UML

Table

Parameter Name

Parameter Type

Code System / Value Set or Pattern

Multiplicity

Comments

Questions

JSON Object/Attribute Mapping

"application/json"

Mapping

ExomAG / HGQN Data Model

1

2

Patient

patient

3

ID

ID-String

Pseudonym ID

1

patient.id

4

Gender

Coding:

Code

Administrative Gender:

Code	Display
male	Männlich
female	Weiblich
other	Divers
unknown	Unbekannt

1

patient.gender

Case.sex

5

Birthdate

YearMonth

yyyy-MM

1

Age (in years|months) will be computed by the application for display

patient.birthDate

Case.dateOfBirth

6

Date Of Death

Date

0...1

7

Municipality Code

String

1

8

Site

Coding:

Code

DNPM Site-ID

(Submitter)

0...1

Will be set by DNPM:DIP system upon import of a data set

patient.managingSite

9

10

Patient

Reference[Patient]

1

11

TODO

12

13

14

Episode Of Care

Behandlungs-Episode/-Fall

case

15

ID

ID-String

1

case.id

Case.internalCaseID

16

Custodian / Managing Org.

ID-String

Organization ID

1

17

Transfer TAN

ID-String

Transfer TAN "Modellvorhaben" (TVN)

1

18

Period

Period (Start and (optional) end date)

Datum des ersten Kontakts/Überweisung an das ZSE

1

19

20

Diagnosis

diagnosis

21

ID

ID-String

1

diagnosis.id

22

Patient

Reference[Patient]

1

diagnosis.patient

23

Onset Age

Quantity:

value + unit

time unit: Months or Years

0...1

diagnosis.onsetAge

Case.ageIn{Months|Years}

24

(Genetic) Verification Status

Coding

Code	Display
unsolved	Keine genetische Diagnosestellung
unclear	Genetische Verdachtsdiagnose
solved	Genetische Diagnose gesichert
partially-solved	Klinischer Phänotyp nur partiell gelöst

25

Disease Category / Type

Coding:

Code + System (+ Version?)

Orphanet Rare Disease Ontology (ORDO)

or

ICD-10-GM

or

OMIM

1...N

OMIM: Licensing to clarify

diagnosis.categories

Case.diseaseCategory

26

27

Hospitalization

28

Period

Period (Start and (optional) end date)

0...1

29

Duration

Duration [Days]

1

30

31

HPO-Term

Object entry in Array hpoTerms

32

ID

ID-String

1

hpoTerms[n].id

33

Patient

Reference[Patient]

1

hpoTerms[n].patient

34

Onset Date

YearMonth

1

35

Status History

Status

0...N

36

Value

Coding:

Code

Human Phenotype Ontology

1

hpoTerms[n].value

Case.hpoTerms (respective value)

37

Status

38

Status

Coding

Code	Display
improved	Verbessert
worsened	Verschlechtert
resolved	Weggefallen

39

Date

40

41

Observation: GMFCS

42

ID

ID-String

1

43

Patient

Reference[Patient]

1

44

Date

1

45

Value

Coding:

Code

Gross Motor Function Classification System

Code	Display
I	Level I
II	Level II
III	Level III
IV	Level IV
V	Level V

1

46

47

Lab

48

ID

ID-String

1

Do we really need to model this in DNPM:DIP? What value does this information add?

Lab.labID

49

Name

String

1

Lab.label

50

NGS Report

Object entry in Array ngsReports

51

ID

ID-String

1

ngsReports[n].id

52

Sequencing Lab

Reference[Lab]

1

Do we really need to model this in DNPM:DIP? What value does this information add?

ngsReports[n].performingLab

Case.sequencingLabID

53

Date

0...1

ngsReports[n].recordedOn

Base.befunddatum

54

Type

Coding:

Code

Code	Display
panel	Panel
exome	Exome
genome-short-read	Genome short-read
genome-long-read	Genome long-read

1

ngsReports[n].sequencingType

Case.testConducted

55

Family Controls

Coding: Code

Family control level/depth

Code	Display
single	single
duo	duo
trio	trio
>3	>3

1

familyControls

Case.singleDuoTrio

56

Sequencing Info

Object: Sequencing Info

1

ngsReports[n].metaInfo

Case.wetlabMetaInfo

57

Autozygosity

Observation: Autozygosity

0...1

ngsReports[n].autozygosity

58

Variants

Observation: Variant

0...N

ngsReports[n].variants

59

Sequencing Info

60

Platform

Coding

Code	Display
illu	Illumina
ont	ONT
10xg	10X Genomics
pacb	PacBio
mgi	MGI
ug	Ultima Genomics
other	Other

