BIH-CEI · aslgraefe · Mar 29, 2026 · Dec 12, 2025 · Dec 15, 2025 · Dec 15, 2025
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -170,13 +170,18 @@ templates/
 # Ignore template files from Public folder
 Public/
 
+# ignore dev folders
+dev/
+
 # Temporary REDCap test config
 *.rarelink_test_redcap_config.json
 
 # DS Store
+# macOS metadata
+.DS_Store
+**/.DS_Store
 .DS_Store/
 .DS_Store?
-.DS_Store
 .src/.DS_Store?
 .src/rarelink/.DS_Store?
 .src/rarelink/utils/.DS_Store?

diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@
 #### Packages & Compatibility
 
 [![REDCap](https://img.shields.io/badge/REDCap-API-darkred.svg)](https://www.project-redcap.org/)
-[![RD-CDM](https://img.shields.io/badge/RD--CDM-v2.0.2-blue.svg)](https://github.com/BIH-CEI/rd-cdm)
+[![RD-CDM](https://img.shields.io/badge/RD--CDM-v2.0.3-blue.svg)](https://github.com/BIH-CEI/rd-cdm)
 [![Phenopackets](https://img.shields.io/badge/Phenopackets-v2.0-purple.svg)](https://phenopacket-schema.readthedocs.io/en/latest/)
 [![LinkML](https://img.shields.io/badge/LinkML-1.9.0+-green.svg)](https://linkml.io/)
 [![HL7 FHIR](https://img.shields.io/badge/HL7%20FHIR-R4-orange.svg)](https://hl7.org/fhir/)
@@ -116,37 +116,38 @@ Documentation on [Setting Up a REDCap Project](https://rarelink.readthedocs.io/e
 
 ## Installation
 
-RareLink can be set up using various Python project management approaches. One
- common method is to use a virtual environment. Below is an example where the
-  virtual environment is named `rarelink-venv`, but you can name it as you prefer:
-
+RareLink requires Python ≥3.10 and <3.13.
 ```bash
 python3.12 -m venv .venv
 source .venv/bin/activate
 pip install --upgrade pip
 ```
 
-> **Note**: You need Python ≥3.10 but <3.13 to be able to use RareLink! 
-
-Next, install rarelink through pypi...
-
+### Core install
 ```bash
 pip install rarelink
 ```
 
-... or clone the RareLink repository, navigate to its root directory, and
- install RareLink using:
+This installs everything needed for REDCap interaction, Phenopacket export,
+and the RareLink CLI. It does **not** install Docker, numpy/pandas, or
+documentation/testing tools.
 
-```bash
-git clone https://github.com/BIH-CEI/rarelink.git
-cd rarelink
-pip install .
-```
+### Optional extras
 
-If you want to install development dependencies (e.g., `pytest`), use:
+| Extra | Install command | What it adds |
+|-------|----------------|--------------|
+| `fhir` | `pip install rarelink[fhir]` | Docker SDK for the toFHIR FHIR export pipeline |
+| `data` | `pip install rarelink[data]` | numpy + pandas for tabular data processing |
+| `test` | `pip install rarelink[test]` | pytest and pytest-mock |
+| `docs` | `pip install rarelink[docs]` | Sphinx and documentation themes |
+| `dev` | `pip install rarelink[dev]` | All of the above plus build/twine/jupyter |
 
+For development:
 ```bash
-pip install .[dev]
+git clone https://github.com/BIH-CEI/rarelink.git
+cd rarelink
+pip install -e .[dev]
+pytest
 ```
 
 ### Setting Up the `.env` File

diff --git a/docs/.DS_Store b/docs/.DS_Store
diff --git a/docs/2_rarelink_framework/2_1_rarelink_overview.rst b/docs/2_rarelink_framework/2_1_rarelink_overview.rst
@@ -16,17 +16,17 @@ GA4GH Phenopackets, without the need for additional coding or mapping.
 As a result, RareLink allows researchers and clinicians to collect and process
 RD data seamlessly within the REDCap environment.
 
