| 1 | <?xml version="1.0" encoding="ISO-8859-1"?> |
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| 2 | <definitions targetNamespace="http://mips.gsf.de/hobit/services/psimi" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:http="http://schemas.xmlsoap.org/wsdl/http/" xmlns:mime="http://schemas.xmlsoap.org/wsdl/mime/" xmlns:ns="net:sf:psidev:mi" xmlns:ns1="http://mips.gsf.de/hobit/services/psimi" xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/" xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" xmlns:tns="http://mips.gsf.de/hobit/services/psimi" xmlns:xs="http://www.w3.org/2001/XMLSchema"> |
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| 3 | <types> |
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| 4 | <xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="net:sf:psidev:mi" xmlns="net:sf:psidev:mi" xmlns:xs="http://www.w3.org/2001/XMLSchema"> |
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| 5 | <xs:element name="entrySet"> |
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| 6 | <xs:annotation> |
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| 7 | <xs:documentation>Root element of the Molecular Interaction Format</xs:documentation> |
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| 8 | </xs:annotation> |
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| 9 | <xs:complexType> |
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| 10 | <xs:sequence> |
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| 11 | <xs:element maxOccurs="unbounded" name="entry"> |
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| 12 | <xs:annotation> |
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| 13 | <xs:documentation>Describes one or more interactions as a self-contained unit. Multiple entries from different files can be concatenated into a single entrySet.</xs:documentation> |
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| 14 | </xs:annotation> |
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| 15 | <xs:complexType> |
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| 16 | <xs:sequence> |
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| 17 | <xs:element minOccurs="0" name="source"> |
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| 18 | <xs:annotation> |
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| 19 | <xs:documentation>Desciption of the source of the entry, usually an organisation</xs:documentation> |
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| 20 | </xs:annotation> |
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| 21 | <xs:complexType> |
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| 22 | <xs:sequence> |
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| 23 | <xs:element minOccurs="0" name="names" type="namesType"> |
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| 24 | <xs:annotation> |
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| 25 | <xs:documentation>Name(s) of the data source, for example the organisation name.</xs:documentation> |
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| 26 | </xs:annotation> |
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| 27 | </xs:element> |
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| 28 | <xs:element minOccurs="0" name="bibref" type="bibrefType"> |
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| 29 | <xs:annotation> |
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| 30 | <xs:documentation>Bibliographic reference for the data source. Example: A paper which describes all interactions of the entry.</xs:documentation> |
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| 31 | </xs:annotation> |
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| 32 | </xs:element> |
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| 33 | <xs:element minOccurs="0" name="xref" type="xrefType"> |
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| 34 | <xs:annotation> |
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| 35 | <xs:documentation>Cross reference for the data source. Example: Entry in a database of databases. </xs:documentation> |
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| 36 | </xs:annotation> |
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| 37 | </xs:element> |
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| 38 | <xs:element minOccurs="0" name="attributeList" type="attributeListType"> |
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| 39 | <xs:annotation> |
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| 40 | <xs:documentation>Further description of the source.</xs:documentation> |
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| 41 | </xs:annotation> |
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| 42 | </xs:element> |
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| 43 | </xs:sequence> |
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| 44 | <xs:attribute name="release" type="xs:string" use="optional"/> |
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| 45 | <xs:attribute name="releaseDate" type="xs:date" use="optional"/> |
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| 46 | </xs:complexType> |
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| 47 | </xs:element> |
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| 48 | <xs:element minOccurs="0" name="availabilityList"> |
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| 49 | <xs:annotation> |
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| 50 | <xs:documentation>Data availability statements, for example copyrights</xs:documentation> |
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| 51 | </xs:annotation> |
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| 52 | <xs:complexType> |
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| 53 | <xs:sequence> |
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| 54 | <xs:element default="free" maxOccurs="unbounded" minOccurs="0" name="availability" type="availabilityType"> |
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| 55 | <xs:annotation> |
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| 56 | <xs:documentation>Describes data availability, e.g. through a copyright statement. If no availability is given, the data is assumed to be freely available.</xs:documentation> |
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| 57 | </xs:annotation> |
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| 58 | </xs:element> |
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| 59 | </xs:sequence> |
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| 60 | </xs:complexType> |
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| 61 | </xs:element> |
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| 62 | <xs:element minOccurs="0" name="experimentList"> |
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| 63 | <xs:annotation> |
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| 64 | <xs:documentation>All experiments in which the interactions of this entry have been determined</xs:documentation> |
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| 65 | </xs:annotation> |
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| 66 | <xs:complexType> |
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| 67 | <xs:sequence> |
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| 68 | <xs:element maxOccurs="unbounded" minOccurs="0" name="experimentDescription" type="experimentType"> |
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| 69 | <xs:annotation> |
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| 70 | <xs:documentation>Describes one set of experimental parameters, usually associated with a single publication.</xs:documentation> |
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| 71 | </xs:annotation> |
