1 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
2 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
3 @prefix owl: <http://www.w3.org/2002/07/owl#> .
4 @prefix dc: <http://purl.org/dc/elements/1.1/> .
5 @prefix xml: <http://www.w3.org/XML/1998/namespace> .
6 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
7 @prefix htswlib: <http://jumpgate.caltech.edu/wiki/LibraryOntology#> .
9 # I'm still learning how to do modeling & validation
10 # this version is just using rdfs:Literal for
13 <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
14 dc:title "HTS-Workflow ontology" ;
17 htswlib:Class a rdfs:Class .
19 htswlib:IlluminaFlowcell
20 a rdfs:Class, htswlib:Class ;
21 rdfs:comment "information about a illumina flowcell" ;
22 rdfs:label "Flowcell" .
25 a rdfs:Class, htswlib:Class ;
26 rdfs:comment "information specific to a lane in a flowcell" ;
30 a rdfs:Class, htswlib:Class ;
31 rdfs:comment "a biological library that can be run on a flowcell" ;
32 rdfs:label "library" .
35 a rdfs:Class, htswlib:Class;
36 rdfs:comment "an instrument that converts libraries into sequence reads" ;
37 rdfs:label "Sequencer" .
40 a rdfs:Class, htswlib:Class ;
41 rdfs:comment "What 'species' was our sample created from." ;
42 rdfs:label "Species" .
45 a rdfs:Class, htswlib:Class ;
46 rdfs:comment "Count of reads with locations" ;
47 rdfs:label "Mapped locations" .
52 rdfs:comment "link to our source flowcell" ;
53 rdfs:label "Flowcell" ;
54 rdfs:domain htswlib:IlluminaLane ;
55 rdfs:range htswlib:IlluminaFlowcell .
59 rdfs:comment "which lanes are attached to a flowcell" ;
61 # cheating, only flowcells & libraries can have lanes
62 rdfs:domain htswlib:Library ;
63 rdfs:domain htswlib:IlluminaFlowcell ;
64 rdfs:range htswlib:IlluminaLane .
68 rdfs:comment "Date thing was constructed" ;
69 rdfs:label "made on" ;
70 rdfs:domain htswlib:IlluminaFlowcell ;
71 rdfs:domain htswlib:Library ;
72 rdfs:range rdfs:Literal .
74 htswlib:total_unique_locations
76 rdfs:comment "How many reads mapped uniquely" ;
77 rdfs:label "Unique locations" ;
78 rdfs:domain htswlib:Library ;
79 rdfs:domain htswlib:IlluminaLane ;
80 rdfs:range rdfs:Literal .
84 rdfs:comment "collection of counts against sequence collections" ;
85 rdfs:label "Has mapping" ;
86 rdfs:domain htswlib:Library ;
87 rdfs:domain htswlib:IlluminaLane ;
88 rdfs:range htswlib:MappedCount .
93 rdfs:comment "Serial number of a flowcell, used as unique key" ;
94 rdfs:label "Flowcell ID" ;
95 rdfs:domain htswlib:IlluminaFlowcell ;
96 rdfs:range rdfs:Literal .
98 htswlib:flowcell_notes
100 rdfs:comment "Comments about flowcell" ;
102 rdfs:domain htswlib:IlluminaFlowcell ;
103 rdfs:range rdfs:Literal .
107 rdfs:comment "Control lane used for image analysis/base calling" ;
108 rdfs:label "Control Lane" ;
109 rdfs:domain htswlib:IlluminaFlowcell ;
110 rdfs:range rdfs:Literal .
114 rdfs:comment "How many cycles did we run the sequencer for" ;
115 rdfs:label "Read length" ;
116 rdfs:domain htswlib:IlluminaFlowcell ;
117 rdfs:range rdfs:Literal .
119 htswlib:flowcell_type
121 rdfs:comment "What kind of flowcell, e.g. single, paired." ;
122 rdfs:label "Flowcell Type" ;
123 rdfs:domain htswlib:IlluminaFlowcell ;
124 rdfs:range rdfs:Literal .
126 htswlib:image_software
128 rdfs:comment "Image analysis software name." ;
129 rdfs:label "Image processor" ;
130 rdfs:domain htswlib:IlluminaFlowcell ;
131 rdfs:range rdfs:Literal .
133 htswlib:image_version
135 rdfs:comment "Image analysis software version identifier." ;
136 rdfs:label "Image processor version" ;
137 rdfs:domain htswlib:IlluminaFlowcell ;
138 rdfs:range rdfs:Literal .
140 htswlib:basecall_software
142 rdfs:comment "Base caller software name." ;
143 rdfs:label "Basecaller" ;
144 rdfs:domain htswlib:IlluminaFlowcell ;
145 rdfs:range rdfs:Literal .
147 htswlib:basecall_version
149 rdfs:comment "Base caller software version identifier." ;
150 rdfs:label "Basecaller Version" ;
151 rdfs:domain htswlib:IlluminaFlowcell ;
152 rdfs:range rdfs:Literal .
154 htswlib:alignment_software
156 rdfs:comment "Alignment software name." ;
157 rdfs:label "Alignment software" ;
158 rdfs:domain htswlib:IlluminaFlowcell ;
159 rdfs:range rdfs:Literal .
