ddi-fw 0.0.237__py3-none-any.whl → 0.0.239__py3-none-any.whl

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Files changed (11) hide show
  1. ddi_fw/datasets/__init__.py +1 -4
  2. {ddi_fw-0.0.237.dist-info → ddi_fw-0.0.239.dist-info}/METADATA +1 -1
  3. {ddi_fw-0.0.237.dist-info → ddi_fw-0.0.239.dist-info}/RECORD +5 -11
  4. ddi_fw/drugbank/__init__.py +0 -2
  5. ddi_fw/drugbank/drugbank.xsd +0 -904
  6. ddi_fw/drugbank/drugbank_parser.py +0 -157
  7. ddi_fw/drugbank/drugbank_processor.py +0 -355
  8. ddi_fw/drugbank/drugbank_processor_org.py +0 -272
  9. ddi_fw/drugbank/event_extractor.py +0 -127
  10. {ddi_fw-0.0.237.dist-info → ddi_fw-0.0.239.dist-info}/WHEEL +0 -0
  11. {ddi_fw-0.0.237.dist-info → ddi_fw-0.0.239.dist-info}/top_level.txt +0 -0
ddi_fw/drugbank/drugbank.xsd DELETED
@@ -1,904 +0,0 @@
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- <?xml version="1.0" encoding="UTF-8"?>
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- <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified"
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- targetNamespace="http://www.drugbank.ca" xmlns="http://www.drugbank.ca">
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- <xs:element name="drugbank" type="drugbank-type">
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- <xs:annotation>
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- <xs:documentation>This is the root element for the DrugBank database schema. DrugBank is a database on drug and drug-targets.</xs:documentation>
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- </xs:annotation>
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- </xs:element>
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- <xs:complexType name="drugbank-type">
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- <xs:annotation>
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- <xs:documentation>This is the root element type for the DrugBank database schema.</xs:documentation>
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- </xs:annotation>
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- <xs:sequence>
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- <xs:element name="drug" type="drug-type" maxOccurs="unbounded"/>
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- </xs:sequence>
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- <xs:attribute name="version" type="xs:string" use="required">
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- <xs:annotation>
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- <xs:documentation>The DrugBank version for the exported XML file.</xs:documentation>
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- </xs:annotation>
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- </xs:attribute>
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- <xs:attribute name="exported-on" type="xs:date" use="required">
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- <xs:annotation>
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- <xs:documentation>The date the XML file was exported.</xs:documentation>
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- </xs:annotation>
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- </xs:attribute>
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- </xs:complexType>
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- <xs:complexType name="drug-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="1" name="drugbank-id"
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- type="drugbank-drug-salt-id-type"> </xs:element>
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- <xs:element name="name" type="xs:string"/>
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- <xs:element name="description" type="xs:string"/>
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- <xs:element name="cas-number" type="xs:string"/>
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- <xs:element name="unii" type="xs:string"/>
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- <xs:element name="average-mass" type="xs:float" minOccurs="0"/>
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- <xs:element name="monoisotopic-mass" type="xs:float" minOccurs="0"/>
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- <xs:element name="state" type="state-type" minOccurs="0"/>
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- <xs:element name="groups" type="group-list-type"/>
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- <xs:element name="general-references" type="reference-list-type"/>
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- <xs:element name="synthesis-reference" type="xs:string"/>
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- <xs:element name="indication" type="xs:string"/>
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- <xs:element name="pharmacodynamics" type="xs:string"/>
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- <xs:element name="mechanism-of-action" type="xs:string"/>
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- <xs:element name="toxicity" type="xs:string"/>
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- <xs:element name="metabolism" type="xs:string"/>
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- <xs:element name="absorption" type="xs:string"/>
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- <xs:element name="half-life" type="xs:string"/>
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- <xs:element name="protein-binding" type="xs:string"/>
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- <xs:element name="route-of-elimination" type="xs:string"/>
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- <xs:element name="volume-of-distribution" type="xs:string"/>
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- <xs:element name="clearance" type="xs:string"/>
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- <xs:element name="classification" type="classification-type" minOccurs="0"/>
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- <xs:element name="salts" type="salt-list-type"/>
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- <xs:element name="synonyms" type="synonym-list-type"/>
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- <xs:element name="products" type="product-list-type"/>
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- <xs:element name="international-brands" type="international-brand-list-type"/>
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- <xs:element name="mixtures" type="mixture-list-type"/>
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- <xs:element name="packagers" type="packager-list-type"/>
