qsar-report 0.0.5 → 1.0.0

data/README.md

@@ -1,5 +1,5 @@
 # QSAR-Report
-QMRF and QPRF reporting extension to OpenTox ruby modules and lazar
+QMRF and QPRF reporting extension to OpenTox ruby modules and lazar.
 ## About
 Class for QMRF and QPRF reporting.  
 * QMRF:
@@ -77,3 +77,9 @@ Copyright
 ---------
 Copyright (c) 2016 Christoph Helma, Micha Rautenberg, Denis Gebele. See LICENSE for details.
 
+Lazar QMRF Example
+------------------
+Here is an advanced example of the usage of the gem in lazar code:
+
+{include:file:example/example.rb}
+

data/VERSION

@@ -1 +1 @@
-0.0.5
+1.0.0

data/example/example.rb

@@ -0,0 +1,175 @@
+# require the qsar-report gem
+require "qsar-report"
+
+# generate a new report
+report = OpenTox::QMRFReport.new
+
+# lazar specific data resources for model information
+model = Model::Lazar.find params[:id]
+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 
+
+# QSAR identifier (title) 1.1
+report.value "QSAR_title", "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 => "Contact Email"}
+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 => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"}
+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 => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"}
+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}"
+
+# Type of model 4.1
+report.value "algorithm_type", "#{model.class.to_s.gsub('OpenTox::Model::Lazar','')}"
+
+# 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 => "modified k-nearest neighbor classification with activity specific similarities, weighted voting and exhaustive enumeration of fragments and neighbors"}
+report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1
+
+# Descriptors in the model 4.3
+report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "all statistically relevant paths are used for similarity calculation", :name => "linear fragmens (paths)", :publication_ref => "", :units => "true/false (i.e. present/absent)"}
+report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1
+
+# Descriptor selection 4.4
+report.value "descriptors_selection", "statistical filter (chi-square with Yates correction)"
+
+# 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 => "Contact Email"}
+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)"
+
+# 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 <html><body>. 
+# see Example below   
+
+# 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 => "Contact Email"}
+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.crossvalidations
+  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>"
+
+# 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
+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

data/lib/qmrf-report.rb

@@ -21,6 +21,8 @@ module OpenTox
     SCHEMA_FILE   = File.join(File.dirname(__FILE__),"template/qmrf.xsd")
     # QMRF XML Template file
     TEMPLATE_FILE = File.join(File.dirname(__FILE__),"template/qmrf.xml")
+    # QMRF catalogs. Entries of a catalog can be referenced in certain tags.
+    CATALOGS = ["software_catalog", "algorithms_catalog", "descriptors_catalog", "endpoints_catalog", "publications_catalog", "authors_catalog"]
     # QMRF XML tags with attributes to edit
     ATTRIBUTE_TAGS = ["training_set_availability", "training_set_data", "training_set_descriptors", "dependent_var_availability", "validation_set_availability", "validation_set_data", "validation_set_descriptors", "validation_dependent_var_availability"]
     
@@ -46,7 +48,11 @@ module OpenTox
     end
 
     # Get or Set a value
-    # e.G.: <QSAR_title chapter="1.1" help="" name="QSAR identifier (title)">Title of My QSAR</QSAR_title>
+    # e.G.:
+    #@example change the title
+    #  report.value "QSAR_title", "Title of My QSAR"
+    #  #changes the QSAR_title tag to:
+    #  #<QSAR_title chapter="1.1" help="" name="QSAR identifier (title)">Title of My QSAR</QSAR_title>
     # @param [String] key Nodename e.g.: "QSAR_title"
     # @param [String] value Value to change. If not set the function returns the current value
     # @return [Error]  returns Error message if fails
@@ -58,11 +64,13 @@ module OpenTox
       t.content
     end
 
-    # Set attributes of an report XML tag
-    # e.G.: <training_set_data cas="Yes" chapter="6.2" chemname="Yes" formula="Yes" help="" inchi="Yes" mol="Yes" name="Available information for the training set" smiles="Yes"/>
+    # Set attributes of an report XML tag.
+    # Some of the QMRF XML tags have attributes to be edited. This applies to 6.1 to 6.4 and 7.1 to 7.4 see also: {OpenTox::QMRFReport::ATTRIBUTE_TAGS ATTRIBUTE_TAGS}.   
+    # e.G. "Available information for the training set" at 6.2 of the report: 
+    #  <training_set_data cas="Yes" chapter="6.2" chemname="Yes" formula="Yes" help="" inchi="Yes" mol="Yes" name="Available information for the training set" smiles="Yes"/>
     #@example change_attributes
     #  report.change_attributes "training_set_data", {:inchi => "Yes", :smiles => "Yes"}
-    # @param [String] key Nodename e.g.: "training_set_data"
+    # @param [String] tagname Nodename e.g.: "training_set_data"
     # @param [Hash] valuehash Key-Value Hash of tag attributes to change.
     # @return [Error]  returns Error message if fails
     def change_attributes tagname, valuehash
@@ -74,7 +82,7 @@ module OpenTox
     end
 