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| 72 | </xs:element> |
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| 73 | </xs:sequence> |
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| 74 | </xs:complexType> |
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| 75 | </xs:element> |
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| 76 | <xs:element minOccurs="0" name="interactorList"> |
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| 77 | <xs:annotation> |
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| 78 | <xs:documentation>List of all interactors occurring in the entry</xs:documentation> |
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| 79 | </xs:annotation> |
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| 80 | <xs:complexType> |
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| 81 | <xs:sequence> |
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| 82 | <xs:annotation> |
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| 83 | <xs:documentation>Will be extended in future levels to include other interactor types e.g. small molecules.</xs:documentation> |
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| 84 | </xs:annotation> |
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| 85 | <xs:element maxOccurs="unbounded" minOccurs="0" name="proteinInteractor" type="proteinInteractorType"> |
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| 86 | <xs:annotation> |
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| 87 | <xs:documentation>A protein object participating in an interaction.</xs:documentation> |
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| 88 | </xs:annotation> |
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| 89 | </xs:element> |
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| 90 | </xs:sequence> |
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| 91 | </xs:complexType> |
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| 92 | </xs:element> |
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| 93 | <xs:element name="interactionList"> |
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| 94 | <xs:annotation> |
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| 95 | <xs:documentation>List of interactions</xs:documentation> |
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| 96 | </xs:annotation> |
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| 97 | <xs:complexType> |
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| 98 | <xs:sequence> |
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| 99 | <xs:annotation> |
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| 100 | <xs:documentation>Will be extended in future levels to include other interaction types e.g. biochemical reactions.</xs:documentation> |
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| 101 | </xs:annotation> |
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| 102 | <xs:element maxOccurs="unbounded" name="interaction" type="interactionElementType"> |
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| 103 | <xs:annotation> |
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| 104 | <xs:documentation>A set of molecules interacting.</xs:documentation> |
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| 105 | </xs:annotation> |
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| 106 | </xs:element> |
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| 107 | </xs:sequence> |
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| 108 | </xs:complexType> |
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| 109 | </xs:element> |
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| 110 | <xs:element minOccurs="0" name="attributeList" type="attributeListType"> |
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| 111 | <xs:annotation> |
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| 112 | <xs:documentation>Semi-structured additional description of the data contained in the entry.</xs:documentation> |
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| 113 | </xs:annotation> |
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| 114 | </xs:element> |
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| 115 | </xs:sequence> |
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| 116 | </xs:complexType> |
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| 117 | <xs:key name="experimentKey"> |
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| 118 | <xs:selector xpath="experimentList/experimentDescription"/> |
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| 119 | <xs:field xpath="@id"/> |
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| 120 | </xs:key> |
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| 121 | <xs:keyref name="experimentRef" refer="experimentKey"> |
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| 122 | <xs:selector xpath="interactionList/interaction/experimentsList/experimentRef"/> |
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| 123 | <xs:field xpath="@ref"/> |
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| 124 | </xs:keyref> |
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| 125 | <xs:key name="interactorKey"> |
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| 126 | <xs:selector xpath="interactorList/proteinInteractor"/> |
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| 127 | <xs:field xpath="@id"/> |
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| 128 | </xs:key> |
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| 129 | <xs:keyref name="interactorRef" refer="interactorKey"> |
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| 130 | <xs:selector xpath="interactionList/interaction/participantList/proteinParticipant/proteinInteractorRef"/> |
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| 131 | <xs:field xpath="@ref"/> |
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| 132 | </xs:keyref> |
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| 133 | <xs:key name="availabilityKey"> |
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| 134 | <xs:selector xpath="availabilityList/availabilityDescription"/> |
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| 135 | <xs:field xpath="@id"/> |
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| 136 | </xs:key> |
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| 137 | <xs:keyref name="availabilityRef" refer="availabilityKey"> |
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| 138 | <xs:selector xpath="availabilityList/availability"/> |
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| 139 | <xs:field xpath="@ref"/> |
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| 140 | </xs:keyref> |
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| 141 | </xs:element> |
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| 142 | </xs:sequence> |
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| 143 | <xs:attribute name="level" type="xs:integer" use="required"/> |
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| 144 | <xs:attribute name="version" type="xs:integer" use="required"/> |
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| 145 | </xs:complexType> |
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| 146 | </xs:element> |
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| 147 | <xs:complexType name="dbReferenceType"> |
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| 148 | <xs:annotation> |
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| 149 | <xs:documentation>Refers to a unique object in an external database.</xs:documentation> |
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| 150 | </xs:annotation> |
