Merge pull request #765 from isb-cgc/Deena-Staging-Theme

Deena staging theme

docs/source/sections/Hosted-Data.rst

@@ -37,7 +37,7 @@ Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are avail
      - ISB-CGC Cohort Builder
    * - `APOLLO <data/APOLLO_about.html>`_
      - |checkmark| 
-     - |checkmark| 
+     - |checkmark| *
      - 
    * - `BEATAML <data/BEATAML_about.html>`_
      - |checkmark| 

docs/source/sections/ReleaseNotes/ISB-CGCDataReleases.rst

@@ -2,7 +2,112 @@
 ISB-CGC Data Release Notes
 ############################
 
-*September 16, 2023*
+*October 31, 2023*
+
+New HTAN tables.
+
+**BigQuery tables created**
+
+- isb-cgc-bq.HTAN.tissueOrOrganOfOrigin_to_wholeOrgan_mapping_current
+- isb-cgc-bq.HTAN.imaging_level4_HTAPP_merfish_current
+- isb-cgc-bq.HTAN.imaging_level4_Duke_mibi_current
+- isb-cgc-bq.HTAN.imaging_level4_TNP_TMA_phase3_current
+- isb-cgc-bq.HTAN.imaging_level4_TNP_TMA_phase1_current
+- isb-cgc-bq.HTAN.imaging_level4_HMS_orion_current
+- isb-cgc-bq.HTAN.id_provenance_current
+- isb-cgc-bq.HTAN.schema_current
+- isb-cgc-bq.HTAN.imaging_channel_metadata_current
+- isb-cgc-bq.HTAN.clinical_tier1_therapy_current
+- isb-cgc-bq.HTAN.scRNAseq_level4_metadata_current
+- isb-cgc-bq.HTAN.scRNAseq_level3_metadata_current
+- isb-cgc-bq.HTAN.scRNAseq_level2_metadata_current
+- isb-cgc-bq.HTAN.scRNAseq_level1_metadata_current
+- isb-cgc-bq.HTAN.scATACseq_level4_metadata_current
+- isb-cgc-bq.HTAN.scATACseq_level3_metadata_current
+- isb-cgc-bq.HTAN.scATACseq_level2_metadata_current
+- isb-cgc-bq.HTAN.scATACseq_level1_metadata_current
+- isb-cgc-bq.HTAN.clinical_tier3_brain_current
+- isb-cgc-bq.HTAN.clinical_tier1_moleculartest_current
+- isb-cgc-bq.HTAN.massSpectrometry_level4_metadata_current
+- isb-cgc-bq.HTAN.massSpectrometry_level3_metadata_current
+- isb-cgc-bq.HTAN.massSpectrometry_level1_metadata_current
+- isb-cgc-bq.HTAN.clinical_tier3_lung_current
+- isb-cgc-bq.HTAN.imaging_level4_metadata_current
+- isb-cgc-bq.HTAN.imaging_level3_segmentation_metadata_current
+- isb-cgc-bq.HTAN.imaging_level2_metadata_current
+- isb-cgc-bq.HTAN.hiCseq_level2_metadata_current
+- isb-cgc-bq.HTAN.hiCseq_level1_metadata_current
+- isb-cgc-bq.HTAN.clinical_tier1_followup_current
+- isb-cgc-bq.HTAN.clinical_tier1_familyhistory_current
+- isb-cgc-bq.HTAN.clinical_tier1_exposure_current
+- isb-cgc-bq.HTAN.clinical_tier1_diagnosis_current
+- isb-cgc-bq.HTAN.clinical_tier1_demographics_current
+- isb-cgc-bq.HTAN.clinical_tier2_current
+- isb-cgc-bq.HTAN.bulkWES_level3_metadata_current
+- isb-cgc-bq.HTAN.bulkWES_level2_metadata_current
+- isb-cgc-bq.HTAN.bulkWES_level1_metadata_current
+- isb-cgc-bq.HTAN.bulkRNAseq_level3_metadata_current
+- isb-cgc-bq.HTAN.bulkRNAseq_level2_metadata_current
+- isb-cgc-bq.HTAN.bulkRNAseq_level1_metadata_current
+- isb-cgc-bq.HTAN.bulkMethylationseq_level2_metadata_current
+- isb-cgc-bq.HTAN.bulkMethylationseq_level1_metadata_current
+- isb-cgc-bq.HTAN.clinical_tier3_breast_current
+- isb-cgc-bq.HTAN.biospecimen_current
+- isb-cgc-bq.HTAN.10xvisium_spatialtranscriptomics_scRNAseq_level3_metadata_current
+- isb-cgc-bq.HTAN.10xvisium_spatialtranscriptomics_scRNAseq_level2_metadata_current
+- isb-cgc-bq.HTAN.10xvisium_spatialtranscriptomics_scRNAseq_level1_metadata_current
+- isb-cgc-bq.HTAN.10xvisium_spatialtranscriptomics_auxiliaryfiles_metadata_current
+- isb-cgc-bq.HTAN_versioned.tissueOrOrganOfOrigin_to_wholeOrgan_mapping_r4
+- isb-cgc-bq.HTAN_versioned.imaging_level4_HTAPP_merfish_r4
+- isb-cgc-bq.HTAN_versioned.imaging_level4_Duke_mibi_r4
+- isb-cgc-bq.HTAN_versioned.imaging_level4_TNP_TMA_phase3_r4
+- isb-cgc-bq.HTAN_versioned.imaging_level4_TNP_TMA_phase1_r4
+- isb-cgc-bq.HTAN_versioned.imaging_level4_HMS_orion_r4
+- isb-cgc-bq.HTAN_versioned.id_provenance_r4
+- isb-cgc-bq.HTAN_versioned.schema_r4
+- isb-cgc-bq.HTAN_versioned.imaging_channel_metadata_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier1_therapy_r4
+- isb-cgc-bq.HTAN_versioned.scRNAseq_level4_metadata_r4
+- isb-cgc-bq.HTAN_versioned.scRNAseq_level3_metadata_r4
+- isb-cgc-bq.HTAN_versioned.scRNAseq_level2_metadata_r4
+- isb-cgc-bq.HTAN_versioned.scRNAseq_level1_metadata_r4
+- isb-cgc-bq.HTAN_versioned.scATACseq_level4_metadata_r4
+- isb-cgc-bq.HTAN_versioned.scATACseq_level3_metadata_r4
+- isb-cgc-bq.HTAN_versioned.scATACseq_level2_metadata_r4
+- isb-cgc-bq.HTAN_versioned.scATACseq_level1_metadata_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier3_brain_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier1_moleculartest_r4
+- isb-cgc-bq.HTAN_versioned.massSpectrometry_level4_metadata_r4
+- isb-cgc-bq.HTAN_versioned.massSpectrometry_level3_metadata_r4
+- isb-cgc-bq.HTAN_versioned.massSpectrometry_level1_metadata_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier3_lung_r4
+- isb-cgc-bq.HTAN_versioned.imaging_level4_metadata_r4
+- isb-cgc-bq.HTAN_versioned.imaging_level3_segmentation_metadata_r4
+- isb-cgc-bq.HTAN_versioned.imaging_level2_metadata_r4
+- isb-cgc-bq.HTAN_versioned.hiCseq_level2_metadata_r4
+- isb-cgc-bq.HTAN_versioned.hiCseq_level1_metadata_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier1_followup_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier1_familyhistory_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier1_exposure_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier1_diagnosis_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier1_demographics_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier2_r4
+- isb-cgc-bq.HTAN_versioned.bulkWES_level3_metadata_r4
+- isb-cgc-bq.HTAN_versioned.bulkWES_level2_metadata_r4
+- isb-cgc-bq.HTAN_versioned.bulkWES_level1_metadata_r4
+- isb-cgc-bq.HTAN_versioned.bulkRNAseq_level3_metadata_r4
+- isb-cgc-bq.HTAN_versioned.bulkRNAseq_level2_metadata_r4
+- isb-cgc-bq.HTAN_versioned.bulkRNAseq_level1_metadata_r4
+- isb-cgc-bq.HTAN_versioned.bulkMethylationseq_level2_metadata_r4
+- isb-cgc-bq.HTAN_versioned.bulkMethylationseq_level1_metadata_r4
+- isb-cgc-bq.HTAN_versioned.clinical_tier3_breast_r4
+- isb-cgc-bq.HTAN_versioned.biospecimen_r4
+- isb-cgc-bq.HTAN_versioned.10xvisium_spatialtranscriptomics_scRNAseq_level3_metadata_r4
+- isb-cgc-bq.HTAN_versioned.10xvisium_spatialtranscriptomics_scRNAseq_level2_metadata_r4
+- isb-cgc-bq.HTAN_versioned.10xvisium_spatialtranscriptomics_scRNAseq_level1_metadata_r4
+- isb-cgc-bq.HTAN_versioned.10xvisium_spatialtranscriptomics_auxiliaryfiles_metadata_r4
+
+*October 16, 2023*
 
