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:6.5.6.0 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 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:0060388 name: vitelline envelope namespace: cellular_component def: A glycoprotein-based structure that lies outside the plasma membrane and su rrounds 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 con nective 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 + proteogl ycan = 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 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 [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 dermata n 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-galacto samine 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 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:0070051 name: fibrinogen binding namespace: molecular_function def: Interacting selectively and non-covalently with fibrinogen, a highly solubl e 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-pal mitoylglycoprotein. synonym: "fatty-acyl-CoA:mucus-glycoprotein fatty-acyltransferase activity" EXAC T [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 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 [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 o f glycoprotein to alpha-D-mannosyl-(1->6)-D-mannose and beta-D-N-acetylglucosami nyl-(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-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 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