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+# 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", "<html><head></head><body>
+ <p>
+ 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.
+ </p>
+ <p>
+ The reliability of predictions decreases gradually with increasing
+ distance from the applicability domain (i.e. decreasing confidence index)
+ </p>
+ </body>
+ </html>"
+
+ # 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","<html><head></head><body>
+ <p>
+ 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.
+ </p>
+ </body>
+ </html>"
+
+ # 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","<html><head></head><body><p>Hypothesis about biochemical mechanisms can be derived from individual
+ predictions by inspecting neighbors and relevant fragments.</p>
+ <p>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.</p>
+ <p>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.</p>"
+
+ # 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