Cc4k5.2.0

content/2.cc4k/1.index.md

@@ -6,6 +6,58 @@ navigation:
 
 CC4K (Cancer Classifications for Kids) provides a harmonized, computable pediatric cancer classification framework used across [St. Jude Cloud](https://stjude.cloud) and by the [CCDI Federated API](https://github.com/CBIIT/ccdi-federation-api).
 
+## v0.5.2
+
+Submitted: xx xx, 2026
+
+Click [here](){target="_blank"} to download.
+
+Version 0.5.2 delivers a restructuring update to the CC4K ontology, primarily within the Solid Tumor hierarchy, following pathologist recommendations and sample reclassifications.
+This release renames 6 classifications, repositions 8 nodes within the tree, removes 8 ambiguous nodes, and introduces 6 new disease nodes, with approximately 104 samples reclassified as a result.
+These changes correct classification inconsistencies and replace outdated or ambiguous terms to improve the accuracy of the tree.
+The following sections detail each of these changes.
+
+### A. Renamed (6):
+
+- **Follicular Thyroid Carcinoma** — updated from *Follicular Thyroid, NOS* to reflect a more precise clinical classification.
+- **Oncocytic Thyroid Carcinoma** — replaces *Hurthle Cell Thyroid Cancer*, adopting current WHO terminology.
+- **Poorly Differentiated Thyroid Carcinoma** — updated from *Poorly Differentiated Thyroid Tumor*, adopting WHO accepted terminology.
+- **Renal Cell Carcinoma, NOS** — replaces *Renal Cell Carcinoma* to remove ambiguity, as RCC encompasses many distinct subtypes.
+- **Infantile Hemangioma** — replaces *Infantile Hemangioendothelioma*, a term no longer recommended, in favor of WHO accepted terminology.
+- **Thymic Carcinoma** — replaces *Intrathyroidal Thymic Carcinoma*, realigned with standard clinical terminology.
+
+### B. Rearranged (8):
+
+The following nodes were misclassified and repositioned within the hierarchy following pathologist review and research validation.
+
+| Node                                                                                                                    | Previous Location                                                           | New Location                                                           |
+|-------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------|------------------------------------------------------------------------|
+| Juvenile Xanthogranuloma                                                                                                | Solid Tumor → Renal Tumors                                                  | Hematologic Malignancies → Other Hematologic Malignancies              |
+| Embryonal Sarcoma of the Liver                                                                                          | Solid Tumor → Undifferentiated Tumors                                       | Solid Tumor → Digestive System Tumors → Liver Tumors                   |
+| Spindle Cell Sarcoma, Spindle Cell Tumor, Undifferentiated Round Cell Sarcoma, and Undifferentiated Pleomorphic Sarcoma | Solid Tumor → Undifferentiated Tumors                                       | Solid Tumor → Soft Tissue Tumors → Tumors of Uncertain Differentiation |
+| Neurothekeoma                                                                                                           | Solid Tumors → Soft Tissue Tumors → Fibroblastic and Myofibroblastic Tumors | Solid Tumors → Skin Tumors                                             |
+| Signet Ring Cell Carcinoma                                                                                              | Solid Tumor → Genital Tumors                                                | Solid Tumor → Digestive System Tumors → Gastrointestinal Tumors        |
+
+*Table 1: CC4K v0.5.2 Nodes Repositioned Within the Hierarchy.*
+
+### C. Deprecated (8):
+
+- **Solid Cancer of Unknown Primary; Epithelioid Neoplasm, NOS; Metastatic Tumor, NOS; Mesenchymal Tumor, NOS; Myxoid Neoplasm, NOS; and Primitive Round Cell Neoplasm** — removed as these classifications were deemed ambiguous and imprecise.
+Samples previously tagged to these nodes have been reassigned to *Solid Tumor, NOS*.
+- **Thyroid Hyperplastic Nodule** — removed as this is a subset of *Thyroid Follicular Nodular Disease*, under which its samples have been reassigned.
+- **Myofibroblastic Sarcoma, NOS** — removed as this is a subset of *Myofibroblastic Neoplasm, NOS*, under which its samples have been reassigned.
+
+### D. New (6):
+
+This release adds six new disease classifications identified through curated case studies requiring formal classification within the tree: **Ganglioneuroblastoma, Nodular**; **Renal Cell Carcinoma with MiT Translocations**; **Histiocytic Neoplasm, NOS**; **Hybrid Nerve Sheath Tumor**; **Adamantinoma**; and **Fibroepithelial Tumor**.
+These nodes were informed by pathologist recommendations and ongoing case review, with samples previously assigned to broader classifications found to more accurately fit these newly introduced nodes.
+Their addition improves classification precision and maintains alignment with the WHO 5th Edition Classification of Tumors: Pediatric Tumors.
+
+A number of classifications were recommended for addition to the Solid Tumor tree but were deferred from this release as the current PeCan/Genomics Platform databases do not yet have sample representation for these nodes.
+Development releases, such as this one, prioritize structural accuracy and classification consistency for nodes already represented by samples.
+New nodes introduced primarily in alignment with the latest edition of WHO Pediatric Tumors are being evaluated for inclusion in upcoming releases.
+We welcome feedback on prioritization as we continue to expand the hierarchy.
+
 ## v0.5.1
 
 Submitted: April 14, 2026

content/4.pecan/1.overview/1.getting-started.md

@@ -7,7 +7,7 @@ navigation:
 The PeCan platform presents curated pediatric cancer genomics data including variants, mutational signatures, and gene expression data in addition to histological slide images from over 11,000 hematological, CNS, and non-CNS solid tumor patient samples.
 
