.. _4_2:
Semi-Automatic Import
===========================
While many rare disease centres and hospitals hold specialised data in
unstructured formats, **RareLink's semi-automatic import guide** provides a means
to standardize this information through `LinkML `_ to the :ref:`2_2`.
Using `LinkML-Map `_, you can
convert your local (tabular) data into a :ref:`rarelink_cdm_linkml` JSON
representation conforming to the :ref:`2_2` for subsequent import to REDCap.
A fully automatic conversion tool is not possible, as the :ref:`2_2` is
based on :ref:`1_2` for which **manual and professional annotation of your data to the
ontology terms is required**. However, to make the process as efficient and user-friendly
as possible, we offer a semi-automatic guide with templates and examples that
significantly speed up the process of importing your data. Once your data is
processed and validated against the :ref:`2_2`'s :ref:`rarelink_cdm_linkml`,
you can export it diretly to :ref:`1_3`, import it to your local :ref:`1_6`
project and subsequently export it to :ref:`1_4`.
Make sure to read the following sections in this documentation to make yourself
familiar with the model, the underlying data elements and its ontologies:
- :ref:`1_2`
- :ref:`1_5`
- :ref:`2_2`
If questions remain and you would like to discuss your data import with us,
please do not hesitate to :ref:`12` us. RareLink is a community-driven project
and we are happy to collaborate wherever possible.
.. hint::
In this process, **you are responsible for the semantic mapping and
ontology annotation** of your data elements. This step is critical for
ensuring that your data, including genetic mutations validated with HGVS,
conforms to the RareLink-CDM standard for Phenopackets and FHIR export and
expresses the correct semantic meaning of your data.
_________________________
**Overview**
.. contents::
:local:
:depth: 3
_________________________
Overview of Components
------------------------
The semi-automatic import process involves several key components:
- **RareLink-CDM LinkML Schema**:
The target schema that defines the
structure of your data once converted. It is designed to be as close
as possible to the original REDCap data model while enabling export
to Phenopackets and FHIR. You can find it here:
- :ref:`2_2`
- :ref:`rarelink_cdm_linkml`
- `RareLink-CDM LinkML yaml schema files `_
- `RareLink-CDM LinkML python model and classes `_
- **LinkML Map**:
A framework for specifying and executing mappings between
data models. You will use a SSSOM (Simple Standard for Sharing Ontological
Mappings) file to map your source data to the RareLink-CDM.
- `LinkML Map Documentation `_
- **SSSOM Mapping File**:
A tab-delimited file that defines the mapping from
your local data fields to the target elements in the RareLink-CDM. In the
SSSOM file, the *object_id* column represents the target value—either the
literal value (e.g., a date) or a standardized code (e.g., SNOMEDCT codes for
sex/gender). A RareLink-CDM SSSOM mapping template is provided below
as a starting point for your mappings.
- `SSSOM Specification `_
- **Semantic Ontology Annotation**
The process of encoding each data element with an ontology term defined in the
value sets of the :ref:`2_2` or the ontologies defiend for the respective
fields. This step ensures that the semantic meaning of your data is preserved
and that the mappings are interoperable. This process requires the most
attention and is crucial for the correct interpretation of your data.
To improve the quality of your mappings, you should use the `ISO/TS 21564 MapQual `_
standard for evaluating the quality of data mappings between health information
systems.
The **ISO/TS 21564 MapQual** is an ISO technical specification that defines
best practices for evaluating the quality of data mappings between
health information systems. It provides guidelines for assessing the
semantic consistency, accuracy, and completeness of mappings, ensuring
that data is correctly annotated and interoperable.
Key steps in the encoding process include:
- **Identification:** Identify source data elements that require mapping.
- **Mapping Selection:** Choose appropriate target ontology terms or codes.
- **Semantic Alignment:** Ensure that each mapping preserves the intended
meaning of the source data.
- **Dual Encoding:** Perform encoding and mapping independently by at least
two experts to improve objectivity and reliability.
- **Quality Assessment:** Evaluate mappings for accuracy and completeness
against the established standards.
- **Documentation:** Record mapping decisions, justifications, and quality
metrics for transparency and future reference.
