diff options
Diffstat (limited to 'lib')
| -rw-r--r-- | lib/qmrf-report.rb | 140 | ||||
| -rw-r--r-- | lib/template/qmrf.xml | 146 | ||||
| -rw-r--r-- | lib/template/qmrf.xsd | 2018 |
3 files changed, 2304 insertions, 0 deletions
diff --git a/lib/qmrf-report.rb b/lib/qmrf-report.rb new file mode 100644 index 0000000..fdce433 --- /dev/null +++ b/lib/qmrf-report.rb @@ -0,0 +1,140 @@ +require "nokogiri" + +# OpenTox module +module OpenTox + + #Class for QMRF reporting. + # + #Provides a ruby OpenTox class to prepare an initial version of a QMRF report. + #The XML output is in QMRF version 1.3 and can be finalized with the QMRF editor 2.0 (https://sourceforge.net/projects/qmrf/) + #@example Report + # require "" + # report = OpenTox::QMRFReport.new + # report.change_qmrf_tag "QSAR_title", "My QSAR Title" + # report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"} + # report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1 + # puts report.to_xml + + class QMRFReport + # QMRF XML Schema file + SCHEMA_FILE = File.join(File.dirname(__FILE__),"template/qmrf.xsd") + # QMRF XML Template file + TEMPLATE_FILE = File.join(File.dirname(__FILE__),"template/qmrf.xml") + + attr_accessor :xml, :report + + # Open an existing QMRF xml report + # @param [String] file Name of the file + def open file + xml = File.read("#{file}") + @report = Nokogiri.XML(xml) + end + + # Initialize a new report instance from qmrf template + def initialize + xml = File.read(TEMPLATE_FILE) + @report = Nokogiri.XML(xml) + end + + # returns XML representation (QMRF XML report) of report instance + # @return [String] returns XML + def to_xml + @report.to_xml + end + + # Change a value + # e.G.: <QSAR_title chapter="1.1" help="" name="QSAR identifier (title)">Title of My QSAR</QSAR_title> + # @param [String] key Name of the node + # @param [String] value Value to change + # @return [Error] returns Error message if fails + def change_qmrf_tag key, value + raise "Can not edit attribute #{key} directly. Edit the catalog with 'report.change_catalog(catalog, key, value)'." if ["QSAR_software","QSAR_Algorithm", ""].include? key + t = @report.at_css key + t.content = value + 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] 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 + def change_catalog catalog, id, valuehash + catalog_exists? catalog + if @report.at_css("#{catalog}").at("//*[@id='#{id}']") + valuehash.each do |key, value| + @report.at_css("#{catalog}").at("//*[@id='#{id}']")["#{key}"]= value + end + else + cat = @report.at_css("#{catalog}") + newentry = Nokogiri::XML::Node.new("#{catalog.to_s.gsub(/s?_catalog/,'')}", self.report) + newentry["id"] = id + valuehash.each do |key, value| + newentry["#{key}"] = value + end + cat << newentry + end + end + + # Set reference to a catalog entry. + # e.g.: reference an author entry from authors_catalog to Chapter 2.2 QMRF authors + #@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] id entry node in the catalog + def ref_catalog chapter, catalog, id + catalog_exists? catalog + if @report.at_css("#{catalog}").at("//*[@id='#{id}']") + chap = @report.at_css("#{chapter}") + if chap.at("//*[@idref='#{id}']").nil? + newentry = Nokogiri::XML::Node.new("#{catalog.to_s.gsub(/s?_catalog/,'_ref')}", self.report) + newentry["idref"] = id + chap << newentry + end + else + raise "catalog entry with id: #{id} do not exist." + end + end + + # get value of a QMRF node + # @param [String] key Nodename e.g.: "QSAR_title" + # @return [String] returns value + def get_qmrf_tag key + t = @report.at_css key + t.content + end + + # get an attribute from a catalog entry + # @param [String] catalog Name of the catalog + # @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. + def get_catalog_value catalog, id, key + catalog_exists? catalog + if @report.at_css("#{catalog}").at("//*[@id='#{id}']") + @report.at_css("#{catalog}").at("//*[@id='#{id}']")["#{key}"] + else + return false + end + end + + # 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 + 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 + true + end + + # Validates a report instance against qmrf.xsd (XML Structure Definition) + def validate + xsd = Nokogiri::XML::Schema(File.read(SCHEMA_FILE)) + out = "" + xsd.validate(@report).each do |error| + out << error.message unless error.message == "Element 'algorithm', attribute 'publication_ref': '' is not a valid value of the atomic type 'xs:IDREF'." || error.message == "Element 'descriptor', attribute 'publication_ref': '' is not a valid value of the atomic type 'xs:IDREF'." + end + return out + end + + end +end
\ No newline at end of file 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> diff --git a/lib/template/qmrf.xsd b/lib/template/qmrf.xsd new file mode 100644 index 0000000..4dd8fa1 --- /dev/null +++ b/lib/template/qmrf.xsd @@ -0,0 +1,2018 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!-- QMRF DTD --> +<!-- DOCTYPE QMRF SYSTEM "qmrf.dtd" --> +<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified"> + <xs:element name="QMRF"> + <xs:complexType> + <xs:sequence> + <xs:element ref="QMRF_chapters"/> + <xs:element ref="Catalogs"/> + </xs:sequence> + <xs:attribute name="schema_version" default="1.0"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="1.0"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="version" default="1.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="1.