About Cafe Variome

What is Cafe Variome?

Cafe Variome is a flexible/customisable, web-based, data discovery tool that can be quickly installed by any biomedical data owner or network who wish to make their data discoverable, either to others within their network or the wider scientific community.

Cafe Variome has three main parts:

Data Component

Whereby different records and/or fields can be made differentially discoverable by different users/networks.

Query Component

Including simple and advanced “query-builder” interfaces, optionally constrained by ontologies.

Administration Component

Whereby a data custodian can import data, create and manage federated networks and set access controls.

Data owners retain full control of their data, the data will not leave the owners servers and whether the data is discoverable can be tightly controlled as well as how the data can then be accessed.

Data can be queried using our simple, yet powerful, query builder interface and the responses are strictly limited (i.e., yes/no, or a count of query “hits”) and there is no transfer of original data. This effectively allows for the discovery of the “existence” of sensitive content whilst the data remains secure on the owners servers.

Why is Cafe Variome needed?

There is a considerable need and desire for networks of diagnostic laboratories/disease consortia to be able to check each others databases for the presence of mutations and/or phenotypes they observe in their own patients. But this is countered by the understandable reluctance and impracticality of sharing the content of each group's database with other labs, or indeed with the wider world.

Given the above, a way forward has been devised based upon enabling the 'open discovery' of data (rather than data 'sharing') between networks of diagnostic laboratories or disease consortia that know/trust each other and share an interest in certain causative genes or diseases.

To that end, the Cafe Variome platform has been developed. We are reaching out to groups and projects that could benefit from such a system, allowing them and their fellow labs to securely share data between each other.

Supported data types

Cafe Variome has been developed with flexibility in mind and is able to support many types of biomedical entities or “things”.

So far we have enabled the discovery of: genomic variants, individual research participants’ clinical findings, summary-level genotype and phenotype data across research cohorts, drug structures, and clinical trial outcomes.

To find out how Cafe Variome could enable the discovery of your biomedical data, please contact us.

Cafe Variome for data owners

Data owners/custodians retain full control of their data and only approved data elements (or obfuscated copies thereof) are remotely queried while all data remains on the custodian’s local server.

The administrators dashboard allows for full control over a Cafe Variome installation and the data contained within.

For more information please take a look at our Data Owners section

Cafe Variome for data discovery

Cafe Variome has a simple, yet powerful query builder based on AND/OR queries and returns a response on whether data exists which matches the set criteria or not. The response could be true or false or the number of matching variants held.

For more information please take a look at our Data Discovery section

Frequently Asked Questions

Where can I download a copy of Cafe Variome?

Cafe Variome can be downloaded directly from our Github repositiory.

Where can I find documentation?

Draft user documentation can be found via our Github repositiory.

How can I get recognised for submitting my data?

Identifying and citing datasets:

A key aim of Cafe Variome is to offer incentive/reward-based schemes to encourage data sharing with the scientific community. To enable this, variant reports submitted to the central depot can be assigned a persistent, unique and citable Digital Object Identifier (DOI: http://www.doi.org). The DataCite consortium, is creating a new global registry for research datasets published in online digital repositories, built on the same established DOI infrastructure that is already used widely to identify and cite traditional scholarly publications.

Identification and citing via data DOIs enables variant reports to be cited like journal articles, and thus the aim is to give laboratory personnel more of an incentive to use the Cafe Variome system and be credited for their contributions. Additionally Cafe Variome will help facilitate the gathering of online access statistics (using citation metrics) relating to the use and impact of the published datasets by the research community at various levels of granularity (e.g per datasets, per data creator, per diagnostic lab).

Contributor Recognition:

Cafe Variome is aiming to unambiguously track the identity of persons who contribute data to the system, for the purpose of recognising and rewarding (and hence promoting) such activities. To enable this Cafe Variome users can link their user account with a unique author/contributor identifier utilising the ORCID system. As variant reports are submitted and assigned DOIs, they can be linked with the ORCID ID of the data submitter (and, optionally for his/her co-contributors). The link(s) between the DOI and the ORCID ID(s) will subsequently be deposited into the ORCID registry, thus unambiguously attributing the data publication to the person(s) who contributed to it.

What is Beacon and how can it help me?

Beacon is a genetic mutation sharing platform developed by the Global Alliance for Genomics and Health. A beacon is web service that any institution can implement to share genetic data. A beacon answers questions of the form "Do you have information about the following mutation?" and responds with one of "Yes" or "No", among potentially more information.

Enabling the in-built beacon allows your data to be discovered in more ways, potentially bringing in more collaborators. The beacon returns information which is more limited than Cafe Variome so is a great way to introduce sensitive data to the world. Any collaborators who discover the existence of data via beacon can then contact you and ask for access to your Cafe Variome to allow for a highly controlled information sharing network to be developed.

How is Cafe Variome funded?

Cafe Variome has received funding from the European Community‘s Seventh Framework Programme (FP7/2007-2013) projects GEN2PHEN (grant agreement 200754) and BioSHaRE-EU (grant agreement 200754), and Innovative Medicines Initiative (IMI) projects EMIF (grant agreement 115372) and EPAD (grant agreement 115736)