RareLink-CDM

In this section, we provide an overview of the instruments that are part of the RareLink Common Data Model (CDM), which is based on the RD-CDM. We have implemented the RD-CDM’s definitions, codes, and mappings into the REDCap instruments by encoding the variables and value sets in the REDCap data dictionary. Each section of the model corresponds to a distinct instrument, ensuring consistency and comprehensive data capture.

Hint

Read the REDCap page to understand how REDCap instruments & data dictionaries work.
Read the RD-CDM page for more information on the ontology-based rare disease common data model.

Contents

REDCap Data Dictionary
LinkML Schema
REDCap-inherent rules
REDCap Field Annotations
RareLink-CDM Instruments

REDCap Data Dictionary

The RareLink CDM Data Dictionary is available for download as a CSV file:

Download: RareLink-CDM Data Dictionary (v2.0.6)

… Next steps

… read Set up the RareLink Framework for more information on how to manually import and set up the RareLink-CDM Data Dictionary into your local REDCap project.
… or run the following commands to directly import the data dictionary into your REDCap project using the RareLink CLI:

rarelink setup keys
rarelink setup data-dictionary

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LinkML Schema

The RareLink-CDM has been encoded in the LinkML schema format to allow for interoperability with other data models and standards. The LinkML schema is an open-data modeling language and provides a machine-readable representation of the RareLink-CDM, including the data elements, codes, and mappings to other standards. In other words, the RareLink REDCap instruments are displayed in a structured format that so that LinkML modules and functionalities can be used.

Here you can view the LinkML schema of the RareLink-CDM.

Usage

We use RareLink-CDM-LinkML schema and functionalities in various RareLink modules, for example:

When running rarelink redcap export-records you will see, that the data from the REDCap project is automatically processed to the LinkML presentation of the RareLink-CDM and validated against it. This ensures the data is ready to Phenopackets Module.
Within the data model itself, we use its python classes and properties automatically generated by LinkML schema to ensure consistent use of code systems, versions and codes within one RareLink-CDM version and its mappings.
Since our RareLink-CDM is modeled and defined with LinkML, we can make use of the LinkML Schema Automator for Semi-Automatic Import from existing (tabular) databases. This allows import it into a REDCap project and allows you to Phenopackets Module or FHIR Module.

LinkML - further links

To know more about LinkML, check out:

The LinkML GitHub repository or
the LinkML Schema Documentation.

Feel free to Contact us in case you would like to be connected to the LinkML community or our colleagues from the Monarch Initiative.

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Rules for REDCap codes and codesystems

REDCap variables and choice codes have specific limitations and requirements:

REDCap recommends a maximum of 26 characters for variable names. We have shortened the variable names to adhere to this limitation.
REDCap variables must be unique and must not contain spaces or special characters, i.e. only alphanumeric characters and underscores.
REDCap choice codes must be unique and must not contain spaces or special characters, i.e. only alphanumeric characters and underscores.

To address these, we have defined a set of rules for the REDCap variables and choice codes in the RareLink-CDM Data Dictionary. The rules are as follows:

The REDCap variable names are based on the RD-CDM codes and display names.
The REDCap choices are based on the RD-CDM codes and display names.
The REDCap variable names are shortened to adhere to the 26-character limit.
The REDCap variable names are unique and do not contain spaces or special characters.
The REDCap choice codes are unique and do not contain spaces or special characters.
All codes begin with the official codesystem prefix (e.g. HP, SNOMED, etc.) as a lower case string followed by an underscore and the code.
All codes are defined in the Field Annotations of each data element.

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REDCap Field Annotations

Within the Field Annotation field of each REDCap element, we have defined each element’s metadata according to the RD-CDM standard, including the following:

Variable: Corresponding to the data element code, codesystem, and display name.
Choices: If applicable, the corresponding choices codesystem, and display name.
Version(s): If applicable, the corresponding codesystem versions used in the REDCap data element
Mapping: If applicable, the corresponding mapping to the HL7 FHIR or GA4GH Phenopackets standard.

