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edamdef
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
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:6.6.0.0
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
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 HM
M.
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, structur
e 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" EXAC
T []
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 hig
her 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 ach
ieve 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 whic
h may not be persistent (stable) or unique (the same identifier may identify mul
tiple 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 HM
M.
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, structur
e 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 In
ternet.
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 re
presented as a Uniform Resource Name (URN) with the following EDAM_format: URN:L
SID:<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.
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
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