113 phenopacket pipeline (#115)

* updates * update data dic * updated cli * updates and new structure * clean up and sort * clean up * clean * clean up and move * clean * structure update * fix * updated structure * added process redcap function code * added mapping structure and logic * updated export functions to linkml * updated download records with modulatiry * fix * fixed cli issue * updates and fixes for transfer to linkml schema * update for env cli * added parsing dates and months and years * upda * implemented pipeline first phenopackets * fixed * fix * added fuction timeselement * addded processor and more modularity * created by dynamically generated * update * fix * dwa * fixed label fetching from internal value sets * test * update * fixes * f * fixes * fwa * fixed validation * update * fix and clean * added disease block * delted old test * fixes * updates * fix * fixes * da * updates * fixes * updates * excluded still does not work * fixed excluded * fix * fixed excluded in disease block * clean map_disease * fix * clean up * made disease mapping modular fix * added interpretations block * added genetics e´neaerly completely * updates * del * data dic * update * fixed logic for genetics * finished genetics mapping * added phenotypic * added phenotypes to pipeline * updated * update * added pytest * fix * updated mappings from dogukan * updates * updates final touch * updated overview figure
BIH-CEI · Jan 19, 2025 · d8ee6a8 · d8ee6a8
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diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -190,4 +190,7 @@ rarelink-cdm-processed.json
 rarelink_apiconfig.json
 
 # Local FHIR server configuration
-hapi-fhir
+hapi-fhir
+
+# test data
+.res/phenopackets_test/
diff --git a/docs/.DS_Store b/docs/.DS_Store
diff --git a/docs/1_background/1_0_background_file.rst b/docs/1_background/1_0_background_file.rst
@@ -1,7 +1,7 @@
 .. _1_0:
 
 Background
-==========
+=============
 
 RareLink was developed as a response to the widespread challenges in rare 
 disease (RD) data management, specifically the lack of interoperability and 

diff --git a/docs/1_background/1_2_ontologies.rst b/docs/1_background/1_2_ontologies.rst
@@ -34,6 +34,7 @@ Ontologies used in RareLink
 The following codesystems are used in the RareLink Core Framework:
 
 .. fields: Ontologies Used in RareLink
+
 :`ICD-10 & ICD-11 <https://www.who.int/standards/classifications/classification-of-diseases>`_: 
     The **International Statistical Classification of Diseases** is used for 
     documenting morbidity in healthcare systems, encoding mortality statistics, 
@@ -92,9 +93,8 @@ The following codesystems are used in the RareLink Core Framework:
     The **Sequence Ontology** provides standardized vocabulary for genomic 
     annotation components, enhancing sharing and analysis of genomic information.
 
-
 .. note:: The versions used by the RareLink Core Framework can be found here: 
-    `RareLink Ontologies <
+    `RareLink Ontologies <https://github.com/BIH-CEI/rarelink/blob/develop/src/rarelink_cdm/v2_0_0_dev0/datamodel/rarelink_code_systems.py>`_.
 
 Further Reading
 ---------------

diff --git a/docs/2_rarelink_framework/2_0_rarelink_file.rst b/docs/2_rarelink_framework/2_0_rarelink_file.rst
@@ -3,11 +3,6 @@
 RareLink Framework
 ==================
 
-.. attention::
-   To use your local REDCap project, you will need to set up a local REDCap 
-   instance. For this please contact your local REDCap administratior. A project
-   name could for example be "RareLink - Your local REDCap location". 
-
 In this section we elaborate on the development of the RareLink framework, how 
 it is designed to facilitate the management of rare disease data, and how it
 supports the creation of interoperable and reusable datasets. We provide an