Merge pull request #753 from isb-cgc/master

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isb-cgc · Jan 17, 2024 · b169400 · b169400
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diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,2 +1,3 @@
-sphinx==4.2.0
-docutils==0.16
+sphinx==6.2.1
+sphinx-rtd-theme==1.2.2
+docutils==0.18.1
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -44,23 +44,36 @@ The `ISB-CGC <https://isb-cgc.org>`_ aims to serve the needs of a broad range of
    sections/Web-UI
    sections/DataExplorer
    sections/DataBrowser
+   sections/data/TCGA_Data_Security
+   sections/Gaining-Access-To-Controlled-Access-Data
+
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+   :caption: MORE ISB-CGC RESOURCES
+
    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
 
 .. toctree::
    :hidden:
    :maxdepth: 1
-   :caption: MORE INFORMATION
+   :caption: NOTEBOOKS
 
    sections/HowTos
    sections/RegulomeExplorerNotebooks
    sections/MachineLearningNotebooks
    sections/HTANNotebooks
+   sections/MitelmanDBNotebooks
+
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+   :caption: MORE INFORMATION
+
    sections/TutorialsAndHow-ToGuides
    sections/Releases
    sections/Quick-links-updated

diff --git a/docs/source/sections/HTANNotebooks.rst b/docs/source/sections/HTANNotebooks.rst
@@ -5,7 +5,7 @@ HTAN Notebooks
 `HTAN <https://humantumoratlas.org/>`_ is a National Cancer Institute (NCI)-funded Cancer Moonshot initiative to construct 3-dimensional atlases of the dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease (`Cell April 2020 <https://www.sciencedirect.com/science/article/pii/S0092867420303469>`_).
 
 .. list-table:: 
-   :widths: 100 10 10
+   :widths: 95 15 10
    :align: center
    :header-rows: 0
 
@@ -15,16 +15,22 @@ HTAN Notebooks
    * - Utilizing the HTAN ID Provenance Google BigQuery Table
      - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/HTAN_ID_Provenance_In_BQ.ipynb>`_
      - 
-   * - Investigating HTAN scRNA-seq with BigQuery
+   * - Constructing AnnData Objects with scRNA-seq Data from BigQuery
      - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Building_AnnData_with_Subset_of_Cells_from_BQ.ipynb>`_
      -  
-   * - Explore HTAN single cell RNA seq data
+   * - Exploring HTAN scRNA-seq data
      - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Investigating_Single_Cell_HTAN_Data.ipynb>`_
      - 
-   * - Explore Spatial Cellular and Molecular Relationships
+   * - Identifying Assay Data by Primary Organ Type in ISB-CGC
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Identifying_HTAN_Data_Files_by_Organ_in_ISB_CGC.ipynb>`_
+     - 
+   * - Exploring HTAN MIBI Imaging data
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Analyzing_HTAN_MIBI_Imaging_Data.ipynb>`_
+     - 
+   * - Exploring Spatial Cellular and Molecular Relationships
      - 
      - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/R%20Notebooks/Explore_HTAN_Spatial_Cellular_Relationships.md>`_
-   * - Explore HTAN Clinicial, Biospecimen, and Assay Metadata
+   * - Exploring HTAN Clinical, Biospecimen, and Assay Metadata
      - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Explore_HTAN_Clinical_Biospecimen_Assay_Metadata.ipynb>`_
      - `R <https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/R%20Notebooks/Explore_HTAN_Clinical_Biospecimen_Assay_Metadata.md>`_
 
diff --git a/docs/source/sections/HowToGetStartedonISB-CGC.rst b/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

diff --git a/docs/source/sections/HowTos.rst b/docs/source/sections/HowTos.rst
@@ -12,7 +12,7 @@ I'm a novice, how do I...
 -------------------------
 
 .. list-table:: 
-   :widths: 100 10 10
+   :widths: 95 15 10
    :align: center
    :header-rows: 0
 
