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:6.6.0.0 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: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 is_a: GO:0044421 ! extracellular region part relationship: part_of GO:0005605 ! basal lamina [Term] id: GO:0038026 name: reelin-mediated signaling pathway namespace: biological_process def: A series of molecular signals initiated by the binding of reelin (a secrete d glycoprotein) to a receptor on the surface of a target cell, and ending with r egulation of a downstream cellular process, e.g. transcription. synonym: "reeler-mediated signaling pathway" EXACT [GOC:bf, PR:000013879] synonym: "reelin-mediated signal transduction pathway" EXACT [GOC:bf] synonym: "reelin-mediated signalling pathway" EXACT [GOC:bf] is_a: GO:0007166 ! cell surface receptor signaling pathway created_by: rfoulger creation_date: 2011-08-02T02:06:18Z [Term] id: GO:0016011 name: dystroglycan complex namespace: cellular_component def: A protein complex that includes alpha- and beta-dystroglycan, which are alt ernative products of the same gene; the laminin-binding component of the dystrop hin-associated glycoprotein complex, providing a link between the subsarcolemmal cytoskeleton (in muscle cells) and the extracellular matrix. Alpha-dystroglycan is an extracellular protein binding to alpha-laminin and to beta-dystroglycan; beta-dystroglycan is a transmembrane protein which binds alpha-dystroglycan and dystrophin. is_a: GO:0043234 ! protein complex is_a: GO:0044459 ! plasma membrane part relationship: part_of GO:0016010 ! dystrophin-associated glycoprotein complex [Term] id: GO:0010405 name: arabinogalactan protein metabolic process namespace: biological_process def: The chemical reactions and pathways involving a cell wall arabinogalactan I I glycoprotein, which is composed of a group of core protein of highly varying l ength and domain complexity. These are O-glycosylated at one or more hydroxyprol ine residues by arabinogalactan (AG) type II groups, which consist of (1->3)-bet a-galactan and (1->6)-beta-linked galactan chains connected to each other by (1- >3,1->6)-linked branch points, O-3 and O-6 positions substituted with terminal a rabinosyl residues. Also, rhamnose, fucose, glucuronic and galacturonic acid can be present in the glycan structures. synonym: "arabinogalactan protein metabolism" EXACT [] is_a: GO:0010404 ! cell wall hydroxyproline-rich glycoprotein metabolic process [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:0004569 [Part of this file has been deleted for brevity] def: The chemical reactions and pathways involving chondroitin sulfate proteogly can, any glycoprotein whose glycosaminoglycan units are chondroitin sulfate. Cho ndroitin sulfates are a group of 10-60 kDa glycosaminoglycans, widely distribute d in cartilage and other mammalian connective tissues; the repeat units consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate. subset: gosubset_prok synonym: "chondroitin sulfate proteoglycan metabolism" EXACT [] synonym: "chondroitin sulphate proteoglycan metabolic process" EXACT [] synonym: "chondroitin sulphate proteoglycan metabolism" EXACT [] is_a: GO:0006029 ! proteoglycan metabolic process is_a: GO:0006790 ! sulfur compound metabolic process is_a: GO:0030203 ! glycosaminoglycan metabolic process is_a: GO:0043436 ! oxoacid metabolic process [Term] id: GO:0046884 name: follicle-stimulating hormone secretion namespace: biological_process def: The regulated release of follicle-stimulating hormone, a gonadotropic glyco protein hormone secreted by the anterior pituitary. synonym: "follicle stimulating hormone secretion" EXACT [] synonym: "follitropin secretion" EXACT [] synonym: "FSH secretion" EXACT [] is_a: GO:0032274 ! gonadotropin secretion [Term] id: GO:0018405 name: protein-keratan sulfate linkage via keratan sulfate D-glucuronyl-D-galacto syl-D-galactosyl-D-xylosyl-L-threonine namespace: biological_process def: Keratan sulfate components are covalently linked to a core glycoprotein via O-glycosidic linkages between xylose and threonine residues. subset: gosubset_prok synonym: "protein-keratan sulphate linkage via keratan sulphate D-glucuronyl-D-g alactosyl-D-galactosyl-D-xylosyl-L-threonine" EXACT [] xref: RESID:AA0247 is_a: GO:0018210 ! peptidyl-threonine modification [Term] id: GO:0010408 name: fasciclin-like arabinogalactan protein metabolic process namespace: biological_process def: The chemical reactions and pathways involving the cell wall arabinogalactan II glycoprotein variant which contains both an arabinogalactan protein (AGP) mo tif and a fasciclin domain. synonym: "fasciclin-like arabinogalactan protein metabolism" EXACT [] is_a: GO:0010405 ! arabinogalactan protein metabolic process [Term] id: GO:0006045 name: N-acetylglucosamine biosynthetic process namespace: biological_process def: The chemical reactions and pathways resulting in the formation of N-acetylg lucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide grou p of a glycoprotein. subset: gosubset_prok synonym: "N-acetylglucosamine anabolism" EXACT [] synonym: "N-acetylglucosamine biosynthesis" EXACT [] synonym: "N-acetylglucosamine formation" EXACT [] synonym: "N-acetylglucosamine synthesis" EXACT [] is_a: GO:0006044 ! N-acetylglucosamine metabolic process is_a: GO:1901073 ! glucosamine-containing compound 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 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