edamisid 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 is_identifier_of relation Description edamisid searches the is_identifier_of relations 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 edamisid % edamisid sequence Find EDAM ontology terms by is_identifier_of relation Obo output file [edamisid.obo]: Go to the output files for this example Command line arguments Find EDAM ontology terms by is_identifier_of relation Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-identifier] string Identifier(s) to search for in ontology (Any string) [-outfile] outobo [*.edamisid] 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: -sensitive boolean [N] By default, the query keywords are matched against the EDAM term names (and synonyms) only. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches. -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 edamisid 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: edamisid.obo [Term] id: EDAM:0001063 name: Sequence identifier namespace: identifier def: An identifier of molecular sequence(s) or entries from a molecular sequence database. subset: identifier is_a: EDAM:0000976 ! Identifier (typed) relationship: is_identifier_of EDAM:0002044 ! Sequence [Term] id: EDAM:0001094 name: Sequence type namespace: data def: A label (text token) describing a type of molecular sequence. comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). subset: data is_a: EDAM:0002100 ! Type is_a: EDAM:0002534 ! Sequence parameter relationship: is_identifier_of EDAM:0002044 ! Sequence relationship: is_identifier_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0001066 name: Sequence alignment ID namespace: identifier def: Identifier of a molecular sequence alignment, for example a record from an alignment database. subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0000863 ! Sequence alignment [Term] id: EDAM:0001099 name: UniProt accession (extended) namespace: identifier def: Accession number of a UniProt (protein sequence) database entry. May contai n version or isoform number. subset: identifier regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z 0-9][0-9]" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[OPQ][0-9][A-Z0-9][ A-Z0-9][A-Z0-9][0-9].[0-9]+" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0 is_a: EDAM:0003021 ! UniProt accession relationship: is_identifier_of EDAM:0001208 ! Protein sequence relationship: is_identifier_of EDAM:0000849 ! Sequence record [Term] id: EDAM:0002621 name: TAIR accession (protein) namespace: identifier def: Identifier of a protein sequence from the TAIR database. subset: identifier regex: "AASequence:[0-9]{10}" is_a: EDAM:0001096 ! Sequence identifier (protein) [Part of this file has been deleted for brevity] [Term] id: EDAM:0001115 name: Sequence profile ID namespace: identifier def: Identifier of a sequence profile. comment: A sequence profile typically represents a sequence alignment. subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0001354 ! Sequence profile [Term] id: EDAM:0001096 name: Sequence accession (protein) namespace: identifier def: Accession number of a protein sequence database entry. subset: identifier synonym: "Protein sequence accession number" EXACT [] is_a: EDAM:0001093 ! Sequence accession relationship: is_identifier_of EDAM:0002976 ! Protein sequence [Term] id: EDAM:0001097 name: Sequence accession (nucleic acid) namespace: identifier def: Accession number of a nucleotide sequence database entry. subset: identifier synonym: "Nucleotide sequence accession number" EXACT [] is_a: EDAM:0001093 ! Sequence accession relationship: is_identifier_of EDAM:0002977 ! Nucleotide sequence [Term] id: EDAM:0001064 name: Sequence set ID namespace: identifier def: An identifier of a set of molecular sequence(s). subset: identifier is_a: EDAM:0000976 ! Identifier (typed) is_a: EDAM:0002091 ! Accession relationship: is_identifier_of EDAM:0000850 ! Sequence set [Term] id: EDAM:0001112 name: Sequence cluster ID namespace: identifier def: An identifier of a cluster of molecular sequence(s). subset: identifier is_a: EDAM:0001064 ! Sequence set ID relationship: is_identifier_of EDAM:0001235 ! Sequence cluster 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 edamname Find EDAM ontology terms by name 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 Finds programs by EDAM data wossinput Finds programs by EDAM input data wossoperation Finds programs by EDAM operation wossoutput Finds programs by EDAM output data wossparam Finds programs by EDAM parameter wosstopic Finds 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