From 7003a2f03c78304551e41cb8e8b429e4b5470ae9 Mon Sep 17 00:00:00 2001 From: clarisse-lau Date: Tue, 14 May 2024 16:59:45 -0700 Subject: [PATCH] add BQ drs manifest instructions --- access_controlled/CDS_access.md | 8 ++++++-- open_access/cds_imaging.md | 8 ++++++-- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/access_controlled/CDS_access.md b/access_controlled/CDS_access.md index 0c5801ee..315c3eb3 100644 --- a/access_controlled/CDS_access.md +++ b/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 diff --git a/open_access/cds_imaging.md b/open_access/cds_imaging.md index 3c624d7b..f3e75de8 100644 --- a/open_access/cds_imaging.md +++ b/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