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Diffstat (limited to 'test/data/qmrf_t7.xml')
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1 files changed, 146 insertions, 0 deletions
diff --git a/test/data/qmrf_t7.xml b/test/data/qmrf_t7.xml new file mode 100644 index 0000000..038110e --- /dev/null +++ b/test/data/qmrf_t7.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)">My QSAR Title</QSAR_title> +<QSAR_models chapter="1.2" help="" name="Other related models">My QSAR Model</QSAR_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="in-silico toxicology gmbh" description="lazar toxicity predictions" id="firstsoftware" name="lazar" number="" url="https://lazar.in-silico.ch"/> +<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="MyName M (2016) My Publication Title, QSAR News, 10, 14-22" url="http://myqsarnewsmag.dom"/> +<publication id="publications_catalog_2" title="MyName M (2016) My Second Publication Title, Hornblower, 101ff." url="http://hornblower.dom"/></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> |