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61 change code systems for data model #66

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merged 93 commits into from
Sep 25, 2024
+2,839 −943
Merged

61 change code systems for data model #66

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23e2778
update
aslgraefe Sep 23, 2024
c95be7f
started phenopacketpipeline dev
aslgraefe Sep 23, 2024
7356192
update
aslgraefe Sep 23, 2024
fa6e86e
added template for function
aslgraefe Sep 23, 2024
ce40d6f
update
aslgraefe Sep 23, 2024
02a4d11
updated data dictionary
aslgraefe Sep 23, 2024
1d25206
edited init for imports
aslgraefe Sep 23, 2024
04ae032
updates
aslgraefe Sep 23, 2024
652d1fb
defined todos for phenoapcket pipeline
aslgraefe Sep 23, 2024
5aa455f
old test del
aslgraefe Sep 23, 2024
28ff69b
uncommented codesystems for test
aslgraefe Sep 23, 2024
0194966
edited import for resources
aslgraefe Sep 23, 2024
ad80f45
updated code systems . py with only versions
aslgraefe Sep 23, 2024
3669fd9
fixed bugs and added all column mappings
aslgraefe Sep 23, 2024
9b80550
added todo for preproccess redcap for phenopacket pipeline function
aslgraefe Sep 23, 2024
227ca62
typo
aslgraefe Sep 23, 2024
33787fd
fix init
aslgraefe Sep 23, 2024
8c7f9e1
fixed snomed import
aslgraefe Sep 23, 2024
0a4461b
fixed snomed_ct
aslgraefe Sep 23, 2024
5e6e8d2
fixed smomed ct
aslgraefe Sep 23, 2024
eeece88
added imports
aslgraefe Sep 23, 2024
7ac07ed
fixed import
aslgraefe Sep 23, 2024
d907c3d
fix def phenopacket pipeline
aslgraefe Sep 23, 2024
fe8a0fe
fiox
aslgraefe Sep 23, 2024
84555f2
typos
aslgraefe Sep 23, 2024
5732233
fix
aslgraefe Sep 23, 2024
a29c0e8
fix
aslgraefe Sep 23, 2024
c27d044
fix testing
aslgraefe Sep 23, 2024
a26fd09
updated copryright and authors
aslgraefe Sep 24, 2024
da4ee09
import rarelink cdm
aslgraefe Sep 24, 2024
6fe1d6d
added repetition of sections for data model
aslgraefe Sep 24, 2024
8520a59
fixed patient status not repetitive
aslgraefe Sep 24, 2024
033c242
update lining fix
aslgraefe Sep 24, 2024
b1ed9f4
fixed gene label
aslgraefe Sep 24, 2024
74a4626
added gene label vs
aslgraefe Sep 24, 2024
934dc0c
updated mapping
aslgraefe Sep 24, 2024
39b2572
new version phenopacket mapper
aslgraefe Sep 24, 2024
0adb25d
update pipeline
aslgraefe Sep 24, 2024
e55b3d4
fix indentation
aslgraefe Sep 24, 2024
d0e8ea3
fixed cdm repeating elements
aslgraefe Sep 24, 2024
988058f
edited disease single ones
aslgraefe Sep 24, 2024
f6273fe
updated genomic diagnosis double
aslgraefe Sep 24, 2024
576d700
addded repeating modifiers
aslgraefe Sep 24, 2024
eedf61e
added repeating to pipeline
aslgraefe Sep 24, 2024
9b5a31c
import s
aslgraefe Sep 24, 2024
fe12bef
fix
aslgraefe Sep 24, 2024
60373bc
fix
aslgraefe Sep 24, 2024
10e119c
updated pipeline
aslgraefe Sep 24, 2024
2e07306
update pipeline
aslgraefe Sep 24, 2024
d2f64a1
update init
aslgraefe Sep 24, 2024
cf82177
renamed file
aslgraefe Sep 24, 2024
c9bce58
updated import
aslgraefe Sep 24, 2024
9fd52c7
updated preprocessing value sets
aslgraefe Sep 24, 2024
2f3d7b9
updated name
aslgraefe Sep 24, 2024
53a7a7c
commented out
aslgraefe Sep 24, 2024
989be79
added TODO in pipeliine
aslgraefe Sep 24, 2024
610f118
added another TODO
aslgraefe Sep 24, 2024
c4e13b8
import phenopackets and fix
aslgraefe Sep 25, 2024
07328ea
updated diseasses and ph features
aslgraefe Sep 25, 2024
d64ba09
uncommenteed for now
aslgraefe Sep 25, 2024
11c3323
update zygosity function
aslgraefe Sep 25, 2024
dfe3e56
added functions and import
aslgraefe Sep 25, 2024
00713dc
updates
aslgraefe Sep 25, 2024
6a6defd
addedd class multiple_fields
aslgraefe Sep 25, 2024
db1e469
added multiple field sclass
aslgraefe Sep 25, 2024
b629ce6
added rarelink_cdm_phenopacket_mapping function
aslgraefe Sep 25, 2024
b34ea91
update
aslgraefe Sep 25, 2024
5dc8ac9
edits
