What is Cafe Variome?

Cafe Variome is a complete data sharing solution designed to allow diagnostic/disease networks to share genetic variant and phenotype data between one another, for example to check for the existence of variant found in a patient in another laboratory they know/trust. Cafe Variome instances can be hosted by us or created or using the provided software to interested collaborators and offers users a portal through which to announce, discover and acquire a listing in patients and unaffected individuals.

For a more comprehensive explanation of Cafe Variome please see our recent paper here, our "About" page here or view the features and screenshots here. Please also see the following flyer for brief overviews of the Cafe Variome concept.



Where can I find documentation?

Draft user documentation can be found here, it gives a guide how to use the Cafe Variome system and administrator interface.


How can I get recognised for submitting my data?

Identifying and citing datasets:

A key aim of Cafe Variome "Central" 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.


Under what conditions can I release variants?

Data can be shared (and subsequently discovered) under the following three models:

1. Open Access: like a journal, where variant records are publicly available for access
2. Restricted Access: the user requests access to variant 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 variant record(s)
3. Linked Access: only reports the existence of a variant and the user is linked to the source database in order to access the full record

The first of these models is recommended for maximal sharing in order to benefit the widest range of third parties (see below).


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)