                                  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:6.5.6.0

   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


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_data:1233
name: Sequence set (protein)
namespace: data
def: Any collection of multiple protein sequences and associated metadata that d
o not (typically) correspond to common sequence database records or database ent
ries.
subset: data
is_a: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1234
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_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence

[Term]
id: EDAM_data:2245
name: Sequence set (bootstrapped)
namespace: data
def: A collection of sequences output from a bootstrapping (resampling) procedur
e.
comment: Bootstrapping is often performed in phylogenetic analysis.
subset: data
is_a: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1064
name: Sequence set ID
namespace: identifier
def: An identifier of a set of molecular sequence(s).
subset: identifiers
subset: data
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:0850
name: Sequence set
namespace: data
def: A collection of multiple molecular sequences and associated metadata that d
o not (typically) correspond to molecular sequence database records or entries a
nd which (typically) are derived from some analytical method.
comment: This concept may be used for arbitrary sequence sets and associated dat
a arising from processing.
subset: data
synonym: "sequence_collection" EXACT [SO:0001260]
is_a: EDAM_data:2955 ! Sequence report


  Output files for usage example 2

  File: edamname.obo

[Term]
id: EDAM_data:1233
name: Sequence set (protein)
namespace: data
def: Any collection of multiple protein sequences and associated metadata that d
o not (typically) correspond to common sequence database records or database ent
ries.
subset: data
is_a: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1245
name: Sequence cluster (protein)
namespace: data
def: A cluster of protein sequences.
comment: The sequences are typically related, for example a family of sequences.
subset: data
synonym: "Protein sequence cluster" EXACT [http://edamontology.org]
is_a: EDAM_data:1233 ! Sequence set (protein)
is_a: EDAM_data:1235 ! Sequence cluster

[Term]
id: EDAM_data:1238
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_data:1233 ! Sequence set (protein)
relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification

[Term]
id: EDAM_data:1262
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_data:1233 ! Sequence set (protein)

[Term]
id: EDAM_data:1234
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_data:0850 ! Sequence set
is_a: EDAM_data:2977 ! Nucleic acid sequence

[Term]
id: EDAM_data:1239
name: Restriction digest
namespace: data
def: Restriction digest fragments from digesting a nucleotide sequence with rest
riction sites using a restriction endonuclease.


  [Part of this file has been deleted for brevity]

subset: identifiers
subset: data
synonym: "UniGene ID" EXACT [http://edamontology.org]
synonym: "UniGene identifier" EXACT [http://edamontology.org]
synonym: "UniGene cluster ID" EXACT [http://edamontology.org]
synonym: "UniGene cluster id" EXACT [http://edamontology.org]
is_a: EDAM_data:1112 ! Sequence cluster ID

[Term]
id: EDAM_data:2220
name: Sequence cluster ID (SYSTERS)
namespace: identifier
def: Unique identifier of a sequence cluster from the SYSTERS database.
subset: identifiers
subset: data
synonym: "SYSTERS cluster ID" EXACT [http://edamontology.org]
is_a: EDAM_data:1112 ! Sequence cluster ID

[Term]
id: EDAM_data:2612
name: Sequence cluster ID (CluSTr)
namespace: identifier
def: Unique identifier of a sequence cluster from the CluSTr database.
subset: identifiers
subset: data
synonym: "CluSTr cluster ID" EXACT [http://edamontology.org]
synonym: "CluSTr ID" EXACT [http://edamontology.org]
regex: "[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(.[0-9])?"
is_a: EDAM_data:1112 ! Sequence cluster ID

[Term]
id: EDAM_data:0850
name: Sequence set
namespace: data
def: A collection of multiple molecular sequences and associated metadata that d
o not (typically) correspond to molecular sequence database records or entries a
nd which (typically) are derived from some analytical method.
comment: This concept may be used for arbitrary sequence sets and associated dat
a arising from processing.
subset: data
synonym: "sequence_collection" EXACT [SO:0001260]
is_a: EDAM_data:2955 ! Sequence report

[Term]
id: EDAM_data:1235
name: Sequence cluster
namespace: data
def: A set of sequences that have been clustered or otherwise classified as belo
nging to a group including (typically) sequence cluster information.
comment: The cluster might include sequences identifiers, short descriptions, al
ignment and summary information.
subset: data
is_a: EDAM_data:0850 ! Sequence set
relationship: has_topic EDAM_topic:3052 ! Sequence clusters and classification
relationship: has_topic EDAM_topic:0724 ! 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        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
