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phenoxml.xsd
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phenoxml.xsd
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<?xml version="1.0" encoding="UTF-8"?>
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" targetNamespace="http://www.bioontologies.org/obd/schema/pheno" xmlns:pheno="http://www.bioontologies.org/obd/schema/pheno">
<!--
default namespace = ""
namespace geno = "http://www.gmod.org/schema/genotype"
-->
<!--
Changes:
Version: 0.11
genetic_feature_set -> genotype_feature_link
Version: 0.10
complete revamp from 0_06
-->
<xs:element name="phenoset">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:genotype"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:genetic_feature"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:phenotype"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:phenotype_manifestation"/>
</xs:sequence>
<xs:attribute name="version" type="xs:string"/>
</xs:complexType>
</xs:element>
<xs:element name="genotype">
<xs:annotation>
<xs:documentation>Each genotype record represents a single individual or group of genetically similar individuals</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" ref="pheno:name"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:genotype_feature_link"/>
</xs:sequence>
<xs:attribute name="id" type="pheno:identifier_Type"/>
<xs:attribute name="organism" type="pheno:identifier_Type">
<xs:annotation>
<xs:documentation>NCBI Taxon ID</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="background" type="pheno:identifier_Type">
<xs:annotation>
<xs:documentation>another genotype</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="name" type="pheno:name_Type"/>
<xs:element name="genotype_feature_link">
<xs:complexType>
<xs:attribute name="copy_count" type="xs:int"/>
<xs:attribute name="feature" type="pheno:identifier_Type">
<xs:annotation>
<xs:documentation>a reference to a genetic feature</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="genetic_feature">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" ref="pheno:typeref"/>
<xs:element minOccurs="0" ref="pheno:name"/>
</xs:sequence>
<xs:attribute name="id" use="required" type="pheno:identifier_Type"/>
<xs:attribute name="organism" type="pheno:identifier_Type">
<xs:annotation>
<xs:documentation>optional: same as genotype.organism_id if not specified</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="manifest_in">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:typeref">
<xs:annotation>
<xs:documentation>may be from genetic context ontology</xs:documentation>
</xs:annotation>
</xs:element>
</xs:sequence>
<xs:attribute name="penetrance_percentage" type="xs:float"/>
<xs:attribute name="genotype" type="pheno:identifier_Type"/>
</xs:complexType>
</xs:element>
<xs:element name="phenotype_manifestation">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" ref="pheno:description">
<xs:annotation>
<xs:documentation>free text summary of the entire phenotype manifestation;</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element ref="pheno:manifest_in"/>
<xs:element ref="pheno:phenotype"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:provenance">
<xs:annotation>
<xs:documentation>support or evidence; experimental details</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:envirotype"/>
</xs:sequence>
<xs:attribute name="id" type="pheno:identifier_Type"/>
</xs:complexType>
</xs:element>
<xs:element name="phenotype">
<xs:annotation>
<xs:documentation>a phenotype is a collection of phenotype characters</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" ref="pheno:typeref"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:phenotype_character"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="phenotype_character">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" ref="pheno:description">
<xs:annotation>
<xs:documentation>free text summary of the phenotype character</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element ref="pheno:bearer"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:quality"/>
</xs:sequence>
<xs:attribute name="expressivity_percentage" type="xs:float"/>
</xs:complexType>
</xs:element>
<xs:element name="bearer">
<xs:complexType>
<xs:sequence>
<xs:element ref="pheno:typeref"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="quality">
<xs:complexType>
<xs:sequence>
<xs:element ref="pheno:typeref">
<xs:annotation>
<xs:documentation>quality type. comes from PATO</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element minOccurs="0" ref="pheno:description">
<xs:annotation>
