Merge pull request #697 from isb-cgc/staging

Staging
isb-cgc · Oct 17, 2022 · 2941080 · 2941080
2 parents 5a91cd1 + ad504f0
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diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -47,6 +47,7 @@ The `ISB-CGC <https://isb-cgc.org>`_ aims to serve the needs of a broad range of
    sections/data/Mitelman_about
    sections/the_TP53_database
    sections/SyntheticLethality_resource
+   sections/data/HTAN_about
    sections/ProgrammaticAccess
    sections/data/TCGA_Data_Security
    sections/Gaining-Access-To-Controlled-Access-Data

diff --git a/docs/source/sections/ReleaseNotes/ISB-CGCDataReleases.rst b/docs/source/sections/ReleaseNotes/ISB-CGCDataReleases.rst
@@ -2,6 +2,34 @@
 ISB-CGC Data Release Notes
 ############################
 
+
+*September 23, 2022*
+
+New clinical tables added to isb-cgc-bq for GDC release 34.
+
+**BigQuery tables created**
+
+- isb-cgc-bq.CTSP_versioned.clinical_gdc_r34
+- isb-cgc-bq.CPTAC_versioned.clinical_gdc_r34
+- isb-cgc-bq.BEATAML1_0_versioned.clinical_gdc_r34
+- isb-cgc-bq.CTSP_versioned.clinical_follow_ups_molecular_tests_gdc_r34
+- isb-cgc-bq.CTSP_versioned.clinical_follow_ups_gdc_r34
+- isb-cgc-bq.CTSP_versioned.clinical_diagnoses_treatments_gdc_r34
+- isb-cgc-bq.CTSP_versioned.clinical_diagnoses_gdc_r34
+
+Current clinical tables updated to GDC release 34.
+
+**BigQuery tables updated**
+
+- isb-cgc-bq.CTSP.clinical_gdc_current
+- isb-cgc-bq.CPTAC.clinical_gdc_current
+- isb-cgc-bq.BEATAML1_0.clinical_gdc_current
+- isb-cgc-bq.CTSP.clinical_follow_ups_molecular_tests_gdc_current
+- isb-cgc-bq.CTSP.clinical_follow_ups_gdc_current
+- isb-cgc-bq.CTSP.clinical_diagnoses_treatments_gdc_current
+- isb-cgc-bq.CTSP.clinical_diagnoses_gdc_current
+
+
 *September 22, 2022*
 
 New and updated PDC Quant V2.10 tables

diff --git a/docs/source/sections/ReleaseNotes/MitelmanReleaseNotes.rst b/docs/source/sections/ReleaseNotes/MitelmanReleaseNotes.rst
@@ -6,6 +6,16 @@ To search this database hosted by the ISB-CGC, please visit `Mitelman Database o
 
 For more detailed information about the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer, see `Mitelman Database <https://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/data/Mitelman_about.html>`_.
 
+*October 17, 2022*
+
+Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer quarterly update.
+
+**Updated totals**
+
+- Total number of cases 74,420
+- Total number of unique gene fusions 33,621
+- Total number of genes involved 14,068
+
 *July 27, 2022*
 
 Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer quarterly update.

diff --git a/docs/source/sections/data/HTAN_about.rst b/docs/source/sections/data/HTAN_about.rst
@@ -1,6 +1,6 @@
-*****************
-HTAN Data Set
-*****************
+******************************
+Human Tumor Atlas Network Data
+******************************
 
 About HTAN
 ------------------------------------------------------------------------
@@ -16,6 +16,7 @@ Data (Release 2) was extracted from the HTAN Data Portal via Synapse (https://hu
 
 To explore HTAN data, please see the `HTAN Data Portal <https://humantumoratlas.org/explore/>`_.
 
+Visit our `HTAN Notebooks <../HTANNotebooks.html>`_ page to see examples using the ISB-CGC hosted HTAN data.
 
 Accessing the HTAN Data in Google BigQuery
 ------------------------------------------------