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:6.5.6.0 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_data:1354 name: Sequence profile namespace: data def: Some type of statistical model representing a (typically multiple) sequence alignment. subset: data synonym: "sequence profile" EXACT [http://semanticscience.org/resource/SIO_01053 1] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] id: EDAM_operation:0467 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: operations is_a: EDAM_operation:0267 ! Protein secondary structure prediction [Term] id: EDAM_data:1385 name: Sequence alignment (hybrid) namespace: data def: Alignment of multiple molecular sequences of different types. comment: Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. subset: data is_a: EDAM_data:0863 ! Sequence alignment [Term] id: EDAM_data:1384 name: Sequence alignment (protein) namespace: data def: Alignment of multiple protein sequences. subset: data is_a: EDAM_data:0863 ! Sequence alignment is_a: EDAM_data:3154 ! Protein alignment [Term] id: EDAM_data:0863 name: Sequence alignment namespace: data def: Alignment of multiple molecular sequences. subset: data synonym: "Sequence alignment" EXACT [http://en.wikipedia.org/wiki/Sequence_align ment] synonym: "sequence alignment" EXACT [http://semanticscience.org/resource/SIO_010 066] is_a: EDAM_data:1916 ! Alignment relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] id: EDAM_operation:0520 name: PCR primer design (for conserved primers) [Part of this file has been deleted for brevity] name: Comparative genomics namespace: topic def: Topic concerning the study (typically comparison) of the sequence, structur e or function of multiple genomes. subset: topics xref: BioCatalogue:Comparative Genomics is_a: EDAM_topic:0622 ! Genomics [Term] id: EDAM_data:0850 name: Sequence set namespace: data def: A collection of multiple molecular sequences and associated metadata that d o not (typically) correspond to molecular sequence database records or entries a nd which (typically) are derived from some analytical method. comment: This concept may be used for arbitrary sequence sets and associated dat a arising from processing. subset: data synonym: "sequence_collection" EXACT [SO:0001260] is_a: EDAM_data:2955 ! Sequence report [Term] id: EDAM_operation:0487 name: Haplotype inference namespace: operation def: Infer haplotypes, either alleles at multiple loci that are transmitted toge ther on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. comment: Haplotype inference can help in population genetic studies and the iden tification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haploty pe describes which nucleotide base occurs at each position for a set of common S NPs. Tools might use combinatorial functions (for example parsimony) or a likeli hood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chai n Monte Carlo (MCMC). subset: operations synonym: "Haplotype mapping" EXACT [http://edamontology.org] synonym: "Haplotype reconstruction" EXACT [http://edamontology.org] is_a: EDAM_operation:0283 ! Linkage analysis relationship: has_output EDAM_data:1863 {min_cardinality=1} ! Haplotype map [Term] id: EDAM_format:2001 name: simple namespace: format def: EMBOSS simple multiple alignment format. subset: formats is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_operation:2499 name: Splicing analysis namespace: operation def: Analyse (e.g. characterize and model) alternative splicing events from comp aring multiple nucleic acid sequences. subset: operations synonym: "Splicing modelling" EXACT [http://edamontology.org] is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison is_a: EDAM_operation:2426 ! Modelling and simulation is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:1307 {min_cardinality=1} ! Nucleic acid featu res (splice sites) relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing Output files for usage example 2 File: edamdef.obo [Term] id: EDAM_data:1354 name: Sequence profile namespace: data def: Some type of statistical model representing a (typically multiple) sequence alignment. subset: data synonym: "sequence profile" EXACT [http://semanticscience.org/resource/SIO_01053 1] is_a: EDAM_data:3031 ! Core data relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] id: EDAM_data:1364 name: Hidden Markov model namespace: data def: A hidden Markov model representation of a set or alignment of sequences. subset: data synonym: "HMM" EXACT [http://edamontology.org] is_a: EDAM_data:1354 ! Sequence profile [Term] id: EDAM_data:2854 name: Position-specific scoring matrix namespace: data def: A simple matrix of numbers, where each value (or column of values) is deriv ed derived from analysis of the corresponding position in a sequence alignment. subset: data is_a: EDAM_data:1354 ! Sequence profile is_a: EDAM_data:2082 ! Matrix [Term] id: EDAM_data:1361 name: Position frequency matrix namespace: data def: A profile (typically representing a sequence alignment) that is a simple ma trix of nucleotide (or amino acid) counts per position. subset: data synonym: "PFM" EXACT [http://edamontology.org] is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] id: EDAM_data:1362 name: Position weight matrix namespace: data def: A profile (typically representing a sequence alignment) that is weighted ma trix of nucleotide (or amino acid) counts per position. comment: Contributions of individual sequences to the matrix might be uneven (we ighted). subset: data synonym: "PWM" EXACT [http://edamontology.org] is_a: EDAM_data:2854 ! Position-specific scoring matrix [Term] id: EDAM_data:1363 name: Information content matrix [Part of this file has been deleted for brevity] id: EDAM_data:2245 name: Sequence set (bootstrapped) namespace: data def: A collection of sequences output from a bootstrapping (resampling) procedur e. comment: Bootstrapping is often performed in phylogenetic analysis. subset: data is_a: EDAM_data:0850 ! Sequence set [Term] id: EDAM_operation:0487 name: Haplotype inference namespace: operation def: Infer haplotypes, either alleles at multiple loci that are transmitted toge ther on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. comment: Haplotype inference can help in population genetic studies and the iden tification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haploty pe describes which nucleotide base occurs at each position for a set of common S NPs. Tools might use combinatorial functions (for example parsimony) or a likeli hood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chai n Monte Carlo (MCMC). subset: operations synonym: "Haplotype mapping" EXACT [http://edamontology.org] synonym: "Haplotype reconstruction" EXACT [http://edamontology.org] is_a: EDAM_operation:0283 ! Linkage analysis relationship: has_output EDAM_data:1863 {min_cardinality=1} ! Haplotype map [Term] id: EDAM_format:2001 name: simple namespace: format def: EMBOSS simple multiple alignment format. subset: formats is_a: EDAM_format:2554 ! Alignment format (text) is_a: EDAM_format:2330 ! Textual format [Term] id: EDAM_operation:2499 name: Splicing analysis namespace: operation def: Analyse (e.g. characterize and model) alternative splicing events from comp aring multiple nucleic acid sequences. subset: operations synonym: "Splicing modelling" EXACT [http://edamontology.org] is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison is_a: EDAM_operation:2426 ! Modelling and simulation is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid) relationship: has_output EDAM_data:1307 {min_cardinality=1} ! Nucleic acid featu res (splice sites) relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] id: EDAM_operation:0264 name: Splice transcript prediction namespace: operation def: Predict splicing alternatives or transcript isoforms from analysis of seque nce data. subset: operations is_a: EDAM_operation:2499 ! Splicing analysis relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing 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 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