Commit ae27d286 authored by jcorvi's avatar jcorvi
Browse files

Merge branch 'develop' into 'master'

Develop

See merge request !7
parents 46941991 5e2ba496
Pipeline #26290 passed with stage
in 7 seconds
......@@ -11,8 +11,8 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<maven.compiler.target>11</maven.compiler.target>
<maven.compiler.source>11</maven.compiler.source>
</properties>
<dependencies>
......
acinar hypertrophy
pharmacodynamic effects
lymphocyte depletion
\ No newline at end of file
manifestation_finding.lst:MY_ONTOLOGY:MANIFESTATION_FINDING
observation_qualification.lst:MY_ONTOLOGY:OBSERVATION_QUALIFICATION
risk_level.lst:MY_ONTOLOGY:RISK_LEVEL
sdomain.lst:MY_ONTOLOGY:STUDY_DOMAIN
findings.lst:MY_ONTOLOGY:FINDING
study_testcd.lst:MY_ONTOLOGY:STUDY_TESTCD
negation.lst:MY_ONTOLOGY:NEGATION
increase MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
increased MANUAL_E=INCREASE MANUAL_SEND_CODE=I
increasing MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
increment MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
increases MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
higher MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
high MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
moderately fast MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
decrease MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
decreases MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
decreased MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
decreasing MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
reduction MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
minimal MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
reductions MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
impaired MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
reduced MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
loss MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
losses MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
low MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
lower MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
changed MANUAL_CODE=CHANGE MANUAL_SEND_CODE=C
change MANUAL_CODE=CHANGE MANUAL_SEND_CODE=C
changes MANUAL_CODE=CHANGE MANUAL_SEND_CODE=C
modification MANUAL_CODE=CHANGE MANUAL_SEND_CODE=C
modifications MANUAL_CODE=CHANGE MANUAL_SEND_CODE=C
affected MANUAL_CODE=CHANGE MANUAL_SEND_CODE=C
impact MANUAL_CODE=CHANGE MANUAL_SEND_CODE=C
alterations MANUAL_CODE=CHANGE MANUAL_SEND_CODE=C
transitory MANUAL_CODE=TRANSITORY MANUAL_SEND_CODE=T
slight prolongation MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
prolongations MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
prolongation MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
enlarged MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
greater MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
slightly low MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
slightly less MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
slightly lower MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
significant inhibition MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
inhibited MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
exaggerated MANUAL_CODE=INCREASE MANUAL_SEND_CODE=I
small MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
retarded MANUAL_CODE=DECREASE MANUAL_SEND_CODE=D
detectable MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
present MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
observable MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
observed MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
showed MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
noticed MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
detected MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
detect MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
