-
Notifications
You must be signed in to change notification settings - Fork 26
/
external-byhand.owl
327 lines (183 loc) · 13.8 KB
/
external-byhand.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
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/obi/dev/external-byhand.owl#"
xml:base="http://purl.obolibrary.org/obo/obi/dev/external-byhand.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/obi/dev/external-byhand.owl"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000114 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000118 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000232 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000412 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412"/>
<!-- http://purl.obolibrary.org/obo/RO_0001900 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001900"/>
<!-- http://purl.org/dc/elements/1.1/source -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/source"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000062 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000062">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000111 xml:lang="en">preceded by</obo:IAO_0000111>
<obo:IAO_0000116 xml:lang="en">An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">is preceded by</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">preceded_by</obo:IAO_0000118>
<dc:source>http://www.obofoundry.org/ro/#OBO_REL:preceded_by</dc:source>
<rdfs:label xml:lang="en">preceded by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000063 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000063">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000111 xml:lang="en">precedes</obo:IAO_0000111>
<rdfs:label xml:lang="en">precedes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001000 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001000">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000111>derives from</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">derives from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002087 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002087">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002090"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000118>starts_at_end_of</obo:IAO_0000118>
<rdfs:comment xml:lang="en">X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)</rdfs:comment>
<rdfs:label xml:lang="en">immediately preceded by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002090 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002090">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
<obo:IAO_0000117>David Osumi-Sutherland</obo:IAO_0000117>
<obo:IAO_0000118>ends_at_start_of</obo:IAO_0000118>
<obo:IAO_0000118>meets</obo:IAO_0000118>
<rdfs:comment xml:lang="en">X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)</rdfs:comment>
<rdfs:label xml:lang="en">immediately precedes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002180 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002180">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.</obo:IAO_0000115>
<obo:IAO_0000116>The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.</obo:IAO_0000116>
<obo:IAO_0000232 xml:lang="en">For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.</obo:IAO_0000232>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:label xml:lang="en">has component</rdfs:label>
<rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Submissions:Componency"/>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002215 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002215">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115>A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.</obo:IAO_0000115>
<obo:IAO_0000118>has function realized in</obo:IAO_0000118>
<rdfs:label>capable of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002219 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002219">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002220"/>
<obo:IAO_0000111>surrounded by</obo:IAO_0000111>
<obo:IAO_0000115>x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">surrounded by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002220 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002220"/>
<!-- http://purl.obolibrary.org/obo/RO_0002222 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002222">
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000116>move to BFO?</obo:IAO_0000116>
<obo:IAO_0000119>Allen</obo:IAO_0000119>
<rdfs:comment>A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.</rdfs:comment>
<rdfs:label xml:lang="en">temporal relation</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002223 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002223">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>inverse of starts with</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000119>Allen</obo:IAO_0000119>
<rdfs:label xml:lang="en">starts</rdfs:label>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000003"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000004"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
<!-- http://purl.obolibrary.org/obo/CLO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CLO_0000001">
<obo:IAO_0000115 xml:lang="en">A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CLO_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CLO_0000031">
<obo:IAO_0000115 xml:lang="en">A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). </obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000078 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000078"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Individuals
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000125 -->
<owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000125">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
</owl:Thing>
</rdf:RDF>
<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->