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