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- <xs:element name="manufacturers" type="manufacturer-list-type"/>
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- <xs:element name="prices" type="price-list-type"/>
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- <xs:element name="categories" type="category-list-type"/>
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- <xs:element name="affected-organisms" type="affected-organism-list-type"/>
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- <xs:element name="dosages" type="dosage-list-type"/>
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- <xs:element name="atc-codes" type="atc-code-list-type"/>
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- <xs:element name="ahfs-codes" type="ahfs-code-list-type"/>
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- <xs:element name="pdb-entries" type="pdb-entry-list-type"/>
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- <xs:element name="fda-label" type="xs:anyURI" minOccurs="0"/>
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- <xs:element name="msds" type="xs:anyURI" minOccurs="0"/>
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- <xs:element name="patents" type="patent-list-type"/>
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- <xs:element name="food-interactions" type="food-interaction-list-type"/>
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- <xs:element name="drug-interactions" type="drug-interaction-list-type"/>
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- <xs:element minOccurs="0" name="sequences" type="sequence-list-type"/>
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- <xs:element minOccurs="0" name="calculated-properties" type="calculated-property-list-type"/>
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- <xs:element name="experimental-properties" type="experimental-property-list-type"/>
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- <xs:element name="external-identifiers" type="external-identifier-list-type"/>
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- <xs:element name="external-links" type="external-link-list-type"/>
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- <xs:element name="pathways" type="pathway-list-type"/>
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- <xs:element name="reactions" type="reaction-list-type"/>
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- <xs:element name="snp-effects" type="snp-effect-list-type"/>
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- <xs:element name="snp-adverse-drug-reactions" type="snp-adverse-drug-reaction-list-type"/>
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- <xs:element name="targets" type="target-list-type"/>
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- <xs:element name="enzymes" type="enzyme-list-type"/>
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- <xs:element name="carriers" type="carrier-list-type"/>
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- <xs:element name="transporters" type="transporter-list-type"/>
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- </xs:sequence>
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- <xs:attribute name="type" use="required">
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- <xs:simpleType>
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- <xs:restriction base="xs:string">
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- <xs:enumeration value="small molecule"/>
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- <xs:enumeration value="biotech"/>
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- </xs:restriction>
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- </xs:simpleType>
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- </xs:attribute>
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- <xs:attribute name="created" type="xs:date" use="required"/>
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- <xs:attribute name="updated" type="xs:date" use="required"/>
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- </xs:complexType>
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- <xs:simpleType name="state-type">
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- <xs:restriction base="xs:string">
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- <xs:enumeration value="solid"/>
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- <xs:enumeration value="liquid"/>
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- <xs:enumeration value="gas"/>
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- </xs:restriction>
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- </xs:simpleType>
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- <xs:complexType name="group-list-type">
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- <xs:sequence maxOccurs="6" minOccurs="1">
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- <xs:element name="group" type="group-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:simpleType name="group-type">
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- <xs:annotation>
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- <xs:documentation>Drugs are grouped into a category like approved, experimental, illicit.</xs:documentation>
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- </xs:annotation>
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- <xs:restriction base="xs:string">
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- <xs:enumeration value="approved"/>
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- <xs:enumeration value="illicit"/>
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- <xs:enumeration value="experimental"/>
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- <xs:enumeration value="withdrawn"/>
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- <xs:enumeration value="nutraceutical"/>
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- <xs:enumeration value="investigational"/>
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- <xs:enumeration value="vet_approved"/>
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- </xs:restriction>
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- </xs:simpleType>
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- <xs:complexType name="classification-type">
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- <xs:annotation>
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- <xs:documentation>Drug classification is obtained from ClassyFire (http://classyfire.wishartlab.com).</xs:documentation>
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- </xs:annotation>
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- <xs:sequence>
