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# feature_values.rb
# Feature Value library
# Author: Andreas Maunz
module OpenTox
class Algorithm
class FeatureValues
# Substructure matching
# @param [Hash] keys: compound, feature_dataset, values: OpenTox::Compound, Array of SMARTS strings
# @return [Array] Array with matching Smarts
def self.match(params, subjectid)
features = params[:feature_dataset].features.collect{ |f| f[DC.title] }
params[:compound].match(features)
end
# Substructure matching with number of non-unique hits
# @param [Hash] keys: compound, feature_dataset, values: OpenTox::Compound, Array of SMARTS strings
# @return [Hash] Hash with matching Smarts and number of hits
def self.match_hits(params, subjectid)
features = params[:feature_dataset].features.collect{ |f| f[DC.title] },
params[:compound].match_hits(features)
end
# PC descriptor calculation
# @param [Hash] keys: compound, feature_dataset, pc_type, lib, values: OpenTox::Compound, String, String
# @return [Hash] Hash with feature name as key and value as value
def self.lookup(params, subjectid)
ds = params[:feature_dataset]
ds.build_feature_positions
cmpd_inchi = params[:compound].inchi
cmpd_idxs = ds.compounds.each_with_index.collect{ |cmpd,idx|
idx if cmpd.inchi == cmpd_inchi
}.compact
if cmpd_idxs.size > 0 # We have entries
cmpd_numeric_f = ds.features.collect { |f|
f if f[RDF.type].include? OT.NumericFeature
}.compact
cmpd_data_entries = cmpd_idxs.collect { |idx|
ds.data_entries[idx]
}
cmpd_fingerprints = cmpd_numeric_f.inject({}) { |h,f|
values = cmpd_data_entries.collect { |entry|
val = entry[ds.feature_positions[f.uri]]
val.nil? ? nil : val.to_f
}.compact
h[f.title] = (values.size > 0) ? values.to_scale.median : nil # AM: median for numeric features
h
}
(ds.features - cmpd_numeric_f).each { |f|
values = cmpd_data_entries.collect { |entry|
val = entry[ds.feature_positions[f.uri]]
val.nil? ? nil : val
}.compact
cmpd_fingerprints[f.title] = values.to_scale.mode # AM: mode for the others
}
else # We need lookup
params[:subjectid] = subjectid
[:compound, :feature_dataset].each { |p| params.delete(p) }; [:pc_type, :lib].each { |p| params.delete(p) if params[p] == "" }
single_cmpd_ds = OpenTox::Dataset.new(nil,subjectid)
single_cmpd_ds.parse_rdfxml(RestClient.post("#{$compound[:uri]}/#{cmpd_inchi}/pc", params, {:accept => "application/rdf+xml"}))
single_cmpd_ds.get(true)
single_cmpd_ds.build_feature_positions
cmpd_fingerprints = single_cmpd_ds.features.inject({}) { |h,f|
h[f.title] = single_cmpd_ds.data_entries[0][single_cmpd_ds.feature_positions[f.uri]]
h
}
end
cmpd_fingerprints
end
end
end
end
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