Class Bio::KEGG::KGML
In: lib/bio/db/kegg/kgml.rb
Parent: Object

KGML (KEGG XML) parser

See www.genome.jp/kegg/xml/ for more details on KGML.

Note for older version users

Incompatible attribute names with KGML tags

 <entry>
 :map -> :pathway
 names()
 <subtype>
 edge()

Examples

 file = File.read("kgml/hsa/hsa00010.xml")
 kgml = Bio::KEGG::KGML.new(file)

 # <pathway> attributes
 puts kgml.name
 puts kgml.org
 puts kgml.number
 puts kgml.title
 puts kgml.image
 puts kgml.link

 kgml.entries.each do |entry|
   # <entry> attributes
   puts entry.id
   puts entry.name
   puts entry.type
   puts entry.link
   puts entry.reaction
   # <graphics> attributes
   entry.graphics.each do |graphics|
     puts graphics.name
     puts graphics.type
     puts graphics.x
     puts graphics.y
     puts graphics.width
     puts graphics.height
     puts graphics.fgcolor
     puts graphics.bgcolor
   end
   # <component> attributes
   puts entry.components
   # methood
   puts entry.names
 end

 kgml.relations.each do |relation|
   # <relation> attributes
   puts relation.entry1
   puts relation.entry2
   puts relation.type
   # <subtype> attributes
   puts relation.name
   puts relation.value
 end

 kgml.reactions.each do |reaction|
   # <reaction> attributes
   puts reaction.name
   puts reaction.type
   # <substrate> attributes
   reaction.substrates.each do |substrate|
     puts substrate.id
     puts substrate.name
     # <alt> attributes
     altnames = reaction.alt[entry_id]
     altnames.each do |name|
       puts name
     end
   end
   # <product> attributes
   reaction.products.each do |product|
     puts product.id
     puts product.name
     # <alt> attributes
     altnames = reaction.alt[entry_id]
     altnames.each do |name|
       puts name
     end
   end
 end

References

Methods

new  

Classes and Modules

Class Bio::KEGG::KGML::Entry
Class Bio::KEGG::KGML::Graphics
Class Bio::KEGG::KGML::Product
Class Bio::KEGG::KGML::Reaction
Class Bio::KEGG::KGML::Relation
Class Bio::KEGG::KGML::Substrate
Class Bio::KEGG::KGML::SubstrateProduct

Attributes

entries  [RW]  entry elements (Array containing KGML::Entry objects, or nil)
image  [R]  image URL of this pathway map (String or nil) (‘pathway’ element)
link  [R]  information URL of this pathway map (String or nil) (‘pathway’ element)
name  [R]  KEGG-style ID string of this pathway map (String or nil) (‘pathway’ element)
number  [R]  map number (String or nil) (‘pathway’ element)
org  [R]  "ko" (KEGG Orthology), "ec" (KEGG ENZYME), or the KEGG 3-letter organism code (String or nil) (‘pathway’ element)
reactions  [RW]  reaction elements (Array containing KGML::Reactions objects, or nil)
relations  [RW]  relation elements (Array containing KGML::Relations objects, or nil)
title  [R]  title (String or nil) (‘pathway’ element)

Public Class methods

Creates a new KGML object.


Arguments:

  • (required) str: String containing xml data
Returns:Bio::KEGG::KGML object

[Source]

     # File lib/bio/db/kegg/kgml.rb, line 141
141:   def initialize(xml)
142:     dom = REXML::Document.new(xml)
143:     parse_root(dom)
144:     parse_entry(dom)
145:     parse_relation(dom)
146:     parse_reaction(dom)
147:   end

[Validate]