EMBOSS: edamdef

edamdef

Wiki

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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

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.
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 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

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 higher 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 that 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 to 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, derived 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 HMM.
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 higher 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 that 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 minimal 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, derived 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 all cases this is a list of short sequence tags and the number of times it is observed.
comment: SAGE, MPSS and SBS experiments are usually performed to study gene expression.  The sequence tags are typically subsequently annotated (after a database 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 HMM.
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.

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

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Wiki

Function

Description

Usage

Command line arguments

Input file format

Output file format

Output files for usage example

File: edamdef.obo

Output files for usage example 2

File: edamdef.obo

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments