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:6.6.0.0 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