reorganization

* fixed image link
* added link to default schema for Pedigree
* changed navigation assignment; we should not add a "help" section w/o real need (the whole site is "help")

We will have to reconsider the overall layout of the content navigation at some point ...

docs/pedigree.md

@@ -1,10 +1,10 @@
 # Overview of the JSON schema *pedigree.json*
 
-The JSON schema for the pedigree data (*pedigree.json*) defines how members of a pedigree (family tree) are represented. It includes several key components:
+The [JSON schema for the pedigree data](https://github.com/ga4gh-beacon/beacon-v2/blob/main/models/src/beacon-v2-default-model/common/pedigree.yaml) defines how members of a pedigree (family tree) are represented. It includes several key components:
+
 1. **"id"**: A unique identifier for the **pedigree**, which is distinct from a family ID. This is because one individual can be involved in multiple pedigrees related to different diseases.
-<figure>
-<img src="/docs/img/Pedigree-image1.jpg" alt="Example schema"/>
-</figure>
+
+![Example pedigree schema](/img/Pedigree-image1.jpg)
 
 *Example: in case a proband (Proband 1) is affected by two diseases segregating in the family, they can be found in two pedigrees related to these different diseases (pedigree drawn here from the Proband 1 perspective showing all family members).*
 
@@ -18,11 +18,13 @@ The JSON schema for the pedigree data (*pedigree.json*) defines how members of a
 4. **"numSubjects"**: The total number of individuals in the pedigree. This simplifies queries by providing the total count, helping to avoid reconstructing the family tree repeatedly.
 
 # Asymmetry in "members":
+
 - If the schema is defined from the **proband's perspective**, all members (proband, parents, etc.) are included.
 - If defined from **another individual's perspective** (e.g., the mother), only two entries are included: the individual and the proband.
 This structure helps with flexibility in representing different family views and cases where an individual may appear in multiple pedigrees.
 
 # FAQs and considerations:
+
 **1. Is it necessary to include one pedigree for each disease an individual has?**
 
 **Answer**: No, it is not necessary to create a new pedigree for every disease an individual has. Doing so can overburden the system with redundant information, resulting in many pedigrees that may be of little to no interest. Instead, you should focus on the most relevant or impactful diseases for the family and research context.

mkdocs.yaml

@@ -21,11 +21,10 @@ nav:
         - Changes: changes-todo
         - FAQ ↗: https://genomebeacons.org/FAQ/
         - Beacon News ↗: https://genomebeacons.org/news/
-        - Help:
-            - How to describe a pedigree: pedigree
     - Using Beacons:
         - Genomic Queries: variant-queries
         - Phenotypes and More...: /filters/#using-filters-in-queries
+        - Pedigrees: pedigree
         - Data Delivery:
             - Biosamples, Variants...: records
             - Data Handovers: handovers