Example Field Annotation of 6.2.6 Temporal Pattern:

Variable:
HP:0012824 | Severity
Choices:
- HP:0012827 | Borderline
- HP:0012825 | Mild
- HP:0012826 | Moderate
- HP:0012829 | Profound
- HP:0012828 | Severe
Version(s):
- HPO Version 2026-02-16
Mapping:
- HL7 FHIR Expression v4.0.1: Observation.interpretation
- GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.severity

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RareLink-CDM Instruments

The RareLink-CDM instruments translate the ontology-based Rare Disease Common Data Model (RD-CDM) into REDCap instruments. Slight adjustments to the RD-CDM were made to comply with REDCap’s rule_set, the data dictionary requirements and to ensure alignment with:

international registries (e.g., the European Reference Networks (ERNs)),
the HL7 FHIR International Patient Summary (IPS) v2.0.0,
the HL7 Genomics Reporting v3.0.0 Profiles, and
the GA4GH Phenopacket Schema.

Each instrument corresponds to a specific section of the RD-CDM and its adpations are described in the section below for each section:

(1) Formal Criteria (rarelink_1_formal_criteria)
(2) Personal Information (rarelink_2_personal_information)
(3) Patient Status (rarelink_3_patient_status)
(4) Care Pathway (rarelink_4_care_pathway)
(5) Disease (rarelink_5_disease)
(6.1) Genetic Findings (rarelink_6_1_genetic_findings)
(6.2) Phenotypic Feature (rarelink_6_2_phenotypic_feature)
(6.3) Measurements (rarelink_6_3_measurements)
(6.4) Family History (rarelink_6_4_family_history)
(7) Consent (rarelink_7_consent)
(8) Disability (rarelink_8_disability)

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Tip

When capturing data manually in you REDCap project, we recommend using the Guide for Manual Data Capture! The information below rather details the structure of the RD-CDM within REDCap (i.e. therefore as the RareLink-CDM).

Legend: Structure of the Schema below

Each instrument follows a consistent format for documentation and representation of variables. Below is an explanation of the sections and terms used:

Instrument Header

Each instrument begins with:

Title: The name of the instrument and its corresponding REDCap identifier in parentheses (e.g., rarelink_1_formal_criteria).
Purpose: A brief description of the instrument’s objective.
A box indicating whether the instrument is a Single-Entry Form (used once per individual):

Single-Entry Form

… or a Repeating Form (used multiple times per individual):

Repeated Form

Variables & Adjustments

Each variable is documented with the following attributes:

Variable Name and Description:
- Listed with its sequence number and corresponding identifier (e.g., 1.1 Pseudonym (snomedct_422549004)).
- Includes a brief explanation of the variable’s purpose, if necessary.
Cardinality:
- Specifies whether the variable is Required or Optional and its occurrence:
  - 1..1 for exactly one occurrence,
  - 0..1 for one optional occurence, or
  - 1..* / 0..* for multiple required/optional occurences.
Validation:
- Describes the expected format or encoding for the variable (e.g., Free Text, Dropdown (choices encoded according to RD-CDM), or specific ontology references like BIOPORTAL:MONDO).

Note

All repeating forms are optional, therefore the cardinality is always 0..*. However, as soon as an instrument is used, specific elements may be required (1..1) to comply with specific HL7 FHIR or Phenopacket requirements.

(1) Formal Criteria (`rarelink_1_formal_criteria`)

Purpose: Captures eligibility and registration information for individuals.

Single-Entry Form

Variables & Adjustments:

1.1 Pseudonym (snomedct_422549004)
- Cardinality: Required (1..1)
- Validation: Free Text
1.2 Date of Admission (snomedct_399423000)
- Cardinality: Required (1..1)
- Validation: Date format (YYYY-MM-DD)

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(2) Personal Information (`rarelink_2_personal_information`)

Purpose: Captures demographic and personal details of individuals.

Single-Entry Form

Variables & Adjustments:

2.1 Date of Birth (snomedct_184099003)
- Cardinality: Required (1..1)
- Validation: Date format (YYYY-MM-DD)
2.2 Sex at Birth (loinc_76689_9)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to RD-CDM)
2.3 Karyotypic Sex (snomedct_1296886006)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to RD-CDM)
2.4 Gender Identity (snomedct_263495000)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to RD-CDM)
2.5 Country of Birth (snomedct_370159000)
- Cardinality: Optional
- Validation: Free Text

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(3) Patient Status (`rarelink_3_patient_status`)

Purpose: Tracks changes in patient conditions over time.

