edamname 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 EDAM ontology terms by name Description edamname searches the names and synonyms of EDAM terms and returns matching terms. The input is read from the installed EDAM 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 EDAM namespaces. Usage Here is a sample session with edamname % edamname "*sequence_set*" Find EDAM ontology terms by name Obo output file [edamname.obo]: Go to the output files for this example Example 2 % edamname "*sequence_set*" -subclasses Find EDAM ontology terms by name Obo output file [edamname.obo]: Go to the output files for this example Command line arguments Find EDAM ontology terms by name Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-query] string Name(s) to search for in ontology (Any string) [-outfile] outobo [*.edamname] 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: data (Data entity); entity (Biological entity); format (Data format); identifier (Identifier); operation (Bioinformatics operation); resource (Data resource); topic (Field of bioinformatics study)) Advanced (Unprompted) qualifiers: -subclasses boolean [N] Extend the query matches to include all terms which are specialisations (EDAM 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 edamname queries the EDAM 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: edamname.obo [Term] id: EDAM_data:1233 name: Sequence set (protein) namespace: data def: Any collection of multiple protein sequences and associated metadata that d o not (typically) correspond to common sequence database records or database ent ries. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1064 name: Sequence set ID namespace: identifier def: An identifier of a set of molecular sequence(s). subset: bioinformatics subset: data subset: edam subset: identifiers created_in: "beta12orEarlier" is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession relationship: is_identifier_of EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:0850 name: Sequence set namespace: data def: A collection of multiple molecular sequences and associated metadata that d o not (typically) correspond to molecular sequence database records or entries a nd which (typically) are derived from some analytical method. comment: This concept may be used for arbitrary sequence sets and associated dat a arising from processing. subset: bioinformatics subset: data subset: edam synonym: "SO:0001260" RELATED [] created_in: "beta12orEarlier" is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_data:1234 name: Sequence set (nucleic acid) namespace: data def: Any collection of multiple nucleotide sequences and associated metadata tha t do not (typically) correspond to common sequence database records or database entries. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set is_a: EDAM_data:2977 ! Nucleic acid sequence [Term] id: EDAM_data:2245 name: Sequence set (bootstrapped) namespace: data def: A collection of sequences output from a bootstrapping (resampling) procedur e. comment: Bootstrapping is often performed in phylogenetic analysis. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set Output files for usage example 2 File: edamname.obo [Term] id: EDAM_data:1233 name: Sequence set (protein) namespace: data def: Any collection of multiple protein sequences and associated metadata that d o not (typically) correspond to common sequence database records or database ent ries. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1245 name: Sequence cluster (protein) namespace: data def: A cluster of protein sequences. comment: The sequences are typically related, for example a family of sequences. subset: bioinformatics subset: data subset: edam synonym: "Protein sequence cluster" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_data:1233 ! Sequence set (protein) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1262 name: Peptide molecular weight hits namespace: data def: A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:1233 ! Sequence set (protein) [Term] id: EDAM_data:1238 name: Proteolytic digest namespace: data def: A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:1233 ! Sequence set (protein) relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification [Term] id: EDAM_data:1064 [Part of this file has been deleted for brevity] id: EDAM_data:1246 name: Sequence cluster (nucleic acid) namespace: data def: A cluster of nucleotide sequences. comment: The sequences are typically related, for example a family of sequences. subset: bioinformatics subset: data subset: edam synonym: "Nucleotide sequence cluster" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_data:1234 ! Sequence set (nucleic acid) is_a: EDAM_data:1235 ! Sequence cluster [Term] id: EDAM_data:1239 name: Restriction digest namespace: data def: Restriction digest fragments from digesting a nucleotide sequence with rest riction sites using a restriction endonuclease. subset: bioinformatics subset: data subset: edam xref: SO:0000412 created_in: "beta12orEarlier" is_a: EDAM_data:1234 ! Sequence set (nucleic acid) [Term] id: EDAM_data:2245 name: Sequence set (bootstrapped) namespace: data def: A collection of sequences output from a bootstrapping (resampling) procedur e. comment: Bootstrapping is often performed in phylogenetic analysis. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_data:1235 name: Sequence cluster namespace: data def: A set of sequences that have been clustered or otherwise classified as belo nging to a group including (typically) sequence cluster information. comment: The cluster might include sequences identifiers, short descriptions, al ignment and summary information. subset: bioinformatics subset: data subset: edam created_in: "beta12orEarlier" is_a: EDAM_data:0850 ! Sequence set relationship: has_topic EDAM_topic:0724 ! Protein families relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification Data files The EDAM Ontology is included in EMBOSS as local database edam. 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 drfinddata Find public databases by data type drfindformat Find public databases by format drfindid Find public databases by identifier drfindresource Find public databases by resource 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 godef Find GO ontology terms by definition 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 wossdata Find programs by EDAM data wossinput Find programs by EDAM input data wossoperation Find programs by EDAM operation wossoutput Find programs by EDAM output data wossparam Find programs by EDAM parameter wosstopic Find programs by EDAM topic 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