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="(Q)SAR Model Reporting Format"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="(Q)SAR Model Reporting Format"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="author" default="Joint Research Centre, European Commission"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Joint Research Centre, European Commission"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="date" default="July 2007"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="July 2007"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="contact" default="Joint Research Centre, European Commission"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Joint Research Centre, European Commission"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="email" default="JRC-IHCP-COMPUTOX@ec.europa.eu"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="JRC-IHCP-COMPUTOX@ec.europa.eu"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="url" default="http://ihcp.jrc.ec.europa.eu/"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="http://ihcp.jrc.ec.europa.eu/"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + </xs:complexType> + </xs:element> + <xs:element name="QMRF_chapters"> + <xs:complexType> + <xs:sequence> + <xs:element ref="QSAR_identifier"/> + <xs:element ref="QSAR_General_information"/> + <xs:element ref="QSAR_Endpoint"/> + <xs:element ref="QSAR_Algorithm"/> + <xs:element maxOccurs="unbounded" ref="QSAR_Applicability_domain"/> + <xs:element ref="QSAR_Robustness"/> + <xs:element maxOccurs="unbounded" ref="QSAR_Predictivity"/> + <xs:element ref="QSAR_Interpretation"/> + <xs:element ref="QSAR_Miscelaneous"/> + <xs:element ref="QMRF_Summary"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <!-- Chapter 1 --> + <xs:element name="QSAR_identifier"> + <xs:complexType> + <xs:sequence> + <xs:element ref="QSAR_title"/> + <xs:element ref="QSAR_models"/> + <xs:element ref="QSAR_software"/> + </xs:sequence> + <xs:attribute name="chapter" default="1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="QSAR identifier"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="QSAR identifier"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help"/> + </xs:complexType> + </xs:element> + <xs:element name="QSAR_title"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="1.1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="1.1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="QSAR identifier (title)"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="QSAR identifier (title)"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <xs:element name="QSAR_models"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="1.2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="1.2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Other related models"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Other related models"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <xs:element name="QSAR_software"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="software_ref"/> + </xs:sequence> + <xs:attribute name="chapter" default="1.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="1.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Software coding the model"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Software coding the model"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Reference to Software_catalog --> + <!-- Chapter 2 --> + <xs:element name="QSAR_General_information"> + <xs:complexType> + <xs:sequence> + <xs:element ref="qmrf_date"/> + <xs:element ref="qmrf_authors"/> + <xs:element ref="qmrf_date_revision"/> + <xs:element ref="qmrf_revision"/> + <xs:element ref="model_authors"/> + <xs:element ref="model_date"/> + <xs:element ref="references"/> + <xs:element ref="info_availability"/> + <xs:element ref="related_models"/> + </xs:sequence> + <xs:attribute name="chapter" default="2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="General information"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="General information"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 2.1 Date of QMRF --> + <xs:element name="qmrf_date"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="2.1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="2.1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Date of QMRF"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Date of QMRF"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 2.2. QMRF authors --> + <xs:element name="qmrf_authors"> + <xs:complexType> + <xs:sequence> + <xs:element maxOccurs="unbounded" ref="author_ref"/> + </xs:sequence> + <xs:attribute name="chapter" default="2.2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="2.2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="QMRF author(s) and contact details"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="QMRF author(s) and contact details"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 2.3 Date of QMRF update --> + <xs:element name="qmrf_date_revision"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="2.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="2.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Date of QMRF update(s)"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Date of QMRF update(s)"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 2.4 QMRF update(s) --> + <xs:element name="qmrf_revision"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="2.4"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="2.4"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="QMRF update(s)"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="QMRF update(s)"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Model developers --> + <xs:element name="model_authors"> + <xs:complexType> + <xs:sequence> + <xs:element maxOccurs="unbounded" ref="author_ref"/> + </xs:sequence> + <xs:attribute name="chapter" default="2.5"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="2.5"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Model developer(s) and contact details"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Model developer(s) and contact details"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Date of model development --> + <xs:element name="model_date"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="2.6"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="2.6"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Date of model development and/or publication"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Date of model development and/or publication"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 2.7 Reference(s) to main scientific papers and/or software package --> + <xs:element name="references"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="publication_ref"/> + </xs:sequence> + <xs:attribute name="chapter" default="2.7"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="2.7"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Reference(s) to main scientific papers and/or software