Merge pull request #742 from isb-cgc/staging

Staging

docs/source/sections/HowToGetStartedonISB-CGC.rst

@@ -2,7 +2,7 @@
 Quick-Start Guide
 ******************
 
-ISB-CGC provides both interactive (through a `web application <https://isb-cgc.appspot.com/>`_) and programmatic access to data hosted by institutes such as the Genomic Data Commons (GDC) of the National Cancer Institute (NCI), and the Wellcome Trust Sanger Institute, leveraging many aspects of the Google Cloud Platform. To get started, you'll need a Google Cloud Project. Additionally, to access controlled data, you'll also need `dbGaP authorization <Gaining-Access-To-Controlled-Access-Data.html>`_.
+ISB-CGC provides both interactive (through a `web application <https://isb-cgc.appspot.com/>`_) and programmatic access to data hosted by institutes such as the Genomic Data Commons (GDC) and the Protemoic Data Commons (PDC) of the National Cancer Institute (NCI) and Human Tumor Atlas Network (HTAN), leveraging many aspects of the Google Cloud Platform. To get started, you'll need a Google Cloud Project. Additionally, to access controlled data, you'll also need `dbGaP authorization <Gaining-Access-To-Controlled-Access-Data.html>`_.
 
 .. image:: GettingStarted.png
    :align: center

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

@@ -2,6 +2,60 @@
 ISB-CGC Data Release Notes
 ############################
 
+*August 24, 2023*
+
+New and Updated PDC v3.4 tables.
+
+**BigQuery tables created**
+
+- isb-cgc-bq.TCGA_versioned.per_sample_file_metadata_CPTAC_TCGA_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.per_sample_file_metadata_proteogenomic_translational_research_centers_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.per_sample_file_metadata_CPTAC3_discovery_and_confirmatory_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.quant_proteome_PTRC_HGSOC_FFPE_validation_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.quant_proteome_PTRC_HGSOC_FFPE_discovery_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.quant_phosphoproteome_PTRC_HGSOC_frozen_validation_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.quant_phosphoproteome_PTRC_HGSOC_FFPE_validation_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.quant_phosphoproteome_PTRC_HGSOC_FFPE_discovery_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.quant_proteome_PTRC_HGSOC_frozen_validation_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.quant_acetylome_CPTAC_UCEC_confirmatory_study_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.quant_proteome_CPTAC_UCEC_confirmatory_study_pdc_V3_4
+- isb-cgc-bq.CPTAC_versioned.quant_phosphoproteome_CPTAC_UCEC_confirmatory_study_pdc_V3_4
+- isb-cgc-bq.PDC_metadata_versioned.gene_info_V3_4
+- isb-cgc-bq.PDC_metadata_versioned.refseq_mapping_2023_03
+- isb-cgc-bq.PDC_metadata_versioned.aliquot_to_case_mapping_V3_4
+- isb-cgc-bq.PDC_metadata_versioned.case_metadata_V3_4
+- isb-cgc-bq.PDC_metadata_versioned.file_associated_entity_mapping_V3_4
+- isb-cgc-bq.PDC_metadata_versioned.file_metadata_V3_4
+- isb-cgc-bq.PDC_metadata_versioned.studies_V3_4
+- isb-cgc-bq.CPTAC.quant_proteome_PTRC_HGSOC_FFPE_validation_pdc_current
+- isb-cgc-bq.CPTAC.quant_proteome_PTRC_HGSOC_FFPE_discovery_pdc_current
+- isb-cgc-bq.CPTAC.quant_phosphoproteome_PTRC_HGSOC_frozen_validation_pdc_current
+- isb-cgc-bq.CPTAC.quant_phosphoproteome_PTRC_HGSOC_FFPE_validation_pdc_current
+- isb-cgc-bq.CPTAC.quant_phosphoproteome_PTRC_HGSOC_FFPE_discovery_pdc_current
+- isb-cgc-bq.CPTAC.quant_proteome_PTRC_HGSOC_frozen_validation_pdc_current
+- isb-cgc-bq.CPTAC.quant_acetylome_CPTAC_UCEC_confirmatory_study_pdc_current
+- isb-cgc-bq.CPTAC.quant_proteome_CPTAC_UCEC_confirmatory_study_pdc_current
+- isb-cgc-bq.CPTAC.quant_phosphoproteome_CPTAC_UCEC_confirmatory_study_pdc_current
+
+**BigQuery tables updated**
+
+- isb-cgc-bq.TCGA.per_sample_file_metadata_CPTAC_TCGA_pdc_current
+- isb-cgc-bq.CPTAC.per_sample_file_metadata_proteogenomic_translational_research_centers_pdc_current
+- isb-cgc-bq.CPTAC.per_sample_file_metadata_CPTAC3_discovery_and_confirmatory_pdc_current
+- isb-cgc-bq.PDC_metadata.gene_info_current
+- isb-cgc-bq.PDC_metadata.refseq_mapping_current
+- isb-cgc-bq.PDC_metadata.aliquot_to_case_mapping_current
+- isb-cgc-bq.PDC_metadata.case_metadata_current
+- isb-cgc-bq.CPTAC.clinical_proteogenomic_translational_research_centers_pdc_current
+- isb-cgc-bq.CPTAC_versioned.clinical_proteogenomic_translational_research_centers_pdc_V3_4
+- isb-cgc-bq.CPTAC.clinical_diagnoses_proteogenomic_translational_research_centers_pdc_current
+- isb-cgc-bq.CPTAC_versioned.clinical_diagnoses_proteogenomic_translational_research_centers_pdc_V3_4
+- isb-cgc-bq.CPTAC.clinical_CPTAC3_discovery_and_confirmatory_pdc_current
+- isb-cgc-bq.CPTAC_versioned.clinical_CPTAC3_discovery_and_confirmatory_pdc_V3_4
+- isb-cgc-bq.PDC_metadata.file_associated_entity_mapping_current
+- isb-cgc-bq.PDC_metadata.file_metadata_current
+- isb-cgc-bq.PDC_metadata.studies_current
+
 *July 31, 2023*
 
 New and updated per sample file metadata added to isb-cgc-bq for GDC release 37.