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- <xs:element name="description" type="xs:string"/>
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- <xs:element name="direct-parent" type="xs:string"/>
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- <xs:element name="kingdom" type="xs:string"/>
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- <xs:element name="superclass" type="xs:string"/>
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- <xs:element name="class" type="xs:string"/>
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- <xs:element name="subclass" type="xs:string"/>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="alternative-parent"
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- type="xs:string"/>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="substituent" type="xs:string"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="synonym-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="synonym" type="synonym-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="synonym-type">
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- <xs:simpleContent>
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- <xs:extension base="xs:string">
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- <xs:attribute name="language" type="xs:string"/>
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- <xs:attribute name="coder" type="xs:string"/>
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- </xs:extension>
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- </xs:simpleContent>
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- </xs:complexType>
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- <xs:complexType name="salt-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="salt" type="salt-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="salt-type">
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- <xs:sequence>
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- <xs:element name="drugbank-id" type="drugbank-drug-salt-id-type" maxOccurs="unbounded"
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- minOccurs="0"/>
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- <xs:element name="name" type="xs:string"/>
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- <xs:element name="unii" type="xs:string"/>
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- <xs:element name="cas-number" type="xs:string"/>
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- <xs:element name="inchikey" type="xs:string"/>
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- <xs:element name="average-mass" type="xs:float" minOccurs="0"/>
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- <xs:element name="monoisotopic-mass" type="xs:float" minOccurs="0"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:simpleType name="drugbank-drug-salt-id-value">
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- <xs:restriction base="xs:string">
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- <xs:minLength value="1"/>
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- <xs:whiteSpace value="collapse"/>
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- <xs:pattern value="DB[0-9]{5}"/>
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- <xs:pattern value="DBSALT[0-9]{6}"/>
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- <xs:pattern value="APRD[0-9]{5}"/>
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- <xs:pattern value="BIOD[0-9]{5}"/>
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- <xs:pattern value="BTD[0-9]{5}"/>
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- <xs:pattern value="EXPT[0-9]{5}"/>
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- <xs:pattern value="NUTR[0-9]{5}"/>
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- </xs:restriction>
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- </xs:simpleType>
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- <xs:complexType name="drugbank-drug-salt-id-type">
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- <xs:annotation>
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- <xs:documentation>The DrugBank ID is used to uniquely identify a drug or salt entry. There is a primary ID and several secondary IDs that come from older ID formats or merged entries.</xs:documentation>
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- </xs:annotation>
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- <xs:simpleContent>
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- <xs:extension base="drugbank-drug-salt-id-value">
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- <xs:attribute default="false" name="primary" type="xs:boolean"/>
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- </xs:extension>
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- </xs:simpleContent>
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- </xs:complexType>
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- <xs:complexType name="drugbank-metabolite-id-type">
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- <xs:annotation>
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- <xs:documentation>The metabolite DrugBank ID uniquely identifies a metabolite entry. Multiple IDs indicate a merged entry.</xs:documentation>
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- </xs:annotation>
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- <xs:simpleContent>
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- <xs:extension base="drugbank-metabolite-id-value">
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- <xs:attribute default="false" name="primary" type="xs:boolean"/>
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- </xs:extension>
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- </xs:simpleContent>
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- </xs:complexType>
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- <xs:simpleType name="drugbank-metabolite-id-value">
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- <xs:restriction base="xs:string">
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- <xs:minLength value="1"/>
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- <xs:whiteSpace value="collapse"/>
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- <xs:pattern value="DBMET[0-9]{5}"/>
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- </xs:restriction>
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- </xs:simpleType>
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- <xs:complexType name="article-type">
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- <xs:sequence>