package"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Reference(s) to main scientific papers and/or software package"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 2.8 Availability of information about the model --> + <xs:element name="info_availability"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="2.8"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="2.8"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Availability of information about the model"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Availability of information about the model"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 2.9 Availability of another QMRF for exactly the same model --> + <xs:element name="related_models"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="2.9"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="2.9"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Availability of another QMRF for exactly the same model"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Availability of another QMRF for exactly the same model"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Chapter 3 --> + <xs:element name="QSAR_Endpoint"> + <xs:complexType> + <xs:sequence> + <xs:element ref="model_species"/> + <xs:element ref="model_endpoint"/> + <xs:element ref="endpoint_comments"/> + <xs:element ref="endpoint_units"/> + <xs:element ref="endpoint_variable"/> + <xs:element ref="endpoint_protocol"/> + <xs:element ref="endpoint_data_quality"/> + </xs:sequence> + <xs:attribute name="chapter" default="3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Defining the endpoint - OECD Principle 1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Defining the endpoint - OECD Principle 1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Link to species catalog --> + <xs:element name="model_species"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="3.1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="3.1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Species"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Species"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Link to endpoint catalog --> + <xs:element name="model_endpoint"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="endpoint_ref"/> + </xs:sequence> + <xs:attribute name="chapter" default="3.2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="3.2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Endpoint"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Endpoint"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- endpoints units --> + <xs:element name="endpoint_comments"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="3.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="3.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Comment on endpoint"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Comment on endpoint"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- endpoints units --> + <xs:element name="endpoint_units"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="3.4"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="3.4"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Endpoint units"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Endpoint units"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- dependent variable --> + <xs:element name="endpoint_variable"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="3.5"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="3.5"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Dependent variable"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Dependent variable"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Experimental protocol --> + <xs:element name="endpoint_protocol"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="3.6"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="3.6"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Experimental protocol"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Experimental protocol"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Endpoint data quality --> + <xs:element name="endpoint_data_quality"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="3.7"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="3.7"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Endpoint data quality and variability"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Endpoint data quality and variability"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Chapter 4 --> + <xs:element name="QSAR_Algorithm"> + <xs:complexType> + <xs:sequence> + <xs:element ref="algorithm_type"/> + <xs:element ref="algorithm_explicit"/> + <xs:element ref="algorithms_descriptors"/> + <xs:element ref="descriptors_selection"/> + <xs:element ref="descriptors_generation"/> + <xs:element ref="descriptors_generation_software"/> + <xs:element ref="descriptors_chemicals_ratio"/> + </xs:sequence> + <xs:attribute name="chapter" default="4"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="4"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Defining the algorithm - OECD Principle 2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Defining the algorithm - OECD Principle 2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 4.1 Types of model --> + <xs:element name="algorithm_type"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="4.1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="4.1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Type of model"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Type of model"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 4.2 Explicit algorithm --> + <xs:element name="algorithm_explicit"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="algorithm_ref"/> + <xs:element ref="equation"/> + </xs:sequence> + <xs:attribute name="chapter" default="4.2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="4.2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Explicit algorithm"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Explicit algorithm"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <xs:element name="equation" type="xs:string"/> + <!-- + 4.3 Comments on algorithm - removed in 1.2 + <!ELEMENT algorithm_comments (#PCDATA)> + <!ATTLIST algorithm_comments chapter CDATA #FIXED "4.3" name CDATA #FIXED "Comments on algorithm" help CDATA "" > + --> + <!