aslgraefe Sep 25, 2024
11d7ce6
edit
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edit
aslgraefe Sep 25, 2024
57aa8e2
fix
aslgraefe Sep 25, 2024
b731582
edot
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edit
aslgraefe Sep 25, 2024
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aslgraefe Sep 25, 2024
aca4ed1
fix
aslgraefe Sep 25, 2024
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fix
aslgraefe Sep 25, 2024
c16751d
fixes
aslgraefe Sep 25, 2024
0a8f4b8
fix
aslgraefe Sep 25, 2024
8b1b060
fix
aslgraefe Sep 25, 2024
0fa330a
fix
aslgraefe Sep 25, 2024
f219fa2
clean up
aslgraefe Sep 25, 2024
7563964
change function
aslgraefe Sep 25, 2024
9c4c607
fix
aslgraefe Sep 25, 2024
91de67b
changed name back
aslgraefe Sep 25, 2024
f182335
fix
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05d7b3a
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3d43852
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af7a6a0
try
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fix
aslgraefe Sep 25, 2024
bb0e950
updates
aslgraefe Sep 25, 2024
e00dcbc
added and edited 5 test patients
aslgraefe Sep 25, 2024
2ed3a94
updated test data
aslgraefe Sep 25, 2024
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fixed smomed ct
@aslgraefe
aslgraefe committed Sep 23, 2024
commit 5e6e8d2e512edd2ad1c859ba17ae449867c48f27
206 changes: 103 additions & 103 deletions src/rarelink/rarelink_cdm/rarelink_cdm_vs.py
View file
Original file line number Diff line number Diff line change
@@ -31,14 +31,14 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 2.2 Sex at Birth
vs_2_2 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="248152002",
Coding(system=res.SNOMED_CT, code="248152002",
display="Female"),
Coding(system=res.SNOMED, code="248153007", display="Male"),
Coding(system=res.SNOMED, code="184115007",
Coding(system=res.SNOMED_CT, code="248153007", display="Male"),
Coding(system=res.SNOMED_CT, code="184115007",
display="Patient sex unknown"),
Coding(system=res.SNOMED, code="32570691000036108",
Coding(system=res.SNOMED_CT, code="32570691000036108",
display="Intersex"),
Coding(system=res.SNOMED, code="1220561009",
Coding(system=res.SNOMED_CT, code="1220561009",
display="Not recorded")
],
name="Value set for 2.2 Sex at Birth",
@@ -48,18 +48,18 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 2.3 Karyotypic Sex
vs_2_3 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="261665006",
Coding(system=res.SNOMED_CT, code="261665006",
display="Unknown"),
Coding(system=res.SNOMED, code="734875008", display="XX"),
Coding(system=res.SNOMED, code="734876009", display="XY"),
Coding(system=res.SNOMED, code="80427008", display="X0"),
Coding(system=res.SNOMED, code="65162001", display="XXY"),
Coding(system=res.SNOMED, code="35111009", display="XXX"),
Coding(system=res.SNOMED, code="403760006", display="XXYY"),
Coding(system=res.SNOMED, code="78317008", display="XXXY"),
Coding(system=res.SNOMED, code="10567003", display="XXXX"),
Coding(system=res.SNOMED, code="48930007", display="XYY"),
Coding(system=res.SNOMED, code="74964007", display="Other")
Coding(system=res.SNOMED_CT, code="734875008", display="XX"),
Coding(system=res.SNOMED_CT, code="734876009", display="XY"),
Coding(system=res.SNOMED_CT, code="80427008", display="X0"),
Coding(system=res.SNOMED_CT, code="65162001", display="XXY"),
Coding(system=res.SNOMED_CT, code="35111009", display="XXX"),
Coding(system=res.SNOMED_CT, code="403760006", display="XXYY"),
Coding(system=res.SNOMED_CT, code="78317008", display="XXXY"),
Coding(system=res.SNOMED_CT, code="10567003", display="XXXX"),
Coding(system=res.SNOMED_CT, code="48930007", display="XYY"),
Coding(system=res.SNOMED_CT, code="74964007", display="Other")
],
name="Value set for 2.3 Karyotypic Sex",
description=("The chromosomal sex of an individual.")
