From 3a11ba2918795821600b7113d0758415718d263a Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 11 Jun 2018 12:46:06 +0200 Subject: combine gui with rest --- lib/report.rb | 208 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 208 insertions(+) create mode 100644 lib/report.rb (limited to 'lib/report.rb') diff --git a/lib/report.rb b/lib/report.rb new file mode 100644 index 0000000..f576106 --- /dev/null +++ b/lib/report.rb @@ -0,0 +1,208 @@ +# Get a list of all possible reports to prediction models +# @param [Header] Accept one of text/uri-list, +# @return [text/uri-list] list of all prediction models +get "/report/?" do + models = Model::Validation.all + case @accept + when "text/uri-list" + uri_list = models.collect{|model| uri("/report/#{model.model_id}")} + return uri_list.join("\n") + "\n" + when "application/json" + models = JSON.parse models.to_json + list = [] + models.each{|m| list << uri("/report/#{m["model_id"]["$oid"]}")} + return list.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end + +get "/report/:id/?" do + case @accept + when "application/xml" + model = Model::Lazar.find params[:id] + not_found_error "Model with id: #{params[:id]} not found." unless model + prediction_model = Model::Validation.find_by :model_id => params[:id] + validation_template = File.join(File.dirname(__FILE__),"../views/model_details.haml") + + if File.directory?("#{File.dirname(__FILE__)}/../../lazar") + lazar_commit = `cd #{File.dirname(__FILE__)}/../../lazar; git rev-parse HEAD`.strip + lazar_commit = "https://github.com/opentox/lazar/tree/#{lazar_commit}" + else + lazar_commit = "https://github.com/opentox/lazar/releases/tag/v#{Gem.loaded_specs["lazar"].version}" + end + + report = OpenTox::QMRFReport.new + + # QSAR Identifier Title 1.1 + report.value "QSAR_title", "Lazar model for #{prediction_model.species} #{prediction_model.endpoint}" + + # Software coding the model 1.3 + report.change_catalog :software_catalog, :firstsoftware, {:name => "lazar", :description => "lazar Lazy Structure- Activity Relationships", :number => "1", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} + report.ref_catalog :QSAR_software, :software_catalog, :firstsoftware + + # Date of QMRF 2.1 + report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}" + + # QMRF author(s) and contact details 2.1 + report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"} + report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor + + # Model developer(s) and contact details 2.5 + report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"} + report.ref_catalog :model_authors, :authors_catalog, :modelauthor + + # Date of model development and/or publication 2.6 + report.value "model_date", "#{Time.parse(model.created_at.to_s).strftime('%Y')}" + + # Reference(s) to main scientific papers and/or software package 2.7 + report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Maunz, Guetlein, Rautenberg, Vorgrimmler, Gebele and Helma (2013), lazar: a modular predictive toxicology framework ", :url => "http://dx.doi.org/10.3389/fphar.2013.00038"} + report.ref_catalog :references, :publications_catalog, :publications_catalog_1 + + # Reference(s) to main scientific papers and/or software package 2.7 + report.change_catalog :publications_catalog, :publications_catalog_2, {:title => "Maunz A and Helma C (2008) Prediction of chemical toxicity with local support vector regression and activity-specific kernels. SAR & QSAR in Environmental Research 19 (5-6), 413-431", :url => "http://dx.doi.org/10.1080/10629360802358430"} + report.ref_catalog :references, :publications_catalog, :publications_catalog_2 + + # Species 3.1 + report.value "model_species", prediction_model.species + + # Endpoint 3.2 + report.change_catalog :endpoints_catalog, :endpoints_catalog_1, {:name => prediction_model.endpoint, :group => ""} + report.ref_catalog :model_endpoint, :endpoints_catalog, :endpoints_catalog_1 + + # Endpoint Units 3.4 + report.value "endpoint_units", "#{prediction_model.unit}" + + model_type = model.class.to_s.gsub('OpenTox::Model::Lazar','') + + # Type of model 4.1 + report.value "algorithm_type", "#{model_type}" + + # Explicit algorithm 4.2 + report.change_catalog :algorithms_catalog, :algorithms_catalog_1, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Neighbor algorithm: #{model.algorithms["similarity"]["method"].gsub('_',' ').titleize}#{(model.algorithms["similarity"][:min] ? ' with similarity > ' + model.algorithms["similarity"][:min].to_s : '')}"} + report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1 + report.change_catalog :algorithms_catalog, :algorithms_catalog_3, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "modified k-nearest neighbor #{model_type}"} + report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_3 + if model.algorithms["prediction"] + pred_algorithm_params = (model.algorithms["prediction"][:method] == "rf" ? "random forest" : model.algorithms["prediction"][:method]) + end + report.change_catalog :algorithms_catalog, :algorithms_catalog_2, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Prediction algorithm: #{model.algorithms["prediction"].to_s.gsub('OpenTox::Algorithm::','').gsub('_',' ').gsub('.', ' with ')} #{(pred_algorithm_params ? pred_algorithm_params : '')}"} + report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_2 + + # Descriptors in the model 4.3 + if model.algorithms["descriptors"][:type] + report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "", :name => "#{model.algorithms["descriptors"][:type]}", :publication_ref => "", :units => ""} + report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1 + end + + # Descriptor selection 4.4 + report.value "descriptors_selection", "#{model.algorithms["feature_selection"].gsub('_',' ')} #{model.algorithms["feature_selection"].collect{|k,v| k.to_s + ': ' + v.to_s}.join(', ')}" if model.algorithms["feature_selection"] + + # Algorithm and descriptor generation 4.5 + report.value "descriptors_generation", "exhaustive breadth first search for paths in chemical graphs (simplified MolFea algorithm)" + + # Software name and version for descriptor generation 4.6 + report.change_catalog :software_catalog, :software_catalog_2, {:name => "lazar, submitted version: #{lazar_commit}", :description => "simplified MolFea algorithm", :number => "2", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} + report.ref_catalog :descriptors_generation_software, :software_catalog, :software_catalog_2 + + # Chemicals/Descriptors ratio 4.7 + report.value "descriptors_chemicals_ratio", "not applicable (classification based on activities of neighbors, descriptors are used for similarity calculation)" + + # Description of the applicability domain of the model 5.1 + report.value "app_domain_description", " +