-.. figure:: ../_static/res/rarelink_overview.svg
+.. figure:: ../_static/res/rarelink_overview.png
 
     Overview of the RareLink framework integrated with a local REDCap instance. 
-    The framework comprises the RareLink instruments based on the RD-CDM, the 
-    RareLink API, the toFHIR & CDIS module for export and import to HL7 FHIR IPS
-    and Genomic Reporting Resources, and the RareLink-Phenopackets module for 
+    The framework comprises the REDCap instruments based on the `RD-CDM <https://www.nature.com/articles/s41597-025-04558-z>`_,  
+    the RareLink API, the toFHIR & CDIS module for export and import to HL7 FHIR 
+    IPS and Genomic Reporting Resources, and the RareLink-Phenopackets module for 
     direct export to GA4GH Phenopackets. Additionally, the LinkML-based import 
     mapper facilitates data import from tabular databases into REDCap, while 
     the Manual Data Capture Guide assists with the manual data capture of 
-    RD-CDM data in a local REDCap project. Click `here <https://github.com/BIH-CEI/rarelink/blob/develop/docs/_static/res/rarelink_overview.svg>`_ 
-    to see the figure in full size.
+    RD-CDM data in a local REDCap project. The framework is also configurable
+    for disease-specific extensions or custom data models.
 
 .. note:: 
     You will need your own REDCap instance to deploy the RareLink framework.

diff --git a/docs/2_rarelink_framework/2_2_rarelink_cdm.rst b/docs/2_rarelink_framework/2_2_rarelink_cdm.rst
@@ -161,7 +161,7 @@ Example Field Annotation of 6.2.6 Temporal Pattern:
     - HP:0012829 | Profound  
     - HP:0012828 | Severe  
     Version(s): 
-    - HPO Version 2025-05-06  
+    - HPO Version 2026-02-16  
     Mapping: 
     - HL7 FHIR Expression v4.0.1: Observation.interpretation  
     - GA4GH Phenopacket Schema v2.0 Element: PhenotypicFeature.severity
@@ -315,7 +315,7 @@ ______________________________________________________________
   - Cardinality: Required (1..1)
   - Validation: Date format (YYYY-MM-DD)
 
-- 2.2 Sex at Birth (``snomedct_281053000``)
+- 2.2 Sex at Birth (``loinc_76689_9``)
 
   - Cardinality: Optional
   - Validation: Dropdown (choices encoded according to :ref:`1_5`)

diff --git a/docs/3_installation/3_1_setup_rarelink_framework.rst b/docs/3_installation/3_1_setup_rarelink_framework.rst
@@ -24,41 +24,57 @@ Follow these steps to set up the project locally and run tests.
       source .venv/bin/activate  # On macOS/Linux
       .venv\Scripts\activate     # On Windows
 
-3. Install dependencies:
+3. Install RareLink:
 
 .. code-block:: bash
 
-      pip install .
+      pip install rarelink
+
+This installs everything needed for REDCap interaction, Phenopacket export,
+and the RareLink CLI.
+
+For optional features, install the relevant extras:
+
+.. code-block:: bash
+
+      pip install rarelink[fhir]    # adds Docker SDK for the toFHIR pipeline
+      pip install rarelink[data]    # adds numpy and pandas for tabular data processing
+
+For development (includes testing, docs, and all optional extras):
+
+.. code-block:: bash
+
+      pip install -e .[dev]
 
 4. Configure all api keys necessary to use rarelink by running the following
 command:
 
 .. code-block:: bash
 
-    rarelink setup keys 
+    rarelink setup keys
 
     This command will prompt you to enter the following keys:
     - BioPortal API key
     - REDCap API key
     - REDCap URL
     - REDCap project ID
 
-.. note:: 
+.. note::
     You can create your free BioPortal account here: `BioPortal <https://bioportal.bioontology.org/>`_
 
 5. Run tests:
-   Use `pytest` to run the test suite.
-
+
 .. code-block:: bash
 
+      pip install rarelink[test]
       pytest
 
 _____________________________________________________________________________________
 
 RareLink Framework CLI config
 ------------------------------------
 
-Use the following commands to update the framework and its components, view 
+Use the following commands to update the framework and its components, view
 its status or reset the framework. See :ref:`2_3` for more information.
 