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- <xs:element name="ref-id" type="xs:string" maxOccurs="1" minOccurs="0"/>
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- <xs:element name="pubmed-id" type="xs:string"/>
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- <xs:element name="citation" type="xs:string"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="textbook-type">
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- <xs:sequence>
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- <xs:element name="ref-id" type="xs:string" maxOccurs="1" minOccurs="0"/>
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- <xs:element name="isbn" type="xs:string"/>
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- <xs:element name="citation" type="xs:string"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="link-type">
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- <xs:sequence>
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- <xs:element name="ref-id" type="xs:string" maxOccurs="1" minOccurs="0"/>
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- <xs:element name="title" type="xs:string"/>
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- <xs:element name="url" type="xs:anyURI"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="attachment-type">
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- <xs:sequence>
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- <xs:element name="ref-id" type="xs:string" maxOccurs="1" minOccurs="0"/>
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- <xs:element name="title" type="xs:string"/>
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- <xs:element name="url" type="xs:anyURI"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="article-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="article" type="article-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="textbook-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="textbook" type="textbook-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="link-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="link" type="link-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="attachment-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="attachment" type="attachment-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="reference-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="1" minOccurs="1" name="articles" type="article-list-type">
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- <xs:annotation>
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- <xs:documentation>Articles are typically PubMed references, although there are some references which do not have a PubMed ID.</xs:documentation>
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- </xs:annotation>
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- </xs:element>
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- <xs:element maxOccurs="1" minOccurs="1" name="textbooks" type="textbook-list-type"/>
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- <xs:element maxOccurs="1" minOccurs="1" name="links" type="link-list-type"/>
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- <xs:element maxOccurs="1" minOccurs="1" name="attachments" type="attachment-list-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="international-brand-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="international-brand"
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- type="international-brand-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="international-brand-type">
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- <xs:sequence>
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- <xs:element name="name" type="xs:string"/>
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- <xs:element name="company" type="xs:string"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="product-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="product" type="product-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="product-type">
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- <xs:sequence>
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- <xs:element name="name" type="xs:string"/>
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- <xs:element name="labeller" type="xs:string"/>
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- <xs:element name="ndc-id" type="xs:string"/>
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- <xs:element name="ndc-product-code" type="xs:string"/>
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- <xs:element name="dpd-id" type="xs:string" nillable="true">
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- <xs:annotation>
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- <xs:documentation>DPD ID from the Canadian Drug Product Database. Only present for drugs that are marketed in Canada.</xs:documentation>
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- </xs:annotation>
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- </xs:element>
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- <xs:element name="ema-product-code" type="xs:string" nillable="true">
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- <xs:annotation>
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- <xs:documentation>EMA product code from the European Medicines Agency Database. Only present for products that are authorised by central procedure for marketing in the European Union.</xs:documentation>
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- </xs:annotation>
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- </xs:element>
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- <xs:element name="ema-ma-number" type="xs:string" nillable="true">
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- <xs:annotation>
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- <xs:documentation>EMA marketing authorisation number from the European Medicines Agency Database. Only present for products that are authorised by central procedure for marketing in the European Union.</xs:documentation>
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- </xs:annotation>
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- </xs:element>
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- <xs:element name="started-marketing-on" type="xs:string"/>
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- <xs:element name="ended-marketing-on" type="xs:string"/>
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- <xs:element name="dosage-form" type="xs:string"/>
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- <xs:element name="strength" type="xs:string"/>
