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README.md
seed-cbioportal_mm10_v2.3.1.sql.gz
seed-cbioportal_mm10_v2.4.0.sql.gz

README.md

cBioPortal Seed Database for Mouse

These files are MySQL database dump files for seeding a new instance of the cBioPortal database for mouse. They contain all the necessary background data for a properly functioning cBioPortal website, including cancer types, genes and uniprot-mappings.

The database schema and cBioPortal release follows different numbering cycles since cBioPortal 1.5.0 and database schema 2.1.0. This means that the version numbers won't be identical.

cBioPortal mouse instance

When using a cBioPortal instance with mouse data, the "chromosome plot" displayed in the Patient View is not supported (see issue). Also make sure the reference genome in portal.properties is set to mm10.

Latest mouse seed database

Seed database schema 2.4.0

This schema is required for cBioPortal release versions:

  • 1.9.0

When using a release version > 1.9.0, a migration step to a new database schema might be required. The migration process is described here.

Schema 2.4.0: SQL file with create table statements
Seed database : seed-cbioportal_mm10_v2.4.0.sql.gz
md5sum 1014ed1f9d72103f2b46e5615aacbc2f

Previous mouse seed databases

Seed database schema 2.3.1

This schema is required for cBioPortal release versions:

  • 1.7.1
  • 1.7.2
  • 1.7.3
  • 1.8.0

When using a release version > 1.8.0, a migration step to a new database schema might be required. The migration process is described here.

Schema 2.3.1: SQL file with create table statements for portal release 1.7.3
Seed database: cbioportal-seed SQL (.gz) file

Seed database schema 2.1.0

This schema is required for older cBioPortal release versions:

  • 1.5.0
  • 1.5.1
  • 1.5.2

When using this older seed database with a release version > 1.5.2, a migration step to a new database schema is required. The migration process is described here.

Schema 2.1.0: SQL file with create table statements for portal release 1.5.0
Seed database: cbioportal-seed SQL (.gz) file)

For developers

Updating the seed database for Datahub is described here.