                                   edamdef



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   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
