From d132e8441b8878861d0b2d0a4563b35387f0e3e9 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 14 Jan 2016 14:52:25 +0100 Subject: initial import --- Gemfile | 2 + data/marina.json | 3282 ++++ data/multi-walled-nano-tubes.json | 430 + data/nanowiki.json | 30302 ++++++++++++++++++++++++++++++++++++ data/protein-corona.json | 20614 ++++++++++++++++++++++++ import.rb | 72 + lib/nano-lazar.rb | 1 + lib/nanoparticle.rb | 9 + nano-lazar.gemspec | 22 + 9 files changed, 54734 insertions(+) create mode 100644 Gemfile create mode 100644 data/marina.json create mode 100644 data/multi-walled-nano-tubes.json create mode 100644 data/nanowiki.json create mode 100644 data/protein-corona.json create mode 100644 import.rb create mode 100644 lib/nano-lazar.rb create mode 100644 lib/nanoparticle.rb create mode 100644 nano-lazar.gemspec diff --git a/Gemfile b/Gemfile new file mode 100644 index 0000000..1aa98e4 --- /dev/null +++ b/Gemfile @@ -0,0 +1,2 @@ +source "http://rubygems.org" +gemspec diff 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"URI":"https://apps.ideaconsult.net/enanomapper/dataset/Default", + "type":"Dataset" + }, + "annotation":[] + +}, +"https://apps.ideaconsult.net/enanomapper/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault":{ + + "type":"Feature", + "title":"CasRN", + "units":"", + "isNominal":false, + "isNumeric":false, + "isMultiValue":false, + "sameAs":"http://www.opentox.org/api/1.1#CASRN", + "isModelPredictionFeature":false, + "creator":"http://ambit.sourceforge.net", + "order":0, + "source":{ + "URI":"https://apps.ideaconsult.net/enanomapper/dataset/Default", + "type":"Dataset" + }, + "annotation":[] + +}} +} diff --git a/import.rb b/import.rb new file mode 100644 index 0000000..b086a8c --- /dev/null +++ b/import.rb @@ -0,0 +1,72 @@ +require 'json' +require 'yaml' +require_relative "lib/nano-lazar.rb" +include OpenTox + +nanomaterials = [] +names = [] + +["nanowiki.json", "protein-corona.json", "marina.json"].each do |f| + JSON.parse(File.read(File.join("data",f)))["dataEntry"].each do |substance| + nm = Nanomaterial.new + nm.uri = substance["compound"]["URI"] + 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 + #component = substance["composition"]#["component"] + 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 + nanomaterials << nm + end +end +puts "Total imported: #{nanomaterials.size}" +puts "With TOX data: #{nanomaterials.select{|n| n.tox}.size}" +puts "With nanoparticle characterisation: #{nanomaterials.select{|n| n.p_chem}.size}" +puts "With TOX data and particle characterisation: #{nanomaterials.select{|n| n.tox and n.p_chem}.size}" +#puts names.sort.uniq.to_yaml +#p nanomaterials.collect{|n| n.uri}.uniq.size diff --git a/lib/nano-lazar.rb b/lib/nano-lazar.rb new file mode 100644 index 0000000..718133c --- /dev/null +++ b/lib/nano-lazar.rb @@ -0,0 +1 @@ +Dir[File.join(File.dirname(__FILE__),"*")].each {|f| require_relative f} diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb new file mode 100644 index 0000000..3a293ee --- /dev/null +++ b/lib/nanoparticle.rb @@ -0,0 +1,9 @@ +module OpenTox + + class Nanomaterial + include OpenTox + + attr_accessor :uri, :tox, :p_chem, :core, :coating + + end +end diff --git a/nano-lazar.gemspec b/nano-lazar.gemspec new file mode 100644 index 0000000..2e40218 --- /dev/null +++ b/nano-lazar.gemspec @@ -0,0 +1,22 @@ +# -*- encoding: utf-8 -*- +$:.push File.expand_path("../lib", __FILE__) + +Gem::Specification.new do |s| + s.name = "lazar" + s.version = File.read("./VERSION").strip + s.authors = ["Christoph Helma, Micha Rautenberg, David Vorgrimmler, Denis Gebele"] + s.email = ["helma@in-silico.ch"] + s.homepage = "http://github.com/opentox/nano-lazar" + s.summary = %q{Lazar nanotoxicity framework} + s.description = %q{Libraries for nanoparticle lazy structure-activity relationships and read-across.} + s.license = 'GPL-3' + + s.rubyforge_project = "lazar" + s.files = `git ls-files`.split("\n") + s.test_files = `git ls-files -- {test,spec,features}/*`.split("\n") + s.require_paths = ["lib"] + + # specify any dependencies here; for example: + s.add_runtime_dependency "bundler" + s.add_runtime_dependency "lazar" +end -- cgit v1.2.3