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- <xs:element name="route" type="xs:string"/>
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- <xs:element name="fda-application-number" type="xs:string"/>
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- <xs:element name="generic" type="xs:boolean"/>
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- <xs:element name="over-the-counter" type="xs:boolean"/>
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- <xs:element name="approved" type="xs:boolean"/>
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- <xs:element name="country" type="product-country-type" maxOccurs="1"/>
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- <xs:element name="source" type="product-source-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="mixture-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="mixture" type="mixture-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="mixture-type">
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- <xs:sequence>
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- <xs:element name="name" type="xs:string"/>
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- <xs:element name="ingredients" type="xs:string"/>
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- <xs:element maxOccurs="1" minOccurs="0" name="supplemental-ingredients" type="xs:string"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="packager-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="packager" type="packager-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="packager-type">
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- <xs:sequence>
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- <xs:element name="name" type="xs:string"/>
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- <xs:element name="url" type="xs:string"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="manufacturer-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="manufacturer"
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- type="manufacturer-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="manufacturer-type">
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- <xs:simpleContent>
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- <xs:extension base="xs:string">
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- <xs:attribute name="generic" type="xs:boolean"/>
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- <xs:attribute name="url" type="xs:anyURI"/>
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- </xs:extension>
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- </xs:simpleContent>
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- </xs:complexType>
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- <xs:complexType name="price-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="price" type="price-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="price-type">
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- <xs:annotation>
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- <xs:documentation>The price for the given drug in US or Canadian currency.</xs:documentation>
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- </xs:annotation>
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- <xs:sequence>
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- <xs:element name="description" type="xs:string"/>
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- <xs:element name="cost">
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- <xs:complexType>
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- <xs:simpleContent>
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- <xs:extension base="xs:string">
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- <xs:attribute name="currency" type="xs:string" use="required"/>
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- </xs:extension>
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- </xs:simpleContent>
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- </xs:complexType>
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- </xs:element>
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- <xs:element name="unit" type="xs:string"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="category-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="category" type="category-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="category-type">
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- <xs:sequence>
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- <xs:element name="category" type="xs:string"/>
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- <xs:element name="mesh-id" type="xs:string"> </xs:element>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="affected-organism-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="affected-organism"
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- type="xs:string"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="dosage-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="dosage" type="dosage-type"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="dosage-type">
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- <xs:sequence>
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- <xs:element name="form" type="xs:string"/>
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- <xs:element name="route" type="xs:string"/>
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- <xs:element name="strength" type="xs:string"/>
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- </xs:sequence>
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- </xs:complexType>
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- <xs:complexType name="atc-code-list-type">
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- <xs:sequence>
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- <xs:element maxOccurs="unbounded" minOccurs="0" name="atc-code" type="atc-code-type"/>
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- </xs:sequence>
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- </xs:complexType>
414
- <xs:complexType name="atc-code-type">
415
- <xs:sequence>
416
- <xs:element maxOccurs="4" minOccurs="4" name="level" type="atc-code-level-type"/>
417
- </xs:sequence>
418
- <xs:attribute name="code" type="xs:string"/>
419
- </xs:complexType>
420
- <xs:complexType name="atc-code-level-type">
421
- <xs:simpleContent>
422
- <xs:extension base="xs:string">
423
- <xs:attribute name="code" type="xs:string" use="required"/>
424
- </xs:extension>
425
- </xs:simpleContent>
426
- </xs:complexType>
427
- <xs:complexType name="ahfs-code-list-type">
428
- <xs:sequence>
429
