EMBOSS: edamdef manual

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:6.6.0.0

   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

-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

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

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

-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

-warning

boolean

Report warnings

Boolean value Yes/No

-error

boolean

Report errors

Boolean value Yes/No

-fatal

boolean

Report fatal errors

Boolean value Yes/No

-die

boolean

Report dying program messages

Boolean value Yes/No

-version

boolean

Report version number and exit

Boolean value Yes/No

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_format:1391
name: HMMER-aln
namespace: format
def: FASTA-style format for multiple sequences aligned by HMMER package to an HMM.
subset: bioinformatics
subset: edam
subset: formats
created_in: "beta12orEarlier"
is_a: EDAM_format:2200 ! FASTA-like (text)
is_a: EDAM_format:2330 ! Textual format
is_a: EDAM_format:2554 ! Alignment format (text)

[Term]
id: EDAM_data:1383
name: Sequence alignment (nucleic acid)
namespace: data
def: Alignment of multiple nucleotide sequences.
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:0863 ! Sequence alignment
is_a: EDAM_data:2084 ! Nucleic acid report

[Term]
id: EDAM_topic:0797
name: Comparative genomics
namespace: topic
def: Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes.
subset: bioinformatics
subset: edam
subset: topics
xref: BioCatalogue:Comparative Genomics
created_in: "beta12orEarlier"
is_a: EDAM_topic:0622 ! Genomics

[Term]
id: EDAM_format:2001
name: EMBOSS simple format
namespace: format
def: EMBOSS simple multiple alignment format.
subset: bioinformatics
subset: edam
subset: formats
created_in: "beta12orEarlier"
is_a: EDAM_format:2330 ! Textual format
is_a: EDAM_format:2554 ! Alignment format (text)

[Term]


  [Part of this file has been deleted for brevity]

subset: operations
synonym: "Multiple sequence alignment (phylogenetic tree-based)" EXACT []
synonym: "Phylogenetic tree-based multiple sequence alignment construction" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:0492 ! Multiple sequence alignment construction
relationship: has_topic EDAM_topic:0084 ! Phylogenetics

[Term]
id: EDAM_operation:0498
name: Multiple sequence alignment construction (consensus)
namespace: operation
def: Align two or more molecular sequences using multiple methods to achieve higher quality.
subset: bioinformatics
subset: edam
subset: operations
synonym: "Consensus multiple sequence alignment construction" EXACT []
synonym: "Multiple sequence alignment (consensus)" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:0492 ! Multiple sequence alignment construction

[Term]
id: EDAM_operation:0434
name: Integrated gene prediction
namespace: operation
def: Predict whole gene structure using a combination of multiple methods to achieve better predictions.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0425 ! Whole gene prediction

[Term]
id: EDAM_data:0842
name: Identifier
namespace: identifier
def: A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).
subset: bioinformatics
subset: data
subset: edam
subset: identifiers
synonym: "WSIO_data:005" EXACT []
synonym: "http://purl.org/dc/elements/1.1/identifier" NARROW []
synonym: "ID" EXACT []
synonym: "SIO:000115" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_data:0006 ! Data
disjoint_from: EDAM_data:2048 ! Report
disjoint_from: EDAM_data:2527 ! Parameter
disjoint_from: EDAM_data:3031 ! Core data
relationship: is_identifier_of EDAM_data:0006 ! Data

Output files for usage example 2

File: edamdef.obo

[Term]
id: EDAM_format:1391
name: HMMER-aln
namespace: format
def: FASTA-style format for multiple sequences aligned by HMMER package to an HMM.
subset: bioinformatics
subset: edam
subset: formats
created_in: "beta12orEarlier"
is_a: EDAM_format:2200 ! FASTA-like (text)
is_a: EDAM_format:2330 ! Textual format
is_a: EDAM_format:2554 ! Alignment format (text)

[Term]
id: EDAM_data:1383
name: Sequence alignment (nucleic acid)
namespace: data
def: Alignment of multiple nucleotide sequences.
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:0863 ! Sequence alignment
is_a: EDAM_data:2084 ! Nucleic acid report

[Term]
id: EDAM_data:1386
name: Sequence alignment (nucleic acid pair)
namespace: data
def: Alignment of exactly two nucleotide sequences.
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:1381 ! Sequence alignment (pair)
is_a: EDAM_data:1383 ! Sequence alignment (nucleic acid)

[Term]
id: EDAM_topic:0797
name: Comparative genomics
namespace: topic
def: Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes.
subset: bioinformatics
subset: edam
subset: topics
xref: BioCatalogue:Comparative Genomics
created_in: "beta12orEarlier"
is_a: EDAM_topic:0622 ! Genomics

[Term]


  [Part of this file has been deleted for brevity]

regex: "[0-9]+"
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:1047
name: URI
namespace: data
def: A string of characters that name or otherwise identify a resource on the Internet.
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:0842 ! Identifier

[Term]
id: EDAM_data:1052
name: URL
namespace: data
def: A Uniform Resource Locator (URL).
subset: bioinformatics
subset: data
subset: edam
xref: Moby:Link
xref: Moby:URL
created_in: "beta12orEarlier"
is_a: EDAM_data:1047 ! URI

[Term]
id: EDAM_data:1053
name: URN
namespace: data
def: A Uniform Resource Name (URN).
subset: bioinformatics
subset: data
subset: edam
created_in: "beta12orEarlier"
is_a: EDAM_data:1047 ! URI

[Term]
id: EDAM_data:1055
name: LSID
namespace: data
def: A Life Science Identifier (LSID) - a unique identifier of some data.
comment: LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following EDAM_format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>]
subset: bioinformatics
subset: data
subset: edam
synonym: "Life Science Identifier" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_data:1053 ! URN

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	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

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