See www.genome.jp/kegg/xml/ for
more details on KGML.
Note for older version users
- Most of incompatible attribute names with KGML tags
are now deprecated. Use the names of KGML tags
instead of old incompatible names that will be removed in the future.
- Bio::KGML::Entry#id (entry_id is deprecated)
- Bio::KGML::Entry#type (category is deprecated)
- Bio::KGML::Relation#entry1 (node1 is deprecated)
- Bio::KGML::Relation#entry2 (node2 is deprecated)
- Bio::KGML::Relation#type (rel is deprecated)
- Bio::KGML::Reaction#name (entry_id is deprecated)
- Bio::KGML::Reaction#type (direction is deprecated)
- New class Bio::KGML::Graphics and new
method Bio::KGML::Entry#graphics. Because two or more graphics elements may
exist, following attribute methods in Bio::KGML::Entry are now deprecated
and will be removed in the future. See rdoc of these methods for details.
- Incompatible changes: Bio::KEGG::KGML::Reaction#substrates now returns an
array containing Bio::KEGG::KGML::Substrate objects, and
Bio::KEGG::KGML::Reaction#products now returns an array containing Bio::KEGG::KGML::Product objects. The changes
enable us to get id of substrates and products.
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