- <xs:element maxOccurs="unbounded" minOccurs="0" name="ahfs-code" type="xs:string"/>
430
- </xs:sequence>
431
- </xs:complexType>
432
- <xs:complexType name="pdb-entry-list-type">
433
- <xs:sequence>
434
- <xs:element maxOccurs="unbounded" minOccurs="0" name="pdb-entry" type="xs:string"/>
435
- </xs:sequence>
436
- </xs:complexType>
437
- <xs:complexType name="patent-list-type">
438
- <xs:sequence>
439
- <xs:element maxOccurs="unbounded" minOccurs="0" name="patent" type="patent-type"/>
440
- </xs:sequence>
441
- </xs:complexType>
442
- <xs:complexType name="patent-type">
443
- <xs:sequence>
444
- <xs:element name="number" type="xs:string"/>
445
- <xs:element name="country" type="xs:string"/>
446
- <xs:element name="approved" type="xs:string"/>
447
- <xs:element name="expires" type="xs:string"/>
448
- <xs:element name="pediatric-extension" type="xs:boolean"/>
449
- </xs:sequence>
450
- </xs:complexType>
451
- <xs:complexType name="food-interaction-list-type">
452
- <xs:sequence>
453
- <xs:element maxOccurs="unbounded" minOccurs="0" name="food-interaction" type="xs:string"
454
- />
455
- </xs:sequence>
456
- </xs:complexType>
457
- <xs:complexType name="drug-interaction-list-type">
458
- <xs:sequence>
459
- <xs:element maxOccurs="unbounded" minOccurs="0" name="drug-interaction"
460
- type="drug-interaction-type"/>
461
- </xs:sequence>
462
- </xs:complexType>
463
- <xs:complexType name="drug-interaction-type">
464
- <xs:sequence>
465
- <xs:element name="drugbank-id" type="drugbank-drug-salt-id-type"/>
466
- <xs:element name="name" type="xs:string"/>
467
- <xs:element name="description" type="xs:string"/>
468
- </xs:sequence>
469
- </xs:complexType>
470
- <xs:complexType name="sequence-list-type">
471
- <xs:sequence>
472
- <xs:element maxOccurs="unbounded" minOccurs="0" name="sequence">
473
- <xs:complexType>
474
- <xs:simpleContent>
475
- <xs:extension base="xs:string">
476
- <xs:attribute fixed="FASTA" name="format" type="xs:string"/>
477
- </xs:extension>
478
- </xs:simpleContent>
479
- </xs:complexType>
480
- </xs:element>
481
- </xs:sequence>
482
- </xs:complexType>
483
- <xs:complexType name="calculated-property-list-type">
484
- <xs:sequence>
485
- <xs:element maxOccurs="unbounded" minOccurs="0" name="property"
486
- type="calculated-property-type"/>
487
- </xs:sequence>
488
- </xs:complexType>
489
- <xs:complexType name="calculated-property-type">
490
- <xs:sequence>
491
- <xs:element name="kind" type="calculated-property-kind-type"/>
492
- <xs:element name="value" type="xs:string"/>
493
- <xs:element name="source" type="calculated-property-source-type"/>
494
- </xs:sequence>
495
- </xs:complexType>
496
- <xs:simpleType name="calculated-property-source-type">
497
- <xs:restriction base="xs:string">
498
- <xs:enumeration value="ChemAxon"/>
499
- <xs:enumeration value="ALOGPS"/>
500
- </xs:restriction>
501
- </xs:simpleType>
502
- <xs:simpleType name="calculated-property-kind-type">
503
- <xs:restriction base="xs:string">
504
- <xs:enumeration value="logP"/>
505
- <xs:enumeration value="logS"/>
506
- <xs:enumeration value="Water Solubility"/>
507
- <xs:enumeration value="IUPAC Name"/>
508
- <xs:enumeration value="Traditional IUPAC Name"/>
509
- <xs:enumeration value="Molecular Weight"/>
510
- <xs:enumeration value="Monoisotopic Weight"/>
511
- <xs:enumeration value="SMILES"/>
512
- <xs:enumeration value="Molecular Formula"/>
513
- <xs:enumeration value="InChI"/>
514
- <xs:enumeration value="InChIKey"/>
515
- <xs:enumeration value="Polar Surface Area (PSA)"/>
516
- <xs:enumeration value="Refractivity"/>
517
- <xs:enumeration value="Polarizability"/>
518
- <xs:enumeration value="Rotatable Bond Count"/>
519
- <xs:enumeration value="H Bond Acceptor Count"/>
520
- <xs:enumeration value="H Bond Donor Count"/>
521
- <xs:enumeration value="pKa (strongest acidic)"/>
522
- <xs:enumeration value="pKa (strongest basic)"/>
523
- <xs:enumeration value="Physiological Charge"/>
524
- <xs:enumeration value="Number of Rings"/>
525
- <xs:enumeration value="Bioavailability"/>
526
- <xs:enumeration value="Rule of Five"/>
527
- <xs:enumeration value="Ghose Filter"/>
528
- <xs:enumeration value="MDDR-Like Rule"/>
529
- <xs:enumeration value="Veber's Rule"/>
530
- </xs:restriction>
531
- </xs:simpleType>
532
- <xs:complexType name="experimental-property-list-type">
533
- <xs:sequence>
534
- <xs:element maxOccurs="unbounded" minOccurs="0" name="property"
535
- type="experimental-property-type"/>
536
- </xs:sequence>
537
- </xs:complexType>
538
- <xs:complexType name="experimental-property-type">
539
- <xs:sequence>
540
- <xs:element name="kind" type="experimental-property-kind-type"/>
541
- <xs:element name="value" type="xs:string"/>
542
- <xs:element name="source" type="xs:string"/>
543
- </xs:sequence>
544
- </xs:complexType>
545
- <xs:simpleType name="experimental-property-kind-type">
546
- <xs:restriction base="xs:string">
547
- <xs:enumeration value="Water Solubility"/>
548
- <xs:enumeration value="Melting Point"/>
549
- <xs:enumeration value="Boiling Point"/>
550
- <xs:enumeration value="logP"/>
551
- <xs:enumeration value="logS"/>
552
- <xs:enumeration value="Hydrophobicity"/>
553
- <xs:enumeration value="Isoelectric Point"/>
554
- <xs:enumeration value="caco2 Permeability"/>
555
- <xs:enumeration value="pKa"/>
556
- <xs:enumeration value="Molecular Weight"/>
557
- <xs:enumeration value="Molecular Formula"/>
558
- <xs:enumeration value="Radioactivity"/>
559
- </xs:restriction>
560
- </xs:simpleType>
561
- <xs:complexType name="external-identifier-list-type">
562
- <xs:sequence>
563
- <xs:element maxOccurs="unbounded" minOccurs="0" name="external-identifier"
564
- type="external-identifier-type"/>
565
- </xs:sequence>
566
- </xs:complexType>
567
- <xs:complexType name="external-identifier-type">
568
- <xs:sequence>
569
- <xs:element name="resource" type="external-identifier-resource-type"/>
570
- <xs:element name="identifier" type="xs:string"/>
571
- </xs:sequence>
572
- </xs:complexType>
573
- <xs:simpleType name="external-identifier-resource-type">
574
- <xs:restriction base="xs:string">
575
- <xs:enumeration value="UniProtKB"/>
576
- <xs:enumeration value="Wikipedia"/>
577
- <xs:enumeration value="ChEBI"/>
578
- <xs:enumeration value="ChEMBL"/>
579
- <xs:enumeration value="PubChem Compound"/>
580
- <xs:enumeration value="PubChem Substance"/>
581
- <xs:enumeration value="Drugs Product Database (DPD)"/>
582
- <xs:enumeration value="KEGG Compound"/>
583
- <xs:enumeration value="KEGG Drug"/>
584
- <xs:enumeration value="ChemSpider"/>
585
- <xs:enumeration value="BindingDB"/>
586
- <xs:enumeration value="National Drug Code Directory"/>
587
- <xs:enumeration value="GenBank"/>
588
- <xs:enumeration value="Therapeutic Targets Database"/>
589
