edamdef 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 definition Description edamdef searches the definition 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 edamdef % edamdef multiple Find EDAM ontology terms by definition Obo output file [edamdef.obo]: Go to the output files for this example Example 2 % edamdef multiple -subclasses Find EDAM ontology terms by definition Obo output file [edamdef.obo]: Go to the output files for this example Command line arguments Find EDAM ontology terms by definition Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-query] string Definition word(s) to search for in ontology (Any string) [-outfile] outobo [*.edamdef] 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: -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 edamdef 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: edamdef.obo [Term] id: EDAM:0002001 name: simple namespace: format def: EMBOSS simple multiple alignment format. subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0000498 name: Multiple sequence alignment (consensus) namespace: operation def: Align two or more molecular sequences using multiple methods to achieve hig her quality. subset: operation is_a: EDAM:0000492 ! Multiple sequence alignment [Term] id: EDAM:0001234 name: Sequence set (nucleic acid) namespace: data def: Any collection of multiple nucleotide sequences and associated metadata tha t do not (typically) correspond to common sequence database records or database entries. subset: data is_a: EDAM:0000850 ! Sequence set is_a: EDAM:0002977 ! Nucleic acid sequence [Term] id: EDAM:0000863 name: Sequence alignment namespace: data def: Alignment of multiple molecular sequences. subset: data is_a: EDAM:0001916 ! Alignment relationship: in_topic EDAM:0000182 ! Sequence alignment [Term] id: EDAM:0001961 name: stockholm namespace: format def: Stockholm multiple sequence alignment format (used by Pfam and Rfam). subset: format spec: http://en.wikipedia.org/wiki/Stockholm_format is_a: EDAM:0002330 ! Text is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0000434 name: Integrated gene prediction namespace: operation [Part of this file has been deleted for brevity] name: Sequence alignment (nucleic acid) namespace: data def: Alignment of multiple nucleotide sequences. subset: data is_a: EDAM:0000863 ! Sequence alignment is_a: EDAM:0002084 ! Nucleic acid report [Term] id: EDAM:0000467 name: Protein secondary structure prediction (integrated) namespace: operation def: Predict secondary structure of protein sequence(s) using multiple methods t o achieve better predictions. subset: operation is_a: EDAM:0000267 ! Protein secondary structure prediction [Term] id: EDAM:0000928 name: Gene expression profile namespace: data def: Data quantifying the level of expression of (typically) multiple genes, der ived for example from microarray experiments. subset: data synonym: "Gene expression pattern" EXACT [] is_a: EDAM:0002541 ! Gene expression data relationship: in_topic EDAM:0000197 ! Gene expression and regulation [Term] id: EDAM:0001391 name: hmmer-aln namespace: format def: FASTA-style format for multiple sequences aligned by HMMER package to an HM M. subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0000520 name: PCR primer design (for conserved primers) namespace: operation def: Design primers that are conserved across multiple genomes or species. subset: operation is_a: EDAM:0000308 ! PCR primer design [Term] id: EDAM:0001392 name: dialign namespace: format def: Multiple sequences aligned by DIALIGN package. subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text Output files for usage example 2 File: edamdef.obo [Term] id: EDAM:0002001 name: simple namespace: format def: EMBOSS simple multiple alignment format. subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0000498 name: Multiple sequence alignment (consensus) namespace: operation def: Align two or more molecular sequences using multiple methods to achieve hig her quality. subset: operation is_a: EDAM:0000492 ! Multiple sequence alignment [Term] id: EDAM:0001234 name: Sequence set (nucleic acid) namespace: data def: Any collection of multiple nucleotide sequences and associated metadata tha t do not (typically) correspond to common sequence database records or database entries. subset: data is_a: EDAM:0000850 ! Sequence set is_a: EDAM:0002977 ! Nucleic acid sequence [Term] id: EDAM:0001240 name: PCR primers namespace: data def: Oligonucleotide primer(s) for PCR and DNA amplification, for example a mini mal primer set. subset: data is_a: EDAM:0001234 ! Sequence set (nucleic acid) [Term] id: EDAM:0001246 name: Sequence cluster (nucleic acid) namespace: data def: A cluster of nucleotide sequences. comment: The sequences are typically related, for example a family of sequences. subset: data synonym: "Nucleotide sequence cluster" EXACT [] is_a: EDAM:0001234 ! Sequence set (nucleic acid) is_a: EDAM:0001235 ! Sequence cluster [Term] id: EDAM:0002198 name: Gene cluster namespace: data def: A cluster of similar genes. [Part of this file has been deleted for brevity] def: Data quantifying the level of expression of (typically) multiple genes, der ived for example from microarray experiments. subset: data synonym: "Gene expression pattern" EXACT [] is_a: EDAM:0002541 ! Gene expression data relationship: in_topic EDAM:0000197 ! Gene expression and regulation [Term] id: EDAM:0002535 name: Sequence tag profile namespace: data def: Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In al l cases this is a list of short sequence tags and the number of times it is obse rved. comment: SAGE, MPSS and SBS experiments are usually performed to study gene expr ession. The sequence tags are typically subsequently annotated (after a databas e search) with the mRNA (and therefore gene) the tag was extracted from. subset: data synonym: "Sequencing-based expression profile" EXACT [] is_a: EDAM:0002028 ! Experimental data is_a: EDAM:0000928 ! Gene expression profile [Term] id: EDAM:0000936 name: Sequence tag profile (with gene assignment) namespace: data def: Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers . subset: data is_a: EDAM:0002535 ! Sequence tag profile [Term] id: EDAM:0001391 name: hmmer-aln namespace: format def: FASTA-style format for multiple sequences aligned by HMMER package to an HM M. subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text [Term] id: EDAM:0000520 name: PCR primer design (for conserved primers) namespace: operation def: Design primers that are conserved across multiple genomes or species. subset: operation is_a: EDAM:0000308 ! PCR primer design [Term] id: EDAM:0001392 name: dialign namespace: format def: Multiple sequences aligned by DIALIGN package. subset: format is_a: EDAM:0002554 ! Alignment format (text) is_a: EDAM:0002330 ! Text 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 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 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