 .. code-block:: bash
@@ -91,32 +107,37 @@ ________________________________________________________________________________
 Phenopacket Pipeline Configuration
 ___________________________________
 
-Via the RareLink CLI type:
+The Phenopacket export pipeline requires a BioPortal API key and a
+``CREATED_BY`` value, both configured via:
 
 .. code-block:: bash
 
-    to be implemented
+    rarelink setup keys
 
-This command guides you through setting up the Phenopacket pipeline for RareLink.
-You will be prompted to enter:
-- Your location where to store the Phenopackets.
+Once configured, export Phenopackets with:
+
+.. code-block:: bash
+
+    rarelink phenopackets export --help
 
 _____________________________________________________________________________________
 
 FHIR Pipeline Configuration
 ___________________________
 
+.. note::
+    The FHIR pipeline requires the ``fhir`` extra: ``pip install rarelink[fhir]``
+
 .. code-block:: bash
 
     rarelink fhir setup
 
-This command guides you through setting up the FHIR pipeline for RareLink. 
+This command guides you through setting up the FHIR pipeline for RareLink.
 You will be prompted to enter:
 
 - Your FHIR server URL.
 - If required, your FHIR server username & password.
 
-.. note:: 
-    All sensitive information will also be stored in the 
-    hidden configuration file.
-
+.. note::
+    All sensitive information will also be stored in the
+    hidden configuration file.
diff --git a/docs/4_user_guide/4_1_manual_data_capture.rst b/docs/4_user_guide/4_1_manual_data_capture.rst
@@ -354,7 +354,8 @@ Fields:
 
     1. Validate mutations using `ClinVar <https://www.ncbi.nlm.nih.gov/clinvar/>`_
        or `Varsome <https://varsome.com/>`_.
-    2. Confirm the expression with the `HGVS Validator <https://lhcforms.nlm.nih.gov/fhir/hgvs-validator/>`_.
+    2. Confirm the expression with the `Variant Validator <https://variantvalidator.org/service/validate/>`_ 
+       or the `HGVS Validator <https://lhcforms.nlm.nih.gov/fhir/hgvs-validator/>`_.
     3. If the validation fails, enter the details in the **6.1.6 Genetic Mutation String** field.
     4. ``*``: **Are you sure the entered HGVS expression was validated using 
        the variant validator?** - this field is mandatory to ensure the

diff --git a/docs/4_user_guide/4_2_import_mapper.rst b/docs/4_user_guide/4_2_import_mapper.rst
@@ -187,7 +187,7 @@ The template contains the following columns:
   RareLink-CDM schema, for example:
 
   - ``rarelink_cdm:snomedct_184099003`` for 2.1 Date of birth, or 
-  - ``rarelink_cdm:snomedct_281053000`` for 2.2 Sex at birth. 
+  - ``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
@@ -198,7 +198,7 @@ The template contains the following columns:
   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., "SNOMEDCT:248152002" for female) or the code from the code system defined
+  (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
@@ -255,7 +255,7 @@ Below you can find a **snippet of the RareLink-CDM SSSOM Template File:**
    #
    # === Personal Information (Singular) ===
    <record_id>	"<source_label>"	rarelink_cdm:snomedct_184099003	"2.1 Date of birth"	<dob>	-	lexical	<mapping_date>	manual
-   <record_id>	"<source_label>"	rarelink_cdm:snomedct_281053000	"2.2 Sex at birth"	<SNOMEDCT_sex_code>	<sex_label>	lexical	<mapping_date>	manual
+   <record_id>	"<source_label>"	rarelink_cdm:loinc_76689_9	"2.2 Sex at birth"	<SNOMEDCT_sex_code>	<sex_label>	lexical	<mapping_date>	manual
    <record_id>	"<source_label>"	rarelink_cdm:snomedct_1296886006	"2.3 Karyotypic Sex"	<karyotype_code>	<karyotype_label>	lexical	<mapping_date>	manual
    <record_id>	"<source_label>"	rarelink_cdm:snomedct_263493000	"2.4 Gender Identity"	<SNOMEDCT_gender_code>	<gender_identity_label>	lexical	<mapping_date>	manual
    <record_id>	"<source_label>"	rarelink_cdm:snomedct_370159000	"2.5 Country of birth"	<ISO3166_code>	<ISO3166_code>	lexical	<mapping_date>	manual
@@ -447,7 +447,7 @@ 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:snomedct_281053000	"2.2 Sex at birth"	SNOMEDCT:248152002	Female	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
@@ -475,7 +475,7 @@ schema.
    # 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:snomedct_281053000	"2.2 Sex at birth"	SNOMEDCT:248153007	Male	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