recognized MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
perceived MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
identified MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
indicated MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
indicate MANUAL_CODE=PRESENT MANUAL_SEND_CODE=P
\ No newline at end of file
never
neither
nobody
no
none
nor
nothing
nowhere
not
rather
without
\ No newline at end of file
transitory MANUAL_CODE=TRANSITORY MANUAL_SEND_CODE=T
reversible MANUAL_CODE=TRANSITORY MANUAL_SEND_CODE=R
\ No newline at end of file
noel MANUAL_CODE=NOEL_RISK_LEVEL MANUAL_SEND_CODE=NOEL
no observed effect level MANUAL_CODE=NOEL_RISK_LEVEL MANUAL_SEND_CODE=NOEL
no-observed-effect level MANUAL_CODE=NOEL_RISK_LEVEL MANUAL_SEND_CODE=NOEL
no-observed-effect-level MANUAL_CODE=NOEL_RISK_LEVEL MANUAL_SEND_CODE=NOEL
loel MANUAL_CODE=LOEL_RISK_LEVEL MANUAL_SEND_CODE=LOEL
lowest observed effect level MANUAL_CODE=LOEL_RISK_LEVEL MANUAL_SEND_CODE=LOEL
lowest-observed-effect level MANUAL_CODE=LOEL_RISK_LEVEL MANUAL_SEND_CODE=LOEL
lowest-observed-effect-level MANUAL_CODE=LOEL_RISK_LEVEL MANUAL_SEND_CODE=LOEL
noael MANUAL_CODE=NOAEL_RISK_LEVEL MANUAL_SEND_CODE=NOAEL
no observed adverse effect level MANUAL_CODE=NOAEL_RISK_LEVEL MANUAL_SEND_CODE=NOAEL
no-observed-adverse-effect level MANUAL_CODE=NOAEL_RISK_LEVEL MANUAL_SEND_CODE=NOAEL
no-observed-adverse-effect-level MANUAL_CODE=NOAEL_RISK_LEVEL MANUAL_SEND_CODE=NOAEL
loael MANUAL_CODE=LOAEL_RISK_LEVEL MANUAL_SEND_CODE=LOAEL
lowest observed adverse effect level MANUAL_CODE=LOAEL_RISK_LEVEL MANUAL_SEND_CODE=LOAEL
lowest-observed-adverse-effect level MANUAL_CODE=LOAEL_RISK_LEVEL MANUAL_SEND_CODE=LOAEL
lowest-observed-adverse-effect-level MANUAL_CODE=LOAEL_RISK_LEVEL MANUAL_SEND_CODE=LOAEL
lowest concentration MANUAL_CODE=LOAEL_RISK_LEVEL MANUAL_SEND_CODE=LOAEL
\ No newline at end of file
depression in body weight gain MANUAL_SEND_DOMAIN_CODE=BG MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95083
clinical MANUAL_SEND_DOMAIN_CODE=CL MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95086
clinical study MANUAL_SEND_DOMAIN_CODE=CL MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95086
clinical findings MANUAL_SEND_DOMAIN_CODE=CL MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95086
clinical observations MANUAL_SEND_DOMAIN_CODE=CL MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95086
general observation MANUAL_SEND_DOMAIN_CODE=CL MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95086
cardiovascular MANUAL_SEND_DOMAIN_CODE=CV MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C102605
heart condition MANUAL_SEND_DOMAIN_CODE=CV MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C102605
cardiovascular function MANUAL_SEND_DOMAIN_CODE=CV MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C102605
cardiovascular system MANUAL_SEND_DOMAIN_CODE=CV MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C102605
heart disease MANUAL_SEND_DOMAIN_CODE=CV MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C102605
cardiology MANUAL_SEND_DOMAIN_CODE=CV MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C102605
cardiovascular abnormality MANUAL_SEND_DOMAIN_CODE=CV MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C102605
cardiac muscle MANUAL_SEND_DOMAIN_CODE=CV MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C102605
cardiac MANUAL_SEND_DOMAIN_CODE=CV MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C102605
cardiotoxicity MANUAL_SEND_DOMAIN_CODE=CV MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C102605
macroscopic findings MANUAL_SEND_DOMAIN_CODE=MA MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95094
macroscopic examinations MANUAL_SEND_DOMAIN_CODE=MA MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95094
macroscopic examination MANUAL_SEND_DOMAIN_CODE=MA MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95094
macroscopic MANUAL_SEND_DOMAIN_CODE=MA MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95094