@@ -66,7 +66,7 @@ I'm an advanced user, how do I...
 -------------------------
 
 .. list-table:: 
-   :widths: 100 10 10
+   :widths: 95 15 10
    :align: center
    :header-rows: 0
 

diff --git a/docs/source/sections/MachineLearningNotebooks.rst b/docs/source/sections/MachineLearningNotebooks.rst
@@ -4,7 +4,7 @@ Machine Learning Notebooks
 Machine learning methods have enabled researchers to leverage and integrate the vast amounts of diverse cancer data to reveal new insights, develop better diagnostics, and improve therapy. ISB-CGC offers examples of how to use Google Cloud resources to train and use machine learning models for a variety of cancer applications and datasets.
 
 .. list-table:: 
-   :widths: 100 10 10
+   :widths: 95 15 10
    :align: center
    :header-rows: 0
 

diff --git a/docs/source/sections/MitelmanDBNotebooks.rst b/docs/source/sections/MitelmanDBNotebooks.rst
@@ -0,0 +1,20 @@
+**************************
+MitelmanDB Notebooks
+**************************
+
+The `Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer <https://mitelmandatabase.isb-cgc.org/>`_  is devoted to genes, chromosomes, and cancer. The Mitelman Database is supported by NCI (National Cancer Institute), the Swedish Cancer Society and the Swedish Childhood Cancer. `The Mitelman Database <https://mitelmandatabase.isb-cgc.org/>`_ is available from ISB-CGC to access and search the data.
+
+.. list-table:: 
+   :widths: 95 15 10
+   :align: center
+   :header-rows: 0
+
+   * - Exploring and comparing the Mitelman DB, CytoConverter, and TCGA datasets
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/MitelmanDB/Exploring_and_comparing_MitelmanDB_CytoConverter_and_TCGA_datasets.ipynb>`_
+     - 
+   * - Cytogenetics and Data Subsets in the Mitelman Database
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/MitelmanDB/Mitelman_Cytogenetics_Subsets.ipynb>`_
+     - 
+   * - Correlations between Mitelman and TCGA datasets
+     - `Python <https://github.com/isb-cgc/Community-Notebooks/blob/master/MitelmanDB/Correlations_MitelmanDB_and_TCGA_datasets.ipynb>`_
+     -  
diff --git a/docs/source/sections/RegulomeExplorerNotebooks.rst b/docs/source/sections/RegulomeExplorerNotebooks.rst
@@ -6,7 +6,7 @@ Integrated statistical analysis and exploration of multiple genomic and clinical
 Bioinformatics notebooks
 =======================
 .. list-table:: 
-   :widths: 100 10 10
+   :widths: 95 15 10
    :align: center
    :header-rows: 0
 

diff --git a/docs/source/sections/ReleaseNotes/ISB-CGCDataReleases.rst b/docs/source/sections/ReleaseNotes/ISB-CGCDataReleases.rst
@@ -2,10 +2,164 @@
 ISB-CGC Data Release Notes
 ############################
 