-- 4.3 Descriptors in model --> + <xs:element name="algorithms_descriptors"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="descriptor_ref"/> + </xs:sequence> + <xs:attribute name="chapter" default="4.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="4.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Descriptors in the model"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Descriptors in the model"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 4.4 Descriptor selection --> + <xs:element name="descriptors_selection"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="4.4"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="4.4"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Descriptor selection"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Descriptor selection"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 4.5 Descriptor generator --> + <xs:element name="descriptors_generation"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="4.5"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="4.5"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Algorithm and descriptor generation"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Algorithm and descriptor generation"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 4.6 Software name and version for descriptor generation todo - ref to Software catalog --> + <xs:element name="descriptors_generation_software"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="software_ref"/> + </xs:sequence> + <xs:attribute name="chapter" default="4.6"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="4.6"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Software name and version for descriptor generation"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Software name and version for descriptor generation"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + <xs:attribute name="options"/> + </xs:complexType> + </xs:element> + <!-- 4.7 Descriptors/Chemicals ratio --> + <xs:element name="descriptors_chemicals_ratio"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="4.7"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="4.7"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Chemicals/Descriptors ratio"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Chemicals/Descriptors ratio"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Chapter 5 --> + <xs:element name="QSAR_Applicability_domain"> + <xs:complexType> + <xs:sequence> + <xs:element ref="app_domain_description"/> + <xs:element ref="app_domain_method"/> + <xs:element ref="app_domain_software"/> + <xs:element ref="applicability_limits"/> + </xs:sequence> + <xs:attribute name="chapter" default="5"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="5"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Defining the applicability domain - OECD Principle 3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Defining the applicability domain - OECD Principle 3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 5.1 Description of the applicability domain of the model --> + <xs:element name="app_domain_description"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="5.1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="5.1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Description of the applicability domain of the model"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Description of the applicability domain of the model"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 5.2 Description of the applicability domain of the model --> + <xs:element name="app_domain_method"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="5.2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="5.2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Method used to assess the applicability domain"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Method used to assess the applicability domain"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 5.3 Software name and version for applicability domain assessment --> + <xs:element name="app_domain_software"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="software_ref"/> + </xs:sequence> + <xs:attribute name="chapter" default="5.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="5.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Software name and version for applicability domain assessment"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Software name and version for applicability domain assessment"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 5.4 Description of the applicability domain of the model --> + <xs:element name="applicability_limits"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="5.4"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="5.4"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Limits of applicability"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Limits of applicability"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Chapter 6 --> + <xs:element name="QSAR_Robustness"> + <xs:complexType> + <xs:sequence> + <xs:element ref="training_set_availability"/> + <xs:element ref="training_set_data"/> + <xs:element ref="training_set_descriptors"/> + <xs:element ref="dependent_var_availability"/> + <xs:element ref="other_info"/> + <xs:element ref="preprocessing"/> + <xs:element ref="goodness_of_fit"/> + <xs:element ref="loo"/> + <xs:element ref="lmo"/> + <xs:element ref="yscrambling"/> + <xs:element ref="bootstrap"/> + <xs:element ref="other_statistics"/> + </xs:sequence> + <xs:attribute name="chapter" default="6"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Internal validation - OECD Principle 4"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Internal validation - OECD Principle 4"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.1 Availability of the training set --> + <xs:element name="training_set_availability"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="answer" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Availability of the training set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Availability of the training set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.2 Available information for the training set --> + <xs:element name="training_set_data"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Available information for the training set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Available information for the training set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + <xs:attribute name="chemname" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="cas" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="smiles" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="inchi" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="mol" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="formula" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + </xs:complexType> + </xs:element> + <!