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goname
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 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
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 th
e 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-acety
l-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" NAR
ROW [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-acetylglucosaminyltransferas
e I activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetyl-D-glucosamine:3-(alpha-D-mannosyl)-beta-D-mannosyl-glycop
rotein 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-acetylglucos
aminyltransferase I activity" EXACT [EC:2.4.1.101]
synonym: "UDP-N-acetylglucosaminyl:alpha-3-D-mannoside beta-1,2-N-acetylglucosam
inyltransferase 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-acetylglucosaminyl
transferase activity"
xref: RHEA:11459
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
[Term]
id: GO:0047253
name: alpha-1,6-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase act
ivity
namespace: molecular_function
def: Catalysis of the reaction: N-acetyl-beta-D-glucosaminyl-1,6-beta-D-(N-acety
l-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-gl
ucosaminyl-1,4-beta)-D-mannosyl-R + UDP.
synonym: "mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyl-transferase activi
ty" EXACT []
synonym: "mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyltransferase activit
y" EXACT [EC:2.4.1.201]
synonym: "N-acetylglucosaminyltransferase VI activity" RELATED [EC:2.4.1.201]
synonym: "N-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferas
e 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" EXA
CT [EC:2.4.1.201]
synonym: "uridine diphosphoacetylglucosamine-glycopeptide beta-1->4-acetylglucos
aminyltransferase VI" RELATED [EC:2.4.1.201]
synonym: "uridine diphosphoacetylglucosamine-glycopeptide beta-1->4-acetylglucos
aminyltransferase 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-i
nositol = 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" EXAC
T [EC:4.6.1.14]
synonym: "6-(alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol diacyl-sn-glyc
erol-lyase [6-(alpha-D-glucosaminyl)-1D-myo-inositol 1,2-cyclic phosphate-formin
g]" 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" EXA
CT [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 (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
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