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:6.5.6.0 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:0036071 name: N-glycan fucosylation namespace: biological_process def: The process of transferring a fucosyl group to an N-glycan. An N-glycan is the carbohydrate portion of an N-glycoprotein when attached to a nitrogen from a sparagine or arginine side-chains. synonym: "glycoprotein fucosylation" RELATED [GOC:bf] is_a: GO:0036065 ! fucosylation [Term] id: GO:0035977 name: protein deglycosylation involved in glycoprotein catabolic process namespace: biological_process def: The removal of sugar residues from a glycosylated protein that contributes to the breakdown of a glycoprotein. is_a: GO:0006517 ! protein deglycosylation relationship: part_of GO:0006516 ! glycoprotein catabolic process [Term] id: GO:0034436 name: glycoprotein transport namespace: biological_process def: The directed movement of a glycoprotein, any protein that contains covalent ly bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. is_a: GO:0015031 ! protein transport [Term] id: GO:0008424 name: glycoprotein 6-alpha-L-fucosyltransferase activity namespace: molecular_function def: Catalysis of the reaction: N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha- D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]- beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-gluco saminyl}-L-asparagine + GDP-L-fucose = N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2) -alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-( 1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-[alpha-L-fucos yl-(1->6)]-N-acetyl-beta-D-glucosaminyl}asparagine + GDP + H(+). synonym: "FucT" RELATED [EC:2.4.1.68] synonym: "GDP-fucose--glycoprotein fucosyltransferase activity" EXACT [EC:2.4.1. 68] synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha(1,6)fucosyltransferase a ctivity" EXACT [EC:2.4.1.68] synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha(1->6)fucosyltransferase activity" EXACT [EC:2.4.1.68] synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha-(1,6)fucosyltransferase activity" EXACT [EC:2.4.1.68] synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha-(1->6)fucosyltransferase activity" EXACT [EC:2.4.1.68] synonym: "GDP-L-fucose--glycoprotein fucosyltransferase activity" EXACT [EC:2.4. 1.68] synonym: "GDPfucose-glycoprotein fucosyltransferase activity" EXACT [EC:2.4.1.68 ] synonym: "glycoprotein fucosyltransferase activity" BROAD [EC:2.4.1.68] synonym: "guanosine diphosphofucose--glycoprotein fucosyltransferase activity" E XACT [EC:2.4.1.68] xref: EC:2.4.1.68 xref: KEGG:R05988 xref: MetaCyc:2.4.1.68-RXN xref: Reactome:REACT_25399 "Addition of alpha 1,6 fucose to the first GlcNAc of the N-glycan, Homo sapiens" xref: RHEA:12988 is_a: GO:0046921 ! alpha-(1->6)-fucosyltransferase activity [Term] id: GO:0018010 name: glycoprotein N-palmitoyltransferase activity namespace: molecular_function def: Catalysis of the reaction: palmitoyl-CoA + glycoprotein = CoA + N-palmitoyl glycoprotein. [Part of this file has been deleted for brevity] synonym: "cell wall hydroxyproline-rich glycoprotein metabolism" EXACT [] is_a: GO:0010384 ! cell wall proteoglycan metabolic process [Term] id: GO:0004653 name: polypeptide N-acetylgalactosaminyltransferase activity namespace: molecular_function def: Catalysis of the reaction: UDP-N-acetyl-D-galactosamine + polypeptide = UDP + N-acetyl-D-galactosaminyl-polypeptide. This reaction is the modification of s erine or threonine residues in polypeptide chains by the transfer of a N-acetylg alactose from UDP-N-acetylgalactose to the hydroxyl group of the amino acid; it is the first step in O-glycan biosynthesis. synonym: "glycoprotein acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1 .41] synonym: "polypeptide-N-acetylgalactosamine transferase activity" EXACT [EC:2.4. 1.41] synonym: "protein-UDP acetylgalactosaminyltransferase activity" EXACT [EC:2.4.1. 41] synonym: "UDP-acetylgalactosamine-glycoprotein acetylgalactosaminyltransferase a ctivity" EXACT [EC:2.4.1.41] synonym: "UDP-acetylgalactosamine:peptide-N-galactosaminyltransferase activity" EXACT [EC:2.4.1.41] synonym: "UDP-GalNAc:polypeptide N-acetylgalactosaminyl transferase activity" EX ACT [EC:2.4.1.41] synonym: "UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase activity" EXA CT [EC:2.4.1.41] synonym: "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminylt ransferase activity" EXACT [EC:2.4.1.41] synonym: "UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyl-transf erase activity" EXACT [EC:2.4.1.41] synonym: "UDP-N-acetylgalactosamine-glycoprotein N-acetylgalactosaminyltransfera se activity" EXACT [EC:2.4.1.41] synonym: "UDP-N-acetylgalactosamine-protein N-acetylgalactosaminyltransferase ac tivity" EXACT [EC:2.4.1.41] synonym: "UDP-N-acetylgalactosamine:kappa-casein polypeptide N-acetylgalactosami nyltransferase activity" EXACT [EC:2.4.1.41] synonym: "UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferas e activity" EXACT [EC:2.4.1.41] synonym: "UDP-N-acetylgalactosamine:protein N-acetylgalactosaminyl transferase a ctivity" EXACT [EC:2.4.1.41] synonym: "uridine diphosphoacetylgalactosamine-glycoprotein acetylgalactosaminyl transferase activity" EXACT [EC:2.4.1.41] xref: EC:2.4.1.41 xref: MetaCyc:2.4.1.41-RXN xref: Reactome:REACT_115586 "Addition of GalNAc to mucins to form the Tn antigen , Homo sapiens" is_a: GO:0008376 ! acetylgalactosaminyltransferase activity [Term] id: GO:0003827 name: alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase acti vity namespace: molecular_function def: Catalysis of the reaction: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R + UDP-N-a cetyl-alpha-D-glucosamine = 3-(2-[N-acetyl-beta-D-glucosaminyl]-alpha-D-mannosyl )-beta-D-mannosyl-R + H(+) + UDP. synonym: "alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.101] synonym: "alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransfera se activity" EXACT [EC:2.4.1.101] synonym: "alpha-1,3-mannosylglycoprotein beta-1,2-N-acetylglucosaminyltransferas e activity" EXACT [] synonym: "GnTI" RELATED [EC:2.4.1.101] 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:REACT_25236 "Addition of GlcNAc to the glycan on the A arm, Homo sapiens" xref: RHEA:11459 is_a: GO:0008375 ! acetylglucosaminyltransferase 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