-- 6.3 Data for each descriptor variable for the training set --> + <xs:element name="training_set_descriptors"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Data for each descriptor variable for the training set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Data for each descriptor variable for the training set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="answer" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="All"/> + <xs:enumeration value="Some"/> + <xs:enumeration value="No"/> + <xs:enumeration value="Unknown"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.4 Data for the dependent variable for the training set --> + <xs:element name="dependent_var_availability"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.4"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.4"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Data for the dependent variable for the training set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Data for the dependent variable for the training set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="answer" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="All"/> + <xs:enumeration value="Some"/> + <xs:enumeration value="No"/> + <xs:enumeration value="Unknown"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.5 Other information about the training set --> + <xs:element name="other_info"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.5"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.5"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Other information about the training set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Other information about the training set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.6 Pre-processing of data before modelling --> + <xs:element name="preprocessing"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.6"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.6"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Pre-processing of data before modelling"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Pre-processing of data before modelling"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.7 Statistics for goodness-of-fit --> + <xs:element name="goodness_of_fit"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.7"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.7"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Statistics for goodness-of-fit"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Statistics for goodness-of-fit"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.8 Robustness - Statistics obtained by leave-one-out cross-validation --> + <xs:element name="loo"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.8"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.8"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Robustness - Statistics obtained by leave-one-out cross-validation"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Robustness - Statistics obtained by leave-one-out cross-validation"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.9 Robustness - Statistics obtained by leave-many-out cross-validation --> + <xs:element name="lmo"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.9"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.9"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Robustness - Statistics obtained by leave-many-out cross-validation"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Robustness - Statistics obtained by leave-many-out cross-validation"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.10 Robustness - Statistics obtained by Y-scrambling --> + <xs:element name="yscrambling"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.10"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.10"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Robustness - Statistics obtained by Y-scrambling"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Robustness - Statistics obtained by Y-scrambling"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.11 Robustness - Statistics obtained by bootstrap --> + <xs:element name="bootstrap"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.11"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.11"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Robustness - Statistics obtained by bootstrap"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Robustness - Statistics obtained by bootstrap"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 6.12 Robustness - Statistics obtained by other methods --> + <xs:element name="other_statistics"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="6.12"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="6.12"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Robustness - Statistics obtained by other methods"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Robustness - Statistics obtained by other methods"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Chapter 7 --> + <xs:element name="QSAR_Predictivity"> + <xs:complexType> + <xs:sequence> + <xs:element ref="validation_set_availability"/> + <xs:element ref="validation_set_data"/> + <xs:element ref="validation_set_descriptors"/> + <xs:element ref="validation_dependent_var_availability"/> + <xs:element ref="validation_other_info"/> + <xs:element ref="experimental_design"/> + <xs:element ref="validation_predictivity"/> + <xs:element ref="validation_assessment"/> + <xs:element