source:
trunk/bio/core/core.xml
@
23732
| Revision 23732, 8.0 KB checked in by julie, 15 months ago (diff) | |
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make chromosome and gene sequence features instead of bioentities |
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| 1 | <?xml version="1.0"?> |
| 2 | <model name="genomic" package="org.intermine.model.bio"> |
| 3 | |
| 4 | <class name="Author" is-interface="true"> |
| 5 | <attribute name="name" type="java.lang.String"/> |
| 6 | <collection name="publications" referenced-type="Publication" reverse-reference="authors"/> |
| 7 | </class> |
| 8 | |
| 9 | <class name="BioEntity" is-interface="true"> |
| 10 | <attribute name="primaryIdentifier" type="java.lang.String"/> |
| 11 | <attribute name="secondaryIdentifier" type="java.lang.String"/> |
| 12 | <attribute name="symbol" type="java.lang.String"/> |
| 13 | <attribute name="name" type="java.lang.String"/> |
| 14 | <reference name="organism" referenced-type="Organism"/> |
| 15 | <collection name="locatedFeatures" referenced-type="Location" reverse-reference="locatedOn"/> |
| 16 | <collection name="locations" referenced-type="Location" reverse-reference="feature" /> |
| 17 | <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject"/> |
| 18 | <collection name="synonyms" referenced-type="Synonym" reverse-reference="subject"/> |
| 19 | <collection name="dataSets" referenced-type="DataSet" reverse-reference="bioEntities"/> |
| 20 | <collection name="publications" referenced-type="Publication"/> |
| 21 | <collection name="crossReferences" referenced-type="CrossReference" reverse-reference="subject"/> |
| 22 | </class> |
| 23 | |
| 24 | <class name="Chromosome" extends="SequenceFeature" is-interface="true"/> |
| 25 | |
| 26 | <class name="Comment" is-interface="true"> |
| 27 | <attribute name="text" type="java.lang.String"/> |
| 28 | <attribute name="type" type="java.lang.String"/> |
| 29 | </class> |
| 30 | |
| 31 | <class name="CrossReference" is-interface="true"> |
| 32 | <attribute name="identifier" type="java.lang.String"/> |
| 33 | <reference name="source" referenced-type="DataSource"/> |
| 34 | <reference name="subject" referenced-type="BioEntity" reverse-reference="crossReferences" /> |
| 35 | <collection name="dataSets" referenced-type="DataSet"/> |
| 36 | </class> |
| 37 | |
| 38 | <class name="DataSource" is-interface="true"> |
| 39 | <attribute name="name" type="java.lang.String"/> |
| 40 | <attribute name="url" type="java.lang.String"/> |
| 41 | <attribute name="description" type="java.lang.String"/> |
| 42 | <collection name="dataSets" referenced-type="DataSet" reverse-reference="dataSource"/> |
| 43 | </class> |
| 44 | |
| 45 | <class name="DataSet" is-interface="true"> |
| 46 | <attribute name="name" type="java.lang.String"/> |
| 47 | <attribute name="url" type="java.lang.String"/> |
| 48 | <attribute name="description" type="java.lang.String"/> |
| 49 | <attribute name="version" type="java.lang.String"/> |
| 50 | <reference name="dataSource" referenced-type="DataSource" reverse-reference="dataSets"/> |
| 51 | <collection name="bioEntities" referenced-type="BioEntity" reverse-reference="dataSets"/> |
| 52 | </class> |
| 53 | |
| 54 | <class name="Gene" extends="SequenceFeature" is-interface="true"> |
| 55 | <attribute name="symbol" type="java.lang.String"/> |
| 56 | <attribute name="ncbiGeneNumber" type="java.lang.String"/> |
| 57 | <collection name="proteins" referenced-type="Protein" reverse-reference="genes"/> |
| 58 | </class> |
| 59 | |
| 60 | <class name="Location" is-interface="true"> |
| 61 | <attribute name="start" type="java.lang.Integer"/> |
| 62 | <attribute name="end" type="java.lang.Integer"/> |
| 63 | <attribute name="strand" type="java.lang.String"/> |
| 64 | <reference name="feature" referenced-type="BioEntity" reverse-reference="locations"/> |
| 65 | <reference name="locatedOn" referenced-type="BioEntity" reverse-reference="locatedFeatures"/> |
| 66 | <collection name="dataSets" referenced-type="DataSet"/> |
| 67 | </class> |
| 68 | |
| 69 | <class name="Ontology" is-interface="true"> |
| 70 | <attribute name="name" type="java.lang.String"/> |
| 71 | <attribute name="url" type="java.lang.String"/> |
| 72 | </class> |
| 73 | |
| 74 | <class name="OntologyTerm" is-interface="true"> |
| 75 | <attribute name="identifier" type="java.lang.String"/> |
| 76 | <attribute name="name" type="java.lang.String"/> |
| 77 | <attribute name="description" type="java.lang.String"/> |
| 78 | <attribute name="namespace" type="java.lang.String"/> |
| 79 | <attribute name="obsolete" type="java.lang.Boolean"/> |
| 80 | <reference name="ontology" referenced-type="Ontology"/> |
| 81 | <collection name="relations" referenced-type="OntologyRelation" /> |