macroscopical MANUAL_SEND_DOMAIN_CODE=MA MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95094
macroscopical findings MANUAL_SEND_DOMAIN_CODE=MA MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95094
macroscopical examinations MANUAL_SEND_DOMAIN_CODE=MA MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95094
macroscopical examination MANUAL_SEND_DOMAIN_CODE=MA MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95094
microscopic findings MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
macroscopically MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
microscopic examination MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
microscopic examinations MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
microscopic MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
microscopical MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
microscopical findings MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
microscopical examination MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histopathology examination MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histopathology examination MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histopathology finding MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histopathology findings MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histological findings MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histologic findings MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histologic MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histopathology MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histological MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histopathological MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histopathologic findings MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
histomorphological MANUAL_SEND_DOMAIN_CODE=MI MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95095
organ measurement MANUAL_SEND_DOMAIN_CODE=OM MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49605
organ-measurement MANUAL_SEND_DOMAIN_CODE=OM MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49605
organ weights MANUAL_SEND_DOMAIN_CODE=OM MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49605
organ weight MANUAL_SEND_DOMAIN_CODE=OM MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49605
pharmacokinetics MANUAL_SEND_DOMAIN_CODE=PP MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49607
pharmacological medicine MANUAL_SEND_DOMAIN_CODE=PP MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49607
pharmacology MANUAL_SEND_DOMAIN_CODE=PP MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49607
tumor finding MANUAL_SEND_DOMAIN_CODE=TF MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95100
tumor MANUAL_SEND_DOMAIN_CODE=TF MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95100
cancerous growth MANUAL_SEND_DOMAIN_CODE=TF MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95100
malignant growth MANUAL_SEND_DOMAIN_CODE=TF MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95100
cancer MANUAL_SEND_DOMAIN_CODE=TF MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95100
tumefaction MANUAL_SEND_DOMAIN_CODE=TF MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95100
sarcoma MANUAL_SEND_DOMAIN_CODE=TF MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95100
carcinoma MANUAL_SEND_DOMAIN_CODE=TF MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95100
neoplasm MANUAL_SEND_DOMAIN_CODE=TF MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95100
tumor examination MANUAL_SEND_DOMAIN_CODE=TF MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95100
respiratory findings MANUAL_SEND_DOMAIN_CODE=RE MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95098
respiratory examination MANUAL_SEND_DOMAIN_CODE=RE MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95098
respiratory inspection MANUAL_SEND_DOMAIN_CODE=RE MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95098
