                                   edamdef



Wiki

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   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
