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goname |
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Optionally the search can be restricted to specified GO namespaces.
% goname glycoprotein Find GO ontology terms by name Obo output file [goname.obo]: |
Go to the output files for this example
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. |
|
* | ||||||
| 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 | ||||||
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.
[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 |
| 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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.