| 82 | <collection name="synonyms" referenced-type="OntologyTermSynonym" /> |
| 83 | <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="ontologyTerm" /> |
| 84 | <collection name="parents" referenced-type="OntologyTerm" /> |
| 85 | <collection name="dataSets" referenced-type="DataSet" /> |
| 86 | </class> |
| 87 | |
| 88 | <class name="OntologyRelation" is-interface="true"> |
| 89 | <reference name="parentTerm" referenced-type="OntologyTerm" /> |
| 90 | <reference name="childTerm" referenced-type="OntologyTerm" /> |
| 91 | <attribute name="relationship" type="java.lang.String"/> |
| 92 | <attribute name="direct" type="java.lang.Boolean"/> |
| 93 | <attribute name="redundant" type="java.lang.Boolean"/> |
| 94 | </class> |
| 95 | |
| 96 | <class name="OntologyAnnotation" is-interface="true"> |
| 97 | <attribute name="qualifier" type="java.lang.String"/> |
| 98 | <reference name="subject" referenced-type="BioEntity" reverse-reference="ontologyAnnotations"/> |
| 99 | <collection name="dataSets" referenced-type="DataSet" /> |
| 100 | <collection name="publications" referenced-type="Publication" /> |
| 101 | <reference name="ontologyTerm" referenced-type="OntologyTerm" reverse-reference="ontologyAnnotations"/> |
| 102 | </class> |
| 103 | |
| 104 | <class name="OntologyTermSynonym" is-interface="true"> |
| 105 | <attribute name="name" type="java.lang.String"/> |
| 106 | <attribute name="type" type="java.lang.String"/> |
| 107 | </class> |
| 108 | |
| 109 | <class name="Organism" is-interface="true"> |
| 110 | <attribute name="genus" type="java.lang.String"/> |
| 111 | <attribute name="taxonId" type="java.lang.Integer"/> |
| 112 | <attribute name="species" type="java.lang.String"/> |
| 113 | <attribute name="commonName" type="java.lang.String"/> |
| 114 | <attribute name="shortName" type="java.lang.String"/> |
| 115 | <attribute name="name" type="java.lang.String"/> |
| 116 | </class> |
| 117 | |
| 118 | <class name="Protein" extends="BioEntity" is-interface="true"> |
| 119 | <attribute name="md5checksum" type="java.lang.String"/> |
| 120 | <attribute name="primaryAccession" type="java.lang.String"/> |
| 121 | <attribute name="length" type="java.lang.Integer"/> |
| 122 | <attribute name="molecularWeight" type="java.lang.Integer"/> |
| 123 | <reference name="sequence" referenced-type="Sequence"/> |
| 124 | <collection name="genes" referenced-type="Gene" reverse-reference="proteins"/> |
| 125 | </class> |
| 126 | |
| 127 | <class name="Publication" is-interface="true"> |
| 128 | <attribute name="title" type="java.lang.String"/> |
| 129 | <attribute name="issue" type="java.lang.String"/> |
| 130 | <attribute name="pubMedId" type="java.lang.String"/> |
| 131 | <attribute name="pages" type="java.lang.String"/> |
| 132 | <attribute name="year" type="java.lang.Integer"/> |
| 133 | <attribute name="volume" type="java.lang.String"/> |
| 134 | <attribute name="journal" type="java.lang.String"/> |
| 135 | <attribute name="firstAuthor" type="java.lang.String"/> |
| 136 | <collection name="authors" referenced-type="Author" reverse-reference="publications" /> |
| 137 | </class> |
| 138 | |
| 139 | <class name="SOTerm" extends="OntologyTerm" is-interface="true"/> |
| 140 | |
| 141 | <class name="Sequence" is-interface="true"> |
| 142 | <attribute name="residues" type="org.intermine.objectstore.query.ClobAccess"/> |
| 143 | <attribute name="length" type="int"/> |
| 144 | <attribute name="md5checksum" type="java.lang.String"/> |
| 145 | </class> |
| 146 | |
| 147 | <class name="SequenceCollection" extends="BioEntity" is-interface="true"> |
| 148 | <reference name="sequenceOntologyTerm" referenced-type="SOTerm"/> |
| 149 | </class> |
| 150 | |
| 151 | <class name="SequenceFeature" extends="BioEntity" is-interface="true"> |
| 152 | <attribute name="score" type="java.lang.Double"/> |
| 153 | <attribute name="scoreType" type="java.lang.String"/> |
| 154 | <attribute name="length" type="java.lang.Integer"/> |
| 155 | <reference name="sequence" referenced-type="Sequence"/> |
| 156 | <reference name="chromosome" referenced-type="Chromosome" /> |
| 157 | <reference name="chromosomeLocation" referenced-type="Location" /> |
| 158 | <reference name="sequenceOntologyTerm" referenced-type="SOTerm"/> |
| 159 | <collection name="overlappingFeatures" referenced-type="SequenceFeature" /> |
| 160 | </class> |
| 161 | |
| 162 | <class name="Synonym" is-interface="true"> |
| 163 | <attribute name="value" type="java.lang.String"/> |
| 164 | <reference name="subject" referenced-type="BioEntity" reverse-reference="synonyms"/> |
| 165 | <collection name="dataSets" referenced-type="DataSet"/> |
| 166 | </class> |
| 167 | |
| 168 | </model> |
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