edamhasoutput 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 has_output relation Description edamhasoutput searches the has_output 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 edamhasoutput % edamhasoutput sequence Find EDAM ontology terms by has_output relation Obo output file [edamhasoutput.obo]: Go to the output files for this example Command line arguments Find EDAM ontology terms by has_output relation Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-identifier] string Identifier(s) to search for in ontology (Any string) [-outfile] outobo [*.edamhasoutput] 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 edamhasoutput 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: edamhasoutput.obo [Term] id: EDAM:0001813 name: Sequence retrieval namespace: operation def: Query a sequence data resource (typically a database) and retrieve sequence s and / or annotation. comment: This includes direct retrieval methods (e.g. the dbfetch program) but n ot those that perform calculations on the sequence. subset: operation synonym: "Data retrieval (sequences)" EXACT [] is_a: EDAM:0002422 ! Data retrieval is_a: EDAM:0002446 ! Sequence processing relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} [Term] id: EDAM:0000290 name: Sequence redundancy removal namespace: operation def: Compare two or more molecular sequences, identify and remove redundant sequ ences based on some criteria. subset: operation is_a: EDAM:0000291 ! Sequence clustering relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} relationship: in_topic EDAM:0000164 ! Sequence clustering [Term] id: EDAM:0002446 name: Sequence processing namespace: operation def: Process (read and / or write) one or more molecular sequences and associate d annotation. subset: operation is_a: EDAM:0002503 ! Sequence data processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=0} relationship: has_output EDAM:0002044 ! Sequence {minCardinality=0} [Term] id: EDAM:0000288 name: Sequence word comparison namespace: operation def: Find exact character or word matches between molecular sequences without fu ll sequence alignment. subset: operation is_a: EDAM:0002451 ! Sequence comparison relationship: has_output EDAM:0000861 ! Sequence word alignment {minCardinality= 1} [Term] id: EDAM:0000292 name: Sequence alignment namespace: operation def: Align (identify equivalent sites within) molecular sequences. subset: operation synonym: "Sequence alignment generation" EXACT [] is_a: EDAM:0002463 ! Sequence alignment processing is_a: EDAM:0002451 ! Sequence comparison [Part of this file has been deleted for brevity] is_a: EDAM:0002421 ! Database search is_a: EDAM:0000239 ! Sequence motif recognition is_a: EDAM:0002995 ! Sequence classification relationship: has_output EDAM:0001298 ! Sequence features (motifs) {minCardinali ty=0} relationship: in_topic EDAM:0000158 ! Sequence motifs [Term] id: EDAM:0000234 name: Sequence complexity calculation namespace: operation def: Calculate sequence complexity, for example to find low-complexity regions i n sequences. subset: operation is_a: EDAM:0000236 ! Sequence composition calculation relationship: has_output EDAM:0001259 ! Sequence property (complexity) {minCardi nality=1} relationship: in_topic EDAM:0000642 ! Low complexity sequence [Term] id: EDAM:0000253 name: Sequence feature detection namespace: operation def: Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. subset: operation is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002423 ! Prediction, detection and recognition relationship: has_output EDAM:0001255 ! Sequence features {minCardinality=1} relationship: in_topic EDAM:0000160 ! Sequence features [Term] id: EDAM:0000301 name: Sequence-3D profile alignment namespace: operation def: Align molecular sequence(s) to structural (3D) profile(s) or template(s) (r epresenting a structure or structure alignment). comment: Methods might perform one-to-one, one-to-many or many-to-many compariso ns. subset: operation is_a: EDAM:0000303 ! Protein fold recognition is_a: EDAM:0002928 ! Alignment is_a: EDAM:0002403 ! Sequence analysis relationship: has_input EDAM:0000889 ! Structural (3D) profile {minCardinality=2 } relationship: has_output EDAM:0000891 ! Sequence-3D profile alignment {minCardin ality=1} relationship: in_topic EDAM:0000184 ! Threading [Term] id: EDAM:0000235 name: Sequence ambiguity calculation namespace: operation def: Calculate sequence ambiguity, for example identity regions in protein or nu cleotide sequences with many ambiguity codes. subset: operation is_a: EDAM:0000236 ! Sequence composition calculation relationship: has_output EDAM:0001260 ! Sequence property (ambiguity) {minCardin ality=1} relationship: in_topic EDAM:0000157 ! Sequence composition 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 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 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