Frequently Asked Questions

  1. What is Cafe Variome?
  2. How can I get recognised for submitting my data?
  3. What data should I share?
  4. Under what conditions can I release my data?
  5. How can I submit my data?
  6. Where can I download submitted variants in bulk?
  7. Why should I share my data and who will benefit?
  8. How is Cafe Variome funded?

 

What is Cafe Variome?

Cafe Variome is designed to function as a clearinghouse and exchange portal for gene variant (mutation) data produced by diagnostics laboratories, 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. Cafe Variome is not a 'database' for the hosting/display/release of data, but a shop window for finding data. As such, it holds only core info for each record, and uses this merely to enable holistic searching across resources. For a more comprehensive explanation of Cafe Variome please see here. Please also see the following presentation and poster for brief overviews of the Cafe Variome concept.

 

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 are 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 recognizing and rewarding (and hence promoting) such activities. To enable this data submitters will link their user account with a unique author/contributor identifier in the system being built by ORCID. As variant reports are submitted and assigned DOIs, they will 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 data should I share?

See the following documentation for guidelines regarding required and optional fields for submission:

Cafe Variome aims to leave the submitter in control of their data at all times and you are encouraged to share as much information as you feel comfortable with, the following document outlines the Cafe Variome data policy. 

 

Under what conditions can I release my data?

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

  1. Open Access: variant records are publicly available for access
  2. Restricted Access: variants can be downloaded only after having sought and received specific permission from the data submitter/owner
  3. Linked Access: only the variant's existence is reported, along with a link to the original data source

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

In addition to these three policies we also allow submitters to assign a licence to their datasets,  for example to specify that the data may only be used for non-commercial use.

 

How can I submit my data?

You may submit data in a number of ways to Cafe Variome:

  1. Using "Cafe Variome enabled" versions of data analysis tools which automatically push diagnostic data to Cafe Variome. Currently the Gensearch software offers this functionality, we are currently working with the providers of the Alamut software to introduce similar functionality. Other software tool providers are encouraged to contact us discuss doing so like-wise.
  2. Upload now online by first registering with Cafe Variome and then using the online upload tool on the following page
  3. Contact us and we can arrange the setup of a secure FTP account that you may use to transfer variants
  4. Contact us and we can work you to develop automated pipelines to routinely push data to Cafe Variome

 

Where can I download submitted variants in bulk?

The variants submitted from diagnostic laboratories that are flagged as openAccess can be downloaded from here. Please note that all other content (e.g. dbSNP, UniProt, PhenCode, HGMD) is NOT available for bulk download, you must go to the source of these variants and request permission from the data owner(s) instead.

 

Why should I share my data and who will benefit?

People with data to be shared can place the full record details online (with controlled access as per their preferences) in their own or other standard databases. I.e., it is not our desire or expectation that data generators should only place (core) content to Cafe Variome, but by also locating such information with Cafe Variome they can ensure much better visibility and discoverability of their data, enable more holistic/comprehensive information accessibility for the field, and have their outputs more widely used, accredited, and ultimately rewarded.

Many third parties will benefit, including investigators, the scientific community (such as locus-specific databases), funding agencies and, most importantly, the public. Our aim is remove all practical hurdles that prevent the existence of valuable mutation observations from being announced to the world for easy discovery and consideration in research and clinical healthcare settings.

 

How is Cafe Variome funded?

Cafe Variome has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement number 200754 - the GEN2PHEN project.