ISB-CGC first release

hi all,



thought some of you might be interested in this!  i'm hopeful of adding a
sparql endpt. to this at some point, particularly the metadata (see the
clinical and biospecimen bigquery tables) and would welcome, thoughts, help
from anyone.



cheers,

michael



Michael Miller

Software Engineer

Institute for Systems Biology
------------------------------

We are very excited to announce a new public resource just released by the
ISB-CGC team.  Although much of the TCGA data has been open-access for
years, it hasn't necessarily been easy to work with.  Based on years of
experience working with the TCGA data, we have designed a set of BigQuery
tables for all of the major open-access data types from clinical data to
gene expression and DNA methylation to somatic mutation calls.  Now *you* can
use the processing power of Google's infrastructure to explore and analyze
this data from Python or R, or by trying out SQL queries directly from the
BigQuery web UI. Details about these BigQuery tables as well as sample
queries and analyses are available in two public github repositories: i
sb-cgc/examples-Python <https://github.com/isb-cgc/examples-Python> and
isb-cgc/examples-R <https://github.com/isb-cgc/examples-R>.  We will
continue adding to these repos and welcome your suggestions for new
analyses!

You will need to have access to a Google Cloud Platform (GCP) project in
order to use BigQuery.  If you don't already have one, you can sign up for
a free-trial <https://cloud.google.com/free-trial/> or contact us to become
part of the community evaluation phase of our Cancer Genomics Cloud pilot.
(You can also find more information about this NCI-funded program here
<https://cbiit.nci.nih.gov/ncip/nci-cancer-genomics-cloud-pilots>.)

If you've never used BigQuery, take a look at the quick-start documentation
<https://cloud.google.com/bigquery/web-ui-quickstart> which includes
information about how to access and query public datasets.  In order to add
the ISB-CGC public BigQuery datasets to the left panel of your BigQuery Web
UI, click on the down arrow icon next to your project name, then click *Switch
to Project*, then *Display Project...* and enter *isb-cgc* in the *Add
Project* pop-up and click *OK*.

If you have any questions about ISB-CGC or have use-cases or research
questions you would like to discuss with us, feel free to write to us.  And
please share this information with your colleagues!



the ISB-CGC team

info@isb-cgc.org

www.isb-cgc.org