- <xs:enumeration value="PharmGKB"/>
590
- <xs:enumeration value="PDB"/>
591
- <xs:enumeration value="IUPHAR"/>
592
- <xs:enumeration value="Guide to Pharmacology"/>
593
- <xs:enumeration value="ZINC"/>
594
- <xs:enumeration value="RxCUI"/>
595
- </xs:restriction>
596
- </xs:simpleType>
597
- <xs:complexType name="external-link-list-type">
598
- <xs:sequence>
599
- <xs:element maxOccurs="unbounded" minOccurs="0" name="external-link"
600
- type="external-link-type"/>
601
- </xs:sequence>
602
- </xs:complexType>
603
- <xs:complexType name="external-link-type">
604
- <xs:sequence>
605
- <xs:element name="resource" type="external-link-resource-type"/>
606
- <xs:element name="url" type="xs:string"/>
607
- </xs:sequence>
608
- </xs:complexType>
609
- <xs:simpleType name="external-link-resource-type">
610
- <xs:restriction base="xs:string">
611
- <xs:enumeration value="RxList"/>
612
- <xs:enumeration value="PDRhealth"/>
613
- <xs:enumeration value="Drugs.com"/>
614
- </xs:restriction>
615
- </xs:simpleType>
616
- <xs:complexType name="pathway-list-type">
617
- <xs:sequence>
618
- <xs:element maxOccurs="unbounded" minOccurs="0" name="pathway" type="pathway-type"/>
619
- </xs:sequence>
620
- </xs:complexType>
621
- <xs:complexType name="pathway-type">
622
- <xs:sequence>
623
- <xs:element name="smpdb-id" type="xs:string"/>
624
- <xs:element name="name" type="xs:string"/>
625
- <xs:element name="category" type="xs:string"/>
626
- <xs:element name="drugs" type="pathway-drug-list-type"/>
627
- <xs:element name="enzymes" type="pathway-enzyme-list-type"/>
628
- </xs:sequence>
629
- </xs:complexType>
630
- <xs:complexType name="pathway-drug-list-type">
631
- <xs:sequence>
632
- <xs:element maxOccurs="unbounded" minOccurs="1" name="drug" type="pathway-drug-type"/>
633
- </xs:sequence>
634
- </xs:complexType>
635
- <xs:complexType name="pathway-drug-type">
636
- <xs:sequence>
637
- <xs:element name="drugbank-id" type="drugbank-drug-salt-id-type"/>
638
- <xs:element name="name" type="xs:string"/>
639
- </xs:sequence>
640
- </xs:complexType>
641
- <xs:complexType name="pathway-enzyme-list-type">
642
- <xs:sequence>
643
- <xs:element maxOccurs="unbounded" minOccurs="0" name="uniprot-id" type="xs:string"/>
644
- </xs:sequence>
645
- </xs:complexType>
646
- <xs:complexType name="reaction-list-type">
647
- <xs:sequence>
648
- <xs:element maxOccurs="unbounded" minOccurs="0" name="reaction" type="reaction-type"/>
649
- </xs:sequence>
650
- </xs:complexType>
651
- <xs:complexType name="reaction-type">
652
- <xs:sequence>
653
- <xs:element name="sequence" type="xs:string"/>
654
- <xs:element name="left-element" type="reaction-element-type"/>
655
- <xs:element name="right-element" type="reaction-element-type"/>
656
- <xs:element name="enzymes" type="reaction-enzyme-list-type"/>
657
- </xs:sequence>
658
- </xs:complexType>
659
- <xs:complexType name="reaction-element-type">
660
- <xs:sequence>
661
- <xs:element name="drugbank-id" type="xs:string"/>
662
- <xs:element name="name" type="xs:string"/>
663
- </xs:sequence>
664
- </xs:complexType>
665
- <xs:complexType name="reaction-enzyme-list-type">
666
- <xs:sequence>
667
- <xs:element maxOccurs="unbounded" minOccurs="0" name="enzyme"
668
- type="reaction-enzyme-type"/>
669
- </xs:sequence>
670
- </xs:complexType>
671
- <xs:complexType name="reaction-enzyme-type">
672
- <xs:sequence>
673
- <xs:element name="drugbank-id" type="xs:string"/>
674
- <xs:element name="name" type="xs:string"/>
675
- <xs:element name="uniprot-id" type="xs:string"/>
676
- </xs:sequence>
677
- </xs:complexType>
678
- <xs:complexType name="snp-effect-list-type">
679
- <xs:sequence>
680
- <xs:element maxOccurs="unbounded" minOccurs="0" name="effect" type="snp-effect-type"/>
681
- </xs:sequence>
682
- </xs:complexType>
683
- <xs:complexType name="snp-effect-type">
684
- <xs:sequence maxOccurs="unbounded" minOccurs="0">
685
- <xs:element maxOccurs="1" minOccurs="1" name="protein-name" type="xs:string"/>
686
- <xs:element name="gene-symbol" type="xs:string"/>
687
- <xs:element name="uniprot-id" type="xs:string"/>
688
- <xs:element name="rs-id" type="xs:string"/>
689
- <xs:element name="allele" type="xs:string"/>
690
- <xs:element name="defining-change" type="xs:string"/>
691
- <xs:element name="description" type="xs:string"/>
692
- <xs:element name="pubmed-id" type="xs:string"/>
693
- </xs:sequence>
694
- </xs:complexType>
695
- <xs:complexType name="snp-adverse-drug-reaction-list-type">
696
- <xs:sequence>
697
- <xs:element maxOccurs="unbounded" minOccurs="0" name="reaction"
698
- type="snp-adverse-drug-reaction-type"/>
699
- </xs:sequence>
700
- </xs:complexType>
701
- <xs:complexType name="snp-adverse-drug-reaction-type">
702
- <xs:sequence maxOccurs="unbounded" minOccurs="0">
703
- <xs:element maxOccurs="1" minOccurs="1" name="protein-name" type="xs:string"/>
704
- <xs:element name="gene-symbol" type="xs:string"/>
705
- <xs:element name="uniprot-id" type="xs:string"/>
706
- <xs:element name="rs-id" type="xs:string"/>
707
- <xs:element name="allele" type="xs:string"/>
708
- <xs:element name="adverse-reaction" type="xs:string"/>
709
- <xs:element name="description" type="xs:string"/>
710
- <xs:element name="pubmed-id" type="xs:string"/>
711
- </xs:sequence>
712
- </xs:complexType>
713
- <xs:complexType name="polypeptide-list-type">
714
- <xs:sequence>
715
- <xs:element maxOccurs="unbounded" minOccurs="0" name="polypeptide"
716
- type="polypeptide-type"/>
717
- </xs:sequence>
718
- </xs:complexType>
719
- <xs:complexType name="polypeptide-type">
720
- <xs:sequence>
721
- <xs:element name="name" type="xs:string"/>
722
- <xs:element name="general-function" type="xs:string"/>
723
- <xs:element name="specific-function" type="xs:string"/>
724
- <xs:element name="gene-name" type="xs:string"/>
725
- <xs:element name="locus" type="xs:string"/>
726
- <xs:element name="cellular-location" type="xs:string"/>
727
- <xs:element name="transmembrane-regions" type="xs:string"/>
728
- <xs:element name="signal-regions" type="xs:string"/>
729
- <xs:element name="theoretical-pi" type="xs:string"/>
730
- <xs:element name="molecular-weight" type="xs:string"/>
731
- <xs:element name="chromosome-location" type="xs:string"/>
732
- <xs:element name="organism">
733
- <xs:complexType>
734
- <xs:simpleContent>
735
- <xs:extension base="xs:string">
736
- <xs:attribute name="ncbi-taxonomy-id" type="xs:string"/>
737
- </xs:extension>
738
- </xs:simpleContent>
739
- </xs:complexType>
740
- </xs:element>
741
- <xs:element name="external-identifiers" type="polypeptide-external-identifier-list-type"/>
742
- <xs:element name="synonyms" type="polypeptide-synonym-list-type"/>
743
- <xs:element name="amino-acid-sequence" type="sequence-type" minOccurs="1"/>
