Merge pull request #16 from ncihtan/main

Getting updates from main before adding more changes for specific assay docs, HTAN index date

access_controlled/CDS_access.md

@@ -16,7 +16,7 @@ To access data via CDS, first generate a CDS Data Repository Service (DRS) manif
 
 1. CDS Portal
 2. HTAN Data Portal
-3. Google BigQuery (Coming Soon!)
+3. Google BigQuery
 
 ## 1. Generating a Manifest File from the CDS Portal
 
@@ -71,7 +71,11 @@ Click **Download Manifest**, which will download a local file called `cds_manife
 ![HTAN Portal: Download DRS Manifest](../img/cds_genomics3.png)
 
 
-## 3. Generating a Manifest File from Google BigQuery (Coming Soon!)
+## 3. Generating a Manifest File from Google BigQuery
+HTAN metadata and a mapping of HTAN Data File IDs to CDS DRS URIs are available as Google BigQuery tables via the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC) (see [Google BigQuery](https://docs.humantumoratlas.org/open_access/biq_query/)). These tables can be used to subset data to a cohort of interest, and obtain DRS URIs of files to access. 
+
+For a step-by-step guide on how to generate a DRS manifest file using Google BigQuery, please see the Python notebook [Creating_CDS_Data_Import_Manifests_Using_BQ.ipynb](https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Creating_CDS_Data_Import_Manifests_Using_BQ.ipynb).
+
 
 
 # Accessing Data

open_access/cds_imaging.md

@@ -14,7 +14,7 @@ To access data via CDS, first generate a CDS Data Repository Service (DRS) manif
 
 1. CDS Portal
 2. HTAN Data Portal
-3. Google BigQuery (Coming Soon!)
+3. Google BigQuery
 
 ## 1. Generating a Manifest File from the CDS Portal
 
@@ -57,7 +57,11 @@ Click **Download Manifest**, which will download a local file called `cds_manife
 ![HTAN Portal: Download DRS Manifest](../img/cds_img3.png)
 
 
-## 3. Generating a Manifest File from Google BigQuery (Coming Soon!)
+## 3. Generating a Manifest File from Google BigQuery
+HTAN metadata and a mapping of HTAN Data File IDs to CDS DRS URIs are available as Google BigQuery tables via the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC) (see [Google BigQuery](https://docs.humantumoratlas.org/open_access/biq_query/)). These tables can be used to subset data to a cohort of interest, and obtain DRS URIs of files to access. 
+
+For a step-by-step guide on how to generate a DRS manifest file using Google BigQuery, please see the Python notebook [Creating_CDS_Data_Import_Manifests_Using_BQ.ipynb](https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Creating_CDS_Data_Import_Manifests_Using_BQ.ipynb).
+
 
 
 # Accessing Data

overview/centers.md

@@ -14,7 +14,7 @@ HTAN currently consists of ten research centers, and two pilot projects. There a
 | HTA4   | Children’s Hospital of Philadelphia     | Tumor Atlas      | Pediatric                         |
 | HTA5   | Dana-Farber Cancer Institute            | Tumor Atlas      | Multiple Cancer Types             |
 | HTA6   | Duke University                         | Pre-Cancer Atlas | Breast                            |
-| HTA7   | Harvard Medical School                  | Pre-Cancer Atlas | Melanoma and Clonal Hematopoiesis |
+| HTA7   | Harvard Medical School                  | Pre-Cancer Atlas | Melanoma, Colorectal Cancer, and Clonal Hematopoiesis |
 | HTA8   | Memorial Sloan Kettering Cancer Center  | Tumor Atlas      | Multiple Cancer Types             |
 | HTA9   | Oregon Health Science University        | Tumor Atlas      | Breast                            |
 | HTA10  | Stanford University                     | Pre-Cancer Atlas | Familial Adenomatous Polyposis    |