@@ -68,15 +68,15 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 2.4 Gender Identity
vs_2_4 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="446141000124107",
Coding(system=res.SNOMED_CT, code="446141000124107",
display="Female gender identity"),
Coding(system=res.SNOMED, code="446151000124109",
Coding(system=res.SNOMED_CT, code="446151000124109",
display="Male gender identity"),
Coding(system=res.SNOMED, code="394743007",
Coding(system=res.SNOMED_CT, code="394743007",
display="Gender unknown"),
Coding(system=res.SNOMED, code="33791000087105",
Coding(system=res.SNOMED_CT, code="33791000087105",
display="Identifies as nonbinary gender"),
Coding(system=res.SNOMED, code="1220561009",
Coding(system=res.SNOMED_CT, code="1220561009",
display="Not recorded")
],
name="Value set for 2.4 Gender Identity",
@@ -95,13 +95,13 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 3.1 Vital Status
vs_3_1 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="438949009", display="Alive"),
Coding(system=res.SNOMED, code="419099009", display="Dead"),
Coding(system=res.SNOMED, code="399307001",
Coding(system=res.SNOMED_CT, code="438949009", display="Alive"),
Coding(system=res.SNOMED_CT, code="419099009", display="Dead"),
Coding(system=res.SNOMED_CT, code="399307001",
display="Unknown - Lost in follow-up"),
Coding(system=res.SNOMED, code="185924006",
Coding(system=res.SNOMED_CT, code="185924006",
display="Unknown - Opted-out"),
Coding(system=res.SNOMED, code="261665006",
Coding(system=res.SNOMED_CT, code="261665006",
display="Unknown - Other Reason")
],
name="Value set for 3.1 Vital Status",
@@ -128,19 +128,19 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 3.4 Age Category
vs_3_4 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="3658006", display="Infancy"),
Coding(system=res.SNOMED, code="713153009",
Coding(system=res.SNOMED_CT, code="3658006", display="Infancy"),
Coding(system=res.SNOMED_CT, code="713153009",
display="Toddler"),
Coding(system=res.SNOMED, code="255398004",
Coding(system=res.SNOMED_CT, code="255398004",
display="Childhood"),
Coding(system=res.SNOMED, code="263659003",
Coding(system=res.SNOMED_CT, code="263659003",
display="Adolescence"),
Coding(system=res.SNOMED, code="41847000",
Coding(system=res.SNOMED_CT, code="41847000",
display="Adulthood"),
Coding(system=res.SNOMED, code="303112003",
Coding(system=res.SNOMED_CT, code="303112003",
display="Fetal period"),
Coding(system=res.SNOMED, code="419099009", display="Dead"),
Coding(system=res.SNOMED, code="261665006",
Coding(system=res.SNOMED_CT, code="419099009", display="Dead"),
Coding(system=res.SNOMED_CT, code="261665006",
display="Unknown")
],
name="Value set for 3.4 Age Category",
@@ -157,8 +157,8 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 3.6 Undiagnosed RD Case
vs_3_6 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="373066001", display="Yes"),
Coding(system=res.SNOMED, code="373067005", display="No")
Coding(system=res.SNOMED_CT, code="373066001", display="Yes"),
Coding(system=res.SNOMED_CT, code="373067005", display="No")
],
name="Value set for 3.6 Undiagnosed RD Case",
description=("Identifies cases where an RD diagnosis has not been established.")