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| 151 | <xs:attribute name="db" type="xs:string" use="required"/> |
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| 152 | <xs:attribute name="id" type="xs:string" use="required"/> |
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| 153 | <xs:attribute name="secondary" type="xs:string" use="optional"/> |
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| 154 | <xs:attribute name="version" type="xs:string" use="optional"/> |
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| 155 | </xs:complexType> |
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| 156 | <xs:complexType name="labelType"> |
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| 157 | <xs:annotation> |
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| 158 | <xs:documentation>A short alphanumeric label identifying an object. Not necessarily unique.</xs:documentation> |
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| 159 | </xs:annotation> |
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| 160 | <xs:simpleContent> |
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| 161 | <xs:extension base="xs:string"/> |
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| 162 | </xs:simpleContent> |
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| 163 | </xs:complexType> |
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| 164 | <xs:complexType name="fullNameType"> |
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| 165 | <xs:annotation> |
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| 166 | <xs:documentation>Full, descriptive object name.</xs:documentation> |
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| 167 | </xs:annotation> |
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| 168 | <xs:simpleContent> |
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| 169 | <xs:extension base="xs:string"/> |
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| 170 | </xs:simpleContent> |
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| 171 | </xs:complexType> |
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| 172 | <xs:complexType name="bioSourceType"> |
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| 173 | <xs:annotation> |
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| 174 | <xs:documentation>Describes the biological source of an object, in simple form only the NCBI taxid.</xs:documentation> |
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| 175 | </xs:annotation> |
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| 176 | <xs:sequence> |
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| 177 | <xs:element minOccurs="0" name="names" type="namesType"> |
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| 178 | <xs:annotation> |
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| 179 | <xs:documentation>The names of the organism. The short label should be a common name if it exists. The full name should be the full name of the species (i.e. genus species).</xs:documentation> |
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| 180 | </xs:annotation> |
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| 181 | </xs:element> |
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| 182 | <xs:element minOccurs="0" name="cellType" type="openCvType"> |
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| 183 | <xs:annotation> |
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| 184 | <xs:documentation>Description of the cell type. Currently no species-independent controlled vocabulary for cell types is available, therefore the choice of reference database(s) is open to the data provider.</xs:documentation> |
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| 185 | </xs:annotation> |
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| 186 | </xs:element> |
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| 187 | <xs:element minOccurs="0" name="compartment" type="openCvType"> |
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| 188 | <xs:annotation> |
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| 189 | <xs:documentation>The subcellular compartement of the object. It is strongly recommended to refer to the Gene Ontology cellular component in this element.</xs:documentation> |
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| 190 | </xs:annotation> |
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| 191 | </xs:element> |
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| 192 | <xs:element minOccurs="0" name="tissue" type="openCvType"> |
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| 193 | <xs:annotation> |
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| 194 | <xs:documentation>Description of the source tissue. Currently no species-independent controlled vocabulary for tissues is available, therefore the choice of reference database(s) is open to the data provider.</xs:documentation> |
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| 195 | </xs:annotation> |
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| 196 | </xs:element> |
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| 197 | </xs:sequence> |
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| 198 | </xs:complexType> |
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| 199 | <xs:complexType name="featureType"> |
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| 200 | <xs:annotation> |
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| 201 | <xs:documentation>A feature, e.g. domain, on a sequence.</xs:documentation> |
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| 202 | </xs:annotation> |
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| 203 | <xs:sequence> |
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| 204 | <xs:element minOccurs="0" name="xref" type="xrefType"> |
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| 205 | <xs:annotation> |
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| 206 | <xs:documentation>Reference to an external feature description, for example InterPro entry.</xs:documentation> |
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| 207 | </xs:annotation> |
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| 208 | </xs:element> |
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| 209 | <xs:element minOccurs="0" name="featureDescription" type="cvType"> |
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| 210 | <xs:annotation> |
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| 211 | <xs:documentation>Description and classification of the feature</xs:documentation> |
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| 212 | </xs:annotation> |
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| 213 | </xs:element> |
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| 214 | <xs:element name="location" type="baseLocationType"> |
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| 215 | <xs:annotation> |
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| 216 | <xs:documentation>Location of the feature on the sequence of the interactor</xs:documentation> |
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| 217 | </xs:annotation> |
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| 218 | </xs:element> |
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| 219 | <xs:element minOccurs="0" name="featureDetection" type="cvType"> |
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| 220 | <xs:annotation> |
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| 221 | <xs:documentation>Experimental method used to identify the feature.</xs:documentation> |
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| 222 | </xs:annotation> |
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| 223 | </xs:element> |
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| 224 | </xs:sequence> |
