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EMBOSS: edamname
edamname

 

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Function

Find EDAM ontology terms by name

Description

edamname searches the names and synonyms 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 edamname


% edamname "*sequence_set*" 
Find EDAM ontology terms by name
Obo output file [edamname.obo]: 

Go to the output files for this example

Example 2


% edamname "*sequence_set*" -subclasses 
Find EDAM ontology terms by name
Obo output file [edamname.obo]: 

Go to the output files for this example

Command line arguments

Find EDAM ontology terms by name
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-query]             string     Name(s) to search for in ontology (Any
                                  string)
  [-outfile]           outobo     [*.edamname] 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 Name(s) to search for in ontology Any string  
[-outfile]
(Parameter 2)
outobo Output ontology term file name OBO ontology term(s) <*>.edamname
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

edamname 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: edamname.obo

[Term]
id: EDAM:0001064
name: Sequence set ID
namespace: identifier
def: An identifier of a set of molecular sequence(s).
subset: identifier
is_a: EDAM:0000976 ! Identifier (typed)
is_a: EDAM:0002091 ! Accession
relationship: is_identifier_of EDAM:0000850 ! Sequence set

[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:0001233
name: Sequence set (protein)
namespace: data
def: Any collection of multiple protein 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

[Term]
id: EDAM:0002245
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:0000850 ! Sequence set

[Term]
id: EDAM:0002874
name: Sequence set (polymorphic)
namespace: data
def: A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata.
subset: data
is_a: EDAM:0001234 ! Sequence set (nucleic acid)

[Term]
id: EDAM:0000850
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 term may be used for arbitrary sequence sets and associated data arising from processing.
subset: data
is_a: EDAM:0002955 ! Sequence report

Output files for usage example 2

File: edamname.obo

[Term]
id: EDAM:0001064
name: Sequence set ID
namespace: identifier
def: An identifier of a set of molecular sequence(s).
subset: identifier
is_a: EDAM:0000976 ! Identifier (typed)
is_a: EDAM:0002091 ! Accession
relationship: is_identifier_of EDAM:0000850 ! Sequence set

[Term]
id: EDAM:0001112
name: Sequence cluster ID
namespace: identifier
def: An identifier of a cluster of molecular sequence(s).
subset: identifier
is_a: EDAM:0001064 ! Sequence set ID
relationship: is_identifier_of EDAM:0001235 ! Sequence cluster

[Term]
id: EDAM:0002612
name: Sequence cluster ID (CluSTr)
namespace: identifier
def: Unique identifier of a sequence cluster from the CluSTr database.
subset: identifier
synonym: "CluSTr cluster ID" EXACT []
synonym: "CluSTr ID" EXACT []
regex: "[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(.[0-9])?"
is_a: EDAM:0001112 ! Sequence cluster ID

[Term]
id: EDAM:0002220
name: Sequence cluster ID (SYSTERS)
namespace: identifier
def: Unique identifier of a sequence cluster from the SYSTERS database.
subset: identifier
synonym: "SYSTERS cluster ID" EXACT []
is_a: EDAM:0001112 ! Sequence cluster ID

[Term]
id: EDAM:0002346
name: Sequence cluster ID (UniRef)
namespace: identifier
def: Unique identifier of an entry from the UniRef database.
subset: identifier
synonym: "UniRef entry accession" EXACT []
synonym: "UniRef cluster id" EXACT []
is_a: EDAM:0001112 ! Sequence cluster ID

[Term]


  [Part of this file has been deleted for brevity]

comment: The sequences are typically related, for example a family of sequences.
subset: data
synonym: "Protein sequence cluster" EXACT []
is_a: EDAM:0001233 ! Sequence set (protein)
is_a: EDAM:0001235 ! Sequence cluster

[Term]
id: EDAM:0001238
name: Proteolytic digest
namespace: data
def: A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses.
subset: data
is_a: EDAM:0001233 ! Sequence set (protein)

[Term]
id: EDAM:0001262
name: Peptide molecular weight hits
namespace: data
def: A report on peptide fragments of certain molecular weight(s) in one or more protein sequences.
subset: data
is_a: EDAM:0001233 ! Sequence set (protein)

[Term]
id: EDAM:0002245
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:0000850 ! Sequence set

[Term]
id: EDAM:0000850
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 term may be used for arbitrary sequence sets and associated data arising from processing.
subset: data
is_a: EDAM:0002955 ! Sequence report

[Term]
id: EDAM:0001235
name: Sequence cluster
namespace: data
def: A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.
comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information.
subset: data
is_a: EDAM:0000850 ! Sequence set
relationship: in_topic EDAM:0000164 ! Sequence clustering
relationship: in_topic EDAM:0000724 ! Protein families

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
edamdef Find EDAM ontology terms by definition
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
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 © 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