Please help by correcting and extending the Wiki pages.
Optionally the search can be restricted to specified GO namespaces.
% godef glycoprotein Find GO ontology terms by definition Obo output file [godef.obo]:
Go to the output files for this example
Find GO ontology terms by definition Version: EMBOSS:18.104.22.168 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
|Standard (Mandatory) qualifiers|
|string||Definition word(s) to search for in ontology||Any string|
|outobo||Output ontology term file name||OBO ontology term(s)||<*>.godef|
|Additional (Optional) qualifiers|
|-namespace||list||By default all terms are returned. Searches can be limited to one or a few namespaces.||
|Advanced (Unprompted) qualifiers|
|-subclasses||boolean||Extend the query matches to include all terms which are specialisations (GO sub-classes) of the matched type.||Boolean value Yes/No||No|
|-obsolete||boolean||The default behaviour is to not use or return obsolete terms. This option if set will include all terms.||Boolean value Yes/No||No|
|"-outfile" associated outobo qualifiers|
|string||Output directory||Any string|
|string||Ontology term output format||Any string|
|-auto||boolean||Turn off prompts||Boolean value Yes/No||N|
|-stdout||boolean||Write first file to standard output||Boolean value Yes/No||N|
|-filter||boolean||Read first file from standard input, write first file to standard output||Boolean value Yes/No||N|
|-options||boolean||Prompt for standard and additional values||Boolean value Yes/No||N|
|-debug||boolean||Write debug output to program.dbg||Boolean value Yes/No||N|
|-verbose||boolean||Report some/full command line options||Boolean value Yes/No||Y|
|-help||boolean||Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose||Boolean value Yes/No||N|
|-warning||boolean||Report warnings||Boolean value Yes/No||Y|
|-error||boolean||Report errors||Boolean value Yes/No||Y|
|-fatal||boolean||Report fatal errors||Boolean value Yes/No||Y|
|-die||boolean||Report dying program messages||Boolean value Yes/No||Y|
|-version||boolean||Report version number and exit||Boolean value Yes/No||N|
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.
[Term] id: GO:0043256 name: laminin complex namespace: cellular_component def: A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural 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 secreted glycoprotein) to a receptor on the surface of a target cell, and ending with regulation 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 alternative products of the same gene; the laminin-binding component of the dystrophin-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 II glycoprotein, which is composed of a group of core protein of highly varying length and domain complexity. These are O-glycosylated at one or more hydroxyproline residues by arabinogalactan (AG) type II groups, which consist of (1->3)-beta-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 arabinosyl 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-rich 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 proteoglycan, any glycoprotein whose glycosaminoglycan units are chondroitin sulfate. Chondroitin sulfates are a group of 10-60 kDa glycosaminoglycans, widely distributed 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 glycoprotein 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-galactosyl-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-galactosyl-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) motif 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-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group 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
|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|
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.