_________________________
Steps When Importing Data
--------------------------
The semi-automatic import process consists of the following steps:
1. Mapping
____________
You begin by defining mappings from your local, tabular database to the
RareLink-CDM using a SSSOM mapping file provided by RareLink. The RareLink-CDM
has no strict minimal requirements beyond the formal criteria fields. However,
if an instrument is used, the corresponding required fields must be mapped.
Depending on the purpose of your data, additional fields should be included;
for instance, registry data should map consent fields, while analyses involving
measurements and genetics require the respective clinical and laboratory fields.
.. tip::
For more precise analyses and a more balanced cohort, we recommend defining a
ruleset for the fields mapped and encoded of your local database.
____
1.1 Understanding the RareLink-CDM data model
""""""""""""""""""""""""""""""""""""""""""""""""
You should familiarize yourself with the RareLink-CDM schema in detail to
understand the target data model, the structure of the data elements and
REDCap instruments, and the recommended ontologies. For this, please go through
the data model and its derivate in REDCap in detail:
- :ref:`1_5`
- Read the `paper on the RareLink-CDM `_
- :ref:`2_2` and its :ref:`rarelink_cdm_linkml`
.. note::
When selecting one data field from a REDCap instrument, you must also map
all fields or define the code or a constant for all fields that are required
by the instrument. You can find the required fields in the :ref:`cdm_overview`
documentation where the cardinality is set to **required (1..1)**.
____
1.2 Mapping Your Data
""""""""""""""""""""""""
Use the provided SSSOM template file to map your local data to the RareLink-CDM.
This template defines standard target predicates and codes, ensuring consistency
in your mappings and facilitating interoperability.
**RareLink-CDM SSSOM Template File**
This template file is designed to assist users in creating mappings from their
local data sources to the RareLink-CDM target schema. It follows the SSSOM
(Simple Standard for Sharing Ontological Mappings) specification and includes
both required and additional optional columns to improve traceability and
clarity of the mapping process.
The template contains the following columns:
- **subject_id**:
A unique identifier for the source record or data element. This value
identifies which record in your local database is being mapped.
- **subject_label**:
A human-readable label for the source record. This provides context
for the mapping and helps users quickly identify the data element.
- **predicate_id**:
The mapping relation that specifies the target element in the :ref:`rarelink_cdm_linkml` of
the :ref:`2_2`. Use the ``default_prefix:slot_name`` from the
RareLink-CDM schema, for example:
- ``rarelink_cdm:snomedct_184099003`` for 2.1 Date of birth, or
- ``rarelink_cdm:loinc_76689_9`` for 2.2 Sex at birth.
- **predicate_label**:
The title of the target element from the schema, i.e. the *name* of the element
itself. This column provides a human-readable description of the target element being mapped.
For the examples above, these would be ``2.1 Date of birth`` and ``2.2 Sex at birth``respectively.
- **object_id**:
The target value in the RareLink-CDM. For literal fields, such as dates,
this is the actual value (e.g., "1970-02-15"). For coded fields, such as
sex, the object_id is the standardized code from the value set
(e.g., "LOINC:76689-9" for female) or the code from the code system defined
by the data element (e.g., "HP:0001250" for a phenotype in element 6.2.1).
- **object_label**: The human-readable label for the target value either from the
RareLink-CDM value sets or the code system defined by the data element. In
the case of dates, a "-" is sufficient.
- **match_type**:
Describes the type of mapping used. Commonly this is set to "lexical"
when the mapping is based on a direct textual match.
- **mapping_date**:
The date when the mapping was created. This column adds traceability
and helps with versioning of your mappings.
- **mapping_tool**:
The tool or method used to generate the mapping. For example, "manual"
indicates that the mapping was curated by a human expert.
.. hint::
:download:`download the TSV template file directly `.
This template provides a minimal yet robust framework for defining your
mappings. It ensures that each mapping row clearly specifies which source
element is linked to which target element and how that connection was made.
By following this template, you can ensure that your mappings are consistent,
interoperable, and well-documented key requirements for successful data
integration in the RareLink-CDM.