1

61

Kit

String

1

62

Observation: Autozygosity

63

ID

ID-String

1

ngsReports[n].autozygosity.id

64

Patient

Reference[Patient]

1

ngsReports[n].autozygosity.patient

65

Value

Float

Range: 0 - 1

1

DEFINITION ???

ngsReports[n].autozygosity.value

Case.autozygosity

66

Observation: Variant (Base class)

67

ID

ID-String

1

ngsReports[n].variants[m].id

68

Patient

Reference[Patient]

1

ngsReports[n].variants[m].id

69

Gene(s)

Coding: Code

HGNC:ID

0...N

System will resolve the gene symbol from HGNC gene set for use as display

ngsReports[n].variants[m].genes

70

Localization

Coding

Code	Display
coding-region	Coding Region
splicing-region	Splicing Region
regulatory-region	Regulatory Region
intronic	Intronic
intergenic	Intergenic

0...N

71

gDNA Change

Coding: Code

ngsReports[n].variants[m].gDNAChange

72

cDNA Change

Coding: Code

ngsReports[n].variants[m].cDNAChange

73

Protein change

Coding: Code

ngsReports[n].variants[m].proteinChange

74

ACMG Class

Code	Display
1	Benign
2	Likely benign
3	Uncertain significance
4	Likely pathogenic
5	Pathogenic

0...1

ngsReports[n].variants[m].acmgClass

75

ACMG Criteria

Object: ACMG Criterion

0...N

ngsReports[n].variants[m].acmgCriteria

76

Zygosity

Coding: Code

Code	Display
heterozygous	Heterozygous
homozygous	Homozygous
comp-het	Compound heterozygous
hemi	Hemizygous
homoplasmic	Homoplasmic
heteroplasmic	Heteroplasmic

0...1

ngsReports[n].variants[m].zygosity

77

Segregation Analysis

Coding: Code

Code	Display
not-performed	not performed
de-novo	de-novo
from-father	Transmitted from father
from-mother	Transmitted from mother

0...1

ngsReports[n].variants[m].segregationAnalysis

78

Mode of inheritance

Coding: Code

Code	Display
dominant	Dominant
recessive	Recessive
X-linked	X-linked
mitochondrial	Mitochondrial
unclear	Unclear

0...1

ngsReports[n].variants[m].modeOfInheritance

79

Significance for case

Code	Display
primary	Variant in context of patient's disease
incidental	Incidental finding
candidate	Candidate variant

0...1

ngsReports[n].variants[m].significance

80

ClinVar ID

External ID [ClinVar]

ClinVar variant ID

0...1

81

Publications

Reference[Publication]

PubMed ID (or DOI?)

0...N

82

Object: ACMG Criterion

83

Value

Coding: Code

ACMG Criteria

Code	Display
PVS1
PS1
PS2
PS3
PS4
PM1
PM2
PM3
PM4
PM5
PM6
PP1
PP2
PP3
PP4
PP5
BA1
BS1
BS2
BS3
BS4
BP1
BP2
BP3
BP4
BP5
BP6
BP7

1

84

Modifier

Coding: Code

Code	Display
pvs	very strong pathogenic
ps	strong pathogenic
pm	medium pathogenic
pp	supporting pathogenic
ba	stand-alone benign
bs	strong benign
bp	supporting benign
bm	medium benign

0...1

85

86

Structural Variant (SV): Variant

Object entry in Array ngsReports[n].variants

87

ISCN Description

Coding: Code

ISCN Description

0...1

ngsReports[n].variants[m].iscnDescription

-

88

89

Small Variant: Variant

SNVs and small indels

90

Chromosome

Coding: Code

Code: { chr1 - chr22, chrX, chrY, chrMT }

1

91

Position

Int

GRCh38 coordinates in VCF-style

1

92

Ref

String

ref sequence in VCF-style

1

93

Alt

String

alternative/observed sequence in VCF-style

1

94

95

Copy Number Variant (CNV): Variant

96

Chromosome

Coding: Code

Code: { chr1 - chr22, chrX, chrY, chrMT }

1

97

Start Position

Int

GRCh38 coordinate

1

98

End Position

Int

GRCh38 coordinate

1

99

Type

Coding: Code

CNV Type

Code	Display
gain	Gain
loss	Loss

1

100

101

Care Plan

102

ID

ID-String

1

103

Patient

Reference[Patient]

1

104

Recording Date

Date

1

105

Sequencing Requested

Boolean

0...1

106

Therapy Recommendations

Object: Therapy Recommendation

0...N

107

Study Enrollment Recommendation

Object: Study Enrollment Recommendation

0...1

108

Recommendation (Base Class)

109

ID

ID-String

1

110

Patient

Reference[Patient]

1

111

Date

1

112

Supporting Variants

Reference[Variant]

0...N

113

Notes

String

0...1

114

Therapy Recommendation

115

Therapy Type/Category

Coding

???