respiratory system MANUAL_SEND_DOMAIN_CODE=RE MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95098
pulmonary system MANUAL_SEND_DOMAIN_CODE=RE MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95098
pulmonary examination MANUAL_SEND_DOMAIN_CODE=RE MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95098
pulmonary inspection MANUAL_SEND_DOMAIN_CODE=RE MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95098
cause of death MANUAL_SEND_DOMAIN_CODE=DD MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95087
death diagnosis MANUAL_SEND_DOMAIN_CODE=DD MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95087
necrosis MANUAL_SEND_DOMAIN_CODE=DD MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95087
necrosis diagnosis MANUAL_SEND_DOMAIN_CODE=DD MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95087
cause of necrosis MANUAL_SEND_DOMAIN_CODE=DD MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95087
necropsy findings MANUAL_SEND_DOMAIN_CODE=DD MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95087
necropsy finding MANUAL_SEND_DOMAIN_CODE=DD MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95087
necropsy MANUAL_SEND_DOMAIN_CODE=DD MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95087
dead details MANUAL_SEND_DOMAIN_CODE=DD MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95087
death diagnosis MANUAL_SEND_DOMAIN_CODE=DD MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95087
drinking MANUAL_SEND_DOMAIN_CODE=FW MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95090
consumption MANUAL_SEND_DOMAIN_CODE=FW MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C95090
ecg MANUAL_SEND_DOMAIN_CODE=EG MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49626
electrocardiographic MANUAL_SEND_DOMAIN_CODE=EG MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49626
laboratory findings MANUAL_SEND_DOMAIN_CODE=LB MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49592
vital signs MANUAL_SEND_DOMAIN_CODE=VS MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C111113 MANUAL_SEND_DOMAIN_ID=C49622
\ No newline at end of file
weights MANUAL_SEND_DOMAIN_CODE=OM CDISC_SEND_CODE=WEIGHT MANUAL_CODELIST=OMTESTCD MANUAL_CODELIST_ID=C25208 MANUAL_SEND_CODE_ID=C89977
body weight MANUAL_SEND_DOMAIN_CODE=BW CDISC_SEND_CODE=BW MANUAL_CODELIST=BWTESTCD MANUAL_CODELIST_ID=C89962 MANUAL_SEND_CODE_ID=C81328
body mass MANUAL_SEND_DOMAIN_CODE=BW CDISC_SEND_CODE=BW MANUAL_CODELIST=BWTESTCD MANUAL_CODELIST_ID=C89962 MANUAL_SEND_CODE_ID=C81328
body weight MANUAL_SEND_DOMAIN_CODE=BW CDISC_SEND_CODE=BW MANUAL_CODELIST=BWTESTCD MANUAL_CODELIST_ID=C89962 MANUAL_SEND_CODE_ID=C81328
body weights MANUAL_SEND_DOMAIN_CODE=BW CDISC_SEND_CODE=BW MANUAL_CODELIST=BWTESTCD MANUAL_CODELIST_ID=C89962 MANUAL_SEND_CODE_ID=C81328
body-weight MANUAL_SEND_DOMAIN_CODE=BW CDISC_SEND_CODE=BW MANUAL_CODELIST=BWTESTCD MANUAL_CODELIST_ID=C89962 MANUAL_SEND_CODE_ID=C81328
body heaviness MANUAL_SEND_DOMAIN_CODE=BW CDISC_SEND_CODE=BW MANUAL_CODELIST=BWTESTCD MANUAL_CODELIST_ID=C89962 MANUAL_SEND_CODE_ID=C81328
body density MANUAL_SEND_DOMAIN_CODE=BW CDISC_SEND_CODE=BW MANUAL_CODELIST=BWTESTCD MANUAL_CODELIST_ID=C89962 MANUAL_SEND_CODE_ID=C81328
body weight gain MANUAL_SEND_DOMAIN_CODE=BG CDISC_SEND_CODE=BWGAIN MANUAL_CODELIST=BGTESTCD MANUAL_CODELIST_ID=C89960 MANUAL_SEND_CODE_ID=C62754
body-weight-gain MANUAL_SEND_DOMAIN_CODE=BG CDISC_SEND_CODE=BWGAIN MANUAL_CODELIST=BGTESTCD MANUAL_CODELIST_ID=C89960 MANUAL_SEND_CODE_ID=C62754
food consumption MANUAL_SEND_DOMAIN_CODE=FW CDISC_SEND_CODE=FC MANUAL_CODELIST=FWTESTCD MANUAL_CODELIST_ID=C89970 MANUAL_SEND_CODE_ID=C90384
water consumption MANUAL_SEND_DOMAIN_CODE=FW CDISC_SEND_CODE=WC MANUAL_CODELIST=FWTESTCD MANUAL_CODELIST_ID=C89970 MANUAL_SEND_CODE_ID=C90484
food intake MANUAL_SEND_DOMAIN_CODE=FW CDISC_SEND_CODE=FC MANUAL_CODELIST=FWTESTCD MANUAL_CODELIST_ID=C89970 MANUAL_SEND_CODE_ID=C90384
