC:4.6.1.14]
synonym: "glycosylphosphatidylinositol-specific phospholipase C activity" EXACT [EC:4.6.1.14]
synonym: "GPI-PLC activity" EXACT [EC:4.6.1.14]
synonym: "GPI-specific phospholipase C activity" EXACT [EC:4.6.1.14]
synonym: "variant-surface-glycoprotein phospholipase C activity" EXACT []
synonym: "VSG-lipase activity" EXACT [EC:4.6.1.14]
xref: EC:4.6.1.14
xref: MetaCyc:3.1.4.47-RXN
is_a: GO:0009975 ! cyclase activity
is_a: GO:0016849 ! phosphorus-oxygen lyase 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
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 © 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