Below you can find a **snippet of the RareLink-CDM SSSOM Template File:**
.. code-block:: tsv
# RareLink-CDM SSSOM Template File
# This template maps source data elements from a registry CSV file to the target RareLink-CDM schema.
# SSSOM documentation: https://mapping-commons.github.io/sssom/
# RareLink-CDM LinkML schema: https://github.com/BIH-CEI/rarelink/tree/develop/src/rarelink/rarelink_cdm/schema_definitions
#
# Columns:
# subject_id : Unique identifier for the source record ().
# subject_label : Human-readable label for the source record ().
# predicate_id : Fully qualified target element (e.g., rarelink_cdm:snomedct_184099003).
# predicate_label : Title of the target element from the schema.
# object_id : Target value – a literal (e.g., date, numeric) or a standardized code with prefix.
# object_label : Human-readable label for the target value (use "-" for dates/numerics when no label is needed).
# match_type : Mapping derivation type (e.g., "lexical").
# mapping_date : Date when the mapping was created ().
# mapping_tool : Method used to create the mapping (e.g., "manual").
#
subject_id subject_label predicate_id predicate_label object_id object_label match_type mapping_date mapping_tool
# === Formal Criteria (Singular) ===
"" rarelink_cdm:snomedct_422549004 "1.1 Pseudonym" lexical manual
"" rarelink_cdm:snomedct_399423000 "1.2 Date of admission" lexical manual
#
# === Personal Information (Singular) ===
"" rarelink_cdm:snomedct_184099003 "2.1 Date of birth" - lexical manual
"" rarelink_cdm:loinc_76689_9 "2.2 Sex at birth" lexical manual
"" rarelink_cdm:snomedct_1296886006 "2.3 Karyotypic Sex" lexical manual
"" rarelink_cdm:snomedct_263493000 "2.4 Gender Identity" lexical manual
"" rarelink_cdm:snomedct_370159000 "2.5 Country of birth" lexical manual
#
# === Patient Status (Repeating Allowed) ===
"" rarelink_cdm:snomedct_278844005 "3.1 Vital Status" lexical manual
"" rarelink_cdm:snomedct_398299004 "3.2 Time of Death" lexical manual
"" rarelink_cdm:snomedct_184305005 "3.3 Cause of Death" lexical manual
"" rarelink_cdm:snomedct_105727008 "3.4 Age Category" lexical manual
"" rarelink_cdm:snomedct_412726003 "3.5 Length of Gestation at Birth" lexical manual
"" rarelink_cdm:snomedct_723663001 "3.6 Undiagnosed RD Case" lexical manual
#
# === Care Pathway (Repeating Allowed) ===
"" rarelink_cdm:hl7fhir_enc_period_start "4.1 Encounter Start" - lexical manual
"" rarelink_cdm:hl7fhir_enc_period_end "4.2 Encounter End" - lexical manual
"" rarelink_cdm:snomedct_305058001 "4.3 Encounter Status" lexical manual
"" rarelink_cdm:hl7fhir_encounter_class "4.4 Encounter Class" lexical manual
#
# === Disease Information (Repeating Allowed) ===
"" rarelink_cdm:disease_coding "5.0 Disease Coding System" lexical manual
"" rarelink_cdm:snomedct_64572001_mondo "5.1 Disease [MONDO]" lexical manual
# [...]
# === Phenotypic Features (Repeating Allowed) ===
"" rarelink_cdm:snomedct_8116006 "6.2.1 Phenotypic Feature" lexical manual
"" rarelink_cdm:snomedct_363778006 "6.2.2 Phenotypic Feature Status" lexical manual
"" rarelink_cdm:snomedct_8116006_onset "6.2.3 Determination Date" - lexical manual
"" rarelink_cdm:snomedct_8116006_resolut "6.2.4 Resolution Date" - lexical manual
"" rarelink_cdm:hp_0003674 "6.2.5 Age of Onset" lexical manual
"" rarelink_cdm:hp_0011008 "6.2.6 Temporal Pattern" lexical manual
"" rarelink_cdm:hp_0012824 "6.2.7 Phenotype Severity" lexical manual
# additional phenotype (if applicable)
"" rarelink_cdm:snomedct_8116006 "6.2.1 Phenotypic Feature" lexical manual
"" rarelink_cdm:snomedct_8116006_onset "6.2.3 Determination Date" - lexical manual