     # Change a catalog
-    # @param [String] catalog Name of the catalog - One of "software_catalog", "algorithms_catalog", "descriptors_catalog", "endpoints_catalog", "publications_catalog", "authors_catalog" in QMRF v1.3
+    # @param [String] catalog Name of the catalog - One of {OpenTox::QMRFReport::CATALOGS CATALOGS}.
     # @param [String] id Single entry node in the catalog e.G.: "<software contact='mycontact@mydomain.dom' description="My QSAR Software " id="software_catalog_2" name="MySoftware" number="" url="https://mydomain.dom"/>
     # @param [Hash] valuehash Key-Value Hash with attributes for a single catalog node
     # @return [Error]  returns Error message if fails
@@ -100,7 +108,7 @@ module OpenTox
     #@example ref_catalog
     #  report.ref_catalog 'qmrf_authors', 'authors_catalog', 'firstauthor'
     # @param [String] chapter Name of the chapter to add the catalog reference. e.g.: qmrf_authors, model_authors, QSAR_software, ...
-    # @param [String] catalog Name of the catalog 
+    # @param [String] catalog Name of the catalog. One of {OpenTox::QMRFReport::CATALOGS CATALOGS}.
     # @param [String] id entry node in the catalog
     def ref_catalog chapter, catalog, id
       catalog_exists? catalog
@@ -117,7 +125,7 @@ module OpenTox
     end
 
     # get an attribute from a catalog entry
-    # @param [String] catalog Name of the catalog
+    # @param [String] catalog Name of the catalog. One of {OpenTox::QMRFReport::CATALOGS CATALOGS}.
     # @param [String] id entry id in the catalog
     # @param [String] key returns value of a key in a catalog node
     # @return [String, false] returns value of a key in a catalog node or false if catalog entry do not exists.
@@ -132,9 +140,9 @@ module OpenTox
 
     # Check if a catalog exists in this QMRF version
     # @param [String] catalog Catalog
-    # @return [Error, true]  returns true or Error if a catalog do not exists
+    # @return [Error, true]  returns true or Error if a catalog do not exists. See also {OpenTox::QMRFReport::CATALOGS CATALOGS}.
     def catalog_exists? catalog
-      raise "Unknown catalog: #{catalog}" unless ["software_catalog", "algorithms_catalog", "descriptors_catalog", "endpoints_catalog", "publications_catalog", "authors_catalog"].include? catalog.to_s
+      raise "Unknown catalog: #{catalog}" unless CATALOGS.include? catalog.to_s
       true
     end
 

data/qsar-report.gemspec

@@ -3,15 +3,15 @@
 Gem::Specification.new do |s|
   s.name        = "qsar-report"
   s.version     = File.read("./VERSION")
-  s.date        = "2016-09-14"
+  s.date        = "2016-09-16"
   s.authors     = ["Micha Rautenberg"]
   s.email       = ["rautenberg@in-silico.ch"]
-  s.homepage    = "http://github.com/opentox/qsar-report"
+  s.homepage    = "https://github.com/opentox/qsar-report"
   s.summary     = %q{qsar-report}
   s.description = %q{QMRF and QPRF reporting for OpenTox ruby module and Lazar Toxicology Predictions}
   s.license     = 'GPL-3.0'
-
-  #s.rubyforge_project = "qsar-report"
+  s.metadata = { "issue_tracker" => "https://github.com/opentox/qsar-report/issues" }
+   
 
   s.files       = `git ls-files`.split("\n")
   s.required_ruby_version = '>= 2.0.0'
@@ -20,4 +20,4 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency "haml", '~> 4.0'
   s.add_runtime_dependency "json", '~> 1.8'
 
