CSC

% edamdef multiple 
Find EDAM ontology terms by definition
Obo output file [edamdef.obo]: 

% edamdef multiple -subclasses 
Find EDAM ontology terms by definition
Obo output file [edamdef.obo]: 

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

[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 higher 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 that 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 to 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, derived 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 HMM.
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

[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 higher 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 that 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 minimal 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, derived 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 all cases this is a list of short sequence tags and the number of times it is observed.
comment: SAGE, MPSS and SBS experiments are usually performed to study gene expression.  The sequence tags are typically subsequently annotated (after a database 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 HMM.
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