                                   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:6.4.0.0

   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


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 hig
her 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 tha
t 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 t
o 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, der
ived 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 HM
M.
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 hig
her 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 tha
t 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 mini
mal 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, der
ived 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 al
l cases this is a list of short sequence tags and the number of times it is obse
rved.
comment: SAGE, MPSS and SBS experiments are usually performed to study gene expr
ession.  The sequence tags are typically subsequently annotated (after a databas
e 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 HM
M.
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.

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        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 (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
