|   | goname | 
Please help by correcting and extending the Wiki pages.
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:6.6.0.0
   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
 | 
| 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: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 activity namespace: molecular_function def: Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + N-acetyl-beta-D-glucosaminyl-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-acetyl-beta-D-glucosaminyl-1,2-(N-acetyl-beta-D-glucosaminyl-1,6)-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. Only branched mannose glycopeptides with non-reducing N-acetylglucosamine terminal residues act as acceptors. synonym: "alpha-1,3(6)-mannosylglycoprotein beta-1,6-N-acetylglucosaminyltransferase activity" EXACT [] synonym: "alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity" EXACT [] synonym: "alpha-mannoside beta-1,6-N-acetylglucosaminyltransferase activity" EXACT [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" EXACT [EC:2.4.1.155] synonym: "UDP-N-acetylglucosamine:alpha-mannoside-beta-1,6 N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.155] synonym: "UDP-N-acetylglucosamine:alpha-mannoside-beta1,6 N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.155] synonym: "uridine diphosphoacetylglucosamine-alpha-mannoside beta-1->6-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.155] synonym: "uridine diphosphoacetylglucosamine-alpha-mannoside beta1->6-acetylglucosaminyltransferase 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 sapiens" 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-rich 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 activity" EXACT [EC:2.3.1.45] synonym: "acetyl-CoA:N-acetylneuraminate-7- or 8-O-acetyltransferase activity" EXACT [EC:2.3.1.45] synonym: "acetyl-CoA:N-acetylneuraminate-9(7)-O-acetyltransferase activity" EXACT [EC:2.3.1.45] synonym: "acetyl-CoA:N-acetylneuraminate-9(or 7)-O-acetyltransferase activity" EXACT [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-linked N-acetylgalactosamine residue in an O-glycan. synonym: "Core 1 GalT" RELATED [] synonym: "UDP-galactose:glycoprotein-N-acetyl-D-galactosamine 3-beta-D-galactosyltransferase activity" EXACT [EC:2.4.1.122] synonym: "UDPgalactose:glycoprotein-N-acetyl-D-galactosamine 3-beta-D-galactosyltransferase activity" EXACT [EC:2.4.1.122] synonym: "uridine diphosphogalactose-mucin beta-(1->3)-galactosyltransferase activity" 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 forming 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 glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide 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 | 
| 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.