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godef |
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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:6.5.6.0
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
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| Qualifier | Type | Description | Allowed values | Default | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||
| [-query] (Parameter 1) |
string | Definition word(s) to search for in ontology | Any string | |||||||
| [-outfile] (Parameter 2) |
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 | ||||||
| Associated qualifiers | ||||||||||
| "-outfile" associated outobo qualifiers | ||||||||||
| -odirectory2 -odirectory_outfile |
string | Output directory | Any string | |||||||
| -oformat2 -oformat_outfile |
string | Ontology term output format | Any string | |||||||
| General qualifiers | ||||||||||
| -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:2.3.1.142] synonym: "protein acyltransferase activity" EXACT [EC:2.3.1.142] xref: EC:2.3.1.142 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:3.2.1.152] xref: EC:3.2.1.152 xref: MetaCyc:3.2.1.152-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 |
| 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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.