From c05766e3e87319dde06bace83c5aac5620d76be7 Mon Sep 17 00:00:00 2001
From: rautenberg <rautenberg@in-silico.ch>
Date: Fri, 19 Aug 2016 16:24:44 +0200
Subject: iniitial commit

---
 lib/template/qmrf.xml | 146 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 146 insertions(+)
 create mode 100644 lib/template/qmrf.xml

(limited to 'lib/template/qmrf.xml')

diff --git a/lib/template/qmrf.xml b/lib/template/qmrf.xml
new file mode 100644
index 0000000..56dee5e
--- /dev/null
+++ b/lib/template/qmrf.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="Yes" mol="Yes" name="Available information for the training set" smiles="Yes"/>
+<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>
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