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| 225 | </xs:complexType> |
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| 226 | <xs:complexType name="xrefType"> |
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| 227 | <xs:annotation> |
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| 228 | <xs:documentation>Crossreference to an external database.</xs:documentation> |
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| 229 | </xs:annotation> |
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| 230 | <xs:sequence> |
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| 231 | <xs:element name="primaryRef" type="dbReferenceType"> |
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| 232 | <xs:annotation> |
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| 233 | <xs:documentation>Primary reference to an external database.</xs:documentation> |
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| 234 | </xs:annotation> |
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| 235 | </xs:element> |
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| 236 | <xs:element maxOccurs="unbounded" minOccurs="0" name="secondaryRef" type="dbReferenceType"> |
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| 237 | <xs:annotation> |
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| 238 | <xs:documentation>Further external objects describing the object.</xs:documentation> |
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| 239 | </xs:annotation> |
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| 240 | </xs:element> |
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| 241 | </xs:sequence> |
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| 242 | </xs:complexType> |
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| 243 | <!-- Feature location definition begins --> |
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| 244 | <xs:complexType name="positionType"> |
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| 245 | <xs:annotation> |
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| 246 | <xs:documentation>A specified position a a sequence.</xs:documentation> |
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| 247 | </xs:annotation> |
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| 248 | <xs:attribute name="position" type="xs:long" use="required"/> |
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| 249 | </xs:complexType> |
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| 250 | <xs:complexType name="intervalType"> |
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| 251 | <xs:annotation> |
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| 252 | <xs:documentation>A interval on a sequence.</xs:documentation> |
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| 253 | </xs:annotation> |
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| 254 | <xs:attribute name="begin" type="xs:long" use="required"/> |
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| 255 | <xs:attribute name="end" type="xs:long" use="required"/> |
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| 256 | </xs:complexType> |
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| 257 | <xs:complexType name="baseLocationType"> |
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| 258 | <xs:annotation> |
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| 259 | <xs:documentation>A location can be either a position, site or have a start and end, only start, only end or is an empty element if the position is unknown.</xs:documentation> |
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| 260 | </xs:annotation> |
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| 261 | <xs:choice> |
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| 262 | <xs:sequence> |
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| 263 | <xs:choice minOccurs="0"> |
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| 264 | <xs:element name="begin" type="positionType"/> |
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| 265 | <xs:element name="beginInterval" type="intervalType"/> |
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| 266 | </xs:choice> |
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| 267 | <xs:choice minOccurs="0"> |
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| 268 | <xs:element name="end" type="positionType"/> |
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| 269 | <xs:element name="endInterval" type="intervalType"/> |
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| 270 | </xs:choice> |
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| 271 | </xs:sequence> |
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| 272 | <xs:element name="position" type="positionType"/> |
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| 273 | <xs:element name="positionInterval" type="intervalType"/> |
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| 274 | <xs:element name="site" type="positionType"/> |
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| 275 | </xs:choice> |
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| 276 | </xs:complexType> |
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| 277 | <!-- Feature location definition ends --> |
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| 278 | <xs:complexType name="experimentType"> |
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| 279 | <xs:annotation> |
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| 280 | <xs:documentation>Describes one set of experimental parameters.</xs:documentation> |
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| 281 | </xs:annotation> |
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| 282 | <xs:sequence> |
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| 283 | <xs:element minOccurs="0" name="names" type="namesType"/> |
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| 284 | <xs:element minOccurs="0" name="bibref" type="bibrefType"> |
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| 285 | <xs:annotation> |
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| 286 | <xs:documentation>Publication describing the experiment.</xs:documentation> |
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| 287 | </xs:annotation> |
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| 288 | </xs:element> |
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| 289 | <xs:element minOccurs="0" name="xref" type="xrefType"> |
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| 290 | <xs:annotation> |
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| 291 | <xs:documentation>Refers to external database description of the experiment.</xs:documentation> |
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| 292 | </xs:annotation> |
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| 293 | </xs:element> |
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| 294 | <xs:element minOccurs="0" name="hostOrganism"> |
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| 295 | <xs:annotation> |
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| 296 | <xs:documentation>The host organism in which the experiment has been performed.</xs:documentation> |
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| 297 | </xs:annotation> |
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| 298 | <xs:complexType> |
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| 299 | <xs:complexContent> |
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| 300 | <xs:extension base="bioSourceType"> |
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| 301 | <xs:attribute name="ncbiTaxId" type="xs:integer" use="required"/> |
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| 302 | </xs:extension> |
