<commit_before>* [Introduction](#introduction)
* [Seed Database](#seed-database)
* [Study staging files](#study-staging-files)
* [Complete cBioPortal database](#complete-cbioportal-database)

# Introduction
This page describes the various files available for download.

# Seed Database
The seed database is a MySQL dump for seeding a new instance of the cBioPortal. Instructions for loading the seed database can be found [here](Import-the-Seed-Database.md). The seed database for human can be downloaded from [cBioPortal Datahub](https://github.com/cBioPortal/datahub/tree/master/seedDB). A mouse version can be found [here](https://github.com/cBioPortal/datahub/tree/master/seedDB_mouse).

# Study staging files
Staging files for the studies on cbioportal.org can be download from the [Data Sets section](https://www.cbioportal.org/data_sets.jsp). These studies can be validated and loaded in a local cBioPortal instances using the [validator and importer](Data-Loading.md). Any issues with a downloaded study can be reported on [cBioPortal DataHub](https://github.com/cBioPortal/datahub/).

#### Example studies
TCGA Provisional studies often contain many different data types. These are excellent examples to use as reference when creating your own staging files. A detailed description on supported data types can be found in the [File Formats documentation](File-Formats.md).

# Complete cBioPortal database
A MySQL database dump of the complete cbioportal.org database can be found here:
http://download.cbioportal.org/mysql-snapshots/public-portal-dump.latest.sql.gz<commit_msg>Add user focused download section to docs<commit_after>* [Introduction](#introduction)
* [User Downloads](#user-downloads)
    * [Datasets Page](#datasets-page)
    * [Datahub](#datahub)
    * [API and API Clients](#api-and-api-clients)
* [Instance Maintainer Downloads](#instance-maintainer-downloads)
    * [Seed Database](#seed-database) 
    * [Study staging files](#study-staging-files)
    * [Complete cBioPortal Database](#complete-cbioportal-database)

# Introduction
This page describes the various files available for download. The first section is targeted towards [users](#user-downloads) of cBioPortal. The second section towards [maintainers](#instance-maintainer-downloads) of cBioPortal instances.

## User Downloads
There are several ways in which one can download data from cBioPortal including manual and programmatic approaches. See options outlined below.

### Datasets Page
A zip file for each study on [cbioportal.org](https://www.cbioportal.org) can be download from the [Datasets Page](https://www.cbioportal.org/datasets). One can also use the R client [cBioPortalData](https://docs.cbioportal.org/6.-web-api-and-clients/api-and-api-clients#cbioportaldata-recommended) to programmatically download all of these files.

### Datahub
The files for each study are also available from our [datahub repository](https://github.com/cBioPortal/datahub). This is basically the extracted version of the zip files in the [Datasets Page](https://www.cbioportal.org/datasets). Note that this is a git LFS repo so if you are familiar with git you might prefer using this option.

### API and API Clients
Besides downloading all the study data one can also request slices of the data using the API. A slice of the data could e.g. be "give me all the mutation data for one patient" or "get me all EGFR mutations for a particular group of samples". There are API clients available in a variety of languages including bash, R and Python. See for more information the [API documentation](https://docs.cbioportal.org/6.-web-api-and-clients/api-and-api-clients). 

## Instance Maintainer Downloads
As an instance maintainer of cBioPortal there are a variety of files that might be helpful. See below.

### Study staging files
Staging files for the studies on cbioportal.org can be download from the [Datasets Page](https://www.cbioportal.org/datasets). These studies can be validated and loaded in a local cBioPortal instances using the [validator and importer](Data-Loading.md). Any issues with a downloaded study can be reported on [cBioPortal DataHub](https://github.com/cBioPortal/datahub/).

#### Example studies
TCGA Provisional studies often contain many different data types. These are excellent examples to use as reference when creating your own staging files. A detailed description on supported data types can be found in the [File Formats documentation](File-Formats.md).

### Complete cBioPortal database
A MySQL database dump of the complete cbioportal.org database can be found here:
http://download.cbioportal.org/mysql-snapshots/public-portal-dump.latest.sql.gz

### Seed Database
The seed database is a MySQL dump for seeding a new instance of the cBioPortal. Instructions for loading the seed database can be found [here](Import-the-Seed-Database.md). The seed database for human can be downloaded from [cBioPortal Datahub](https://github.com/cBioPortal/datahub/tree/master/seedDB). A mouse version can be found [here](https://github.com/cBioPortal/datahub/tree/master/seedDB_mouse).

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