ref="validation_comments"/> + </xs:sequence> + <xs:attribute name="chapter" default="7"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="7"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="External validation - OECD Principle 4"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="External validation - OECD Principle 4"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 7.1 Availability of the external validation set --> + <xs:element name="validation_set_availability"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="7.1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="7.1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="answer" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Availability of the external validation set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Availability of the external validation set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 7.2 Available information for the external validation set --> + <xs:element name="validation_set_data"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="7.2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="7.2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Available information for the external validation set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Available information for the external validation set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + <xs:attribute name="chemname" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="cas" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="smiles" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="inchi" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="mol" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="formula" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + </xs:complexType> + </xs:element> + <!-- 7.3 Data for each descriptor variable for the external validation set --> + <xs:element name="validation_set_descriptors"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="7.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="7.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Data for each descriptor variable for the external validation set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Data for each descriptor variable for the external validation set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="answer" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="All"/> + <xs:enumeration value="Some"/> + <xs:enumeration value="No"/> + <xs:enumeration value="Unknown"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 7.4 Data for the dependent variable for the external validation set --> + <xs:element name="validation_dependent_var_availability"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="7.4"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="7.4"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Data for the dependent variable for the external validation set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Data for the dependent variable for the external validation set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="answer" use="required"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="All"/> + <xs:enumeration value="Some"/> + <xs:enumeration value="No"/> + <xs:enumeration value="Unknown"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 7.5 Other information about the external validation set --> + <xs:element name="validation_other_info"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="7.5"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="7.5"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Other information about the external validation set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Other information about the external validation set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 7.6 Experimental design for data splitting --> + <xs:element name="experimental_design"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="7.6"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="7.6"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Experimental design of test set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Experimental design of test set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 7.7 Predictivity - Statistics obtained by external validation --> + <xs:element name="validation_predictivity"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="7.7"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="7.7"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Predictivity - Statistics obtained by external validation"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Predictivity - Statistics obtained by external validation"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 7.8 Predictivity - Assessment of the external validation set --> + <xs:element name="validation_assessment"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="7.8"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="7.8"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Predictivity - Assessment of the external validation set"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Predictivity - Assessment of the external validation set"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 7.9 Comments on the external validation of the model --> + <xs:element name="validation_comments"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="7.9"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="7.9"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Comments on the external validation of the model"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Comments on the external validation of the model"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Chapter 8 --> + <xs:element name="QSAR_Interpretation"> + <xs:complexType> + <xs:sequence> + <xs:element ref="mechanistic_basis"/> + <xs:element ref="mechanistic_basis_comments"/> + <xs:element ref="mechanistic_basis_info"/> + </xs:sequence> + <xs:attribute name="chapter" default="8"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="8"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Providing a mechanistic interpretation - OECD Principle 5"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Providing