+ The applicability domain (AD) of the training set is characterized by + the confidence index of a prediction (high confidence index: close to + the applicability domain of the training set/reliable prediction, low + confidence: far from the applicability domain of the + trainingset/unreliable prediction). The confidence index considers (i) + the similarity and number of neighbors and (ii) contradictory examples + within the neighbors. A formal definition can be found in Helma 2006. +

+

+ The reliability of predictions decreases gradually with increasing + distance from the applicability domain (i.e. decreasing confidence index) +

+ + " + + # Method used to assess the applicability domain 5.2 + report.value "app_domain_method", "see Helma 2006 and Maunz 2008" + + # Software name and version for applicability domain assessment 5.3 + report.change_catalog :software_catalog, :software_catalog_3, {:name => "lazar, submitted version: #{lazar_commit}", :description => "integrated into main lazar algorithm", :number => "3", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} + report.ref_catalog :app_domain_software, :software_catalog, :software_catalog_3 + + # Limits of applicability 5.4 + report.value "applicability_limits", "Predictions with low confidence index, unknown substructures and neighbors that might act by different mechanisms" + + # Availability of the training set 6.1 + report.change_attributes "training_set_availability", {:answer => "Yes"} + + # Available information for the training set 6.2 + report.change_attributes "training_set_data", {:cas => "Yes", :chemname => "Yes", :formula => "Yes", :inchi => "Yes", :mol => "Yes", :smiles => "Yes"} + + # Data for each descriptor variable for the training set 6.3 + report.change_attributes "training_set_descriptors", {:answer => "No"} + + # Data for the dependent variable for the training set 6.4 + report.change_attributes "dependent_var_availability", {:answer => "All"} + + # Other information about the training set 6.5 + report.value "other_info", "#{prediction_model.source}" + + # Pre-processing of data before modelling 6.6 + report.value "preprocessing", (model.class == OpenTox::Model::LazarRegression ? "-log10 transformation" : "none") + + # Robustness - Statistics obtained by leave-many-out cross-validation 6.9 + if prediction_model.repeated_crossvalidation + crossvalidations = prediction_model.crossvalidations + out = haml File.read(validation_template), :layout=> false, :locals => {:model => prediction_model} + report.value "lmo", out + end + + # Mechanistic basis of the model 8.1 + report.value "mechanistic_basis"," +

+ Compounds with similar structures (neighbors) are assumed to have + similar activities as the query compound. For the determination of + activity specific similarities only statistically relevant subtructures + (paths) are used. For this reason there is a priori no bias towards + specific mechanistic hypothesis. +

+ + " + + # A priori or a posteriori mechanistic interpretation 8.2 + report.value "mechanistic_basis_comments","a posteriori for individual predictions" + + # Other information about the mechanistic interpretation 8.3 + report.value "mechanistic_basis_info","

Hypothesis about biochemical mechanisms can be derived from individual + predictions by inspecting neighbors and relevant fragments.

+

Neighbors are compounds that are similar in respect to a certain + endpoint and it is likely that compounds with high similarity act by + similar mechanisms as the query compound. Links at the webinterface + prove an easy access to additional experimental data and literature + citations for the neighbors and the query structure.

+

Activating and deactivating parts of the query compound are highlighted + in red and green on the webinterface. Fragments that are unknown (or too + infrequent for statistical evaluation are marked in yellow and + additional statistical information about the individual fragments can be + retrieved. Please note that lazar predictions are based on neighbors and + not on fragments. Fragments and their statistical significance are used + for the calculation of activity specific similarities.

" + + # Bibliography 9.2 + report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1 + report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_2 + report.change_catalog :publications_catalog, :publications_catalog_3, {:title => "Helma (2006), Lazy structure-activity relationships (lazar) for the prediction of rodent carcinogenicity and Salmonella mutagenicity.", :url => "http://dx.doi.org/10.1007/s11030-005-9001-5"} + report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_3 + + # output + response['Content-Type'] = "application/xml" + return report.to_xml + else + bad_request_error "Mime type #{@accept} is not supported." + end + +end -- cgit v1.2.3