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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:184.108.40.206 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:0060388 name: vitelline envelope namespace: cellular_component def: A glycoprotein-based structure that lies outside the plasma membrane and surrounds the egg before fertilization. synonym: "fertilization membrane" RELATED  is_a: GO:0035805 ! egg coat [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:0050698 name: proteoglycan sulfotransferase activity namespace: molecular_function def: Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + proteoglycan = adenosine 3',5'-bisphosphate + proteoglycan sulfate. A proteoglycan is a glycoprotein whose carbohydrate units are glycosaminoglycans. synonym: "proteoglycan sulfate transfer" RELATED  synonym: "proteoglycan sulphotransferase activity" EXACT  xref: EC:2.8.2.- is_a: GO:0008146 ! sulfotransferase activity [Term] id: GO:0050654 name: chondroitin sulfate proteoglycan metabolic process namespace: biological_process 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 [Term] id: GO:0050651 name: dermatan sulfate proteoglycan biosynthetic process namespace: biological_process def: The chemical reactions and pathways resulting in the formation of dermatan sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are dermatan sulfate (chondroitin sulfate B). Dermatan sulfate is a glycosaminoglycan with repeats consisting of beta-(1,4)-linked L-iduronyl-beta-(1,3)-N-acetyl-D-galactosamine 4-sulfate units. subset: gosubset_prok synonym: "chondroitin sulfate B proteoglycan biosynthesis" EXACT  synonym: "chondroitin sulfate B proteoglycan biosynthetic process" EXACT  synonym: "dermatan sulfate proteoglycan anabolism" EXACT  synonym: "dermatan sulfate proteoglycan biosynthesis" EXACT  synonym: "dermatan sulfate proteoglycan formation" EXACT  synonym: "dermatan sulfate proteoglycan synthesis" EXACT  [Part of this file has been deleted for brevity] 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:0070051 name: fibrinogen binding namespace: molecular_function def: Interacting selectively and non-covalently with fibrinogen, a highly soluble hexameric glycoprotein complex that is found in blood plasma and is converted to fibrin by thrombin in the coagulation cascade. is_a: GO:0032403 ! protein complex binding [Term] id: GO:0047965 name: glycoprotein O-fatty-acyltransferase activity namespace: molecular_function def: Catalysis of the reaction: palmitoyl-CoA + mucus glycoprotein = CoA + O-palmitoylglycoprotein. synonym: "fatty-acyl-CoA:mucus-glycoprotein fatty-acyltransferase activity" EXACT [EC:220.127.116.11] synonym: "protein acyltransferase activity" EXACT [EC:18.104.22.168] xref: EC:22.214.171.124 xref: MetaCyc:GLYCOPROTEIN-O-FATTY-ACYLTRANSFERASE-RXN is_a: GO:0016416 ! O-palmitoyltransferase activity [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 [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:126.96.36.199] xref: EC:188.8.131.52 xref: MetaCyc:184.108.40.206-RXN is_a: GO:0004567 ! beta-mannosidase activity [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
|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.