@@ -218,7 +218,7 @@ class RareLink_CDM_v2_0_0_ValueSets:
Coding(system=res.HL7FHIR, code="hh", display="Home Health"),
Coding(system=res.HL7FHIR, code="rdc",
display="RD Specialist Center"),
Coding(system=res.SNOMED, code="261665006", display="Unknown")
Coding(system=res.SNOMED_CT, code="261665006", display="Unknown")
],
name="Value set for 4.4 Encounter Class",
description=("The class of an encounter of the individual at the time of "
@@ -258,11 +258,11 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 5.3 Age at Onset
vs_5_3 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="118189007",
Coding(system=res.SNOMED_CT, code="118189007",
display="Prenatal"),
Coding(system=res.SNOMED, code="3950001", display="Birth"),
Coding(system=res.SNOMED, code="410672004", display="Date"),
Coding(system=res.SNOMED, code="261665006", display="Unknown")
Coding(system=res.SNOMED_CT, code="3950001", display="Birth"),
Coding(system=res.SNOMED_CT, code="410672004", display="Date"),
Coding(system=res.SNOMED_CT, code="261665006", display="Unknown")
],
name="Value set for 5.3 Age at Onset",
description=("The age at the onset of the first symptoms or signs "
@@ -282,11 +282,11 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 5.5 Age at Diagnosis
vs_5_5 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="118189007",
Coding(system=res.SNOMED_CT, code="118189007",
display="Prenatal"),
Coding(system=res.SNOMED, code="3950001", display="Birth"),
Coding(system=res.SNOMED, code="410672004", display="Date"),
Coding(system=res.SNOMED, code="261665006",
Coding(system=res.SNOMED_CT, code="3950001", display="Birth"),
Coding(system=res.SNOMED_CT, code="410672004", display="Date"),
Coding(system=res.SNOMED_CT, code="261665006",
display="Unknown")
],
name="Value set for 5.5 Age at Diagnosis",
@@ -301,10 +301,10 @@ class RareLink_CDM_v2_0_0_ValueSets:
"day of the month or the 1st month of the year, respectively.")
)

# 5.7 Body Site [SNOMED CT]
# 5.7 Body Site [SNOMED_CT CT]
vs_5_7 = ValueSet(
elements=[res.SNOMED],
name="Value set for 5.7 Body Site [SNOMED CT]",
elements=[res.SNOMED_CT],
name="Value set for 5.7 Body Site [SNOMED_CT CT]",
description=("The specific body site affected by disease is encoded using all "
"descendants of SCT Body Structure (123037004).")
)
@@ -332,10 +332,10 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 5.9 Severity
vs_5_9 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="24484000", display="Severe"),
Coding(system=res.SNOMED, code="6736007",
Coding(system=res.SNOMED_CT, code="24484000", display="Severe"),
Coding(system=res.SNOMED_CT, code="6736007",
display="Moderate"),
Coding(system=res.SNOMED, code="255604002", display="Mild")
Coding(system=res.SNOMED_CT, code="255604002", display="Mild")
],
name="Value set for 5.9 Severity",
description=("The severity of the disease is categorised"
@@ -653,9 +653,9 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 6.2.3 Status
vs_6_2_3 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="410605003",
Coding(system=res.SNOMED_CT, code="410605003",
display="Confirmed present"),
Coding(system=res.SNOMED, code="723511001", display="Refuted")
Coding(system=res.SNOMED_CT, code="723511001", display="Refuted")
],
name="Value set for 6.2.3 Status",
description=("The current status of the phenotypic feature, indicating "
@@ -664,7 +664,7 @@ class RareLink_CDM_v2_0_0_ValueSets:

# 6.2.4 Modifier
vs_6_2_4 = ValueSet(
elements=[res.HPO, res.NCBITaxon, res.SNOMED],
elements=[res.HPO, res.NCBITaxon, res.SNOMED_CT],
name="Value set for 6.2.4 Modifier",
description=("Further clinical modifiers to describe a specific "
"phenotypic feature, such as severity or linked\
@@ -684,13 +684,13 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 6.3.1 Propositus/-a