Code	Display
symptomatic-therapy	Symptomatische nicht-medikamentöse Therapie (Fördermaßnahmen)
symptomatic-medication-administration	Symptomatische medikamentöse Therapie (bspw. antispastische Medikation)
symptomatic-intervention	Symptomatische interventionelle Therapie (Operationen, Injektionen)
causal-medication-administration	Kausale Therapie (medikamentös)
causal-intervention	Kausale Therapie (interventionell)

1

116

Medication

Coding

ATC ???

0...N

117

Study Enrollment Recommendation

118

Studies

Reference[Study]

Study Number(s)

0...N

119

Clinical Management Recommendation

120

Type

Coding

Ref. TNAMSE

Code	Display
disease-specific-ambulatory-care	Indikatorerkrankungsspezifische Ambulanz
university-ambulatory-care	Andere Hochschulambulanz
local-crd	Eigenes ZSE
other-crd	Anderes ZSE
other-ambulatory-care	Andere Ambulanz
gp	Hausarzt
specialist	Niedergelassener Facharzt

121

122

Therapy Follow-up Documentation

123

History

Therapy

1...N

124

Therapy

therapy

125

ID

ID-String

1

therapy.id

126

Patient

Reference[Patient]

1

therapy.patient

127

Recorded On

Date

1

128

Period

0...1

129

Type/Category

Coding

see. Therapy Recommendation Type/Category

1

130

Medication

Coding

see. Therapy Recommendation Medication

0...N

131

Notes

String

0...N

therapy.notes

132

133

134

PatientRecord

135

Patient

1

patient

136

Diagnosis

1

diagnosis

137

Case

1

case

138

HPO-Terms

Observation: HPO-Term

1...N

hpoTerms

139

GMFCS Status History

Observation: GMFCS

0...N

140

Hospitalization

0...1

141

Care Plans

Care Plan

1...N

142

NGS-Report

0...N

ngsReports

143

Therapy Documentation

Therapy

0...N

therapy

API Docs

Documentation of the DNPM:DIP node's "ETL API", i.e. for upload of RD Patient Record data, can be found at:

https://github.com/KohlbacherLab/dnpm-dip-api-gateway/tree/main/app/controllers#example-data-and-etl-api

This also includes an endpoint to get a JSON Schema of the representation of an RD Patient Record.

Demo System

A Demo System exposing the above REST API is available at: https://dnpm.bwhealthcloud.de

IMPORTANT: This System is meant for demonstration/testing purposes only – DO NOT use its validation endpoint with real data! The validation API will also be available in your local installation of the DNPM:DIP node, so you will eventually be able to validate your real data in a protected local operations setting.

Quick Links:

JSON Schema: https://dnpm.bwhealthcloud.de/api/rd/etl/patient-record/schema
Random-generated JSON Example: https://dnpm.bwhealthcloud.de/api/rd/fake/data/patient-record

Datenintegrationsplattform SE:dip

Data Model - SE:dip

UML

Table

Patient

Episode Of Care

Diagnosis

Hospitalization

HPO-Term

Status

Observation: GMFCS

Lab

NGS Report

Sequencing Info

Observation: Autozygosity

Observation: Variant (Base class)

Object: ACMG Criterion

Structural Variant (SV): Variant

Small Variant: Variant

Copy Number Variant (CNV): Variant

Care Plan

Recommendation (Base Class)

Therapy Recommendation

Study Enrollment Recommendation

Clinical Management Recommendation

Therapy Follow-up Documentation

Therapy

PatientRecord

API Docs

Demo System

UML

Table

Patient

Consent

Episode Of Care

Diagnosis

Hospitalization

HPO-Term

Status

Observation: GMFCS

Lab

NGS Report

Sequencing Info

Observation: Autozygosity

Observation: Variant (Base class)

Object: ACMG Criterion

Structural Variant (SV): Variant

Small Variant: Variant

Copy Number Variant (CNV): Variant

Care Plan

Recommendation (Base Class)

Therapy Recommendation

Study Enrollment Recommendation

Clinical Management Recommendation

Therapy Follow-up Documentation

Therapy

PatientRecord

API Docs

Demo System