Variables & Adjustments:

Date of Completion for the Sheet (patient_status_date)
- Novel Variable: Date of completion for the sheet
- Cardinality: Required (1..1)
- Validation: Date format (YYYY-MM-DD)
3.1 Vital Status (snomedct_278844005)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
3.2 Time of Death (snomedct_398299004)
- Cardinality: Optional
- Validation: Date format (YYYY-MM-DD)
3.3 Cause of Death [ICD10CM] (snomedct_184305005)
- Cardinality: Optional
- Validation: BIOPORTAL:ICD10CM
3.4 Age Category (snomedct_105727008)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
3.5 Length of Gestation at Birth [weeks+days] (snomedct_412726003)
- Cardinality: Optional
- Validation: Free Text
3.6 Undiagnosed RD Case (snomedct_723663001)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)

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(4) Care Pathway (`rarelink_4_care_pathway`)

Purpose: Tracks details of individual encounters in the care pathway.

Repeated Form

Variables & Adjustments:

4.1 Encounter Start (hl7fhir_enc_period_start)
- Cardinality: Optional
- Validation: Date format (YYYY-MM-DD)
4.2 Encounter End (hl7fhir_enc_period_end)
- Cardinality: Optional
- Validation: Date format (YYYY-MM-DD)
4.3 Encounter Status (snomedct_305058001)
- Cardinality: Required (1..1)
- Validation: Dropdown (choices encoded according to ref:1_5)
4.4 Encounter Class (hl7fhir_encounter_class)
- Cardinality: Required (1..1)
- Validation: Dropdown (choices encoded according to ref:1_5)

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(5) Disease (`rarelink_5_disease`)

Purpose: Captures detailed information about the diseases affecting individuals.

Repeated Form

Variables & Adjustments:

Disease Coding (disease_coding)
- Novel Variable: Selection of code system for disease information (only one code system allowed per disease entry. We recommend using MONDO).
- Cardinality: Required (1..1)
- Validation: Dropdown (choices encoded according to ref:1_5)

Disease Information (Grouped Fields):

The following fields capture the disease information using different encoding systems. The relevant field depends on the choice made in disease_coding:

5.1 Disease [MONDO] (snomedct_64572001_mondo)
- Cardinality: Required (1..1) if disease_coding = ‘mondo’
- Validation: BIOPORTAL:MONDO
5.1 Disease [ORDO] (snomedct_64572001_ordo)
- Cardinality: Required (1..1) if disease_coding = ‘ordo’
- Validation: BIOPORTAL:ORDO
5.1 Disease [ICD10CM] (snomedct_64572001_icd10cm)
- Cardinality: Required (1..1) if disease_coding = ‘icd10cm’
- Validation: BIOPORTAL:ICD10CM
5.1 Disease [ICD11] (snomedct_64572001_icd11)
- Cardinality: Required (1..1) if disease_coding = ‘icd11’
- Validation: Free Text (BIOPORTAL does not support ICD11 yet)
5.1 Disease [OMIM_P] (snomedct_64572001_omim_p)
- Cardinality: Required (1..1) if disease_coding = ‘omim’
- Validation: BIOPORTAL:OMIM

Additional Fields:

5.2 Verification Status (loinc_99498_8)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
5.3 Age at Onset (snomedct_424850005)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
5.4 Date of Onset (snomedct_298059007)
- Cardinality: Optional
- Validation: Date format (YYYY-MM-DD)
5.5 Age at Diagnosis (snomedct_423493009)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
5.6 Date of Diagnosis (snomedct_432213005)
- Cardinality: Optional
- Validation: Date format (YYYY-MM-DD)
5.7 Body Site [SNOMED CT] (snomedct_363698007)
- Cardinality: Optional
- Validation: BIOPORTAL:SNOMEDCT
5.8 Clinical Status (snomedct_263493007)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
5.9 Disease Severity (snomedct_246112005)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)

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(6.1) Genetic Findings (`rarelink_6_1_genetic_findings`)

Purpose: Captures information about genetic variants and their clinical significance.