+*September 16, 2023*
+
+New masked somatic mutation data added to isb-cgc-bq for GDC release 37.
+
+**BigQuery tables created**
+
+- isb-cgc-bq.CPTAC_versioned.masked_somatic_mutation_hg38_gdc_r36
+- isb-cgc-bq.HCMI_versioned.masked_somatic_mutation_hg38_gdc_r36
+- isb-cgc-bq.TARGET_versioned.masked_somatic_mutation_hg38_gdc_r36
+
+**BigQuery tables updated**
+
+- isb-cgc-bq.CPTAC.masked_somatic_mutation_hg38_gdc_current
+- isb-cgc-bq.HCMI.masked_somatic_mutation_hg38_gdc_current
+- isb-cgc-bq.TARGET.masked_somatic_mutation_hg38_gdc_current
+
+*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.
+
+**BigQuery tables created**
+
+- isb-cgc-bq.TRIO_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.GENIE_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.VAREPOP_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.WCDT_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.ORGANOID_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.OHSU_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.NCICCR_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.CMI_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.BEATAML1_0_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.MMRF_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.REBC_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.CPTAC_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.CDDP_EAGLE_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.EXC_RESPONDERS_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.MP2PRT_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.MATCH_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.CTSP_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.CGCI_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.HCMI_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.TARGET_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.FM_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.TCGA_versioned.per_sample_file_metadata_hg38_gdc_r37
+- isb-cgc-bq.CCLE_versioned.per_sample_file_metadata_hg19_gdc_r37
+- isb-cgc-bq.TCGA_versioned.per_sample_file_metadata_hg19_gdc_r37
+- isb-cgc-bq.TARGET_versioned.per_sample_file_metadata_hg19_gdc_r37
+
+**BigQuery tables updated**
+
+- isb-cgc-bq.TRIO.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.GENIE.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.VAREPOP.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.WCDT.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.ORGANOID.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.OHSU.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.NCICCR.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.CMI.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.BEATAML1_0.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.MMRF.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.REBC.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.CPTAC.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.MP2PRT.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.CTSP.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.CGCI.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.HCMI.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.TARGET.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.FM.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.CCLE.per_sample_file_metadata_hg19_gdc_current
+- isb-cgc-bq.TCGA.per_sample_file_metadata_hg19_gdc_current
+- isb-cgc-bq.TARGET.per_sample_file_metadata_hg19_gdc_current
+- isb-cgc-bq.MATCH.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.EXC_RESPONDERS.per_sample_file_metadata_hg38_gdc_current
+- isb-cgc-bq.CDDP_EAGLE.per_sample_file_metadata_hg38_gdc_current
+
+*July 20, 2023*
+
+New GDC Gene Level Copy Number tables.
+
+**BigQuery tables created**
+
+- isb-cgc-bq.CPTAC_versioned.copy_number_gene_level_hg38_gdc_r36
+- isb-cgc-bq.TARGET_versioned.copy_number_gene_level_hg38_gdc_r36
+- isb-cgc-bq.REBC_versioned.copy_number_gene_level_hg38_gdc_r36
+- isb-cgc-bq.CGCI_versioned.copy_number_gene_level_hg38_gdc_r36
+- isb-cgc-bq.HCMI_versioned.copy_number_gene_level_hg38_gdc_r36
+- isb-cgc-bq.MP2PRT_versioned.copy_number_gene_level_hg38_gdc_r36
+- isb-cgc-bq.CDDP_EAGLE_versioned.copy_number_gene_level_hg38_gdc_r36
+- isb-cgc-bq.TCGA_versioned.copy_number_gene_level_hg38_gdc_r36
+- isb-cgc-bq.CPTAC.copy_number_gene_level_hg38_gdc_current
+- isb-cgc-bq.TARGET.copy_number_gene_level_hg38_gdc_current
+- isb-cgc-bq.REBC.copy_number_gene_level_hg38_gdc_current
+- isb-cgc-bq.CGCI.copy_number_gene_level_hg38_gdc_current
+- isb-cgc-bq.HCMI.copy_number_gene_level_hg38_gdc_current
+- isb-cgc-bq.MP2PRT.copy_number_gene_level_hg38_gdc_current
+- isb-cgc-bq.CDDP_EAGLE.copy_number_gene_level_hg38_gdc_current
+- isb-cgc-bq.TCGA.copy_number_gene_level_hg38_gdc_current
+
 *June 5, 2023*
 
 New and Updated PDC v3.0 tables. New and Updated HTAN tables.
 
+**BigQuery tables created**
+
 - 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

diff --git a/docs/source/sections/ReleaseNotes/WebAppReleaseNotes.rst b/docs/source/sections/ReleaseNotes/WebAppReleaseNotes.rst
@@ -2,6 +2,9 @@
 ISB-CGC Web App Release Notes
 #############################
 
+*November 27, 2023* 
+
+- On the ISB-CGC Help-->Video Tutorials page, the Introduction video has been replaced with a new version. Two obsolete videos "Image Viewers" and "Exporting Cohort" were removed.
 
 *May 3, 2023*