161 htswlib:alignment_version
163 rdfs:comment "Alignment software version identifier." ;
164 rdfs:label "Aligner" ;
165 rdfs:domain htswlib:IlluminaFlowcell ;
166 rdfs:range rdfs:Literal .
170 rdfs:comment "Which sequencer sequenced this flowcell" ;
171 rdfs:label "Sequenced By" ;
172 rdfs:domain htswlib:IlluminaFlowcell ;
173 rdfs:range htswlib:Sequencer .
175 htswlib:sequencer_model
177 rdfs:comment "What model of sequencer was this flowcell run on." ;
178 rdfs:label "Sequencer model" ;
179 rdfs:domain htswlib:Sequencer ;
180 rdfs:range rdfs:Literal .
182 htswlib:sequencer_instrument
184 rdfs:comment "Sequencer instrument identifier." ;
185 rdfs:label "Instrument ID " ;
186 rdfs:domain htswlib:Sequencer ;
187 rdfs:range rdfs:Literal .
189 htswlib:sequencer_name
191 rdfs:comment "Local name for sequencer." ;
192 rdfs:label "Sequencer name " ;
193 rdfs:domain htswlib:Sequencer ;
194 rdfs:range rdfs:Literal .
197 # library only properties
200 rdfs:comment "Library unique identifier" ;
201 rdfs:label "Library ID" ;
202 rdfs:domain htswlib:Library ;
203 rdfs:range rdfs:Literal .
207 rdfs:comment "human readable name" ;
209 rdfs:range rdfs:Literal .
213 rdfs:comment """what type of library are we, which is primarily
214 determined by the type of adaptors ligated onto
215 sequence fragments.""" ;
216 rdfs:label "Library Type" ;
217 rdfs:domain htswlib:Library ;
218 rdfs:range rdfs:Literal .
220 htswlib:stopping_point
222 rdfs:comment "Protocol stopping point" ;
223 rdfs:label "Stopping Point" ;
224 rdfs:domain htswlib:Library ;
225 rdfs:range rdfs:Literal .
227 htswlib:concentration
229 rdfs:comment "Concentration of sample in nanograms per microliter" ;
230 rdfs:label "Concentration" ;
231 rdfs:domain htswlib:Library ;
232 rdfs:range rdfs:Literal .
236 rdfs:comment "The expected size of the sample sequence" ;
237 rdfs:label "Insert Size" ;
238 rdfs:domain htswlib:Library ;
239 rdfs:range rdfs:Literal .
243 rdfs:comment "The estimated fragment sizes cut from gel";
244 rdfs:label "Gel Cut" ;
245 rdfs:domain htswlib:Library ;
246 rdfs:range rdfs:Literal .
250 rdfs:comment "Name of person who created library" ;
251 rdfs:label "Made by" ;
252 rdfs:domain htswlib:Library ;
253 rdfs:range rdfs:Literal .
255 htswlib:multiplex_index
257 rdfs:comment "multiplex sequence" ;
259 rdfs:domain htswlib:Library ;
260 rdfs:range rdfs:Literal .
264 rdfs:comment "Description of source material" ;
265 rdfs:label "cell line" ;
266 rdfs:domain htswlib:Library ;
267 rdfs:range rdfs:Literal .
269 htswlib:experiment_type
271 rdfs:comment "What type of sequencing is this. e.g. RNA-Seq, DeNovo etc." ;
272 rdfs:label "Experiment Type" ;
273 rdfs:domain htswlib:Library ;
274 rdfs:range rdfs:Literal .
278 rdfs:comment "Entity associated with this sample" ;
279 rdfs:label "affiliation" ;
280 rdfs:domain htswlib:Library ;
281 rdfs:range rdfs:Literal .
285 rdfs:comment "Scientific name of sample species" ;
286 rdfs:label "Species" ;
287 rdfs:domain htswlib:Library ;
288 #rdfs:domain htswlib:IlluminaLane;
289 rdfs:range htswlib:Species .
293 rdfs:comment "Which replicate this was" ;
294 rdfs:label "replicate" ;
295 rdfs:domain htswlib:Library ;
296 rdfs:range rdfs:Literal .
298 # lane only properties
301 rdfs:comment "Which lane were we run in" ;
302 rdfs:label "lane id" ;
303 rdfs:domain htswlib:IlluminaLane ;
304 rdfs:range rdfs:Literal .
306 # FIXME: should this be note?
309 rdfs:comment "Comment about an object" ;
310 rdfs:range rdfs:Literal .
314 rdfs:comment "which library was run on this lane." ;
315 rdfs:label "Library" ;
316 rdfs:domain htswlib:IlluminaLane ;
317 rdfs:range htswlib:Library .
322 rdfs:comment "Scientific name of species" ;
323 rdfs:label "Species" ;
324 rdfs:domain htswlib:Species ;
325 rdfs:range rdfs:Literal .
327 # mapped count properties
330 rdfs:comment "A sequence collection, genome, chromosome, spike in, etc.";
331 rdfs:label "Mapped to" ;
332 rdfs:domain htswlib:MappedCount ;
333 rdfs:range rdfs:Literal .
337 rdfs:comment "Number of read locations" ;
339 rdfs:domain htswlib:MappedCount ;
340 rdfs:range rdfs:Literal .