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| 303 | </xs:complexContent> |
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| 304 | </xs:complexType> |
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| 305 | </xs:element> |
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| 306 | <xs:element name="interactionDetection" type="cvType"> |
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| 307 | <xs:annotation> |
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| 308 | <xs:documentation>Experimental method to determine the interaction. External controlled vocabulary.</xs:documentation> |
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| 309 | </xs:annotation> |
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| 310 | </xs:element> |
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| 311 | <xs:element minOccurs="0" name="participantDetection" type="cvType"> |
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| 312 | <xs:annotation> |
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| 313 | <xs:documentation>Experimental method to determine the interactors involved in the interaction. External controlled vocabulary.</xs:documentation> |
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| 314 | </xs:annotation> |
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| 315 | </xs:element> |
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| 316 | <xs:element minOccurs="0" name="featureDetection" type="cvType"> |
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| 317 | <xs:annotation> |
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| 318 | <xs:documentation>Experimental method to determine the features of interactors. External controlled vocabulary.</xs:documentation> |
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| 319 | </xs:annotation> |
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| 320 | </xs:element> |
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| 321 | <xs:element minOccurs="0" name="confidence"> |
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| 322 | <xs:annotation> |
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| 323 | <xs:documentation>Confidence in this experiment. Usually a statistical measure.</xs:documentation> |
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| 324 | </xs:annotation> |
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| 325 | <xs:complexType> |
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| 326 | <xs:attribute name="unit" type="xs:string" use="required"/> |
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| 327 | <xs:attribute name="value" type="xs:string" use="required"/> |
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| 328 | </xs:complexType> |
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| 329 | </xs:element> |
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| 330 | <xs:element minOccurs="0" name="attributeList" type="attributeListType"> |
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| 331 | <xs:annotation> |
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| 332 | <xs:documentation>Semi-structured additional description of the experiment.</xs:documentation> |
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| 333 | </xs:annotation> |
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| 334 | </xs:element> |
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| 335 | </xs:sequence> |
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| 336 | <xs:attribute name="id" type="xs:int" use="optional"/> |
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| 337 | </xs:complexType> |
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| 338 | <xs:complexType name="refType"> |
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| 339 | <xs:annotation> |
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| 340 | <xs:documentation>Refers to an object within the same file by its id.</xs:documentation> |
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| 341 | </xs:annotation> |
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| 342 | <xs:attribute name="ref" type="xs:string" use="required"/> |
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| 343 | </xs:complexType> |
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| 344 | <xs:complexType name="attributeListType"> |
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| 345 | <xs:annotation> |
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| 346 | <xs:documentation>A list of additional attributes. Open tag-value list to allow the inclusion of additional data.</xs:documentation> |
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| 347 | </xs:annotation> |
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| 348 | <xs:sequence> |
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| 349 | <xs:element maxOccurs="unbounded" name="attribute"> |
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| 350 | <xs:complexType> |
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| 351 | <xs:simpleContent> |
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| 352 | <xs:extension base="xs:string"> |
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| 353 | <xs:attribute name="name" type="xs:string" use="required"/> |
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| 354 | </xs:extension> |
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| 355 | </xs:simpleContent> |
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| 356 | </xs:complexType> |
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| 357 | </xs:element> |
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| 358 | </xs:sequence> |
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| 359 | </xs:complexType> |
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| 360 | <xs:complexType name="bibrefType"> |
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| 361 | <xs:annotation> |
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| 362 | <xs:documentation>Bibliographic reference.</xs:documentation> |
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| 363 | </xs:annotation> |
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| 364 | <xs:choice> |
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| 365 | <xs:element name="xref" type="xrefType"> |
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| 366 | <xs:annotation> |
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| 367 | <xs:documentation>Bibliographic reference in external database, usually PubMed.</xs:documentation> |
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| 368 | </xs:annotation> |
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| 369 | </xs:element> |
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| 370 | <xs:element name="attributeList" type="attributeListType"> |
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| 371 | <xs:annotation> |
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| 372 | <xs:documentation>Alternative description of bibliographic reference if no external database entry is available.</xs:documentation> |
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| 373 | </xs:annotation> |
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| 374 | </xs:element> |
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| 375 | </xs:choice> |
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| 376 | </xs:complexType> |
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| 377 | <xs:complexType name="namesType"> |
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| 378 | <xs:annotation> |
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| 379 | <xs:documentation>Names for an object.</xs:documentation> |
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| 380 | </xs:annotation> |