-end
+end

data/test/all.rb

@@ -1,3 +1,3 @@
-["qmrf-report.rb","qprf-report.rb"].each do |test|
+["qmrf-report.rb", "qprf-report.rb"].each do |test|
   require_relative test
-end
+end

data/test/data/qmrf_t9n.xml

@@ -0,0 +1,146 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE QMRF PUBLIC "http://qmrf.sourceforge.net/qmrf.dtd" "qmrf.dtd">
+<QMRF author="Joint Research Centre, European Commission" contact="Joint Research Centre, European Commission" date="July 2007" email="JRC-IHCP-COMPUTOX@ec.europa.eu" name="(Q)SAR Model Reporting Format" schema_version="1.0" url="http://ihcp.jrc.ec.europa.eu/" version="1.3">
+<QMRF_chapters>
+<QSAR_identifier chapter="1" help="" name="QSAR identifier">
+<QSAR_title chapter="1.1" help="" name="QSAR identifier (title)"/>
+<QSAR_models chapter="1.2" help="" name="Other related models"/>
+<QSAR_software chapter="1.3" help="" name="Software coding the model">
+			
+      <software_ref idref="firstsoftware"/>
+</QSAR_software>
+</QSAR_identifier>
+<QSAR_General_information chapter="2" help="" name="General information">
+<qmrf_date chapter="2.1" help="" name="Date of QMRF"/>
+<qmrf_authors chapter="2.2" help="" name="QMRF author(s) and contact details">
+		
+      <author_ref idref="firstauthor"/>
+</qmrf_authors>
+<qmrf_date_revision chapter="2.3" help="" name="Date of QMRF update(s)"/>
+<qmrf_revision chapter="2.4" help="" name="QMRF update(s)"/>
+<model_authors chapter="2.5" help="" name="Model developer(s) and contact details">
+		
+      <author_ref idref="modelauthor"/>
+</model_authors>
+<model_date chapter="2.6" help="" name="Date of model development and/or publication"/>
+<references chapter="2.7" help="" name="Reference(s) to main scientific papers and/or software package">
+
+      </references>
+<info_availability chapter="2.8" help="" name="Availability of information about the model"/>
+<related_models chapter="2.9" help="" name="Availability of another QMRF for exactly the same model"/>
+</QSAR_General_information>
+<QSAR_Endpoint chapter="3" help="" name="Defining the endpoint - OECD Principle 1">
+<model_species chapter="3.1" help="" name="Species"/>
+<model_endpoint chapter="3.2" help="" name="Endpoint">
+
+      </model_endpoint>
+<endpoint_comments chapter="3.3" help="" name="Comment on endpoint"/>
+<endpoint_units chapter="3.4" help="" name="Endpoint units"/>
+<endpoint_variable chapter="3.5" help="" name="Dependent variable"/>
+<endpoint_protocol chapter="3.6" help="" name="Experimental protocol"/>
+<endpoint_data_quality chapter="3.7" help="" name="Endpoint data quality and variability"/>
+</QSAR_Endpoint>
+<QSAR_Algorithm chapter="4" help="" name="Defining the algorithm - OECD Principle 2">
+<algorithm_type chapter="4.1" help="" name="Type of model"/>
+<algorithm_explicit chapter="4.2" help="" name="Explicit algorithm">
+<algorithm_ref idref="algorithms_catalog_1"/>
+<equation/>
+</algorithm_explicit>
+<algorithms_descriptors chapter="4.3" help="" name="Descriptors in the model">
+      
+      <descriptor_ref idref="descriptors_catalog_1"/>
+</algorithms_descriptors>
+<descriptors_selection chapter="4.4" help="" name="Descriptor selection"/>
+<descriptors_generation chapter="4.5" help="" name="Algorithm and descriptor generation"/>
+<descriptors_generation_software chapter="4.6" help="" name="Software name and version for descriptor generation" options="">
+				
+      <software_ref idref="software_catalog_2"/>
+</descriptors_generation_software>
+<descriptors_chemicals_ratio chapter="4.7" help="" name="Chemicals/Descriptors ratio"/>
+</QSAR_Algorithm>
+<QSAR_Applicability_domain chapter="5" help="" name="Defining the applicability domain - OECD Principle 3">
+<app_domain_description chapter="5.1" help="" name="Description of the applicability domain of the model"/>
+<app_domain_method chapter="5.2" help="" name="Method used to assess the applicability domain"/>
+<app_domain_software chapter="5.3" help="" name="Software name and version for applicability domain assessment">
+
+      <software_ref idref="software_catalog_3"/>
+</app_domain_software>
+<applicability_limits chapter="5.4" help="" name="Limits of applicability"/>
+</QSAR_Applicability_domain>
+<QSAR_Robustness chapter="6" help="" name="Internal validation - OECD Principle 4">
+<training_set_availability answer="Yes" chapter="6.1" help="" name="Availability of the training set"/>
+<training_set_data cas="Yes" chapter="6.2" chemname="Yes" formula="Yes" help="" inchi="No" mol="Yes" name="Available information for the training set" smiles="No"/>
