edamhasinput 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_input relation Description edamhasinput searches the has_input relations of EDAM terms and returns matching terms. The input is read from the installed EDAM databas. 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 edamhasinput % edamhasinput sequence Find EDAM ontology terms by has_input relation Obo output file [edamhasinput.obo]: Go to the output files for this example Command line arguments Find EDAM ontology terms by has_input relation Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-identifier] string Identifier(s) to search for in ontology (Any string) [-outfile] outobo [*.edamhasinput] 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 edamhasinput 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: edamhasinput.obo [Term] id: EDAM:0002403 name: Sequence analysis namespace: operation def: Analyse one or more known molecular sequences. subset: operation is_a: EDAM:0002446 ! Sequence processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} relationship: has_output EDAM:0002955 ! Sequence report {minCardinality=1} relationship: in_topic EDAM:0000080 ! Sequence [Term] id: EDAM:0001780 name: Sequence submission namespace: operation def: Submit a molecular sequence to a database. subset: operation is_a: EDAM:0002446 ! Sequence processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} relationship: in_topic EDAM:0000091 ! Data handling [Term] id: EDAM:0000564 name: Sequence rendering namespace: operation def: Visualise, format or render a molecular sequence, possibly with sequence fe atures or properties shown. subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002446 ! Sequence processing relationship: has_input EDAM:0002044 ! Sequence {minCardinality=1} relationship: has_output EDAM:0002969 ! Sequence image or plot {minCardinality=1 } [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:0000346 name: Sequence database search (by sequence) namespace: operation def: Search a sequence database and retrieve sequences that are similar to a que ry sequence. subset: operation synonym: "Sequence similarity search" EXACT [] is_a: EDAM:0000338 ! Sequence database search [Part of this file has been deleted for brevity] namespace: operation def: Design and optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. subset: operation is_a: EDAM:0002419 ! Primer and probe design relationship: has_input EDAM:0002977 ! Nucleic acid sequence relationship: has_output EDAM:0000932 ! Oligonucleotide probe data {minCardinali ty=1} relationship: in_topic EDAM:0000200 ! Microarrays relationship: in_topic EDAM:0000632 ! Molecular probes or primers [Term] id: EDAM:0002478 name: Sequence analysis (nucleic acid) namespace: operation def: Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). subset: operation is_a: EDAM:0002403 ! Sequence analysis is_a: EDAM:0002501 ! Nucleic acid data processing relationship: has_input EDAM:0002977 ! Nucleic acid sequence {minCardinality=1} relationship: in_topic EDAM:0000640 ! Nucleic acid sequences [Term] id: EDAM:0002452 name: Sequence cluster processing namespace: operation def: Process (read and / or write) a sequence cluster. subset: operation is_a: EDAM:0002503 ! Sequence data processing relationship: has_input EDAM:0001235 ! Sequence cluster {minCardinality=0} relationship: has_output EDAM:0001235 ! Sequence cluster {minCardinality=0} relationship: in_topic EDAM:0000164 ! Sequence clustering [Term] id: EDAM:0000566 name: Sequence cluster rendering namespace: operation def: Visualise, format or render sequence clusters. subset: operation is_a: EDAM:0000337 ! Plotting and rendering is_a: EDAM:0002452 ! Sequence cluster processing relationship: has_input EDAM:0001235 ! Sequence cluster {minCardinality=1} [Term] id: EDAM:0000368 name: Sequence masking namespace: operation def: Mask characters in a molecular sequence (replacing those characters with a mask character). comment: For example, SNPs or repeats in a DNA sequence might be masked. subset: operation is_a: EDAM:0000231 ! Sequence editing relationship: has_input EDAM:0000851 ! Sequence mask character {minCardinality=1 } 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 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 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