Let your data be discovered with Cafe Variome


Cafe Variome can help you publish your data and share it with others in a number of different ways but most importantly, as the data owner, you have full control over your data and who can discover and access it.

Choose which Cafe Variome is most suited to your needs:

Cafe Variome Central


Cafe Variome "Central" (https://central.cafevariome.org) was designed to function as a clearinghouse and exchange portal for gene variant data produced by diagnostics laboratories and all available variants from public repositories, offering users a portal through which to announce, discover and acquire a comprehensive listing of observed neutral and disease-causing gene variants in patients and unaffected individuals.

Hosted and "in-a-box" versions


We recognise that some users may not wish to use the central version of Cafe Variome and instead create their own private installations. In order to facilitate this we offer both a fully hosted version (on University of Leicester servers) and an in-a-box version to interested collaborators.

Contact us to discuss either of these options.


Automate data upload with diagnostic software

Cafe Variome has worked closely with the providers of mutation interpretation software used in diagnostic laboratories to produce versions of these tools that will allow you to submit sequence variants directly to a Cafe Variome installation.

The following software now offers this functionality:

- Gensearch (PhenoSystems). See the following page for details of how to submit.

- Alamut (Interactive Biosoftware). See the following page for details of how to submit.

Providers of other diagnostic software are encouraged to contact us to discuss enabling similar functionality in their own tools.


Or upload to Cafe Variome manually

If you do not use software that is currently supported by Cafe Variome or you wish to upload variants in bulk you may use the built in data import facility to import variants.

Variants can be added through the curators interface of Cafe Variome, contact us in order to have your account set as a curator.


Making Data Selectively Discoverable

Your data can only be discovered by people who you have provided access to your Cafe Variome installation.

Datasets can quickly and easily be set to discoverable or undiscoverable within the Cafe Variome dashboard.

If you have enabled the optional in-built beacon for genomic variants data then you can tailor the beacon to only return information about variants you want to be discoverable.

Additional information about Beacons can be found in our FAQs. Alternatively you can explore the beacon within Cafe Variome Central.


Making Data Selectively Accessible

To give you fine-grained control over how your data can be accessed three accessibility models can be applied to data as described below:

Open Access: like a journal, where variant records are publicly available for access

Restricted Access: the user requests access to variant records from the data owner/submitter, the user must either belong to a pre-approved group or must request access from the data owner in order to access the record(s)

Linked Access: only reports on the existence of a variant, the user must be linked to the source database in order to access the full record(s)

Features

Please contact us if you wish to trial Cafe Variome.