forked from mcwbbc/rgd_owl_ontology
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathRGD_Core_Ontology.owl
276 lines (275 loc) · 14.8 KB
/
RGD_Core_Ontology.owl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
<?xml version="1.0"?>
<rdf:RDF
xmlns="http://www.purl.org/RGD/core#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:swrl="http://www.w3.org/2003/11/swrl#"
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xml:base="http://www.purl.org/RGD/core">
<owl:Ontology rdf:about=""/>
<owl:Class rdf:ID="Location">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>This class describes the cytogenetic or genomic location of a MappableObject</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Location</rdfs:label>
</owl:Class>
<owl:Class rdf:ID="Qtl">
<rdfs:subClassOf>
<owl:Class rdf:ID="MappableObject"/>
</rdfs:subClassOf>
<owl:disjointWith>
<owl:Class rdf:ID="Marker"/>
</owl:disjointWith>
<owl:disjointWith>
<owl:Class rdf:ID="Gene"/>
</owl:disjointWith>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>A QTL object in RGD; a genomic segment which has been demonstrated to have a statistically significant linkage to a specific measurable phenotypic trait and in which there is presumed to be one or more genes or genomic elements that contribute to the control of that trait, along with a complex array of other genomic elements.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>QTL</rdfs:label>
</owl:Class>
<owl:Class rdf:ID="OntologyAnnotation">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Ontology Annotation</rdfs:label>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>An association between an ontology term and an RGD object</rdfs:comment>
</owl:Class>
<owl:Class rdf:about="#Gene">
<owl:disjointWith>
<owl:Class rdf:about="#Marker"/>
</owl:disjointWith>
<owl:disjointWith rdf:resource="#Qtl"/>
<rdfs:subClassOf>
<owl:Class rdf:about="#MappableObject"/>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>A gene object in RGD; a genomic segment which has been shown or predicted to be able to produce an RNA through the process of transcription.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Gene</rdfs:label>
</owl:Class>
<owl:Class rdf:ID="Strain">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>an RGD Strain object; a group of rats which share a genetic background, for example an inbred strain is a lineage of rats which have been rendered essentially genetically identical to each other and distinct from other strains by 20 or more generations of brother-sister matings. Other strains have been produced by genetic and/or genomic manipulations such as introduction of an exogenous gene or chromosomal segment, or mutation of one or more loci. Some strains are outbred, meaning individuals of those strains are by definition not genetically identical.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Strain</rdfs:label>
<rdfs:subClassOf>
<owl:Class rdf:ID="RgdObject"/>
</rdfs:subClassOf>
</owl:Class>
<owl:Class rdf:ID="Est">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>An expressed sequence tag; a short sub-sequence of a transcribed nucleotide sequence which may or may not be polymorphic between strains or individuals. When polymorphic, it can be used to track the parental source of the surrounding DNA segment through successive generations.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>EST</rdfs:label>
<owl:disjointWith>
<owl:Class rdf:ID="Snp"/>
</owl:disjointWith>
<rdfs:subClassOf>
<owl:Class rdf:about="#Marker"/>
</rdfs:subClassOf>
</owl:Class>
<owl:Class rdf:about="#MappableObject">
<rdfs:subClassOf>
<owl:Class rdf:about="#RgdObject"/>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Any RgdObject to which a Location (genomic, genetic or cytogenetic) can be attached</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Mappable Object</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#RgdObject">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>RGD Object</rdfs:label>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Any object with an RGD ID--specifically genes, strains, QTLs and Markers.</rdfs:comment>
</owl:Class>
<owl:Class rdf:ID="Sslp">
<owl:disjointWith>
<owl:Class rdf:about="#Snp"/>
</owl:disjointWith>
<rdfs:subClassOf>
<owl:Class rdf:about="#Marker"/>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>A simple sequence length polymorphism; a short segment of DNA which contains a variable number of repeated 2-5 nucleotide sequences. The number of times the sequence is repeated depends on the strain or individual allowing these polymorphisms to be used to track the parental source of the surrounding DNA segment through successive generations.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>SSLP</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#Marker">
<rdfs:subClassOf rdf:resource="#MappableObject"/>
<owl:disjointWith rdf:resource="#Qtl"/>
<owl:disjointWith rdf:resource="#Gene"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Marker</rdfs:label>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>An RGD marker object; a small DNA segment or individual nucleotide which has been shown to be polymorphic between different rat strains or between different individuals and which can be used to "follow" the parental (or ancestral) source of a particular DNA region through successive generations.</rdfs:comment>
</owl:Class>
<owl:Class rdf:about="#Snp">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>SNP</rdfs:label>
<owl:disjointWith rdf:resource="#Est"/>
<owl:disjointWith rdf:resource="#Sslp"/>
<rdfs:subClassOf rdf:resource="#Marker"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>A single nucleotide polymorphism; a natrually occurring difference in a single nucleotide at a particular genomic position. The value of the nucleotide is dependent on the strain or individual allowing these polymorphisms to be used to follow the parental source of the surrounding DNA segment through successive generations</rdfs:comment>
</owl:Class>
<owl:ObjectProperty rdf:ID="isStrainFor">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Which QTL(s) this strain was used to determine.</rdfs:comment>
<rdfs:domain rdf:resource="#Strain"/>
<owl:inverseOf>
<owl:ObjectProperty rdf:ID="hasStrain"/>
</owl:inverseOf>