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| 381 | <xs:sequence> |
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| 382 | <xs:element name="shortLabel" type="xs:string"/> |
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| 383 | <xs:element minOccurs="0" name="fullName" type="xs:string"/> |
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| 384 | </xs:sequence> |
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| 385 | </xs:complexType> |
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| 386 | <xs:complexType name="cvType"> |
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| 387 | <xs:annotation> |
|---|
| 388 | <xs:documentation>Reference to an external controlled vocabulary.</xs:documentation> |
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| 389 | </xs:annotation> |
|---|
| 390 | <xs:sequence> |
|---|
| 391 | <xs:element name="names" type="namesType"> |
|---|
| 392 | <xs:annotation> |
|---|
| 393 | <xs:documentation>Name of the controlled vocabulary term.</xs:documentation> |
|---|
| 394 | </xs:annotation> |
|---|
| 395 | </xs:element> |
|---|
| 396 | <xs:element name="xref" type="xrefType"> |
|---|
| 397 | <xs:annotation> |
|---|
| 398 | <xs:documentation>Source of the controlled vocabulary term. E.g. the name of the CV and the term ID.</xs:documentation> |
|---|
| 399 | </xs:annotation> |
|---|
| 400 | </xs:element> |
|---|
| 401 | </xs:sequence> |
|---|
| 402 | </xs:complexType> |
|---|
| 403 | <xs:complexType name="openCvType"> |
|---|
| 404 | <xs:annotation> |
|---|
| 405 | <xs:documentation>Allows to reference an external controlled vocabulary, or to directly include a value if no suitable external definition is available.</xs:documentation> |
|---|
| 406 | </xs:annotation> |
|---|
| 407 | <xs:sequence> |
|---|
| 408 | <xs:element name="names" type="namesType"> |
|---|
| 409 | <xs:annotation> |
|---|
| 410 | <xs:documentation>This contains the controlled vocabulary terms, as a short and optionally as a long form.</xs:documentation> |
|---|
| 411 | </xs:annotation> |
|---|
| 412 | </xs:element> |
|---|
| 413 | <xs:element minOccurs="0" name="xref" type="xrefType"> |
|---|
| 414 | <xs:annotation> |
|---|
| 415 | <xs:documentation>Refers to the term of the controlled vocabulary in an external database.</xs:documentation> |
|---|
| 416 | </xs:annotation> |
|---|
| 417 | </xs:element> |
|---|
| 418 | <xs:element minOccurs="0" name="attributeList" type="attributeListType"> |
|---|
| 419 | <xs:annotation> |
|---|
| 420 | <xs:documentation>If no suitable external controlled vocabulary is available, this attributeList can be used to describe the term. Example: Attribute name: Mouse atlas tissue name; attribute value: spinal cord, day 30.</xs:documentation> |
|---|
| 421 | </xs:annotation> |
|---|
| 422 | </xs:element> |
|---|
| 423 | </xs:sequence> |
|---|
| 424 | </xs:complexType> |
|---|
| 425 | <xs:complexType name="proteinInteractorType"> |
|---|
| 426 | <xs:annotation> |
|---|
| 427 | <xs:documentation>Describes a protein interactor.</xs:documentation> |
|---|
| 428 | </xs:annotation> |
|---|
| 429 | <xs:sequence> |
|---|
| 430 | <xs:element name="names" type="namesType"> |
|---|
| 431 | <xs:annotation> |
|---|
| 432 | <xs:documentation>Protein name(s). The short label is typically a short name that could appear as a label on a diagram.</xs:documentation> |
|---|
| 433 | </xs:annotation> |
|---|
| 434 | </xs:element> |
|---|
| 435 | <xs:element minOccurs="0" name="xref" type="xrefType"> |
|---|
| 436 | <xs:annotation> |
|---|
| 437 | <xs:documentation>An interactor should have an xref whenever possible. If the interactor is not available in external databases, it must be characterised within this proteinInteractor object e.g. by its sequence.</xs:documentation> |
|---|
| 438 | </xs:annotation> |
|---|
| 439 | </xs:element> |
|---|
| 440 | <xs:element minOccurs="0" name="organism"> |
|---|
| 441 | <xs:annotation> |
|---|
| 442 | <xs:documentation>The normal source organism of the interactor. If a human protein has been expressed in yeast, this attribute would describe human.</xs:documentation> |
|---|
| 443 | </xs:annotation> |
|---|
| 444 | <xs:complexType> |
|---|
| 445 | <xs:complexContent> |
|---|
| 446 | <xs:extension base="bioSourceType"> |
|---|
| 447 | <xs:attribute name="ncbiTaxId" type="xs:integer" use="required"/> |
|---|
| 448 | </xs:extension> |
|---|
| 449 | </xs:complexContent> |
|---|
| 450 | </xs:complexType> |
|---|
| 451 | </xs:element> |
|---|
| 452 | <xs:element minOccurs="0" name="sequence" type="xs:string"> |
|---|
| 453 | <xs:annotation> |
|---|
| 454 | <xs:documentation>Amino acid sequence in uppercase</xs:documentation> |
|---|
| 455 | </xs:annotation> |
|---|
| 456 | </xs:element> |
|---|
| 457 | </xs:sequence> |
|---|
| 458 | <xs:attribute name="id" type="xs:int" use="optional"/> |
|---|
| 459 | </xs:complexType> |
|---|
| 460 | <xs:complexType name="availabilityType"> |
|---|
| 461 | <xs:annotation> |
|---|
| 462 | <xs:documentation>A text describing the availability of data, e.g. a copyright statement.</xs:documentation> |
|---|
| 463 | </xs:annotation> |
|---|
| 464 | <xs:simpleContent> |
|---|
| 465 | <xs:extension base="xs:string"> |
|---|
| 466 | <xs:attribute name="id" type="xs:int" use="optional"/> |
|---|
| 467 | </xs:extension> |
|---|
| 468 | </xs:simpleContent> |
|---|
| 469 | </xs:complexType> |
|---|
| 470 | <xs:complexType name="interactionElementType"> |
|---|
| 471 | <xs:annotation> |
|---|
| 472 | <xs:documentation>A molecular interaction.</xs:documentation> |
|---|
| 473 | </xs:annotation> |
|---|
| 474 | <xs:sequence> |
|---|
| 475 | <xs:element minOccurs="0" name="names" type="namesType"> |
|---|
| 476 | <xs:annotation> |
|---|
| 477 | <xs:documentation>Name(s) of the interaction.</xs:documentation> |
|---|
| 478 | </xs:annotation> |
|---|
| 479 | </xs:element> |
|---|
| 480 | <xs:choice minOccurs="0"> |
|---|
| 481 | <xs:annotation> |
|---|
| 482 | <xs:documentation>Either refer to an already defined availability statement in this entry or insert description.</xs:documentation> |
|---|
| 483 | </xs:annotation> |
|---|
| 484 | <xs:element name="availabilityRef" type="refType"> |
|---|
| 485 | <xs:annotation> |
|---|
| 486 | <xs:documentation>References an availability statement already present in this entry.</xs:documentation> |
|---|
| 487 | </xs:annotation> |
|---|
| 488 | </xs:element> |
|---|
| 489 | <xs:element name="availabilityDescription" type="availabilityType"> |
|---|
| 490 | <xs:annotation> |
|---|
| 491 | <xs:documentation>Describes the availability of the interaction data. If no availability is given, the data is assumed to be freely available.</xs:documentation> |
|---|
| 492 | </xs:annotation> |
|---|
| 493 | </xs:element> |
|---|
| 494 | </xs:choice> |
|---|
| 495 | <xs:element name="experimentList"> |
|---|
| 496 | <xs:annotation> |
|---|
| 497 | <xs:documentation>List of experiments in which this interaction has been determined.</xs:documentation> |
|---|
| 498 | </xs:annotation> |
|---|
| 499 | <xs:complexType> |
|---|
| 500 | <xs:choice maxOccurs="unbounded"> |
|---|
| 501 | <xs:annotation> |
|---|
| 502 | <xs:documentation>Either refer to an already defined experiment in this entry or insert description.</xs:documentation> |
|---|
| 503 | </xs:annotation> |
|---|
| 504 | <xs:element name="experimentRef" type="refType"> |
|---|
| 505 | <xs:annotation> |
|---|
| 506 | <xs:documentation>References an experiment already present in this entry.</xs:documentation> |
|---|
| 507 | </xs:annotation> |
|---|
| 508 | </xs:element> |
|---|
| 509 | <xs:element name="experimentDescription" type="experimentType"> |
|---|
| 510 | <xs:annotation> |
|---|
| 511 | <xs:documentation>An experiment in which this interaction has been determined.</xs:documentation> |
|---|