a mechanistic interpretation - OECD Principle 5"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 8.1 Mechanistic basis of the model: --> + <xs:element name="mechanistic_basis"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="8.1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="8.1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Mechanistic basis of the model"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Mechanistic basis of the model"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 8.2 A priori or a posteriori mechanistic interpretation --> + <xs:element name="mechanistic_basis_comments"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="8.2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="8.2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="A priori or a posteriori mechanistic interpretation"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="A priori or a posteriori mechanistic interpretation"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 8.3 Other information about the mechanistic interpretation --> + <xs:element name="mechanistic_basis_info"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="8.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="8.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Other information about the mechanistic interpretation"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Other information about the mechanistic interpretation"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Chapter 9 --> + <xs:element name="QSAR_Miscelaneous"> + <xs:complexType> + <xs:sequence> + <xs:element ref="comments"/> + <xs:element ref="bibliography"/> + <xs:element ref="attachments"/> + </xs:sequence> + <xs:attribute name="chapter" default="9"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="9"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Miscellaneous information"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Miscellaneous information"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 9.1 Comments --> + <xs:element name="comments"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="9.1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="9.1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Comments"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Comments"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 9.2 Bibliography --> + <xs:element name="bibliography"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="publication_ref"/> + </xs:sequence> + <xs:attribute name="chapter" default="9.2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="9.2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Bibliography"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Bibliography"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 9.3 Supporting information --> + <!-- added embedded attribute, expecting CDATA in Base64 v1.2 --> + <xs:element name="attachments"> + <xs:complexType> + <xs:sequence> + <xs:element ref="attachment_training_data"/> + <xs:element ref="attachment_validation_data"/> + <xs:element ref="attachment_documents"/> + </xs:sequence> + <xs:attribute name="chapter" default="9.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="9.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Supporting information"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Supporting information"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <xs:element name="attachment_training_data"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="molecules"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <xs:element name="attachment_validation_data"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="molecules"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <xs:element name="attachment_documents"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="document"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <xs:element name="molecules"> + <xs:complexType> + <xs:attribute name="embedded"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="url" use="required"/> + <xs:attribute name="filetype"/> + <xs:attribute name="description"/> + </xs:complexType> + </xs:element> + <!-- http://www.ch.ic.ac.uk/chemime/Chemical MIME types --> + <xs:element name="document"> + <xs:complexType> + <xs:attribute name="embedded"> + <xs:simpleType> + <xs:restriction base="xs:token"> + <xs:enumeration value="Yes"/> + <xs:enumeration value="No"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="url" use="required"/> + <xs:attribute name="filetype"/> + <xs:attribute name="description"/> + </xs:complexType> + </xs:element> + <!-- 10. Summary (ECB Inventory) --> + <xs:element name="QMRF_Summary"> + <xs:complexType> + <xs:sequence> + <xs:element ref="QMRF_number"/> + <xs:element ref="date_publication"/> + <xs:element ref="keywords"/> + <xs:element ref="summary_comments"/> + </xs:sequence> + <xs:attribute name="chapter" default="10"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="10"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Summary (JRC QSAR Model Database)"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Summary (JRC QSAR Model Database)"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- 10.1 QMRF number --> + <xs:element name="QMRF_number"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="10.1"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="10.1"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="QMRF number"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="QMRF number"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <xs:element name="date_publication"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="10.2"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="10.2"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Publication date"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Publication date"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <xs:element name="keywords"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="10.3"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="10.3"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Keywords"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Keywords"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <xs:element name="summary_comments"> + <xs:complexType mixed="true"> + <xs:attribute name="chapter" default="10.4"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="10.4"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="name" default="Comments"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="Comments"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + <xs:attribute name="help" default=""/> + </xs:complexType> + </xs:element> + <!