<rdfs:range rdf:resource="#Qtl"/>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:ID="hasLocation">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>hasLocation describes the location of the mappable object; it joins a MappableObject to a Location.</rdfs:comment>
<rdfs:range rdf:resource="#Location"/>
<rdfs:domain rdf:resource="#MappableObject"/>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:ID="hasMarker">
<rdfs:domain rdf:resource="#Qtl"/>
<owl:inverseOf>
<owl:ObjectProperty rdf:ID="isMarkerFor"/>
</owl:inverseOf>
<rdfs:range rdf:resource="#Marker"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Associates a QTL with one or more markers. A QTL can have up to three markers--two flanking markers and/or a peak marker.</rdfs:comment>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:ID="isCandidateGeneFor">
<owl:inverseOf>
<owl:ObjectProperty rdf:ID="hasCandidateGene"/>
</owl:inverseOf>
<rdfs:range rdf:resource="#Qtl"/>
<rdfs:domain rdf:resource="#Gene"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>links a gene which is a candidate gene for a QTL to that QTL; inverse of property "hasCandidateGene"</rdfs:comment>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#isMarkerFor">
<owl:inverseOf rdf:resource="#hasMarker"/>
<rdfs:domain rdf:resource="#Marker"/>
<rdfs:range rdf:resource="#Qtl"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Inverse of hasMarker--defines which QTL(s) this marker is associated with.</rdfs:comment>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasStrain">
<owl:inverseOf rdf:resource="#isStrainFor"/>
<rdfs:domain rdf:resource="#Qtl"/>
<rdfs:range rdf:resource="#Strain"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>This is one of the strains that was used to determine association between a phenotypic trait and a region of the chromosome. Each rat QTL will have two associated strains which were crossed and the progeny genotyped and phenotyped to determine the location of the QTL.</rdfs:comment>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:ID="hasOntologyAnnotation">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>links an annotation to the annotated object</rdfs:comment>
<rdfs:domain rdf:resource="#RgdObject"/>
<rdfs:range rdf:resource="#OntologyAnnotation"/>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:ID="hasPeakMarker">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>This is the marker which defines the peak of the QTL graph. Not all QTLs will have a peak marker defined.</rdfs:comment>
<rdfs:range rdf:resource="#Marker"/>
<rdfs:subPropertyOf rdf:resource="#hasMarker"/>
<rdfs:domain rdf:resource="#Qtl"/>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasCandidateGene">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>links a QTL to a specified candidate gene for that QTL; inverse of property "isCandidateGeneFor"</rdfs:comment>
<rdfs:domain rdf:resource="#Qtl"/>
<rdfs:range rdf:resource="#Gene"/>
<owl:inverseOf rdf:resource="#isCandidateGeneFor"/>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:ID="hasFlankingMarkerUp">
<rdfs:subPropertyOf rdf:resource="#hasMarker"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>This is the upstream marker which defines the 5' end of the QTL. RGD calls this "Flank 1". Not all QTLs will have an upstream marker defined.</rdfs:comment>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:ID="hasFlankingMarkerDwn">
<rdfs:subPropertyOf rdf:resource="#hasMarker"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>This is the downstream marker which defines the 3' end of the QTL. RGD calls this "Flank 2". Not all QTLs will have an downstream marker defined.</rdfs:comment>
</owl:ObjectProperty>
<owl:DatatypeProperty rdf:ID="hasTerm">
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
<rdfs:domain rdf:resource="#OntologyAnnotation"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasCytogeneticBand">
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
<rdfs:domain rdf:resource="#Location"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasOntologyId">
<rdfs:domain rdf:resource="#OntologyAnnotation"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasChromosome">
<rdfs:domain rdf:resource="#Location"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasGenomeAssembly">
<rdfs:domain rdf:resource="#Location"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasSymbol">
<rdfs:domain rdf:resource="#RgdObject"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasAbsPosition">
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
<rdfs:domain rdf:resource="#Location"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasQualifier">
<rdfs:domain rdf:resource="#OntologyAnnotation"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasChrStrand">
<rdfs:domain rdf:resource="#Location"/>
<rdfs:range>
<owl:DataRange>
<owl:oneOf rdf:parseType="Resource">
<rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>+</rdf:first>
<rdf:rest rdf:parseType="Resource">
<rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>-</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</rdf:rest>
</owl:oneOf>
</owl:DataRange>
</rdfs:range>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasChrStop">
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
<rdfs:domain rdf:resource="#Location"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasPValue">
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
<rdfs:domain rdf:resource="#Qtl"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasEvidenceCode">
<rdfs:domain rdf:resource="#OntologyAnnotation"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasLodScore">
<rdfs:domain rdf:resource="#Qtl"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasChrStart">
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
<rdfs:domain rdf:resource="#Location"/>
</owl:DatatypeProperty>
<owl:DatatypeProperty rdf:ID="hasName">
<rdfs:domain rdf:resource="#RgdObject"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
</owl:DatatypeProperty>
<owl:FunctionalProperty rdf:ID="hasRgdId">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Unique identifier for data in the RGD database</rdfs:comment>
<rdfs:domain rdf:resource="#RgdObject"/>
</owl:FunctionalProperty>
</rdf:RDF>
<!-- Created with Protege (with OWL Plugin 3.4.4, Build 579) http://protege.stanford.edu -->