-
Notifications
You must be signed in to change notification settings - Fork 54
/
Copy pathpco_import.owl
251 lines (138 loc) · 11.9 KB
/
pco_import.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
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/envo/imports/pco_import.owl#"
xml:base="http://purl.obolibrary.org/obo/envo/imports/pco_import.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#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/envo/imports/pco_import.owl"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
<!-- 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.org/dc/elements/1.1/contributor -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor"/>
<!-- http://purl.org/dc/elements/1.1/creator -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>
<!-- http://purl.org/dc/elements/1.1/description -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
<!-- http://purl.org/dc/elements/1.1/title -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title"/>
<!-- http://purl.org/dc/terms/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/PCO_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000031"/>
<obo:IAO_0000112>Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A material entity that consists of two or more organisms, viruses, or viroids.</obo:IAO_0000115>
<obo:IAO_0000118>group of organism</obo:IAO_0000118>
<obo:IAO_0000118>organism collection</obo:IAO_0000118>
<rdfs:comment>May be of the same or different species.</rdfs:comment>
<rdfs:label xml:lang="en">collection of organisms</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000018"/>
<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A collection of organisms, all of the same species, that live in the same place.</obo:IAO_0000115>
<obo:IAO_0000119>ISBN:0878932739</obo:IAO_0000119>
<rdfs:comment xml:lang="en">It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms.
Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used.</rdfs:comment>
<rdfs:label xml:lang="en">population of organisms</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000029"/>
<obo:IAO_0000115 xml:lang="en">A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">multispecies community</obo:IAO_0000118>
<obo:IAO_0000119>ISBN:0865423504</obo:IAO_0000119>
<rdfs:comment xml:lang="en">Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community.</rdfs:comment>
<rdfs:label xml:lang="en">ecological community</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_0000018 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000018">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">collection of organisms of the same species</obo:IAO_0000118>
<rdfs:label xml:lang="en">single-species collection of organisms</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_0000029 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000029">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A collection of organisms that consists of two or more organisms from at least two species.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))".</obo:IAO_0000116>
<rdfs:comment xml:lang="en"></rdfs:comment>
<rdfs:label xml:lang="en">multi-species collection of organisms</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000031">
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115>A material entity that is one or more organisms, viruses or viroids.</obo:IAO_0000115>
<rdfs:label xml:lang="en">organismal entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_0000051 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_0000051">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000029"/>
<obo:IAO_0000115 xml:lang="en">A multi-species collection of organisms that consists of two or more microbes from at least two species.</obo:IAO_0000115>
<dc:creator xml:lang="en">https://orcid.org/0000-0001-8815-0078</dc:creator>
<rdfs:label xml:lang="en">multi-species collection of microbes</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PCO_1000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PCO_1000004">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000002"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PCO_0000051"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness.</obo:IAO_0000115>
<obo:IAO_0000116>A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22</obo:IAO_0000116>
<obo:IAO_0000117>http://orcid.org/0000-0002-4366-3088</obo:IAO_0000117>
<obo:IAO_0000119>http://dx.doi.org/10.1038/ismej.2009.88</obo:IAO_0000119>
<oboInOwl:hasBroadSynonym xml:lang="en">microbiota</oboInOwl:hasBroadSynonym>
<rdfs:comment>The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another.</rdfs:comment>
<rdfs:label xml:lang="en">microbial community</rdfs:label>
</owl:Class>
</rdf:RDF>
<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->