| 512 | </xs:annotation> |
|---|
| 513 | </xs:element> |
|---|
| 514 | </xs:choice> |
|---|
| 515 | </xs:complexType> |
|---|
| 516 | </xs:element> |
|---|
| 517 | <xs:element name="participantList"> |
|---|
| 518 | <xs:annotation> |
|---|
| 519 | <xs:documentation>A list of molecules participating in this interaction.</xs:documentation> |
|---|
| 520 | </xs:annotation> |
|---|
| 521 | <xs:complexType> |
|---|
| 522 | <xs:sequence> |
|---|
| 523 | <xs:annotation> |
|---|
| 524 | <xs:documentation>Will be extended in future levels to include other types of participant molecules.</xs:documentation> |
|---|
| 525 | </xs:annotation> |
|---|
| 526 | <xs:element maxOccurs="unbounded" minOccurs="2" name="proteinParticipant" type="proteinParticipantType"> |
|---|
| 527 | <xs:annotation> |
|---|
| 528 | <xs:documentation>An interaction has two or more participants, thereby covering binary and n-ary interactions.</xs:documentation> |
|---|
| 529 | </xs:annotation> |
|---|
| 530 | </xs:element> |
|---|
| 531 | </xs:sequence> |
|---|
| 532 | </xs:complexType> |
|---|
| 533 | </xs:element> |
|---|
| 534 | <xs:element maxOccurs="unbounded" minOccurs="0" name="interactionType" type="cvType"> |
|---|
| 535 | <xs:annotation> |
|---|
| 536 | <xs:documentation>External controlled vocabulary characterising the interaction type, for example "aggregation".</xs:documentation> |
|---|
| 537 | </xs:annotation> |
|---|
| 538 | </xs:element> |
|---|
| 539 | <xs:element minOccurs="0" name="confidence"> |
|---|
| 540 | <xs:annotation> |
|---|
| 541 | <xs:documentation>Confidence in this interaction. Usually a statistical measure.</xs:documentation> |
|---|
| 542 | </xs:annotation> |
|---|
| 543 | <xs:complexType> |
|---|
| 544 | <xs:attribute name="unit" type="xs:string" use="required"/> |
|---|
| 545 | <xs:attribute name="value" type="xs:string" use="required"/> |
|---|
| 546 | </xs:complexType> |
|---|
| 547 | </xs:element> |
|---|
| 548 | <xs:element minOccurs="0" name="xref" type="xrefType"> |
|---|
| 549 | <xs:annotation> |
|---|
| 550 | <xs:documentation>Interaction database ID</xs:documentation> |
|---|
| 551 | </xs:annotation> |
|---|
| 552 | </xs:element> |
|---|
| 553 | <xs:element minOccurs="0" name="attributeList" type="attributeListType"> |
|---|
| 554 | <xs:annotation> |
|---|
| 555 | <xs:documentation>Semi-structured additional description of the data contained in the entry.</xs:documentation> |
|---|
| 556 | </xs:annotation> |
|---|
| 557 | </xs:element> |
|---|
| 558 | </xs:sequence> |
|---|
| 559 | </xs:complexType> |
|---|
| 560 | <xs:complexType name="proteinParticipantType"> |
|---|
| 561 | <xs:annotation> |
|---|
| 562 | <xs:documentation>A protein participating in an interaction.</xs:documentation> |
|---|
| 563 | </xs:annotation> |
|---|
| 564 | <xs:sequence> |
|---|
| 565 | <xs:choice> |
|---|
| 566 | <xs:annotation> |
|---|
| 567 | <xs:documentation>Either refer to an already defined protein interactor in this entry or insert description.</xs:documentation> |
|---|
| 568 | </xs:annotation> |
|---|
| 569 | <xs:element name="proteinInteractorRef" type="refType"> |
|---|
| 570 | <xs:annotation> |
|---|
| 571 | <xs:documentation>References an interactor described in the interactorList of the entry</xs:documentation> |
|---|
| 572 | </xs:annotation> |
|---|
| 573 | </xs:element> |
|---|
| 574 | <xs:element name="proteinInteractor" type="proteinInteractorType"> |
|---|
| 575 | <xs:annotation> |
|---|
| 576 | <xs:documentation>Fully describes an interactor</xs:documentation> |
|---|
| 577 | </xs:annotation> |
|---|
| 578 | </xs:element> |
|---|
| 579 | </xs:choice> |
|---|
| 580 | <xs:element minOccurs="0" name="featureList"> |
|---|
| 581 | <xs:annotation> |
|---|
| 582 | <xs:documentation>Sequence features relevant for the interaction, for example binding domains</xs:documentation> |
|---|
| 583 | </xs:annotation> |
|---|
| 584 | <xs:complexType> |
|---|
| 585 | <xs:sequence> |
|---|
| 586 | <xs:element maxOccurs="unbounded" name="feature" type="featureType"/> |
|---|
| 587 | </xs:sequence> |
|---|
| 588 | </xs:complexType> |
|---|
| 589 | </xs:element> |
|---|
| 590 | <xs:element minOccurs="0" name="confidence"> |
|---|
| 591 | <xs:annotation> |
|---|
| 592 | <xs:documentation>Confidence in participant detection.</xs:documentation> |
|---|
| 593 | </xs:annotation> |
|---|
| 594 | <xs:complexType> |
|---|
| 595 | <xs:attribute name="unit" type="xs:string" use="required"/> |
|---|
| 596 | <xs:attribute name="value" type="xs:string" use="required"/> |
|---|
| 597 | </xs:complexType> |
|---|
| 598 | </xs:element> |
|---|
| 599 | <xs:element minOccurs="0" name="role"> |
|---|
| 600 | <xs:annotation> |
|---|
| 601 | <xs:documentation>The role of the participant in the interaction, e.g. "bait". Choose an enumerated value.</xs:documentation> |
|---|
| 602 | </xs:annotation> |
|---|
| 603 | <xs:simpleType> |
|---|
| 604 | <xs:restriction base="xs:string"> |
|---|
| 605 | <xs:enumeration value="bait"/> |
|---|
| 606 | <xs:enumeration value="prey"/> |
|---|
| 607 | <xs:enumeration value="neutral"/> |
|---|
| 608 | <xs:enumeration value="unspecified"/> |
|---|
| 609 | </xs:restriction> |
|---|
| 610 | </xs:simpleType> |
|---|
| 611 | </xs:element> |
|---|
| 612 | <xs:element minOccurs="0" name="isTaggedProtein" type="xs:boolean"> |
|---|
| 613 | <xs:annotation> |
|---|
| 614 | <xs:documentation>True if the protein has been tagged in the experiment.</xs:documentation> |
|---|
| 615 | </xs:annotation> |
|---|
| 616 | </xs:element> |
|---|
| 617 | <xs:element minOccurs="0" name="isOverexpressedProtein" type="xs:boolean"> |
|---|
| 618 | <xs:annotation> |
|---|
| 619 | <xs:documentation>True if the protein has been overexpressed in the experiment.</xs:documentation> |
|---|
| 620 | </xs:annotation> |
|---|
| 621 | </xs:element> |
|---|
| 622 | </xs:sequence> |
|---|
| 623 | </xs:complexType> |
|---|
| 624 | </xs:schema> |
|---|
| 625 | <xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="http://mips.gsf.de/hobit/services/psimi" xmlns:ns1="http://mips.gsf.de/hobit/services/psimi" xmlns:xs="http://www.w3.org/2001/XMLSchema"> |
|---|
| 626 | <xs:element name="getForInteractor"> |
|---|
| 627 | <xs:annotation> |
|---|
| 628 | <xs:documentation>Interactions for interactors with id</xs:documentation> |
|---|
| 629 | </xs:annotation> |
|---|
| 630 | <xs:complexType> |
|---|
| 631 | <xs:sequence> |
|---|
| 632 | <xs:element name="id" type="xs:string"/> |
|---|
| 633 | </xs:sequence> |
|---|
| 634 | </xs:complexType> |
|---|
| 635 | </xs:element> |
|---|
| 636 | <xs:element name="getForInteractorLike"> |
|---|
| 637 | <xs:annotation> |
|---|
| 638 | <xs:documentation>Interactions for interactors like id</xs:documentation> |
|---|
| 639 | </xs:annotation> |
|---|
| 640 | <xs:complexType> |
|---|
| 641 | <xs:sequence> |
|---|
| 642 | <xs:element name="id" type="xs:string"/> |
|---|
| 643 | </xs:sequence> |
|---|
| 644 | </xs:complexType> |
|---|
| 645 | </xs:element> |
|---|
| 646 | <xs:element name="getBetweenInteractors"> |
|---|
| 647 | <xs:annotation> |
|---|
| 648 | <xs:documentation>Interactions between two interactors</xs:documentation> |
|---|
| 649 | </xs:annotation> |
|---|
| 650 | <xs:complexType> |
|---|
| 651 | <xs:sequence> |
|---|
| 652 | <xs:element maxOccurs="2" name="id" type="xs:string"/> |
|---|
| 653 | </xs:sequence> |
|---|
| 654 | </xs:complexType> |
|---|
| 655 | </xs:element> |
|---|
| 656 | <xs:element name="getForInteractorlist"> |
|---|
| 657 | <xs:annotation> |
|---|
| 658 | <xs:documentation>Interactions for a list of interactors</xs:documentation> |
|---|
| 659 | </xs:annotation> |
|---|
| 660 | <xs:complexType> |
|---|
| 661 | <xs:sequence> |
|---|
| 662 | <xs:element maxOccurs="unbounded" name="id" type="xs:string"/> |
|---|
| 663 | </xs:sequence> |
|---|
