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:6.5.6.0 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_operation:2403 name: Sequence analysis namespace: operation def: Analyse one or more known molecular sequences. subset: operations synonym: "Sequence analysis (general)" EXACT [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 {min_cardinality=1} ! Sequence relationship: has_output EDAM_data:2955 {min_cardinality=1} ! Sequence report relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_operation:0292 name: Sequence alignment construction namespace: operation def: Align (identify equivalent sites within) molecular sequences. subset: operations synonym: "Sequence alignment" EXACT [http://edamontology.org] synonym: "Sequence alignment computation" EXACT [http://edamontology.org] synonym: "Sequence alignment generation" EXACT [http://edamontology.org] is_a: EDAM_operation:2463 ! Sequence alignment processing !(?) is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:2044 {minCardinality=2, note="Applies to both pure/raw sequences and sequence records. Indirectly also to sequence sets or IDs (?)"} ! Sequence relationship: has_output EDAM_data:0863 {min_cardinality=1} ! Sequence alignment relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:1780 name: Sequence submission namespace: operation def: Submit a molecular sequence to a database. subset: operations is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 {min_cardinality=1} ! Sequence relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition [Term] id: EDAM_operation:2446 name: Sequence processing namespace: operation def: Process (read and / or write) one or more molecular sequences and associate d annotation. subset: operations synonym: "Sequence processing (general)" EXACT [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing relationship: has_input EDAM_data:2044 {min_cardinality=0} ! Sequence relationship: has_output EDAM_data:2044 {min_cardinality=0} ! Sequence relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Part of this file has been deleted for brevity] synonym: "PCR primer prediction" EXACT [http://edamontology.org] is_a: EDAM_operation:2419 ! Primer and probe design relationship: has_input EDAM_data:2977 ! Nucleic acid sequence relationship: has_output EDAM_data:1240 {min_cardinality=0} ! PCR primers relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] id: EDAM_operation:2506 name: Sequence alignment analysis (protein) namespace: operation def: Analyse a protein sequence alignment, typically to detect features or make predictions. subset: operations is_a: EDAM_operation:0258 ! Sequence alignment analysis is_a: EDAM_operation:2502 ! Protein data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_input EDAM_data:1384 {min_cardinality=1} ! Sequence alignment (protein) relationship: has_topic EDAM_topic:0741 ! Protein sequence alignment [Term] id: EDAM_operation:0361 name: Sequence annotation namespace: operation def: Annotate a molecular sequence record with terms from a controlled vocabular y. subset: operations is_a: EDAM_operation:0226 ! Annotation relationship: has_input EDAM_data:0849 {min_cardinality=1} ! Sequence record relationship: has_output EDAM_data:0849 {min_cardinality=1} ! Sequence record [Term] id: EDAM_operation:0368 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: operations is_a: EDAM_operation:0231 ! Sequence editing relationship: has_input EDAM_data:0851 {min_cardinality=1} ! Sequence mask chara cter [Term] id: EDAM_operation:3180 name: Sequence assembly evaluation namespace: operation def: Evaluate a DNA sequence assembly, typically for purposes of quality control . subset: operations is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis is_a: EDAM_operation:2425 ! Optimisation and refinement relationship: has_input EDAM_data:0925 ! Sequence assembly relationship: has_output EDAM_data:3181 ! Sequence assembly report relationship: has_topic EDAM_topic:0196 ! Sequence assembly 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 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