Repeated Form

Variables & Adjustments:

Genetic Diagnosis Code (genetic_diagnosis_code)
- Novel Variable: Allows the user to choose the corresponding code system for a genetic diagnosis related to the variant.
- Cardinality: Required (1..1)
- Validation: Dropdown (choices encoded according to ref:1_5)

Genomic Diagnosis (Grouped Fields):

The following fields capture the genomic diagnosis using different code systems. The relevant field depends on the choice made in genetic_diagnosis_code:

6.1.1 Genomic Diagnosis [MONDO] (snomedct_106221001_mondo)
- Cardinality: Required (1..1) if genetic_diagnosis_code = ‘mondo’
- Validation: BIOPORTAL:MONDO
6.1.1 Genomic Diagnosis [OMIM_p] (snomedct_106221001_omim_p)
- Cardinality: Required (1..1) if genetic_diagnosis_code = ‘omim’
- Validation: BIOPORTAL:OMIM

Variant Information:

6.1.2 Progress Status of Interpretation (ga4gh_progress_status)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.1.3 Interpretation Status (ga4gh_interp_status)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.1.4 Structural Variant Analysis Method (loinc_81304_8)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.1.5 Reference Genome (loinc_62374_4)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.1.6 Genetic Mutation String (loinc_lp7824_8)
- Cardinality: Optional
- Validation: Free Text

HGVS Variant Information:

Variant Expression (variant_expression)
- Novel Variable: Ensures users select the type of validated HGVS expression.
- Cardinality: Required (1..1)
- Validation: Dropdown (choices: g.HGVS, c.HGVS, p.HGVS)
6.1.7 Genomic DNA Change [g.HGVS] (loinc_81290_9)
- Cardinality: Required (1..1) if variant_expression = ‘ghgvs’
- Validation: Free Text
6.1.8 Sequence DNA Change [c.HGVS] (loinc_48004_6)
- Cardinality: Required (1..1) if variant_expression = ‘chgvs’
- Validation: Free Text
6.1.9 Amino Acid Change [p.HGVS] (loinc_48005_3)
- Cardinality: Required (1..1) if variant_expression = ‘phgvs’
- Validation: Free Text
Variant Validation (variant_validation)
- Novel Variable: Ensures users confirm that HGVS expressions were validated using the variant validator.
- Cardinality: Required if any HGVS field is filled.
- Validation: Radio (Yes/No)

Variant Information:

6.1.10 Gene [HGNC-NR] (loinc_48018_6)
- Cardinality: Optional
- Validation: BIOPORTAL:HGNC-NR
6.1.11 Zygosity (loinc_53034_5)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.1.11A Zygosity - Other [LOINC] (loinc_53034_5_other)
- Cardinality: Required (1..1) if loinc_53034_5 = ‘Other’
- Validation: BIOPORTAL:LOINC
6.1.12 Genomic Source Class (loinc_48002_0)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.1.13 DNA Change Type (loinc_48019_4)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.1.13A DNA Change Type - Other [LOINC] (loinc_48019_4_other)
- Cardinality: Required (1..1) if loinc_48019_4 = ‘Other’
- Validation: BIOPORTAL:LOINC
6.1.14 Clinical Significance [ACMG] (loinc_53037_8)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.1.15 Therapeutic Actionability (ga4gh_therap_action)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.1.16 Clinical Annotation Level Of Evidence (loinc_93044_6)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)

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(6.2) Phenotypic Feature (`rarelink_6_2_phenotypic_feature`)

Purpose: Captures observed physical and clinical characteristics using standardized terminologies.

Repeated Form

Variables & Adjustments:

6.2.1 Phenotypic Feature (snomedct_8116006)
- Cardinality: Required (1..1)
- Validation: BIOPORTAL:HP
6.2.2 Status (snomedct_363778006)
- Cardinality: Required (1..1)
- Validation: Dropdown (choices encoded according to ref:1_5)
6.2.3 Determination Date (snomedct_8116006_onset)
- Cardinality: Optional
- Validation: Date format (YYYY-MM-DD)
6.2.4 Resolution Date (snomedct_8116006_resolut)
- Cardinality: Optional
- Validation: Date format (YYYY-MM-DD)
6.2.5 Age of Onset (hp_0003674)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.2.6 Temporal Pattern (hp_0011008)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.2.7 Phenotype Severity (hp_0012824)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.2.9 Evidence for the phenotype [ECO] (phenotypicfeature_evidence)
- Cardinality: Optional
- Validation: BIOPORTAL:ECO

Clinical Modifiers adjustments:

The following fields capture clinical modifiers for a specific phenotypic feature that were defined within the RareLink-CDM - based on the general corresponding RD-CDM field:

6.2.8A Clinical Modifier [HP] (hp_0012823_hp1)
- Cardinality: Optional
- Validation: BIOPORTAL:HP
6.2.8B Clinical Modifier [HP] (hp_0012823_hp2)
- Cardinality: Optional (Required if hp_0012823_hp1 is filled)
- Validation: BIOPORTAL:HP
6.2.8C Clinical Modifier [HP] (hp_0012823_hp3)
- Cardinality: Optional (Required if hp_0012823_hp2 is filled)
- Validation: BIOPORTAL:HP
6.2.8D If applicable, what was the causing organism? [NCBITAXON] (hp_0012823_ncbitaxon)
- Cardinality: Optional
- Validation: BIOPORTAL:NCBITAXON
6.2.8E If applicable, what was the primary body site? [SNOMED] (hp_0012823_snomed)
- Cardinality: Optional
- Validation: BIOPORTAL:SNOMEDCT

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(6.3) Measurements (`rarelink_6_3_measurements`)

Purpose: Captures various types of measurements including vital signs, laboratory tests, imaging, procedures, and more, aligned with IPS and Phenopackets profiles.

Repeated Form

Key Adjustments:

Vital Signs Panel: Added 6.3.1A Vital Signs Panel and 6.3.1A Other Vital Sign to align with the IPS vital status profile.
Procedure-Specific Fields: Integrated Procedure as NCIT or SNOMED? and related fields for NCIT and SNOMED procedures to support IPS procedure profiles.
Complex Logic: Highlighted branching logic based on measurement_category to handle vital signs, laboratory, imaging, procedures, and other measurement types.

Variables & Adjustments:

6.3.0A Category (measurement_category)
- Cardinality: Required (1..1)
- Validation: Dropdown (choices encoded according to ref:1_5)
6.3.0B Status (measurement_status)
- Cardinality: Required (1..1)
- Validation: Dropdown (choices encoded according to ref:1_5)

Vital Signs:

6.3.1A Vital Signs Panel (ln_85353_1)
- Cardinality: Optional (if measurement_category = “vital-signs”)
- Validation: Dropdown (choices encoded according to ref:1_5)
6.3.1A Other Vital Sign (ln_85353_1_other)
- Cardinality: Optional (Required if ln_85353_1 = “other”)
- Validation: BIOPORTAL:LOINC

Measurement Details:

6.3.1 Assay (ncit_c60819)
- Cardinality: Optional (if measurement_category ≠ “vital-signs” and ≠ “procedure”)
- Validation: BIOPORTAL:LOINC
6.3.2 Value (ncit_c25712)
- Cardinality: Optional (if measurement_category ≠ “procedure”)
- Validation: Decimal number (e.g., 0.00–999999.99)
6.3.3 Value Unit (ncit_c92571)
- Cardinality: Optional (if measurement_category ≠ “vital-signs” or ln_85353_1_other is filled, and ≠ “procedure”)
- Validation: BIOPORTAL:UO
6.3.4 Interpretation (ncit_c41255)
- Cardinality: Optional (if measurement_category ≠ “procedure”)
- Validation: BIOPORTAL:NCIT
6.3.5 Time Observed (ncit_c82577)
- Cardinality: Required (1..1)
- Validation: Date format (YYYY-MM-DD)

Procedure-Specific Fields:

Procedure as NCIT or SNOMED? (procedure)
- Cardinality: Optional (if measurement_category = “procedure”)
- Validation: Dropdown (choices encoded according to ref:1_5)
6.3.6A Procedure [NCIT] (snomedct_122869004_ncit)
- Cardinality: Optional (if procedure = “ncit”)
- Validation: BIOPORTAL:NCIT
6.3.6B Procedure [SNOMED] (snomedct_122869004_snomed)
- Cardinality: Optional (if procedure = “snomed”)
- Validation: BIOPORTAL:SNOMEDCT
6.3.7 Procedure [SNOMED] (snomedct_122869004)
- Cardinality: Required (1..1, if measurement_category = “procedure”)
- Validation: BIOPORTAL:SNOMEDCT
6.3.7A Body Site [SNOMED] (snomedct_122869004_bdsite)
- Cardinality: Optional (if measurement_category = “procedure”)
- Validation: BIOPORTAL:SNOMEDCT
6.3.7B Procedure Status [SNOMED] (snomedct_122869004_status)
- Cardinality: Required (1..1, if measurement_category = “procedure”)
- Validation: Dropdown (choices encoded according to ref:1_5)

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(6.4) Family History (`rarelink_6_4_family_history`)

Purpose: Captures family history details of the individual, including relationships, health statuses, and genetic information.