vs_6_3_1 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="373066001",
Coding(system=res.SNOMED_CT, code="373066001",
display="Yes"),
Coding(system=res.SNOMED, code="373067005",
Coding(system=res.SNOMED_CT, code="373067005",
display="No"),
Coding(system=res.SNOMED, code="261665006",
Coding(system=res.SNOMED_CT, code="261665006",
display="Unknown"),
Coding(system=res.SNOMED, code="1220561009",
Coding(system=res.SNOMED_CT, code="1220561009",
display="Not recorded")
],
name="Value set for 6.3.1 Propositus/-a",
@@ -703,29 +703,29 @@ class RareLink_CDM_v2_0_0_ValueSets:
# propositus/a
vs_6_3_2 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="65656005",
Coding(system=res.SNOMED_CT, code="65656005",
display="Natural mother"),
Coding(system=res.SNOMED, code="9947008",
Coding(system=res.SNOMED_CT, code="9947008",
display="Natural father"),
Coding(system=res.SNOMED, code="83420006",
Coding(system=res.SNOMED_CT, code="83420006",
display="Natural daughter"),
Coding(system=res.SNOMED, code="113160008",
Coding(system=res.SNOMED_CT, code="113160008",
display="Natural son"),
Coding(system=res.SNOMED, code="60614009",
Coding(system=res.SNOMED_CT, code="60614009",
display="Natural brother"),
Coding(system=res.SNOMED, code="73678001",
Coding(system=res.SNOMED_CT, code="73678001",
display="Natural sister"),
Coding(system=res.SNOMED, code="11286003",
Coding(system=res.SNOMED_CT, code="11286003",
display="Twin sibling"),
Coding(system=res.SNOMED, code="45929001",
Coding(system=res.SNOMED_CT, code="45929001",
display="Half-brother"),
Coding(system=res.SNOMED, code="2272004",
Coding(system=res.SNOMED_CT, code="2272004",
display="Half-sister"),
Coding(system=res.SNOMED, code="62296006",
Coding(system=res.SNOMED_CT, code="62296006",
display="Natural grandfather"),
Coding(system=res.SNOMED, code="17945006",
Coding(system=res.SNOMED_CT, code="17945006",
display="Natural grandmother"),
Coding(system=res.SNOMED, code="1220561009",
Coding(system=res.SNOMED_CT, code="1220561009",
display="Not recorded")
],
name="Value set for 6.3.2 Relationship of the individual to the "
@@ -737,13 +737,13 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 6.3.3 Consanguinity
vs_6_3_3 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="373066001",
Coding(system=res.SNOMED_CT, code="373066001",
display="Yes"),
Coding(system=res.SNOMED, code="373067005",
Coding(system=res.SNOMED_CT, code="373067005",
display="No"),
Coding(system=res.SNOMED, code="261665006",
Coding(system=res.SNOMED_CT, code="261665006",
display="Unknown"),
Coding(system=res.SNOMED, code="1220561009",
Coding(system=res.SNOMED_CT, code="1220561009",
display="Not recorded")
],
name="Value set for 6.3.3 Consanguinity",
@@ -755,29 +755,29 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 6.3.4 Family Member Relationship
vs_6_3_4 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="65656005",
Coding(system=res.SNOMED_CT, code="65656005",
display="Natural mother"),
Coding(system=res.SNOMED, code="9947008",
Coding(system=res.SNOMED_CT, code="9947008",
display="Natural father"),
Coding(system=res.SNOMED, code="83420006",
Coding(system=res.SNOMED_CT, code="83420006",
display="Natural daughter"),
Coding(system=res.SNOMED, code="113160008",
Coding(system=res.SNOMED_CT, code="113160008",
display="Natural son"),
Coding(system=res.SNOMED, code="60614009",
Coding(system=res.SNOMED_CT, code="60614009",
display="Natural brother"),
Coding(system=res.SNOMED, code="73678001",
Coding(system=res.SNOMED_CT, code="73678001",
display="Natural sister"),
Coding(system=res.SNOMED, code="11286003",
Coding(system=res.SNOMED_CT, code="11286003",
display="Twin sibling"),
Coding(system=res.SNOMED, code="45929001",
