From 2b1074342284fbaa5403dd95f970e089f1ace5a6 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 20 Mar 2018 16:58:08 +0100 Subject: updated example structure --- example/example.rb | 70 +++++++++++++++++++++++++++++------------------------- 1 file changed, 38 insertions(+), 32 deletions(-) diff --git a/example/example.rb b/example/example.rb index e268a5c..df26aa3 100644 --- a/example/example.rb +++ b/example/example.rb @@ -10,7 +10,7 @@ prediction_model = Model::Prediction.find_by :model_id => params[:id] validation_template = File.join(File.dirname(__FILE__),"../views/model_details.haml") #detailed validation results from lazar-rest -# Start filling the QMRF report +# Start filling the QMRF report # QSAR identifier (title) 1.1 report.value "QSAR_title", "Model for #{prediction_model.species} #{prediction_model.endpoint}" @@ -22,10 +22,16 @@ 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 +# QMRF author(s) and contact details 2.2 report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"} report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor +# Date of QMRF update(s) 2.3 +report.value "qmrf_date_revision", "" + +# QMRF update(s) 2.4 +report.value "qmrf_revision", "" + # Model developer(s) and contact details 2.5 report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"} report.ref_catalog :model_authors, :authors_catalog, :modelauthor @@ -42,9 +48,9 @@ report.change_catalog :publications_catalog, :publications_catalog_2, {:title => report.ref_catalog :references, :publications_catalog, :publications_catalog_2 # Species 3.1 -report.value "model_species", prediction_model.species +report.value "model_species", prediction_model.species -# Endpoint 3.2 +# 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 @@ -75,23 +81,23 @@ report.ref_catalog :descriptors_generation_software, :software_catalog, :softwar # Chemicals/Descriptors ratio 4.7 report.value "descriptors_chemicals_ratio", "not applicable (classification based on activities of neighbors, descriptors are used for similarity calculation)" -# Some QMRF fields (tag contents) can have formatted HTML contents. -# These contents have to have a complete HTML document structure with basic surrounding tags like . -# see Example below +# Some QMRF fields (tag contents) can have formatted HTML contents. +# These contents have to have a complete HTML document structure with basic surrounding tags like . +# see Example below # 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 + 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 + The reliability of predictions decreases gradually with increasing distance from the applicability domain (i.e. decreasing confidence index)

@@ -100,7 +106,7 @@ report.value "app_domain_description", " # 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 +# 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 => "Contact Email"} report.ref_catalog :app_domain_software, :software_catalog, :software_catalog_3 @@ -135,10 +141,10 @@ 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 + 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.

@@ -148,22 +154,22 @@ report.value "mechanistic_basis"," 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 +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 +

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 +

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.

" -# Reference all publications to the bibliography +# Reference all publications to the bibliography # Bibliography 9.2 report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1 report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_2 @@ -172,4 +178,4 @@ report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_3 # output response['Content-Type'] = "application/xml" -return report.to_xml \ No newline at end of file +return report.to_xml -- cgit v1.2.3