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edamdef |
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Optionally the search can be restricted to specified EDAM namespaces.
% 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
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
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| Qualifier | Type | Description | Allowed values | Default | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||||||
| [-query] (Parameter 1) |
string | Definition word(s) to search for in ontology | Any string | |||||||||||||||
| [-outfile] (Parameter 2) |
outobo | Output ontology term file name | OBO ontology term(s) | <*>.edamdef | ||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||
| -namespace | list | By default all terms are returned. Searches can be limited to one or a few namespaces. |
|
* | ||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||
| -subclasses | boolean | Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type. | Boolean value Yes/No | No | ||||||||||||||
| -obsolete | boolean | The default behaviour is to not use or return obsolete terms. This option if set will include all terms. | Boolean value Yes/No | No | ||||||||||||||
| Associated qualifiers | ||||||||||||||||||
| "-outfile" associated outobo qualifiers | ||||||||||||||||||
| -odirectory2 -odirectory_outfile |
string | Output directory | Any string | |||||||||||||||
| -oformat2 -oformat_outfile |
string | Ontology term output format | Any string | |||||||||||||||
| General qualifiers | ||||||||||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||||||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||||||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||||||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||||||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||||||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||||||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||||||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||||||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||||||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||||||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||||||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||||||||||
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.
[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_010531]
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 to 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_alignment]
synonym: "sequence alignment" EXACT [http://semanticscience.org/resource/SIO_010066]
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, structure 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 do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.
comment: This concept may be used for arbitrary sequence sets and associated data 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 together 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 identification 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 haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain 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 comparing 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 features (splice sites)
relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing
|
[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_010531]
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 derived 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 matrix 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 matrix of nucleotide (or amino acid) counts per position.
comment: Contributions of individual sequences to the matrix might be uneven (weighted).
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) procedure.
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 together 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 identification 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 haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain 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 comparing 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 features (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 sequence data.
subset: operations
is_a: EDAM_operation:2499 ! Splicing analysis
relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing
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| 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 |
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