-- Misc repositories --> + <xs:element name="Catalogs"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="software_catalog"/> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="algorithms_catalog"/> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="descriptors_catalog"/> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="endpoints_catalog"/> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="publications_catalog"/> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="authors_catalog"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <!-- Software catalog --> + <xs:element name="software_catalog"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="software"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <xs:element name="software"> + <xs:complexType> + <xs:attribute name="id" use="required" type="xs:ID"/> + <xs:attribute name="name" use="required"/> + <xs:attribute name="url"/> + <xs:attribute name="number" use="required"/> + <xs:attribute name="description"/> + <xs:attribute name="version"/> + <xs:attribute name="contact"/> + </xs:complexType> + </xs:element> + <xs:element name="software_ref"> + <xs:complexType> + <xs:attribute name="idref" use="required" type="xs:IDREF"/> + <xs:attribute name="catalog" default="software_catalog"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="software_catalog"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + </xs:complexType> + </xs:element> + <!-- Algorithms catalog --> + <xs:element name="algorithms_catalog"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="algorithm"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <xs:element name="algorithm"> + <xs:complexType> + <xs:attribute name="id" use="required" type="xs:ID"/> + <xs:attribute name="definition" use="required"/> + <xs:attribute name="description" use="required"/> + <xs:attribute name="publication_ref" type="xs:IDREF"/> + </xs:complexType> + </xs:element> + <xs:element name="algorithm_ref"> + <xs:complexType> + <xs:attribute name="idref" use="required" type="xs:IDREF"/> + <xs:attribute name="catalog" default="algorithms_catalog"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="algorithms_catalog"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + </xs:complexType> + </xs:element> + <!-- Descriptors catalog --> + <xs:element name="descriptors_catalog"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="descriptor"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <xs:element name="descriptor"> + <xs:complexType> + <xs:attribute name="id" use="required" type="xs:ID"/> + <xs:attribute name="name" use="required"/> + <xs:attribute name="units" use="required"/> + <xs:attribute name="description" use="required"/> + <xs:attribute name="publication_ref" type="xs:IDREF"/> + </xs:complexType> + </xs:element> + <xs:element name="descriptor_ref"> + <xs:complexType> + <xs:attribute name="idref" use="required" type="xs:IDREF"/> + <xs:attribute name="catalog" default="descriptors_catalog"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="descriptors_catalog"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + </xs:complexType> + </xs:element> + <!-- Endpoints catalog --> + <!-- subgroup attribute added version 0.9 --> + <xs:element name="endpoints_catalog"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="endpoint"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <xs:element name="endpoint"> + <xs:complexType> + <xs:attribute name="id" use="required" type="xs:ID"/> + <xs:attribute name="name" use="required"/> + <xs:attribute name="subgroup"/> + <xs:attribute name="group"/> + </xs:complexType> + </xs:element> + <xs:element name="endpoint_ref"> + <xs:complexType> + <xs:attribute name="idref" use="required" type="xs:IDREF"/> + <xs:attribute name="catalog" default="endpoints_catalog"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="endpoints_catalog"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + </xs:complexType> + </xs:element> + <!-- Authors catalog. Number attribute should be unique, will be used in QMRF number generation --> + <xs:element name="authors_catalog"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="author"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <xs:element name="author"> + <xs:complexType> + <xs:attribute name="id" use="required" type="xs:ID"/> + <xs:attribute name="name" use="required"/> + <xs:attribute name="affiliation"/> + <xs:attribute name="contact"/> + <xs:attribute name="url"/> + <xs:attribute name="email"/> + <xs:attribute name="number" use="required"/> + </xs:complexType> + </xs:element> + <xs:element name="author_ref"> + <xs:complexType> + <xs:attribute name="idref" use="required" type="xs:IDREF"/> + <xs:attribute name="catalog" default="authors_catalog"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="authors_catalog"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + </xs:complexType> + </xs:element> + <!-- Publications catalog --> + <xs:element name="publications_catalog"> + <xs:complexType> + <xs:sequence> + <xs:element minOccurs="0" maxOccurs="unbounded" ref="publication"/> + </xs:sequence> + </xs:complexType> + </xs:element> + <xs:element name="publication"> + <xs:complexType> + <xs:attribute name="id" use="required" type="xs:ID"/> + <xs:attribute name="title" use="required"/> + <xs:attribute name="url"/> + </xs:complexType> + </xs:element> + <xs:element name="publication_ref"> + <xs:complexType> + <xs:attribute name="idref" use="required" type="xs:IDREF"/> + <xs:attribute name="number" default=""/> + <xs:attribute name="catalog" default="publications_catalog"> + <xs:simpleType> + <xs:restriction base="xs:string"> + <xs:enumeration value="publications_catalog"/> + </xs:restriction> + </xs:simpleType> + </xs:attribute> + </xs:complexType> + </xs:element> +</xs:schema> |