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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:220.127.116.11 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:0004579 name: dolichyl-diphosphooligosaccharide-protein glycotransferase activity namespace: molecular_function def: Catalysis of the reaction: dolichyl diphosphooligosaccharide + protein L-asparagine = dolichyl diphosphate + a glycoprotein with the oligosaccharide chain attached by glycosylamine linkage to protein L-asparagine. synonym: "asparagine N-glycosyltransferase activity" EXACT [EC:18.104.22.168] synonym: "dolichyl-diphosphooligosaccharide-protein glycosyltransferase activity" EXACT  synonym: "dolichyl-diphosphooligosaccharide:protein-L-asparagine oligopolysaccharidotransferase activity" EXACT [EC:22.214.171.124] synonym: "dolichyldiphosphooligosaccharide-protein glycosyltransferase activity" EXACT [EC:126.96.36.199] synonym: "dolichyldiphosphooligosaccharide-protein oligosaccharyltransferase activity" EXACT [EC:188.8.131.52] synonym: "dolichyldiphosphoryloligosaccharide-protein oligosaccharyltransferase activity" EXACT [EC:184.108.40.206] synonym: "dolichylpyrophosphodiacetylchitobiose-protein glycosyltransferase activity" EXACT [EC:220.127.116.11] synonym: "oligomannosyltransferase activity" RELATED [EC:18.104.22.168] xref: EC:22.214.171.124 xref: MetaCyc:126.96.36.199-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 membrane to the other. The D isomer of N-acetylglucosamine 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. 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-covalently 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 each other and surrounded by an acellular stalk tube composed of cellulose and glycoprotein. 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 immunological 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 confers 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 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 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 of a group of parenchyma cells which secrete a glycoprotein mucilage as a lubricant. 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 connective 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 of glycoprotein to alpha-D-mannosyl-(1->6)-D-mannose and beta-D-N-acetylglucosaminyl-(1->4)-beta-D-N-acetylglucosaminyl sequences. synonym: "endo-beta-mannosidase activity" EXACT [EC:188.8.131.52] xref: EC:184.108.40.206 xref: MetaCyc:220.127.116.11-RXN is_a: GO:0015923 ! mannosidase activity
|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|
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