 New masked somatic mutation data added to isb-cgc-bq for GDC release 37.
 

docs/source/sections/data/COSMIC_about.rst

@@ -0,0 +1,11 @@
+***************
+COSMIC Data Set
+***************
+
+About the Catalog Of Somatic Mutations In Cancer
+-------------------------------------------------
+
+The `Catalogue Of Somatic Mutations In Cancer <https://cancer.sanger.ac.uk/cosmic>`_ (COSMIC) is the world's largest and most comprehensive resource
+for exploring the impact of somatic mutations in human cancer. 
+
+ISB-CGC no longer hosts COSMIC data.

docs/source/sections/data/TCGA-images.rst

@@ -22,9 +22,6 @@ The metadata table also includes the patient identifier in TCGA "barcode" format
 Pathology Images
 ################
 
-.. note::
-   All tissue slide images from the TCGA program are currently unavailable for viewing.  (Diagnostic images will display.)
-
 Over 30,000 TCGA tissue slide images in `SVS <http://openslide.org/formats/aperio/>`_ format, are also available in GCS, in the open-access bucket `gs://gdc-tcga-phs000178-open/ <https://console.cloud.google.com/storage/browser/gdc-tcga-phs000178-open/>`_.
 
 These files were uploaded from the `GDC legacy archive <https://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_format%22,%22value%22:%5B%22SVS%22%5D%7D%7D%5D%7D>`_.