1 +
from rdflib import Graph, Literal, Namespace, URIRef
2 +
from rdflib.extras.infixowl import Class, Ontology, Property, min, only, some
3 + 4 +
CPR = Namespace("http://purl.org/cpr/0.75#")
5 +
INF = Namespace("http://www.loa-cnr.it/ontologies/InformationObjects.owl#")
6 +
EDNS = Namespace("http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#")
7 +
DOLCE = Namespace("http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#")
8 +
REL = Namespace("http://www.geneontology.org/owl#")
9 +
GALEN = Namespace("http://www.co-ode.org/ontologies/galen#")
10 +
TIME = Namespace("http://www.w3.org/2006/time#")
11 +
CYC = Namespace("http://sw.cyc.com/2006/07/27/cyc/")
12 + 13 + 14 +
def infixowl_example():
15 +
g = Graph()
16 +
g.bind("cpr", CPR, override=False)
17 +
g.bind("ro", REL, override=False)
18 +
g.bind("inf", INF, override=False)
19 +
g.bind("edns", EDNS, override=False)
20 +
g.bind("dol", DOLCE, override=False)
21 +
g.bind("time", TIME, override=False)
22 +
g.bind("galen", GALEN, override=False)
23 + 24 +
Class.factoryGraph = g
25 +
Property.factoryGraph = g
26 +
Ontology.factoryGraph = g
27 + 28 +
cprOntology = Ontology(URIRef("http://purl.org/cpr/owl")) # noqa: N806
29 +
cprOntology.imports = [
30 +
URIRef("http://obo.sourceforge.net/relationship/relationship.owl"),
31 +
URIRef(DOLCE),
32 +
URIRef(EDNS),
33 +
URIRef("http://www.w3.org/2006/time#"),
34 +
]
35 +
cprOntology.comment = [
36 +
Literal(
37 +
"""This OWL ontology was generated by Fuxi 0.85b.dev-r107
38 +
(with newly added Infix OWL syntax library). It imports the
39 +
OBO relationship ontology, DOLCE, and OWL time. It formally
40 +
defines a focused, core set of archetypes [Jung, C.]
41 +
replicated in various patient record terminology. This core is
42 +
defined in RDF and follows the normalization principles
43 +
of "rigorous formal ontologies" [Rector, A.]."""
44 +
)
45 +
]
46 +
cprOntology.setVersion(Literal("0.75"))
47 + 48 +
# Relations
49 +
# represented-by
50 +
representationOf = Property( # noqa: N806
51 +
CPR["representation-of"],
52 +
inverseOf=Property(CPR["represented-by"]),
53 +
comment=[
54 +
Literal(
55 +
"""Patient records stand in the cpr:representation-of relation
56 +
with patients"""
57 +
)
58 +
],
59 +
)
60 +
representedBy = Property( # noqa: F841, N806
61 +
CPR["represented-by"], inverseOf=representationOf
62 +
)
63 +
# description-of
64 +
descrOf = Property( # noqa: N806
65 +
CPR["description-of"],
66 +
comment=[
67 +
Literal(
68 +
"""Clinical descriptions stand in the cpr:description-of
69 +
relation with various clinical phenomenon"""
70 +
)
71 +
],
72 +
domain=[Class(CPR["clinical-description"])],
73 +
)
74 +
# cpr:interpreted-by
75 +
interpretedBy = Property( # noqa: F841, N806
76 +
CPR["interpreted-by"],
77 +
comment=[
78 +
Literal(
79 +
"""Signs and symptoms are interpreted by rational physical
80 +
objects (people)"""
81 +
)
82 +
],
83 +
domain=[Class(CPR["medical-sign"]) | Class(CPR["symptom"])],
84 +
range=[Class(CPR.person)],
85 +
)
86 +
# cpr:realized-by
87 +
realizedBy = Property( # noqa: N806
88 +
CPR["realized-by"],
89 +
comment=[
90 +
Literal(
91 +
"""The epistemological relation in which screening acts and
92 +
the problems they realize stand to each other"""
93 +
)
94 +
],
95 +
inverseOf=Property(CPR["realizes"]),
96 +
domain=[Class(CPR["medical-problem"])],
97 +
range=[Class(CPR["screening-act"])],
98 +
)
99 +
# cpr:realizes
100 +
realizes = Property(CPR["realizes"], inverseOf=realizedBy) # noqa: F841
101 + 102 +
# Classes
103 +
# cpr:person
104 +
person = Class(CPR.person)
105 +
person.comment = [
106 +
Literal(
107 +
"""A class which directly corresponds with the “Person” class in
108 +
both GALEN and Cyc"""
109 +
)
110 +
]
111 +
person.subClassOf = [Class(EDNS["rational-physical-object"])]
112 +
person.equivalentClass = [Class(GALEN.Person), Class(CYC.Person)]
113 + 114 +
# cpr:patient
115 +
patient = Class(CPR.patient)
116 +
patient.comment = [
117 +
Literal(
118 +
"""A class which directly corresponds with the “Patient”
119 +
and “MedicalPatient” classes in GALEN / Cyc"""
120 +
)
121 +
]
122 +
# patient.equivalentClass = [Class(GALEN.Patient),Class(CYC.MedicalPatient)]
123 +
patient.subClassOf = [CPR["represented-by"] @ some @ Class(CPR["patient-record"])]
124 +
person += patient
125 + 126 +
# cpr:clinician
127 +
clinician = Class(CPR.person)
128 +
clinician.comment = [
129 +
Literal(
130 +
"""A person who plays the clinician role (typically Nurse,
131 +
Physician / Doctor, etc.)"""
