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# TODO: missing data for protein corona silver particles
require 'json'
require 'yaml'
require 'csv'
require_relative "lib/nano-lazar.rb"
include OpenTox
def feature_name uri
f = @features[uri]
name = f['title']
annotations = f['annotation'].collect{|a| "#{a['p']}: #{a['o']}"}.uniq.join ", "
name << " (#{annotations})" unless annotations.empty?
name << " [#{f['units']}]" if f['units'] and !f['units'].empty?
name
end
nanomaterials = []
feature_names = {}
@features = {}
["nanowiki.json", "protein-corona.json", "marina.json"].each do |f|
bundle = JSON.parse(File.read(File.join("data",f)))
@features.merge! bundle["feature"]
bundle["dataEntry"].each do |substance|
nm = Nanoparticle.new
nm.uri = substance["compound"]["URI"]
nm.name = substance["values"]["https://apps.ideaconsult.net/enanomapper/identifier/name"] if substance["values"]
if substance["composition"]
nr_cores = substance["composition"].select{|c| c["relation"] == "HAS_CORE"}.size
puts "#{substance["compound"]["URI"]} has #{nr_cores} cores" if nr_cores !=1
substance["composition"].each do |composition|
component = composition["component"]
if component
name = component["values"]["https://apps.ideaconsult.net/enanomapper/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
#names << name
if composition["relation"] == "HAS_CORE"
nm.core = name
elsif composition["relation"] == "HAS_COATING"
nm.coating ||= []
nm.coating << name
end
else
#puts substance.to_yaml
end
end
else
#puts substance.to_yaml
end
substance["values"].each do |k,v|
property = nil
if k.match(/TOX/)
nm.tox ||= []
property = "tox"
elsif k.match(/P-CHEM/)
nm.p_chem ||= []
property = "p_chem"
end
if property
v.each do |val|
if val.keys == ["loValue"]
nm.tox << {k => val["loValue"]} if property == "tox"
nm.p_chem << {k => val["loValue"]} if property == "p_chem"
elsif val.keys == ["loQualifier", "loValue"] and val["loQualifier"] == "mean"
nm.tox << {k => val["loValue"]} if property == "tox"
nm.p_chem << {k => val["loValue"]} if property == "p_chem"
elsif val.keys == ["loQualifier", "loValue", "upQualifier", "upValue" ]
nm.tox << {k => (val["loValue"]+val["upValue"])/2} if property == "tox"
nm.p_chem << {k => (val["loValue"]+val["upValue"])/2} if property == "p_chem"
elsif val.keys == ["loQualifier", "loValue"] and val["loQualifier"] == ">="
else
p val
end
end
else
#p k,v
end
end
nm.tox.uniq! if nm.tox
nm.p_chem.uniq! if nm.p_chem
nanomaterials << nm
end
end
puts "Total imported: #{nanomaterials.size}"
puts "With nanoparticle characterisation: #{nanomaterials.select{|n| n.p_chem}.size}"
modelling_data = nanomaterials.select{|n| n.tox and n.p_chem}
puts "With TOX data: #{nanomaterials.select{|n| n.tox}.size}"
puts "With TOX data and particle characterisation: #{modelling_data.size}"
endpoints = modelling_data.collect{|n| n.tox.collect{|t| t.keys}}.flatten.compact.uniq
puts
puts "Endpoints: #{endpoints.size}"
single_value_endpoints = []
endpoint_values = {}
endpoints.each do |e|
i = 0
values = []
modelling_data.each do |n|
n.tox.each do |t|
if t[e]
i += 1
values << t[e]
end
end
end
single_value_endpoints << e if values.uniq.size == 1
endpoint_values[e] = values.size unless values.uniq.size == 1
end
endpoints -= single_value_endpoints
puts "Endpoints with more than one measurement value: #{endpoints.size}"
endpoint_values.select!{|k,v| v > 10}
puts "Endpoints with more than 10 measurements: #{endpoint_values.size}"
endpoints = endpoint_values.keys
puts
puts endpoint_values.sort{|a,b| b[1] <=> a[1]}.collect{|e,v| "#{feature_names[e]}: #{v}"}.join("\n")
endpoint = "https://apps.ideaconsult.net/enanomapper/property/TOX/UNKNOWN_TOXICITY_SECTION/Log2+transformed/94D664CFE4929A0F400A5AD8CA733B52E049A688/E/3ed642f9-1b42-387a-9966-dea5b91e5f8a"
nanomaterials.select!{|nm| nm.tox and nm.tox.collect{|t| t.keys}.flatten.include? endpoint}
p nanomaterials.size
feature_values = {}
nanomaterials.each do |nm|
(nm.p_chem + nm.tox).each do |f|
feature_names[f] = feature_name f # avoid appending annotations/units with each function call, unclear why it happens
p f unless f.size == 1
k = f.keys.first
unless f[k].is_a? String
feature_values[k] ||= []
feature_values[k] << f[k]
end
end
end
# remove empty values
feature_values.select!{|f,vals| vals.uniq.size > 2}
tox_descriptors = feature_values.select{|f,vals| f.match 'TOX'}.keys
p_chem_descriptors = feature_values.select{|f,vals| f.match 'P-CHEM'}.keys
#puts @features.to_yaml
column_names = ["Nanoparticle"] + p_chem_descriptors.collect{|d| feature_names[d]} + tox_descriptors.collect{|d| feature_names[d]}
table = []
CSV.open(File.join(File.dirname(__FILE__),"data","protein_corona_extract.csv"),"w+") do |csv|
csv << column_names
nanomaterials.each do |nm|
if nm.tox and nm.tox.collect{|t| t.keys}.flatten.include? endpoint
#table << []
csv << [nm.name] + p_chem_descriptors.collect{|p| nm.p_chem.collect{|pchem| pchem[p]}.compact.first} + tox_descriptors.collect{|p| nm.p_chem.collect{|pchem| pchem[p]}.compact.first}
end
end
end
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