water intake MANUAL_SEND_DOMAIN_CODE=FW CDISC_SEND_CODE=WC MANUAL_CODELIST=FWTESTCD MANUAL_CODELIST_ID=C89970 MANUAL_SEND_CODE_ID=C95090
food and water consumption MANUAL_SEND_DOMAIN_CODE=FW CDISC_SEND_CODE=FC FWTESTCD=SDOMAIN MANUAL_CODELIST_ID=C89970 MANUAL_SEND_CODE_ID=C90384
food or water consumption MANUAL_SEND_DOMAIN_CODE=FW CDISC_SEND_CODE=FC MANUAL_CODELIST=FWTESTCD MANUAL_CODELIST_ID=C89970 MANUAL_SEND_CODE_ID=C90384
food and water intake MANUAL_SEND_DOMAIN_CODE=FW CDISC_SEND_CODE=FC MANUAL_CODELIST=FWTESTCD MANUAL_CODELIST_ID=C89970 MANUAL_SEND_CODE_ID=C90384
food or water intake MANUAL_SEND_DOMAIN_CODE=FW CDISC_SEND_CODE=FC MANUAL_CODELIST=FWTESTCD MANUAL_CODELIST_ID=C89970 MANUAL_SEND_CODE_ID=C90384
feed intake MANUAL_SEND_DOMAIN_CODE=FW CDISC_SEND_CODE=FC MANUAL_CODELIST=SDOMAIN MANUAL_CODELIST_ID=C89970 MANUAL_SEND_CODE_ID=C90384
feed consumption MANUAL_SEND_DOMAIN_CODE=FW CDISC_SEND_CODE=FC MANUAL_CODELIST=FWTESTCD MANUAL_CODELIST_ID=C89970 MANUAL_SEND_CODE_ID=C90384
exposures MANUAL_SEND_DOMAIN_CODE=PP CDISC_SEND_CODE=PKPARM:2000315 MANUAL_CODELIST=PKPARM MANUAL_CODELIST_ID=C85493 MANUAL_SEND_CODE_ID=PKPARM:2000315
overall weight gain MANUAL_SEND_DOMAIN_CODE=BG CDISC_SEND_CODE=BWGAIN MANUAL_CODELIST=BGTESTCD MANUAL_CODELIST_ID=C89960 MANUAL_SEND_CODE_ID=C62754
\ No newline at end of file
Imports: {
import static gate.Utils.*;
}
Phase:firstphase
Input: Lookup
Options: control = appelt
Rule: basic_mapp
(
{Lookup.majorType=="MY_ONTOLOGY"}
)
:lookup
-->
{
gate.AnnotationSet lookup = (gate.AnnotationSet) bindings.get("lookup");
gate.Annotation ann = (gate.Annotation) lookup.iterator().next();
String content = stringFor(doc, ann);
FeatureMap lookupFeatures = ann.getFeatures();
gate.FeatureMap features = Factory.newFeatureMap();
lookupFeatures.remove("majorType");
features.put("SOURCE","MY_ONTOLOGY");
features.put("text",content);
String minorType = lookupFeatures.get("minorType").toString();
lookupFeatures.remove("minorType");
features.putAll(lookupFeatures);
gate.AnnotationSet tokens = outputAS.get("Token", ann.getStartNode().getOffset(), ann.getEndNode().getOffset());
List<Annotation> tokensList = new ArrayList<Annotation>(tokens);
Collections.sort(tokensList, new gate.util.OffsetComparator());
String lemma = "";
String original_lemma = "";
for (Annotation token : tokensList) {
lemma = lemma + " " + token.getFeatures().get("root").toString();
original_lemma = original_lemma + " " + token.getFeatures().get("original_root").toString();
}
features.put("original_lemma",original_lemma.trim());
features.put("lemma",lemma.trim().toLowerCase());
try{
outputAS.add(lookup.firstNode().getOffset(),lookup.lastNode().getOffset(), minorType, features);
}catch(InvalidOffsetException e){
throw new LuckyException(e);
}
//remove old lookup
inputAS.remove(ann);
}
\ No newline at end of file
Phase:secondphase
Input: Lookup
Options: control = all
Rule: delete_rule
(
{Lookup}
)
:lookup
-->
{
gate.AnnotationSet lookup = (gate.AnnotationSet) bindings.get("lookup");
gate.Annotation ann = (gate.Annotation) lookup.iterator().next();
inputAS.remove(ann);
}
\ No newline at end of file
MultiPhase: Main
Phases:
basic_mapping
remove_false_negation
delete_lookups
\ No newline at end of file
Imports: {
import static gate.Utils.*;
}
Phase:secondphase
Input: Token
Options: control = all
Rule: removeStopwords
(
{Token.word=="no."} | ({Token.word=="no"} {Token.kind=="NUMBER"})
) :stop
-->
{
System.out.println("Negation erronea");
gate.AnnotationSet lookup = (gate.AnnotationSet) bindings.get("stop");
System.out.println(lookup);
AnnotationSet negation = inputAS.get("NEGATION", lookup.iterator().next().getStartNode().getOffset(), lookup.iterator().next().getEndNode().getOffset());
if(negation.size()>0){
try{
outputAS.remove(negation.iterator().next());
} catch(Exception e){
System.out.println("error removing " + negation + " error : " + e);
}
}
}
\ No newline at end of file
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