132 +
)
133 +
]
134 +
person += clinician
135 + 136 +
# bytes
137 +
bytes = Class(CPR.bytes)
138 +
bytes.comment = [
139 +
Literal(
140 +
"""The collection of physical objects which constitute a stream of
141 +
bytes in memory, disk, etc."""
142 +
)
143 +
]
144 +
bytes.subClassOf = [DOLCE["non-agentive-physical-object"]]
145 + 146 +
# cpr:patient-record
147 +
patientRecord = Class(CPR["patient-record"]) # noqa: N806
148 +
patientRecord.comment = [
149 +
Literal(
150 +
"""a class (a representational artifact [REFTERM]) depicting
151 +
relevant clinical information about a specific patient and is
152 +
primarily comprised of one or more
153 +
cpr:clinical-descriptions."""
154 +
)
155 +
]
156 +
patientRecord.seeAlso = [URIRef("")]
157 +
patientRecord.subClassOf = [
158 +
bytes,
159 +
# Class(CYC.InformationBearingThing),
160 +
CPR["representation-of"] @ only @ patient,
161 +
REL.OBO_REL_has_proper_part @ some @ Class(CPR["clinical-description"]),
162 +
]
163 + 164 +
# cpr:medical-problem
165 +
problem = Class(
166 +
CPR["medical-problem"],
167 +
subClassOf=[
168 +
Class(DOLCE.quality),
169 +
realizedBy @ only @ Class(CPR["screening-act"]),
170 +
],
171 +
)
172 +
problem.comment = [
173 +
Literal(
174 +
""".. problems that clearly require the intervention of a health
175 +
care professional. These include acute problems requiring
176 +
hospitalization and chronic problems requiring long-term
177 +
management."""
178 +
)
179 +
]
180 + 181 +
# cpr:clinical-description
182 +
clinDescr = Class(CPR["clinical-description"]) # noqa: N806
183 +
clinDescr.disjointWith = [CPR["patient-record"]]
184 +
clinDescr.comment = [
185 +
Literal(
186 +
"""A class which corresponds (at least syntactically) with the HL7
187 +
RIM Act Class, insofar as its members consist of clinical
188 +
recordings (representational artifacts) of natural phenomena
189 +
of clinical significance"""
190 +
)
191 +
]
192 +
clinDescr.subClassOf = [
193 +
bytes,
194 +
# Class(CYC.InformationBearingThing),
195 +
DOLCE["has-quality"] @ some @ Class(TIME.TemporalEntity),
196 +
descrOf @ min @ Literal(1),
197 +
]
198 + 199 +
# cpr:medical-sign
200 +
sign = Class(
201 +
CPR["medical-sign"],
202 +
subClassOf=[
203 +
problem,
204 +
Property(CPR["interpreted-by"]) @ only @ clinician,
205 +
Property(CPR["interpreted-by"]) @ some @ clinician,
206 +
],
207 +
disjointWith=[CPR.symptom],
208 +
)
209 +
sign.comment = [
210 +
Literal(
211 +
"""A cpr:medical-problem which are specifically interpreted by a
212 +
clinician. As such, this class is informally defined as an
213 +
objective indication of a quality typically detected by a
214 +
physician during a physical examination of a patient."""
215 +
)
216 +
]
217 + 218 +
symptom = Class(
219 +
CPR["symptom"],
220 +
subClassOf=[
221 +
problem,
222 +
Property(CPR["interpreted-by"]) @ only @ patient,
223 +
Property(CPR["interpreted-by"]) @ some @ patient,
224 +
],
225 +
disjointWith=[sign],
226 +
)
227 +
symptom.comment = [
228 +
Literal(
229 +
"""(Medicine) any sensation or change in bodily function that is
230 +
experienced by a patient and is associated with a particular
231 +
disease."""
232 +
)
233 +
]
234 + 235 +
# clinical-act heriarchy
236 +
clinicalAct = Class( # noqa: N806
237 +
CPR["clinical-act"], subClassOf=[Class(EDNS.activity)]
238 +
)
239 + 240 +
therapy = Class(CPR["therapeutic-act"], subClassOf=[clinicalAct])
241 +
therapy += Class(CPR["physical-therapy"], disjointWith=[CPR["medical-therapy"]])
242 +
therapy += Class(
243 +
CPR["psychological-therapy"],
244 +
disjointWith=[CPR["medical-therapy"], CPR["physical-therapy"]],
245 +
)
246 + 247 +
medicalTherapy = Class( # noqa: N806
248 +
CPR["medical-therapy"],
249 +
disjointWith=[CPR["physical-therapy"], CPR["psychological-therapy"]],
250 +
)
251 +
therapy += medicalTherapy
252 +
medicalTherapy += Class(CPR["substance-administration"])
253 + 254 +
diagnosticAct = Class(CPR["diagnostic-act"], subClassOf=[clinicalAct]) # noqa: N806
255 +
diagnosticAct.disjointWith = [CPR["therapeutic-act"]]
256 + 257 +
screeningAct = Class(CPR["screening-act"]) # noqa: N806
258 +
screeningAct += Class(CPR["laboratory-test"])
259 + 260 +
diagnosticAct += screeningAct
261 + 262 +
screeningAct += Class(
263 +
CPR["medical-history-screening-act"],
264 +
disjointWith=[CPR["clinical-examination"], CPR["laboratory-test"]],
265 +
)
266 + 267 +
screeningAct += Class(
268 +
CPR["clinical-examination"],
269 +
disjointWith=[CPR["laboratory-test"], CPR["medical-history-screening-act"]],
270 +
)
271 + 272 +
device = Class( # noqa: F841
273 +
CPR["medical-device"], subClassOf=[Class(GALEN.Device)]
274 +
)
275 + 276 +
print(g.serialize(format="turtle"))
277 + 278 + 279 +
if __name__ == "__main__":
280 +
infixowl_example()
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4