#
# === Measurements (Repeating Allowed) ===
# Measurement 1
"" rarelink_cdm:ncit_c60819 "6.3.1 Assay" lexical manual
"" rarelink_cdm:ncit_c25712 "6.3.2 Measurement Value" lexical manual
"" rarelink_cdm:ncit_c92571 "6.3.3 Unit" lexical manual
"" rarelink_cdm:ncit_c41255 "6.3.4 Interpretation" lexical manual
"" rarelink_cdm:ncit_c82577 "6.3.5 Time Observed" - lexical manual
# Measurement 2
"" rarelink_cdm:ncit_c60819 "6.3.1 Assay" lexical manual
"" rarelink_cdm:ncit_c25712 "6.3.2 Measurement Value" lexical manual
"" rarelink_cdm:ncit_c92571 "6.3.3 Unit" lexical manual
"" rarelink_cdm:ncit_c41255 "6.3.4 Interpretation" lexical manual
"" rarelink_cdm:ncit_c82577 "6.3.5 Time Observed" - lexical manual
# [...]
#
# you cn find the entire template file here: https://github.com/BIH-CEI/rarelink/tree/develop/docs/_static/res/import_mapper_tsvs
.. tip::
You can view and download all the example csv and sssom mapping files:
- `RareLink-CDM SSSOM Mapping Examples `_ or
- :download:`download the TSV template file directly `.
____
2. Semantic Ontology Annotation
_________________________________
According to your mappings, you must encode each data element with its
recommended ontology term of its
- **value set** (e.g.: 2.2. Sex at Birth) or
- **an ontology term of the coding system** defined (e.g. 5.1 Disease [MONDO]).
This step ensures that the semantic meaning of your
data is preserved and that the mappings are interoperable. Within the
:ref:`2_2`'s :ref:`rarelink_cdm_linkml` you will find the slot names, the value set
encodings and the codesystems required for the encoding.
.. note::
As explained above, the `ISO/TS 21564 MapQual `_
should be followed to ensure the quality of your mappings! In the above
section on components you find more details.
Then, write the results into the SSSOM mapping file using the template provided above
into the columns ``object_id`` and ``object_label`` while selecting the correct
``predicate_id`` and ``predicate_label`` from the RareLink-CDM schema's data elements.
.. tip::
Use the user-friendly Ontology Lookup Service (OLS) to find the correct
ontology terms for your data elements. You can access the OLS here: https://www.ebi.ac.uk/ols4/ontologies.
Do not forget to note the versions of the ontologies used and save it as
metadata for your dataset.
____
3. Preparation
_________________________________
Prepare for command execution by ensuring you have:
- A valid source data file (e.g., an Excel or CSV export of your local database)
- Your SSSOM mapping file
- The RareLink-CDM schema file (e.g., ``rarelink_cdm.yaml``)
LinkML-Map will use these inputs to transform your data into JSON that conforms
to the RareLink-CDM model.
Then you can run LinkML Map:
.. code-block:: bash
linkml-tr map-data -T tr.yaml -s
____
4. Execution and Validation
_________________________________
Run the integrated RareLink CLI command (e.g., ``rarelink import``) to perform
the conversion. As part of the execution, validate your data against the RareLink-CDM
LinkML schema using the following command:
.. code-block:: bash
linkml-validate --schema src/rarelink/rarelink_cdm/schema_definitions/rarelink_cdm.yaml
This validation step ensures that your data conforms to the model before
proceeding to further export (such as to Phenopackets) or upload to REDCap.
____
5. Next Steps
_________________________________
After validation, your RareLink-CDM data is ready. You may now choose to export
the data as Phenopackets or upload it to your REDCap project using the command:
.. code-block:: bash
rarelink redcap upload-records
or export it directly to Phenopackets using:
.. code-block:: bash
rarelink phenopackets export
____
Examples
----------
Below we provide an example of a semi-structured tabular database with five
individuals along with their corresponding SSSOM mapping files.
.. tip::
You can view and download all the example csv and sssom mapping files here:
`RareLink-CDM SSSOM Mapping Examples `_.
____
Example: Adult Rare Disease Registry
____________________________________________
Includes clinical, laboratory, patient status, and genetic data.
