edamisid

 

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Function

Find EDAM ontology terms by is_identifier_of relation

Description

edamisid searches the is_identifier_of relations 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 edamisid


% edamisid sequence 
Find EDAM ontology terms by is_identifier_of relation
Obo output file [edamisid.obo]: 

Go to the output files for this example

Command line arguments

Find EDAM ontology terms by is_identifier_of relation
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-identifier]        string     Identifier(s) to search for in ontology (Any
                                  string)
  [-outfile]           outobo     [*.edamisid] 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:
   -sensitive          boolean    [N] By default, the query keywords are
                                  matched against the EDAM term names (and
                                  synonyms) only. This option also matches the
                                  keywords against the EDAM term definitions
                                  and will therefore (typically) report more
                                  matches.
   -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
[-identifier]
(Parameter 1)
string Identifier(s) to search for in ontology Any string  
[-outfile]
(Parameter 2)
outobo Output ontology term file name OBO ontology term(s) <*>.edamisid
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
-sensitive boolean By default, the query keywords are matched against the EDAM term names (and synonyms) only. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches. Boolean value Yes/No No
-subclasses boolean Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type. Boolean value Yes/No 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 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 N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-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 N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

edamisid 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: edamisid.obo

[Term]
id: EDAM_data:1063
name: Sequence identifier
namespace: identifier
def: An identifier of molecular sequence(s) or entries from a molecular sequence database.
subset: identifiers
subset: data
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:0855 ! Sequence metadata
relationship: is_identifier_of EDAM_data:2044 ! Sequence

[Term]
id: EDAM_data:1094
name: Sequence type
namespace: data
def: A label (text token) describing a type of molecular sequence.
comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).
subset: data
is_a: EDAM_data:2100 ! Type
is_a: EDAM_data:2534 ! Sequence parameter
relationship: is_identifier_of EDAM_data:2044 ! Sequence
relationship: is_identifier_of EDAM_data:0849 ! Sequence record

[Term]
id: EDAM_data:1114
name: Sequence motif identifier
namespace: identifier
def: Identifier of a sequence motif, for example an entry from a motif database.
subset: identifiers
subset: data
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:1353 ! Sequence motif

[Term]
id: EDAM_data:1096
name: Sequence accession (protein)
namespace: identifier
def: Accession number of a protein sequence database entry.
subset: identifiers
subset: data
synonym: "Protein sequence accession number" EXACT [http://edamontology.org]
is_a: EDAM_data:1093 ! Sequence accession
relationship: is_identifier_of EDAM_data:2976 ! Protein sequence

[Term]
id: EDAM_data:1112
name: Sequence cluster ID
namespace: identifier
def: An identifier of a cluster of molecular sequence(s).
subset: identifiers


  [Part of this file has been deleted for brevity]

subset: data
is_a: EDAM_data:1093 ! Sequence accession
relationship: is_identifier_of EDAM_data:0849 ! Sequence record

[Term]
id: EDAM_data:2621
name: TAIR accession (protein)
namespace: identifier
def: Identifier of a protein sequence from the TAIR database.
subset: identifiers
subset: data
regex: "AASequence:[0-9]{10}"
is_a: EDAM_data:1096 ! Sequence accession (protein)
is_a: EDAM_data:2387 ! TAIR accession
relationship: is_identifier_of EDAM_data:0849 ! Sequence record

[Term]
id: EDAM_data:1101
name: TREMBL accession
namespace: identifier
def: Identifier of a TREMBL sequence database entry.
subset: identifiers
subset: data
is_a: EDAM_data:3021 ! UniProt accession
synonym: "TREMBL accession number" EXACT [http://edamontology.org]
synonym: "TREMBL ID" EXACT [http://edamontology.org]
relationship: is_identifier_of EDAM_data:0849 ! Sequence record

[Term]
id: EDAM_data:1100
name: PIR identifier
namespace: identifier
def: An identifier of PIR sequence database entry.
subset: identifiers
subset: data
synonym: "PIR accession number" EXACT [http://edamontology.org]
synonym: "PIR ID" EXACT [http://edamontology.org]
is_a: EDAM_data:1096 ! Sequence accession (protein)
relationship: is_identifier_of EDAM_data:0849 ! Sequence record

[Term]
id: EDAM_data:2291
name: UniProt ID
namespace: identifier
def: An identifier of a polypeptide in the UniProt database.
subset: identifiers
subset: data
synonym: "UniProt identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:1096 ! Sequence accession (protein)
relationship: is_identifier_of EDAM_data:0849 ! Sequence record

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
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 © 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