-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbk_mappings.ttl
437 lines (266 loc) · 13.7 KB
/
bk_mappings.ttl
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
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
@prefix : <http://knetminer.org/data/rdf/terms/biokno/ext_mappings#> .
@prefix bk: <http://knetminer.org/data/rdf/terms/biokno/> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix bka: <http://knetminer.org/data/rdf/terms/biokno/attributes/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix agri: <http://agrischemas.org/> .
@prefix bpax: <http://www.biopax.org/release/biopax-level3.owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix schema: <http://schema.org/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix bioschema: <http://bioschemas.org/> .
@base <http://knetminer.org/data/rdf/terms/biokno/ext_mappings> .
<http://knetminer.org/data/rdf/terms/biokno/ext_mappings> rdf:type owl:Ontology ;
owl:imports bk: ,
<http://knetminer.org/data/rdf/terms/biokno/knetminer_extensions/> .
#################################################################
# Annotation properties
#################################################################
### http://agrischemas.org/evidence
agri:evidence rdf:type owl:AnnotationProperty .
### http://knetminer.org/data/rdf/terms/biokno/evidence
bk:evidence rdf:type owl:ObjectProperty;
rdfs:subPropertyOf agri:evidence .
bk:dataSource rdf:type owl:ObjectProperty;
rdfs:subPropertyOf dc:source .
### http://knetminer.org/data/rdf/terms/biokno/attributes/EVIDENCE
bka:EVIDENCE rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf agri:evidence .
bka:ID a owl:DataTypeProperty;
rdfs:subPropertyOf schema:identifier, dcterms:identifier.
schema:identifier a owl:AnnotationProperty.
#################################################################
# Object Properties
#################################################################
### http://knetminer.org/data/rdf/terms/biokno/consumes
bk:consumes rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/cooc_wi
bk:cooc_wi rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/cs_by
bk:cs_by rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/en_by
bk:en_by rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf sio:SIO_010079, bioschema:isEncodedByBioChemEntity .
### http://knetminer.org/data/rdf/terms/biokno/enc
bk:enc rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf sio:SIO_010078, bioschema:encodesBioChemEntity .
### http://knetminer.org/data/rdf/terms/biokno/has_part
bk:has_part rdf:type owl:ObjectProperty;
rdfs:subPropertyOf schema:hasPart .
### http://knetminer.org/data/rdf/terms/biokno/has_participant
bk:has_participant rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/is_a
bk:is_a rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/neg_reg
bk:neg_reg rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/part_of
bk:part_of rdf:type owl:ObjectProperty;
rdfs:subPropertyOf schema:isPartOf .
### http://knetminer.org/data/rdf/terms/biokno/participates_in
bk:participates_in rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/pd_by
bk:pd_by rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/pos_reg
bk:pos_reg rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/produces
bk:produces rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/publication_features
bk:publication_features rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf dc:subject, schema:about.
### http://knetminer.org/data/rdf/terms/biokno/published_in
bk:published_in rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf schema:subjectOf.
bk:pub_in rdf:type owl:ObjectProperty;
rdfs:subPropertyOf schema:subjectOf.
bk:occ_in rdf:type owl:ObjectProperty;
owl:inverseOf schema:mentions.
### http://knetminer.org/data/rdf/terms/biokno/regulates
bk:regulates rdf:type owl:ObjectProperty .
### http://knetminer.org/data/rdf/terms/biokno/relFrom
bk:relFrom rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf rdf:subject .
### http://knetminer.org/data/rdf/terms/biokno/relTo
bk:relTo rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf rdf:object .
### http://knetminer.org/data/rdf/terms/biokno/relTypeRef
bk:relTypeRef rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf rdf:predicate .
### http://purl.org/dc/elements/1.1/subject
dc:subject rdf:type owl:ObjectProperty .
### http://schema.org/subjectOf
schema:subjectOf rdf:type owl:ObjectProperty .
### http://semanticscience.org/resource/SIO_010078
sio:SIO_010078 rdf:type owl:ObjectProperty .
### http://semanticscience.org/resource/SIO_010079
sio:SIO_010079 rdf:type owl:ObjectProperty .