| 664 | </xs:complexType> |
|---|
| 665 | </xs:element> |
|---|
| 666 | <xs:element name="getBetweenInteractorlists"> |
|---|
| 667 | <xs:annotation> |
|---|
| 668 | <xs:documentation>Interactions between two interactor lists</xs:documentation> |
|---|
| 669 | </xs:annotation> |
|---|
| 670 | <xs:complexType> |
|---|
| 671 | <xs:sequence> |
|---|
| 672 | <xs:element maxOccurs="2" name="list"> |
|---|
| 673 | <xs:complexType> |
|---|
| 674 | <xs:sequence> |
|---|
| 675 | <xs:element maxOccurs="unbounded" name="id" type="xs:string"/> |
|---|
| 676 | </xs:sequence> |
|---|
| 677 | </xs:complexType> |
|---|
| 678 | </xs:element> |
|---|
| 679 | </xs:sequence> |
|---|
| 680 | </xs:complexType> |
|---|
| 681 | </xs:element> |
|---|
| 682 | <xs:element name="getForInteractionDetectionMethod"> |
|---|
| 683 | <xs:annotation> |
|---|
| 684 | <xs:documentation>Interactions for a specific method</xs:documentation> |
|---|
| 685 | </xs:annotation> |
|---|
| 686 | <xs:complexType> |
|---|
| 687 | <xs:sequence> |
|---|
| 688 | <xs:element name="method" type="xs:string"/> |
|---|
| 689 | </xs:sequence> |
|---|
| 690 | </xs:complexType> |
|---|
| 691 | </xs:element> |
|---|
| 692 | <xs:element name="getForOrganism"> |
|---|
| 693 | <xs:annotation> |
|---|
| 694 | <xs:documentation>Interactions for a specific organism</xs:documentation> |
|---|
| 695 | </xs:annotation> |
|---|
| 696 | <xs:complexType> |
|---|
| 697 | <xs:sequence> |
|---|
| 698 | <xs:element name="id" type="xs:int"/> |
|---|
| 699 | </xs:sequence> |
|---|
| 700 | </xs:complexType> |
|---|
| 701 | </xs:element> |
|---|
| 702 | <xs:element name="ServiceFailedException"> |
|---|
| 703 | <xs:annotation> |
|---|
| 704 | <xs:documentation>Exception if something goes wrong</xs:documentation> |
|---|
| 705 | </xs:annotation> |
|---|
| 706 | <xs:complexType> |
|---|
| 707 | <xs:sequence> |
|---|
| 708 | <xs:element name="messageType" type="xs:string"/> |
|---|
| 709 | <xs:element name="message" type="xs:string"/> |
|---|
| 710 | </xs:sequence> |
|---|
| 711 | </xs:complexType> |
|---|
| 712 | </xs:element> |
|---|
| 713 | </xs:schema> |
|---|
| 714 | </types> |
|---|
| 715 | <message name="getForInteractiorReq"> |
|---|
| 716 | <part element="ns1:getForInteractor" name="request"/> |
|---|
| 717 | </message> |
|---|
| 718 | <message name="getForInteractiorRes"> |
|---|
| 719 | <part element="ns:entrySet" name="response"/> |
|---|
| 720 | </message> |
|---|
| 721 | <message name="getForInteractorLikeReq"> |
|---|
| 722 | <part element="ns1:getForInteractorLike" name="request"/> |
|---|
| 723 | </message> |
|---|
| 724 | <message name="getForInteractorLikeRes"> |
|---|
| 725 | <part element="ns:entrySet" name="response"/> |
|---|
| 726 | </message> |
|---|
| 727 | <message name="getBetweenInteractorsReq"> |
|---|
| 728 | <part element="ns1:getBetweenInteractors" name="request"/> |
|---|
| 729 | </message> |
|---|
| 730 | <message name="getBetweenInteractorsRes"> |
|---|
| 731 | <part element="ns:entrySet" name="response"/> |
|---|
| 732 | </message> |
|---|
| 733 | <message name="getForInteractorlistReq"> |
|---|
| 734 | <part element="ns1:getForInteractorlist" name="request1"/> |
|---|
| 735 | </message> |
|---|
| 736 | <message name="getForInteractorlistRes"> |
|---|
| 737 | <part element="ns:entrySet" name="response"/> |
|---|
| 738 | </message> |
|---|
| 739 | <message name="getBetweenInteractorlistsReq"> |
|---|
| 740 | <part element="ns1:getBetweenInteractorlists" name="request"/> |
|---|
| 741 | </message> |
|---|
| 742 | <message name="getBetweenInteractorlistsRes"> |
|---|
| 743 | <part element="ns:entrySet" name="response"/> |
|---|
| 744 | </message> |
|---|
| 745 | <message name="getForInteractionDetectionMethodReq"> |
|---|
| 746 | <part element="ns1:getForInteractionDetectionMethod" name="request"/> |
|---|
| 747 | </message> |
|---|
| 748 | <message name="getForInteractionDetectionMethodRes"> |
|---|
| 749 | <part element="ns:entrySet" name="response"/> |
|---|
| 750 | </message> |
|---|
| 751 | <message name="getForOrganismReq"> |
|---|
| 752 | <part element="ns1:getForOrganism" name="request"/> |
|---|
| 753 | </message> |
|---|
| 754 | <message name="getForOrganismRes"> |
|---|
| 755 | <part element="ns:entrySet" name="response"/> |
|---|
| 756 | </message> |
|---|
| 757 | <portType name="PsimiSOAPPortType"> |
|---|
| 758 | <operation name="getForInteractor"> |
|---|
| 759 | <input message="tns:getForInteractiorReq"/> |
|---|
| 760 | <output message="tns:getForInteractiorRes" name="getInteractionRes"/> |
|---|
| 761 | </operation> |
|---|
| 762 | <operation name="getForInteractorLike"> |
|---|
| 763 | <input message="tns:getForInteractorLikeReq"/> |
|---|
| 764 | <output message="tns:getForInteractorLikeRes"/> |
|---|
| 765 | </operation> |
|---|
| 766 | <operation name="getBetweenInteractors"> |
|---|
| 767 | <input message="tns:getBetweenInteractorsReq"/> |
|---|
| 768 | <output message="tns:getBetweenInteractorsRes"/> |
|---|
| 769 | </operation> |
|---|
| 770 | <operation name="getForInteractorlist"> |
|---|
| 771 | <input message="tns:getForInteractorlistReq"/> |
|---|
| 772 | <output message="tns:getForInteractorlistRes"/> |
|---|
| 773 | </operation> |
|---|
| 774 | <operation name="getForInteractionDetectionMethod"> |
|---|
| 775 | <input message="tns:getForInteractionDetectionMethodReq"/> |
|---|
| 776 | <output message="tns:getForInteractionDetectionMethodRes"/> |
|---|
| 777 | </operation> |
|---|
| 778 | <operation name="getForOrganism"> |
|---|
| 779 | <input message="tns:getForOrganismReq"/> |
|---|
| 780 | <output message="tns:getForOrganismRes"/> |
|---|
| 781 | </operation> |
|---|
| 782 | </portType> |
|---|
| 783 | <binding name="PsimiSOAPBinding" type="tns:PsimiSOAPPortType"> |
|---|
| 784 | <soap:binding style="document" transport="http://schemas.xmlsoap.org/soap/http"/> |
|---|
| 785 | <operation name="getForInteractor"> |
|---|
| 786 | <input> |
|---|
| 787 | <soap:body use="literal"/> |
|---|
| 788 | </input> |
|---|
| 789 | <output> |
|---|
| 790 | <soap:body use="literal"/> |
|---|
| 791 | </output> |
|---|
| 792 | </operation> |
|---|
| 793 | <operation name="getForInteractorLike"> |
|---|
| 794 | <input> |
|---|
| 795 | <soap:body use="literal"/> |
|---|
| 796 | </input> |
|---|
| 797 | <output> |
|---|
| 798 | <soap:body use="literal"/> |
|---|
| 799 | </output> |
|---|
| 800 | </operation> |
|---|
| 801 | <operation name="getBetweenInteractors"> |
|---|
| 802 | <input> |
|---|
| 803 | <soap:body use="literal"/> |
|---|
| 804 | </input> |
|---|
| 805 | <output> |
|---|
| 806 | <soap:body use="literal"/> |
|---|
| 807 | </output> |
|---|
| 808 | </operation> |
|---|
| 809 | <operation name="getForInteractorlist"> |
|---|
| 810 | <input> |
|---|
| 811 | <soap:body use="literal"/> |
|---|
| 812 | </input> |
|---|
| 813 | <output> |
|---|
| 814 | <soap:body use="literal"/> |
|---|
| 815 | </output> |
|---|
| 816 | </operation> |
|---|
| 817 | <operation name="getForInteractionDetectionMethod"> |
|---|
| 818 | <input> |
|---|
| 819 | <soap:body use="literal"/> |
|---|
| 820 | </input> |
|---|
| 821 | <output> |
|---|
| 822 | <soap:body use="literal"/> |
|---|
| 823 | </output> |
|---|
| 824 | </operation> |
|---|
| 825 | <operation name="getForOrganism"> |
|---|
| 826 | <input> |
|---|
| 827 | <soap:body use="literal"/> |
|---|
| 828 | </input> |
|---|
| 829 | <output> |
|---|
| 830 | <soap:body use="literal"/> |
|---|
| 831 | </output> |
|---|
| 832 | </operation> |
|---|
| 833 | </binding> |
|---|
| 834 | <service name="serviceName"> |
|---|
| 835 | <port binding="tns:PsimiSOAPBinding" name="PsimiService"> |
|---|
| 836 | <soap:address location="http://mips.gsf.de/proj/hobitws/services/PsimiService"/> |
|---|
| 837 | </port> |
|---|
| 838 | </service> |
|---|
| 839 | </definitions> |
|---|
