godef 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 definition Description godef searches the definition 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 godef % godef glycoprotein Find GO ontology terms by definition Obo output file [godef.obo]: Go to the output files for this example Command line arguments Find GO ontology terms by definition Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-query] string Definition word(s) to search for in ontology (Any string) [-outfile] outobo [*.godef] 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 godef 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: godef.obo [Term] id: GO:0004579 name: dolichyl-diphosphooligosaccharide-protein glycotransferase activity namespace: molecular_function def: Catalysis of the reaction: dolichyl diphosphooligosaccharide + protein L-as paragine = dolichyl diphosphate + a glycoprotein with the oligosaccharide chain attached by glycosylamine linkage to protein L-asparagine. synonym: "asparagine N-glycosyltransferase activity" EXACT [EC:2.4.1.119] synonym: "dolichyl-diphosphooligosaccharide-protein glycosyltransferase activity " EXACT [] synonym: "dolichyl-diphosphooligosaccharide:protein-L-asparagine oligopolysaccha ridotransferase activity" EXACT [EC:2.4.1.119] synonym: "dolichyldiphosphooligosaccharide-protein glycosyltransferase activity" EXACT [EC:2.4.1.119] synonym: "dolichyldiphosphooligosaccharide-protein oligosaccharyltransferase act ivity" EXACT [EC:2.4.1.119] synonym: "dolichyldiphosphoryloligosaccharide-protein oligosaccharyltransferase activity" EXACT [EC:2.4.1.119] synonym: "dolichylpyrophosphodiacetylchitobiose-protein glycosyltransferase acti vity" EXACT [EC:2.4.1.119] synonym: "oligomannosyltransferase activity" RELATED [EC:2.4.1.119] xref: EC:2.4.1.119 xref: MetaCyc:2.4.1.119-RXN xref: Reactome:12500 "dolichyl-diphosphooligosaccharide-protein glycotransferase activity" is_a: GO:0004576 ! oligosaccharyl transferase activity [Term] id: GO:0015572 name: N-acetylglucosamine transmembrane transporter activity namespace: molecular_function def: Catalysis of the transfer of N-acetylglucosamine from one side of the membr ane to the other. The D isomer of N-acetylglucosamine is a common structural uni t of glycoproteins in plants, bacteria and animals; it is often the terminal sug ar of an oligosaccharide group of a glycoprotein. alt_id: GO:0015580 subset: gosubset_prok synonym: "D-GlcNAc transmembrane transporter activity" EXACT [] synonym: "N-Acetyl-D-glucosamine permease" RELATED [] synonym: "N-acetyl-D-glucosamine transmembrane transporter activity" EXACT [] synonym: "N-acetylchitosamine transmembrane transporter activity" EXACT [] synonym: "N-acetylglucosamine permease activity" RELATED [] is_a: GO:0015149 ! hexose transmembrane transporter activity [Term] id: GO:0002162 name: dystroglycan binding namespace: molecular_function def: Interacting selectively and non-covalently with dystroglycan. Dystroglycan is glycoprotein found in non-muscle tissues as well as in muscle tissues, often in association with dystrophin. The native dystroglycan cleaved into two non-cov alently associated subunits, alpha (N-terminal) and beta (C-terminal). is_a: GO:0001948 ! glycoprotein binding [Term] id: GO:0031150 name: sorocarp stalk development namespace: biological_process def: The process whose specific outcome is the progression of the sorocarp stalk over time, from its formation to the mature structure. The sorocarp stalk is a tubular structure that consists of cellulose-covered cells stacked on top of eac h other and surrounded by an acellular stalk tube composed of cellulose and glyc oprotein. An example of this process is found in Dictyostelium discoideum. synonym: "sorophore development" EXACT [] synonym: "stalk development" BROAD [] synonym: "stalk formation" BROAD [] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0031154 ! culmination involved in sorocarp development [Part of this file has been deleted for brevity] synonym: "positive regulation of glycoprotein biosynthetic process of formation of immunological synapse" EXACT [GOC:obol] synonym: "positive regulation of glycoprotein biosynthetic process of immunologi cal synapse formation" EXACT [GOC:obol] is_a: GO:0010560 ! positive regulation of glycoprotein biosynthetic process relationship: part_of GO:0001771 ! immunological synapse formation [Term] id: GO:0016914 name: follicle-stimulating hormone complex namespace: cellular_component def: A gonadotrophic glycoprotein hormone secreted, in mammals, by the anterior pituitary gland; consists of alpha and beta subunits, the latter of which confer s hormonal specificity. synonym: "follicle stimulating hormone complex" EXACT [] synonym: "FSH complex" EXACT [] is_a: GO:0043234 ! protein complex is_a: GO:0044421 ! extracellular region part [Term] id: GO:0043256 name: laminin complex namespace: cellular_component def: A large, extracellular glycoprotein complex composed of three different pol ypeptide chains, alpha, beta and gamma. Provides an integral part of the structu ral scaffolding of basement membranes. subset: goslim_pir is_a: GO:0043234 ! protein complex is_a: GO:0044420 ! extracellular matrix part relationship: part_of GO:0005605 ! basal lamina [Term] id: GO:0048829 name: root cap development namespace: biological_process def: The process whose specific outcome is the progression of the root cap over time, from its formation to the mature structure. The root cap protects the root meristem from friction as the root grows through the soil. The cap is made up o f a group of parenchyma cells which secrete a glycoprotein mucilage as a lubrica nt. is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0048364 ! root development [Term] id: GO:0051541 name: elastin metabolic process namespace: biological_process def: The chemical reactions and pathways involving elastin, a glycoprotein which is randomly coiled and crosslinked to form elastic fibers that are found in con nective tissue. synonym: "elastin metabolism" EXACT [] is_a: GO:0009100 ! glycoprotein metabolic process [Term] id: GO:0033947 name: mannosylglycoprotein endo-beta-mannosidase activity namespace: molecular_function def: Catalysis of the hydrolysis of the alpha-D-mannosyl-(1->6)-beta-D-mannosyl- (1->4)-beta-D-N-acetylglucosaminyl-(1->4)-beta-D-N-acetylglucosaminyl sequence o f glycoprotein to alpha-D-mannosyl-(1->6)-D-mannose and beta-D-N-acetylglucosami nyl-(1->4)-beta-D-N-acetylglucosaminyl sequences. synonym: "endo-beta-mannosidase activity" EXACT [EC:3.2.1.152] xref: EC:3.2.1.152 xref: MetaCyc:3.2.1.152-RXN is_a: GO:0015923 ! mannosidase 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 goname Find GO ontology terms by name 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