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:6.6.0.0 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_operation:0290 name: Sequence redundancy removal namespace: operation def: Compare two or more molecular sequences, identify and remove redundant sequ ences based on some criteria. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" is_a: EDAM_operation:0291 ! Sequence clustering relationship: has_output EDAM_data:2044 ! Sequence relationship: has_topic EDAM_topic:0164 ! Sequence clustering [Term] id: EDAM_operation:1813 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: bioinformatics subset: edam subset: operations synonym: "Data retrieval (sequences)" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_operation:2422 ! Data retrieval is_a: EDAM_operation:2446 ! Sequence processing relationship: has_output EDAM_data:2044 ! Sequence [Term] id: EDAM_operation:2871 name: Sequence tagged site (STS) mapping namespace: operation def: Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). comment: An STS is a short subsequence of known sequence and location that occur s only once in the chromosome or genome that is being mapped. Sources of STSs in clude 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (S SLPs), and random genomic sequences from cloned genomic DNA or database sequence s. subset: bioinformatics subset: edam subset: operations synonym: "Sequence mapping" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_operation:2944 ! Physical mapping relationship: has_output EDAM_data:1279 ! Sequence map [Term] id: EDAM_operation:0310 name: Sequence assembly namespace: operation def: Combine (align and merge) overlapping fragments of a DNA sequence to recons truct the original sequence. comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble con tigs, for example ESTs and genomic DNA fragments, depending on the detected frag ment overlaps. subset: bioinformatics subset: edam [Part of this file has been deleted for brevity] subset: edam subset: operations created_in: "beta12orEarlier" is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2463 ! Sequence alignment processing relationship: has_input EDAM_data:0863 ! Sequence alignment relationship: has_output EDAM_data:1711 ! Sequence alignment image [Term] id: EDAM_operation:0491 name: Pairwise sequence alignment construction namespace: operation def: Align exactly two molecular sequences. comment: Methods might perform one-to-one, one-to-many or many-to-many compariso ns. subset: bioinformatics subset: edam subset: operations synonym: "Pairwise sequence alignment" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_operation:0292 ! Sequence alignment construction relationship: has_output EDAM_data:1381 ! Sequence alignment (pair) [Term] id: EDAM_operation:0483 name: Structured RNA prediction and optimisation namespace: operation def: Predict or optimise RNA sequences (sequence pools) with likely secondary an d tertiary structure for in vitro selection. subset: bioinformatics subset: edam subset: operations synonym: "Nucleic acid folding family identification" EXACT [] synonym: "RNA inverse folding" EXACT [] created_in: "beta12orEarlier" is_a: EDAM_operation:2425 ! Optimisation and refinement is_a: EDAM_operation:3095 ! Nucleic acid design relationship: has_output EDAM_data:1234 ! Sequence set (nucleic acid) relationship: has_topic EDAM_topic:2953 ! Nucleic acid design [Term] id: EDAM_operation:0449 name: Sequence alignment analysis (site correlation) namespace: operation def: Analyse correlations between sites in a molecular sequence alignment. comment: This is typically done to identify possible covarying positions and pre dict contacts or structural constraints in protein structures. subset: bioinformatics subset: edam subset: operations created_in: "beta12orEarlier" is_a: EDAM_operation:0258 ! Sequence alignment analysis relationship: has_output EDAM_data:1416 ! Sequence alignment report (site correl ation) 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 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