.. code-block:: csv
Pseudonym,Sex,Gender,DOB,Disease_Diagnosis,Symptoms,Symptom_Dates,Lab_Measurements,Lab_Measurement_Dates,Patient_Status,Time_at_Last_Visit,Consent_Given,Genetic_Mutation,Zygosity,Mutation_Type,Genomic_Diagnosis
ADR001,Female,Female,1970-02-15,Wilson Disease,"Hepatic dysfunction; tremors","2020-03-10;2020-04-15","Serum ceruloplasmin:12 mg/dL; ALT:85 U/L","2020-03-12;2020-03-12",Alive,2022-10-01,Y,ATP7B:c.3207C>A,Heterozygous,Missense,Wilson Disease confirmed
ADR002,Male,Male,1982-07-30,Fabry Disease,"Angiokeratomas; Acroparesthesias","2019-06-20;2019-07-01","α-Gal A activity:Low; Creatinine:1.2 mg/dL","2019-06-22;2019-06-22",Alive,2021-12-15,Y,GLA:c.936+919G>A,Hemizygous,Deletion,Fabry Disease suspected
ADR003,Female,Female,1965-11-05,Wilson Disease,"Jaundice; Neurological impairment","2018-02-05;2018-03-10","Serum ceruloplasmin:9 mg/dL; Bilirubin:3.2 mg/dL","2018-02-07;2018-02-07",Dead,2018-03-15,N,ATP7B:c.2304insG,Homozygous,Frameshift,Wilson Disease confirmed
ADR004,Female,Female,1978-04-10,Fabry Disease,"Corneal verticillata; Peripheral neuropathy","2021-01-15;2021-01-20","α-Gal A activity:Borderline; ECG:Abnormal","2021-01-16;2021-01-16",Alive,2022-05-10,Y,GLA:c.937G>T,Hemizygous,Nonsense,Fabry Disease confirmed
ADR005,Male,Male,1980-12-20,Fabry Disease,"Renal insufficiency; Cardiac issues","2020-11-05;2020-11-05","α-Gal A activity:Low; eGFR:45 mL/min","2020-11-06;2020-11-06",Alive,2022-08-22,Y,GLA:c.937G>A,Hemizygous,Missense,Fabry Disease confirmed
This dataset comprises records for adult patients diagnosed with rare diseases
such as Wilson Disease and Fabry Disease. It includes essential clinical data
(e.g., date of birth, sex at birth, disease diagnosis, symptoms, lab measurements,
patient status, time at last visit, and genetic mutation details). The accompanying
SSSOM mapping template guides you in mapping these source fields to the RareLink-CDM
schema.
.. code-block:: tsv
# Adult Rare Disease Registry SSSOM Mapping Template
# This template maps key fields from an adult rare disease registry CSV file
# to the RareLink-CDM target schema.
#
subject_id subject_label predicate_id predicate_label object_id object_label match_type mapping_date mapping_tool
ADR001 "Patient ADR001" rarelink_cdm:snomedct_422549004 "1.1 Pseudonym" ADR001 ADR001 lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:snomedct_184099003 "2.1 Date of birth" 1970-02-15 - lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:loinc_76689_9 "2.2 Sex at birth" LOINC:76689-9 Female lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:snomedct_263493000 "2.4 Gender Identity" SNOMEDCT:446141000124107 Female gender identity lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:snomedct_278844005 "3.1 Vital Status" SNOMEDCT:438949009 Alive lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:snomedct_64572001_mondo "5.1 Disease [MONDO]" MONDO:0012345 Wilson Disease lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:loinc_99498_8 "5.2 Verification status" HL7FHIR:confirmed Confirmed lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:snomedct_106221001_mondo "6.1.1 Genetic Diagnosis [MONDO]" MONDO:0012345 Wilson Disease lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:loinc_lp7824_8 "6.1.6 Genetic Mutation String" ATP7B:c.3207C>A - lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:loinc_53034_5 "6.1.11 Zygosity" LOINC:LA6706-1 Heterozygous lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:loinc_48019_4_other "6.1.13 DNA Change Type" LOINC:LA6698-0 Missense lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:snomedct_309370004 "7.1 Consent Status" hl7fhir_active "Active" lexical 2025-01-01 manual
# Repeating elements: Patient ADR001 has two phenotypic features.
ADR001 "Patient ADR001" rarelink_cdm:snomedct_8116006 "6.2.1 Phenotypic Feature" HP:0002480 hepatic encephalopathy lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:snomedct_8116006_onset "6.2.3 Determination Date" 2020-03-10 - lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:snomedct_8116006 "6.2.1 Phenotypic Feature" HP:0001337 tremors lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:snomedct_8116006_onset "6.2.3 Determination Date" 2020-04-15 - lexical 2025-01-01 manual