### http://www.biopax.org/release/biopax-level3.owl#participant
bpax:participant rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf bk:has_participant .
### http://www.biopax.org/release/biopax-level3.owl#product
bpax:product rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf bk:produces .
#################################################################
# Data properties
#################################################################
### http://knetminer.org/data/rdf/terms/biokno/altName
bk:altName rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf skos:altLabel, schema:alternateName, rdfs:label;
rdfs:seeAlso schema:name .
### http://knetminer.org/data/rdf/terms/biokno/name
bk:name rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf rdfs:label.
### http://knetminer.org/data/rdf/terms/biokno/prefName
bk:prefName rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf skos:prefLabel, schema:name, rdfs:label;
rdfs:comment "schema:name is described and used as preferred name, despite being defined as equivalent to dc:title. Here, we prefer to stick to the de-facto meaning, which should ease interoperability." .
### http://knetminer.org/data/rdf/terms/biokno/attributes/AUTHORS
bka:AUTHORS rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf dcterms:creator, agri:authorsList.
agri:authorsList rdf:type owl:AnnotationProperty.
### http://knetminer.org/data/rdf/terms/biokno/attributes/Abstract
bka:Abstract rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf dcterms:description, schema:abstract .
### http://knetminer.org/data/rdf/terms/biokno/attributes/AbstractHeader
bka:AbstractHeader rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf dcterms:title .
### http://knetminer.org/data/rdf/terms/biokno/attributes/FullText
bka:FullText rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf dcterms:description, schema:text .
### http://knetminer.org/data/rdf/terms/biokno/attributes/PVALUE
bka:PVALUE rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf agri:pvalue;
rdfs:comment "TODO: we would like to find a better form of integration with SIO/OBI"@en ;
rdfs:seeAlso obo:OBI_0000175 ,
sio:SIO_000765 .
bka:TFIDF rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf agri:score;
rdfs:seeAlso obo:OBI_0000071.
### http://knetminer.org/data/rdf/terms/biokno/attributes/URL
bka:URL rdf:type owl:DatatypeProperty .
### http://knetminer.org/data/rdf/terms/biokno/attributes/YEAR
bka:YEAR rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf dcterms:issued, schema:datePublished .
bka:PMID rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf agri:pmedId .
### http://purl.org/dc/elements/1.1/creator
dc:creator rdf:type owl:DatatypeProperty .
### http://purl.org/dc/terms/description
dcterms:description rdf:type owl:DatatypeProperty .
### http://purl.org/dc/terms/issued
dcterms:issued rdf:type owl:DatatypeProperty .
### http://purl.org/dc/terms/title
dcterms:title rdf:type owl:DatatypeProperty .
### http://www.biopax.org/release/biopax-level3.owl#name
bpax:name rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf bk:name .
### http://www.biopax.org/release/biopax-level3.owl#standardName
bpax:standardName rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf bk:prefName .
### http://www.w3.org/2004/02/skos/core#altLabel
skos:altLabel rdf:type owl:DatatypeProperty .
### http://www.w3.org/2004/02/skos/core#editorialNote
skos:editorialNote rdf:type owl:DatatypeProperty .
### http://www.w3.org/2004/02/skos/core#prefLabel
skos:prefLabel rdf:type owl:DatatypeProperty .
#################################################################
# Classes
#################################################################
### http://agrischemas.org/BioPathway
agri:BioPathway rdf:type owl:Class ;
owl:equivalentClass bk:Path .
### http://agrischemas.org/ScholarlyPublication
agri:ScholarlyPublication rdf:type owl:Class ;
owl:equivalentClass bk:Publication .
### http://bioschemas.org/BioChemEntity
bioschema:BioChemEntity rdf:type owl:Class .
### http://bioschemas.org/Protein
bioschema:Protein rdf:type owl:Class ;
owl:equivalentClass bpax:Protein .
### http://bioschemas.org/Study
bioschema:Study rdf:type owl:Class ;
owl:equivalentClass bk:Experiment .
### http://knetminer.org/data/rdf/terms/biokno/Concept
bk:Concept rdfs:subClassOf skos:Concept .
### http://knetminer.org/data/rdf/terms/biokno/Experiment
### http://knetminer.org/data/rdf/terms/biokno/Gene
bk:Gene rdf:type owl:Class ;
owl:equivalentClass bpax:Gene, bioschema:Gene .