Coding(system=res.SNOMED_CT, code="45929001",
display="Half-brother"),
Coding(system=res.SNOMED, code="2272004",
Coding(system=res.SNOMED_CT, code="2272004",
display="Half-sister"),
Coding(system=res.SNOMED, code="62296006",
Coding(system=res.SNOMED_CT, code="62296006",
display="Natural grandfather"),
Coding(system=res.SNOMED, code="17945006",
Coding(system=res.SNOMED_CT, code="17945006",
display="Natural grandmother"),
Coding(system=res.SNOMED, code="1220561009",
Coding(system=res.SNOMED_CT, code="1220561009",
display="Not recorded")
],
name="Value set for 6.3.4 Family Member Relationship",
@@ -805,15 +805,15 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 6.3.6 Family Member Sex
vs_6_3_6 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="248152002",
Coding(system=res.SNOMED_CT, code="248152002",
display="Female"),
Coding(system=res.SNOMED, code="248153007",
Coding(system=res.SNOMED_CT, code="248153007",
display="Male"),
Coding(system=res.SNOMED, code="184115007",
Coding(system=res.SNOMED_CT, code="184115007",
display="Patient sex unknown"),
Coding(system=res.SNOMED, code="32570691000036108",
Coding(system=res.SNOMED_CT, code="32570691000036108",
display="Intersex"),
Coding(system=res.SNOMED, code="1220561009",
Coding(system=res.SNOMED_CT, code="1220561009",
display="Not recorded")
],
name="Value set for 6.3.6 Family Member Sex",
@@ -839,11 +839,11 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 6.3.9 Family Member Deceased
vs_6_3_9 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="373066001",
Coding(system=res.SNOMED_CT, code="373066001",
display="Yes"),
Coding(system=res.SNOMED, code="373067005",
Coding(system=res.SNOMED_CT, code="373067005",
display="No"),
Coding(system=res.SNOMED, code="261665006",
Coding(system=res.SNOMED_CT, code="261665006",
display="Unknown")
],
name="Value set for 6.3.9 Family Member Deceased",
@@ -909,9 +909,9 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 7.4 Agreement to be contacted for research purposes
vs_7_4 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="373066001", display="Yes"),
Coding(system=res.SNOMED, code="373067005", display="No"),
Coding(system=res.SNOMED, code="261665006", display="Unknown")
Coding(system=res.SNOMED_CT, code="373066001", display="Yes"),
Coding(system=res.SNOMED_CT, code="373067005", display="No"),
Coding(system=res.SNOMED_CT, code="261665006", display="Unknown")
],
name="Value set for 7.4 Agreement to be contacted for research purposes",
description=("Indicates whether the patient agrees to be contacted for "
@@ -921,9 +921,9 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 7.5 Consent to the reuse of data
vs_7_5 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="373066001", display="Yes"),
Coding(system=res.SNOMED, code="373067005", display="No"),
Coding(system=res.SNOMED, code="261665006", display="Unknown")
Coding(system=res.SNOMED_CT, code="373066001", display="Yes"),
Coding(system=res.SNOMED_CT, code="373067005", display="No"),
Coding(system=res.SNOMED_CT, code="261665006", display="Unknown")
],
name="7.5 Consent to the reuse of data",
description=("Indicates whether the patient consents to the reuse of "
@@ -933,9 +933,9 @@ class RareLink_CDM_v2_0_0_ValueSets:
# 7.6 Biological sample
vs_7_6 = ValueSet(
elements=[
Coding(system=res.SNOMED, code="373066001", display="Yes"),
Coding(system=res.SNOMED, code="373067005", display="No"),
Coding(system=res.SNOMED, code="261665006", display="Unknown")
Coding(system=res.SNOMED_CT, code="373066001", display="Yes"),
Coding(system=res.SNOMED_CT, code="373067005", display="No"),
Coding(system=res.SNOMED_CT, code="261665006", display="Unknown")
],
name="7.6 Biological sample",
description=("Indicates whether a patient's biological sample is "