# Repeating elements: Patient ADR001 has two measurements.
ADR001 "Patient ADR001" rarelink_cdm:ncit_c60819 "6.3.1 Assay" LOINC:2064-4 Ceruloplasmin [Mass/volume] lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:ncit_c25712 "6.3.2 Measurement Value" 12 12 lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:ncit_c92571 "6.3.3 Unit" UO:0010067 milligram per deciliter lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:ncit_c82577 "6.3.5 Time Observed" 2020-03-12 - lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:ncit_c60819 "6.3.1 Assay" LOINC:1742-6 Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:ncit_c25712 "6.3.2 Measurement Value" 85 - lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:ncit_c92571 "6.3.3 Unit" UO:0000179 unit per liter lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:ncit_c82577 "6.3.5 Time Observed" 2020-03-12 - lexical 2025-01-01 manual
#
# Mappings for a second patient (ADR002)
ADR002 "Patient ADR002" rarelink_cdm:snomedct_422549004 "1.1 Pseudonym" ADR002 ADR002 lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:snomedct_184099003 "2.1 Date of birth" 1982-07-30 1982-07-30 lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:loinc_76689_9 "2.2 Sex at birth" SNOMEDCT:248153007 Male lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:snomedct_278844005 "3.1 Vital Status" SNOMEDCT:438949009 Alive lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:snomedct_64572001_mondo "5.1 Disease [MONDO]" MONDO:0010526 Fabry Disease lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:loinc_99498_8 "5.2 Verification status" HL7FHIR:differential Differential lexical 2025-01-01 manual
ADR001 "Patient ADR001" rarelink_cdm:snomedct_106221001_mondo "6.1.1 Genetic Diagnosis [MONDO]" MONDO:0010526 Fabry Disease lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:loinc_lp7824_8 "6.1.6 Genetic Mutation String" GLA:c.936+919G>A - lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:loinc_53034_5 "6.1.11 Zygosity" LOINC:LA6707-9 Hemizygous lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:loinc_48019_4 "6.1.13 DNA Change Type" LOINC:LA6692-3 Deletion lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:snomedct_309370004 "7.1 Consent Status" hl7fhir_active "Active" lexical 2025-01-01 manual
# Repeating elements: Patient ADR002 has two phenotypic features.
ADR002 "Patient ADR002" rarelink_cdm:snomedct_8116006 "6.2.1 Phenotypic Feature" HP:0001071 Angiokeratoma corporis diffusum lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:snomedct_8116006_onset "6.2.3 Determination Date" 2019-06-20 - lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:snomedct_8116006 "6.2.1 Phenotypic Feature" HP:0031006 Acroparesthesias lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:snomedct_8116006_onset "6.2.3 Determination Date" 2019-07-01 - lexical 2025-01-01 manual
# Repeating elements: Patient ADR002 has two measurements.
ADR002 "Patient ADR002" rarelink_cdm:ncit_c60819 "6.3.1 Assay" LOINC:55908-8 Alpha galactosidase A [Enzymatic activity/volume] in DBS lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:ncit_c41255 "6.3.4 Interpretation" NCIT:C78801 Value Below Reference Range lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:ncit_c82577 "6.3.5 Time Observed" 2019-06-22 - lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:ncit_c60819 "6.3.1 Assay" LOINC:2160-0 Creatinine [Mass/volume] in Serum or Plasma lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:ncit_c25712 "6.3.2 Measurement Value" 1.2 - lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:ncit_c92571 "6.3.3 Unit" UO:0010067 milligram per deciliter lexical 2025-01-01 manual
ADR002 "Patient ADR002" rarelink_cdm:ncit_c82577 "6.3.5 Time Observed" 2019-06-22 - lexical 2025-01-01 manual
#
# Mappings for Patient three, four and five are within the file below.
.. tip::
You can view and download all the example csv and sssom mapping files here:
`RareLink-CDM SSSOM Mapping Examples `_.
_____
Additional Resources
----------------------
- `LinkML Map Documentation `_
- `SSSOM Specification `_
- `RareLink-CDM Documentation `_
- `RareLink GitHub Repository `_
- `RareLink-CDM SSSOM Mapping Examples `_
- :download:`download the TSV template file directly `.