<xs:documentation>optional free text</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:related_entity"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:on_condition"/>
<xs:element minOccurs="0" ref="pheno:in_comparison_to">
<xs:annotation>
<xs:documentation>for relative qualities we may want an explicit "yardstick"</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:measurement"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:temporal_qualifier"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:modifier"/>
</xs:sequence>
<xs:attribute name="determinable" type="pheno:classId_Type"/>
<xs:attribute name="count" type="xs:integer"/>
</xs:complexType>
</xs:element>
<xs:element name="related_entity">
<xs:complexType>
<xs:sequence>
<xs:element ref="pheno:typeref"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="on_condition">
<xs:annotation>
<xs:documentation>sometimes a state is only instantiated if a certain condition holds</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element ref="pheno:typeref"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="in_comparison_to">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:typeref"/>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:measurement"/>
</xs:sequence>
<xs:attribute name="relation" type="pheno:classId_Type"/>
<xs:attribute name="about" type="pheno:identifier_Type"/>
</xs:complexType>
</xs:element>
<xs:element name="modifier">
<xs:complexType>
<xs:attribute name="about" use="required" type="pheno:classId_Type"/>
</xs:complexType>
</xs:element>
<xs:element name="measurement">
<xs:complexType>
<xs:sequence>
<xs:element ref="pheno:unit"/>
</xs:sequence>
<xs:attribute name="value" type="xs:float">
<xs:annotation>
<xs:documentation> the only time this would be omitted is if we only have a range</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="min_value" type="xs:float"/>
<xs:attribute name="max_value" type="xs:float"/>
<xs:attribute name="standard_deviation" type="xs:float"/>
<xs:attribute name="standard_error" type="xs:float"/>
<xs:attribute name="assay" type="pheno:identifier_Type">
<xs:annotation>
<xs:documentation>TODO: reference to a particular experiment</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="unit">
<xs:annotation>
<xs:documentation>the unit should come from an SI unit ontology</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element ref="pheno:typeref"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="provenance">
<xs:annotation>
<xs:documentation>evidence: could refer to papers, figures in papers, raw images, etc</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:attribute name="id" use="required" type="pheno:identifier_Type"/>
<xs:attribute name="type" type="pheno:classId_Type"/>
</xs:complexType>
</xs:element>
<xs:element name="envirotype">
<xs:complexType>
<xs:sequence>
<xs:element ref="pheno:typeref"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="typeref">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" maxOccurs="unbounded" ref="pheno:qualifier"/>
</xs:sequence>
<xs:attribute name="about" use="required" type="pheno:classId_Type"/>
</xs:complexType>
</xs:element>
<xs:element name="qualifier">
<xs:complexType>
<xs:sequence>
<xs:element ref="pheno:holds_in_relation_to"/>
</xs:sequence>
<xs:attribute name="relation" use="required" type="pheno:classId_Type"/>
</xs:complexType>
</xs:element>
<xs:element name="holds_in_relation_to">
<xs:complexType>
<xs:sequence>
<xs:element ref="pheno:typeref"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="temporal_qualifier">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" ref="pheno:time_range"/>
</xs:sequence>
<xs:attribute name="relation" type="pheno:classId_Type"/>
</xs:complexType>
</xs:element>
<xs:element name="time_range">
<xs:complexType>
<xs:sequence>
<xs:element minOccurs="0" ref="pheno:typeref"/>
<xs:element minOccurs="0" ref="pheno:measurement"/>
</xs:sequence>
<xs:attribute name="id" type="pheno:identifier_Type"/>
</xs:complexType>
</xs:element>
<xs:element name="description">
<xs:annotation>
<xs:documentation>an optionally-attributed textual description</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute name="id" type="xs:NMTOKEN"/>
<xs:attribute name="attribution" type="pheno:identifier_Type">
<xs:annotation>
<xs:documentation>e.g pubmed ID</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
</xs:element>
<!-- ++ basic types ++ -->
<xs:simpleType name="identifier_Type">
<xs:restriction base="xs:string"/>
</xs:simpleType>
<xs:simpleType name="name_Type">
<xs:restriction base="xs:string"/>
</xs:simpleType>
<xs:simpleType name="classId_Type">
<xs:restriction base="xs:NMTOKEN"/>
</xs:simpleType>
</xs:schema>