+<training_set_descriptors answer="All" chapter="6.3" help="" name="Data for each descriptor variable for the training set"/>
+<dependent_var_availability answer="All" chapter="6.4" help="" name="Data for the dependent variable for the training set"/>
+<other_info chapter="6.5" help="" name="Other information about the training set"/>
+<preprocessing chapter="6.6" help="" name="Pre-processing of data before modelling"/>
+<goodness_of_fit chapter="6.7" help="" name="Statistics for goodness-of-fit"/>
+<loo chapter="6.8" help="" name="Robustness - Statistics obtained by leave-one-out cross-validation"/>
+<lmo chapter="6.9" help="" name="Robustness - Statistics obtained by leave-many-out cross-validation"/>
+<yscrambling chapter="6.10" help="" name="Robustness - Statistics obtained by Y-scrambling"/>
+<bootstrap chapter="6.11" help="" name="Robustness - Statistics obtained by bootstrap"/>
+<other_statistics chapter="6.12" help="" name="Robustness - Statistics obtained by other methods"/>
+</QSAR_Robustness>
+<QSAR_Predictivity chapter="7" help="" name="External validation - OECD Principle 4">
+<validation_set_availability answer="Yes" chapter="7.1" help="" name="Availability of the external validation set"/>
+<validation_set_data cas="Yes" chapter="7.2" chemname="Yes" formula="Yes" help="" inchi="Yes" mol="Yes" name="Available information for the external validation set" smiles="Yes"/>
+<validation_set_descriptors answer="All" chapter="7.3" help="" name="Data for each descriptor variable for the external validation set"/>
+<validation_dependent_var_availability answer="All" chapter="7.4" help="" name="Data for the dependent variable for the external validation set"/>
+<validation_other_info chapter="7.5" help="" name="Other information about the external validation set"/>
+<experimental_design chapter="7.6" help="" name="Experimental design of test set"/>
+<validation_predictivity chapter="7.7" help="" name="Predictivity - Statistics obtained by external validation"/>
+<validation_assessment chapter="7.8" help="" name="Predictivity - Assessment of the external validation set"/>
+<validation_comments chapter="7.9" help="" name="Comments on the external validation of the model"/>
+</QSAR_Predictivity>
+<QSAR_Interpretation chapter="8" help="" name="Providing a mechanistic interpretation - OECD Principle 5">
+<mechanistic_basis chapter="8.1" help="" name="Mechanistic basis of the model"/>
+<mechanistic_basis_comments chapter="8.2" help="" name="A priori or a posteriori mechanistic interpretation"/>
+<mechanistic_basis_info chapter="8.3" help="" name="Other information about the mechanistic interpretation"/>
+</QSAR_Interpretation>
+<QSAR_Miscelaneous chapter="9" help="" name="Miscellaneous information">
+<comments chapter="9.1" help="" name="Comments"/>
+<bibliography chapter="9.2" help="" name="Bibliography">
+				
+      <publication_ref idref="publications_catalog_1"/>
+</bibliography>
+<attachments chapter="9.3" help="" name="Supporting information">
+        
+        
+        
+        
+        
+        
+      <attachment_training_data/>
+<attachment_validation_data/>
+<attachment_documents/>
+</attachments>
+</QSAR_Miscelaneous>
+<QMRF_Summary chapter="10" help="" name="Summary (JRC QSAR Model Database)">
+<QMRF_number chapter="10.1" help="" name="QMRF number">To be entered by JRC</QMRF_number>
+<date_publication chapter="10.2" help="" name="Publication date">To be entered by JRC</date_publication>
+<keywords chapter="10.3" help="" name="Keywords">To be entered by JRC</keywords>
+<summary_comments chapter="10.4" help="" name="Comments">To be entered by JRC</summary_comments>
+</QMRF_Summary>
+</QMRF_chapters>
+<Catalogs>
+<software_catalog>
+<software contact="" description="" id="firstsoftware" name="" number="" url=""/>
+<software contact="" description="" id="software_catalog_2" name="" number="" url=""/>
+<software contact="" description="" id="software_catalog_3" name="" number="" url=""/>
+</software_catalog>
+<algorithms_catalog>
+<algorithm definition="" description="" id="algorithms_catalog_1" publication_ref=""/>
+</algorithms_catalog>
+<descriptors_catalog>
+<descriptor description="" id="descriptors_catalog_1" name="" publication_ref="" units=""/>
+</descriptors_catalog>
+<endpoints_catalog/>
+<publications_catalog>
+<publication id="publications_catalog_1" title="" url=""/>
+</publications_catalog>
+<authors_catalog>
+<author affiliation="" contact="" email="" id="firstauthor" name="" number="" url=""/>
+<author affiliation="" contact="" email="" id="modelauthor" name="" number="" url=""/>
+</authors_catalog>
+</Catalogs>
+</QMRF>