### http://knetminer.org/data/rdf/terms/biokno/Interaction
bk:Interaction rdf:type owl:Class ;
owl:equivalentClass bpax:Interaction .
### http://knetminer.org/data/rdf/terms/biokno/Molecule
bk:Molecule rdf:type owl:Class ;
rdfs:subClassOf bioschema:BioChemEntity .
### http://knetminer.org/data/rdf/terms/biokno/MoleculeComplex
bk:MoleculeComplex rdf:type owl:Class ;
owl:equivalentClass bpax:Complex ;
rdfs:subClassOf bioschema:BioChemEntity;
rdfs:comment "[kNetMiner] TODO: for some reason bk:Protein is made a subclass of this, probably wrong."@en .
### http://knetminer.org/data/rdf/terms/biokno/Participant
bk:Participant rdf:type owl:Class ;
owl:equivalentClass bpax:Entity .
### http://knetminer.org/data/rdf/terms/biokno/Path
bk:Path rdf:type owl:Class ;
owl:equivalentClass sio:SIO_001107 ,
bpax:Pathway .
### http://knetminer.org/data/rdf/terms/biokno/Protein
bk:Protein rdf:type owl:Class ;
owl:equivalentClass sio:SIO_010043 ,
bpax:Protein, bioschema:Protein .
### http://knetminer.org/data/rdf/terms/biokno/Publication
bk:Publication rdf:type owl:Class ;
rdfs:subClassOf schema:CreativeWork .
### http://knetminer.org/data/rdf/terms/biokno/Reaction
bk:Reaction rdf:type owl:Class ;
owl:equivalentClass bpax:BiochemicalReaction ;
rdfs:comment "[kNetMiner] TODO: requires review. Likely, bpax:BiochemicalReaction can model any reaction, whether it's biology-related or not"@en .
### http://knetminer.org/data/rdf/terms/biokno/Relation
bk:Relation rdf:type owl:Class ;
rdfs:subClassOf rdf:Statement .
### http://knetminer.org/data/rdf/terms/biokno/Transport
bk:Transport rdf:type owl:Class ;
owl:equivalentClass bpax:Transport .
### http://schema.org/CreativeWork
schema:CreativeWork rdf:type owl:Class .
### http://semanticscience.org/resource/SIO_001107
sio:SIO_001107 rdf:type owl:Class .
### http://semanticscience.org/resource/SIO_010043
sio:SIO_010043 rdf:type owl:Class .
### http://www.biopax.org/release/biopax-level3.owl#BiochemicalReaction
bpax:BiochemicalReaction rdf:type owl:Class .
### http://www.biopax.org/release/biopax-level3.owl#Complex
bpax:Complex rdf:type owl:Class .
### http://www.biopax.org/release/biopax-level3.owl#Entity
bpax:Entity rdf:type owl:Class .
### http://www.biopax.org/release/biopax-level3.owl#Gene
bpax:Gene rdf:type owl:Class .
### http://www.biopax.org/release/biopax-level3.owl#Interaction
bpax:Interaction rdf:type owl:Class .
### http://www.biopax.org/release/biopax-level3.owl#Pathway
bpax:Pathway rdf:type owl:Class .
### http://www.biopax.org/release/biopax-level3.owl#Protein
bpax:Protein rdf:type owl:Class .
### http://www.biopax.org/release/biopax-level3.owl#Transport
bpax:Transport rdf:type owl:Class .
### http://www.w3.org/2004/02/skos/core#Concept
skos:Concept rdf:type owl:Class .
#################################################################
# Individuals
#################################################################
### http://knetminer.org/data/rdf/terms/biokno/Participant
bk:Participant rdf:type owl:NamedIndividual .
#################################################################
# Annotations
#################################################################
bk:Participant skos:editorialNote "[kNetMiner] TODO: from the description, it seems to correspond to bpax:PhysicalEntity, but we're unsure that there aren't more general real data"@en .
bka:Score a owl:DatatypeProperty;
rdfs:seeAlso obo:OBI_0000071;
rdfs:subPropertyOf agri:score
.
### Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi