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module Mspire
class Mzml
class CV
# note: CV is NOT paramable!
# (required) The short label to be used as a reference tag with which to refer to
# this particular Controlled Vocabulary source description (e.g., from
# the cvLabel attribute, in CVParamType elements).
attr_accessor :id
# (required) The usual name for the resource (e.g. The PSI-MS Controlled Vocabulary).
attr_accessor :full_name
# (required) The URI for the resource.
attr_accessor :uri
# (optional) The version of the CV from which the referred-to terms are drawn.
attr_accessor :version
def initialize(id, full_name, uri, version=nil)
@id, @full_name, @uri, @version = id, full_name, uri, version
end
def to_xml(builder)
atts = {id: @id, fullName: @full_name, :URI => @uri}
atts[:version] = @version if @version
builder.cv( atts )
builder
end
def self.list_xml(objs, builder)
# we don't extend Mzml::List because of custom name below
builder.cvList(count: objs.size) do |cvl_n|
objs.each {|obj| obj.to_xml(cvl_n) }
end
builder
end
def self.from_xml(xml)
self.new(xml[:id], xml[:fullName], xml[:URI], xml[:version])
end
IMS = self.new("IMS", "Imaging MS Ontology", "http://www.maldi-msi.org/download/imzml/imagingMS.obo", "0.9.1")
MS = self.new('MS', "Proteomics Standards Initiative Mass Spectrometry Ontology", "http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo", "3.29.0")
# the version for UO doesn't really exist: seen files where they use the
# download date: DD:MM:YYY. I'm going to use the save date in the header.
UO = self.new("UO", "Unit Ontology", "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo", "12:10:2011")
DEFAULT_CVS = [MS, UO, IMS]
end
end
end
Version data entries
24 entries across 24 versions & 1 rubygems