Repeated Form

Key Adjustments:

Pseudonym Field: Added family_history_pseudonym to identify family members across records.
Required Fields: Marked fields like family_history_pseudonym, snomedct_444018008, and hl7fhir_fmh_status as mandatory for FHIR base resource FamilyMemberHistory compatibility.
Branching Logic: Added logic for deceased family members to ensure fields like loinc_54112_8 and loinc_92662_6 are completed if applicable.

Variables & Adjustments:

6.4.0 Pseudonym (family_history_pseudonym)
- Cardinality: Required (1..1)
- Validation: Free Text
6.4.1 Propositus/-a (snomedct_64245008)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.4.2 Relationship to Index Case (snomedct_408732007)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.4.3 Consanguinity (snomedct_842009)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.4.4 Family Member Relationship (snomedct_444018008)
- Cardinality: Required (1..1)
- Validation: Dropdown (choices encoded according to ref:1_5)
6.4.5 Family Member Record Status (hl7fhir_fmh_status)
- Cardinality: Required (1..1)
- Validation: Dropdown (choices encoded according to ref:1_5)
6.4.6 Family Member Sex (loinc_54123_5)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.4.7 Family Member Age (loinc_54141_7)
- Cardinality: Optional
- Validation: Integer (0–200)
6.4.8 Family Member Date of Birth (loinc_54124_3)
- Cardinality: Optional
- Validation: Date format (YYYY-MM-DD)
6.4.9 Family Member Deceased (snomedct_740604001)
- Cardinality: Optional
- Validation: Dropdown (choices encoded according to ref:1_5)
6.4.10 Family Member Cause of Death [ICD10CM] (loinc_54112_8)
- Cardinality: Optional (available if snomedct_740604001 = “snomedct_373066001”)
- Validation: BIOPORTAL:ICD10CM
6.4.11 Family Member Deceased Age (loinc_92662_6)
- Cardinality: Optional (available if snomedct_740604001 = “snomedct_373066001”)
- Validation: Integer (0–200)
6.4.12 Family Member Disease [MONDO] (loinc_75315_2)
- Cardinality: Optional
- Validation: BIOPORTAL:MONDO

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(8) Disability (`rarelink_8_disability`)

Purpose: Captures information related to the classification of an individual’s functioning and disability.

Single-Entry Form

Key Adjustments:

ICF Integration: The variable rarelink_icf_score allows for the classification of functioning and disability using the International Classification of Functioning, Disability, and Health (ICF) framework.
Documentation Support: Links to relevant documentation and guidance provided to ensure proper data entry and standardization.
Optional Field: The field is optional, catering to cases where detailed disability classification is not required.

Variables & Adjustments:

8.1 Classification of Functioning / Disability (rarelink_icf_score)
- Cardinality: Optional
- Validation: Free Text (encoded according to BIOPORTAL:ICF)

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RareLink-CDM

Contents

REDCap Data Dictionary

… Next steps

LinkML Schema

Usage

LinkML - further links

Rules for REDCap codes and codesystems

REDCap Field Annotations

RareLink-CDM Instruments

Legend: Structure of the Schema below

Instrument Header

Variables & Adjustments

(1) Formal Criteria (rarelink_1_formal_criteria)

(2) Personal Information (rarelink_2_personal_information)

(3) Patient Status (rarelink_3_patient_status)

(4) Care Pathway (rarelink_4_care_pathway)

(5) Disease (rarelink_5_disease)

(6.1) Genetic Findings (rarelink_6_1_genetic_findings)

(6.2) Phenotypic Feature (rarelink_6_2_phenotypic_feature)

(6.3) Measurements (rarelink_6_3_measurements)

(6.4) Family History (rarelink_6_4_family_history)

(7) Consent (rarelink_7_consent)

(8) Disability (rarelink_8_disability)

(1) Formal Criteria (`rarelink_1_formal_criteria`)

(2) Personal Information (`rarelink_2_personal_information`)

(3) Patient Status (`rarelink_3_patient_status`)

(4) Care Pathway (`rarelink_4_care_pathway`)

(5) Disease (`rarelink_5_disease`)

(6.1) Genetic Findings (`rarelink_6_1_genetic_findings`)

(6.2) Phenotypic Feature (`rarelink_6_2_phenotypic_feature`)

(6.3) Measurements (`rarelink_6_3_measurements`)

(6.4) Family History (`rarelink_6_4_family_history`)

(7) Consent (`rarelink_7_consent`)

(8) Disability (`rarelink_8_disability`)