744
- <xs:element name="gene-sequence" type="sequence-type" minOccurs="1"/>
745
- <xs:element name="pfams" type="pfam-list-type"/>
746
- <xs:element name="go-classifiers" type="go-classifier-list-type"/>
747
- </xs:sequence>
748
- <xs:attribute name="id" type="xs:string" use="required"/>
749
- <xs:attribute name="source" type="xs:string" use="required"/>
750
- </xs:complexType>
751
- <xs:complexType name="polypeptide-external-identifier-list-type">
752
- <xs:sequence>
753
- <xs:element maxOccurs="unbounded" minOccurs="0" name="external-identifier"
754
- type="polypeptide-external-identifier-type"/>
755
- </xs:sequence>
756
- </xs:complexType>
757
- <xs:complexType name="polypeptide-external-identifier-type">
758
- <xs:sequence>
759
- <xs:element name="resource" type="polypeptide-external-identifier-resource-type"/>
760
- <xs:element name="identifier" type="xs:string"/>
761
- </xs:sequence>
762
- </xs:complexType>
763
- <xs:simpleType name="polypeptide-external-identifier-resource-type">
764
- <xs:restriction base="xs:string">
765
- <xs:enumeration value="UniProtKB"/>
766
- <xs:enumeration value="UniProt Accession"/>
767
- <xs:enumeration value="HUGO Gene Nomenclature Committee (HGNC)"/>
768
- <xs:enumeration value="Human Protein Reference Database (HPRD)"/>
769
- <xs:enumeration value="GenAtlas"/>
770
- <xs:enumeration value="GeneCards"/>
771
- <xs:enumeration value="GenBank Gene Database"/>
772
- <xs:enumeration value="GenBank Protein Database"/>
773
- <xs:enumeration value="ChEMBL"/>
774
- <xs:enumeration value="IUPHAR"/>
775
- <xs:enumeration value="Guide to Pharmacology"/>
776
- </xs:restriction>
777
- </xs:simpleType>
778
- <xs:complexType name="polypeptide-synonym-list-type">
779
- <xs:sequence>
780
- <xs:element maxOccurs="unbounded" minOccurs="0" name="synonym" type="xs:string"/>
781
- </xs:sequence>
782
- </xs:complexType>
783
- <xs:complexType name="sequence-type">
784
- <xs:simpleContent>
785
- <xs:extension base="xs:string">
786
- <xs:attribute fixed="FASTA" name="format" type="xs:string"/>
787
- </xs:extension>
788
- </xs:simpleContent>
789
- </xs:complexType>
790
- <xs:complexType name="pfam-list-type">
791
- <xs:sequence>
792
- <xs:element maxOccurs="unbounded" minOccurs="0" name="pfam" type="pfam-type"/>
793
- </xs:sequence>
794
- </xs:complexType>
795
- <xs:complexType name="pfam-type">
796
- <xs:sequence>
797
- <xs:element name="identifier" type="xs:string"/>
798
- <xs:element name="name" type="xs:string"/>
799
- </xs:sequence>
800
- </xs:complexType>
801
- <xs:complexType name="go-classifier-list-type">
802
- <xs:sequence>
803
- <xs:element maxOccurs="unbounded" minOccurs="0" name="go-classifier"
804
- type="go-classifier-type"/>
805
- </xs:sequence>
806
- </xs:complexType>
807
- <xs:complexType name="go-classifier-type">
808
- <xs:sequence>
809
- <xs:element name="category" type="xs:string"/>
810
- <xs:element name="description" type="xs:string"/>
811
- </xs:sequence>
812
- </xs:complexType>
813
- <xs:complexType name="action-list-type">
814
- <xs:sequence>
815
- <xs:element name="action" type="xs:string" maxOccurs="unbounded" minOccurs="0"/>
816
- </xs:sequence>
817
- </xs:complexType>
818
- <xs:simpleType name="known-action-type">
819
- <xs:restriction base="xs:string">
820
- <xs:enumeration value="yes"/>
821
- <xs:enumeration value="no"/>
822
- <xs:enumeration value="unknown"/>
823
- </xs:restriction>
824
- </xs:simpleType>
825
- <xs:group name="interactant-group">
826
- <xs:sequence>
827
- <xs:element name="id" type="xs:string"/>
828
- <xs:element name="name" type="xs:string"/>
829
- <xs:element name="organism" type="xs:string"/>
830
- <xs:element name="actions" type="action-list-type"/>
831
- <xs:element name="references" type="reference-list-type"/>
832
- <xs:element name="known-action" type="known-action-type"/>
833
- <xs:element maxOccurs="unbounded" minOccurs="0" name="polypeptide"
834
- type="polypeptide-type"/>
835
- </xs:sequence>
836
- </xs:group>
837
- <xs:complexType name="target-list-type">
838
- <xs:sequence>
839
- <xs:element maxOccurs="unbounded" minOccurs="0" name="target" type="target-type"/>
840
- </xs:sequence>
841
- </xs:complexType>
842
- <xs:complexType name="target-type">
843
- <xs:sequence>
844
- <xs:group ref="interactant-group"/>
845
- </xs:sequence>
846
- <xs:attribute name="position" type="xs:integer" use="optional"/>
847
- </xs:complexType>
848
- <xs:complexType name="enzyme-list-type">
849
- <xs:sequence>
850
- <xs:element maxOccurs="unbounded" minOccurs="0" name="enzyme" type="enzyme-type"/>
851
- </xs:sequence>
852
- </xs:complexType>
853
- <xs:complexType name="enzyme-type">
854
- <xs:sequence>
855
- <xs:group ref="interactant-group"/>
856
- <xs:element name="inhibition-strength" type="xs:string"/>
857
- <xs:element name="induction-strength" type="xs:string"/>
858
- </xs:sequence>
859
- <xs:attribute name="position" type="xs:integer" use="optional"/>
860
- </xs:complexType>
861
- <xs:complexType name="carrier-list-type">
862
- <xs:sequence>
863
- <xs:element maxOccurs="unbounded" minOccurs="0" name="carrier" type="carrier-type"/>
864
- </xs:sequence>
865
- </xs:complexType>
866
- <xs:complexType name="carrier-type">
867
- <xs:sequence>
868
- <xs:group ref="interactant-group"/>
869
- </xs:sequence>
870
- <xs:attribute name="position" type="xs:integer" use="optional"/>
871
- </xs:complexType>
872
- <xs:complexType name="transporter-list-type">
873
- <xs:sequence>
874
- <xs:element maxOccurs="unbounded" minOccurs="0" name="transporter"
875
- type="transporter-type"/>
876
- </xs:sequence>
877
- </xs:complexType>
878
- <xs:complexType name="transporter-type">
879
- <xs:sequence>
880
- <xs:group ref="interactant-group"/>
881
- </xs:sequence>
882
- <xs:attribute name="position" type="xs:integer" use="optional"/>
883
- </xs:complexType>
884
- <xs:simpleType name="product-country-type">
885
- <xs:annotation>
886
- <xs:documentation>Drug products are currently only imported from the U.S. (FDA) and Canada (Canadian Drug Product Database, or DPD).</xs:documentation>
887
- </xs:annotation>
888
- <xs:restriction base="xs:string">
889
- <xs:enumeration value="US"/>
890
- <xs:enumeration value="Canada"/>
891
- <xs:enumeration value="EU"/>
892
- </xs:restriction>
893
- </xs:simpleType>
894
- <xs:simpleType name="product-source-type">
895
- <xs:annotation>
896
- <xs:documentation>Drug products are currently only imported from the FDA and the Canadian Drug Product Database, or DPD.</xs:documentation>
897
- </xs:annotation>
898
- <xs:restriction base="xs:string">
899
- <xs:enumeration value="FDA NDC"/>
900
- <xs:enumeration value="DPD"/>
901
- <xs:enumeration value="EMA"/>
902
- </xs:restriction>
903
- </xs:simpleType>
904
- </xs:schema>