 Data can be explored via a series of data facets containing both retrospective and prospective study cohorts from St. Jude Children's Research Hospital and other trusted institutions and research centers around the world such as [TARGET](https://ocg.cancer.gov/programs/target), [DKFZ](https://www.dkfz.de/en/index.html), and many others.
-Learn more about the data [here](/pecan/overview/methods-and-data).
+[Learn more about the data](/pecan/overview/methods-and-data).
 
 ![logos](/img/pecan/overview/getting-started/logos.png)
 
@@ -49,7 +49,7 @@ Users can expand any node to reveal its subtypes, with sample counts displayed a
 A tooltip on each node provides additional details and quick navigation to each data facet to view the available data.
 The tree can be downloaded as an SVG for external use.
 
-![PeCan Subtype Tree](/img/pecan/overview/getting-started/subtype_tree.png)
+![PeCan Subtype Tree](/img/pecan/overview/getting-started/Subtype_Tree.png)
 
 **Figure 3: Subtype Tree**
 A user is able to explore the tree by selecting the interactive nodes.

deployment/preview/pr178/app.yaml

@@ -0,0 +1,88 @@
+---
+apiVersion: helm.toolkit.fluxcd.io/v2beta1
+kind: HelmRelease
+metadata:
+  name: docs
+  namespace: docs-pr178
+spec:
+  interval: 30m
+  chart:
+    spec:
+      chart: generic
+      version: 1.1.x
+      sourceRef:
+        kind: HelmRepository
+        name: stjudecloud
+        namespace: flux-system
+      interval: 1h
+  values:
+    nameOverride: docs
+    extraDeploy:
+      - |
+        apiVersion: v1
+        kind: Service
+        metadata:
+          name: {{ template "common.names.fullname" . }}-oauth-bridge
+          labels: {{- include "common.labels.standard" . | nindent 4 }}
+            {{- if .Values.commonLabels }}
+            {{- include "common.tplvalues.render" ( dict "value" .Values.commonLabels "context" $ ) | nindent 4 }}
+            {{- end }}
+          {{- if .Values.commonAnnotations }}
+          annotations: {{- include "common.tplvalues.render" ( dict "value" .Values.commonAnnotations "context" $ ) | nindent 4 }}
+          {{- end }}
+        spec:
+          type: ExternalName
+          externalName: oauth2-proxy.oauth2-proxy
+      - |
+        ---
+        apiVersion: networking.k8s.io/v1
+        kind: Ingress
+        metadata:
+          name: {{ .Release.Name }}-oauth
+        spec:
+          ingressClassName: nginx
+          rules:
+          - host: {{ .Values.ingress.hostname }}
+            http:
+              paths:
+                - backend:
+                    service:
+                      name: {{ template "common.names.fullname" . }}-oauth-bridge
+                      port:
+                        number: 80
+                  path: /oauth2
+                  pathType: ImplementationSpecific
+          tls:
+          - hosts:
+            - {{ .Values.ingress.hostname }}
+            secretName: {{ .Values.ingress.hostname }}-tls
+    image:
+      repository: stjudecloud/docs
+      tag: latest # {"$imagepolicy": "flux-system:docs-pr178:tag"}
+    podAnnotations:
+      linkerd.io/inject: enabled
+      config.linkerd.io/proxy-cpu-request: 20m
+    containerPorts:
+      http: 3000
+    service:
+      ports:
+        - name: http
+          protocol: TCP
+          port: 3000
+          targetPort: http
+    ingress:
+      enabled: true
+      hostname: docs-pr178.staging.stjude.cloud
+      path: /
+      annotations:
+        cert-manager.io/cluster-issuer: letsencrypt-prod
+        linkerd.io/inject: ingress
+        nginx.ingress.kubernetes.io/auth-signin: https://$host/oauth2/start?rd=$escaped_request_uri
+        nginx.ingress.kubernetes.io/auth-url: https://$host/oauth2/auth
+        nginx.ingress.kubernetes.io/service-upstream: "true"
+        nginx.ingress.kubernetes.io/enable-modsecurity: "true"
+        nginx.ingress.kubernetes.io/enable-owasp-core-rules: "true"
+      tls:
+        enabled: true
+    datadog:
+      enabled: false