The VarGoats Data Sharing Statement

This document describes the principles of data sharing held by the VarGoats consortium. This document is subject to approval by the VarGoats Steering Committee. Any queries about this document should be sent to Gwenola Tosser-Klopp.

Definitions

Archive
means one of the archives hosted at the EBI, NCBI or DDBJ. These include the ENA, Genbank, ArrayExpress and Geo
VarGoats Participant
means an individual:
* whose Research Institute was included in the Scientific Consortium from VarGoats original proposal, submitted to 2015 CALL FOR PROPOSALS « Large-scale sequencing projects » at FRANCE GENOMIQUE and who is included in a VarGoats working group,
OR
* whose inclusion in a VarGoats working group has been validated by VarGoats Steering Committee,
AND
* who has agreed to the VarGoats core principles.
Data
means any assay or metadata generated for or associated with VarGoats sequencing
Analysis
means any computational process where raw sequencing data is aligned, transformed or combined to produce a new product.
Internal Data
means data that is only accessible via the VarGoats private shared storage.
Private Shared Storage
means a storage space hosted at Genotoul that has password access via the goat genome website HTTP/FTP (http://www.goatgenome.org).
Public Data
means all data available through the VarGoats public HTTP/FTP site, which has no password and is accessible to everyone.

VarGoats recognizes that quickly sharing the data generated by the consortium with the wider community is a priority. Rapid data sharing before publication ensures that everyone can benefit from the data created by VarGoats and can take advantage of improved identification of the variations in these animal genomes to aid their own research.

All raw data produced by France Génomique at Génoscope using DNA provided by partners (with or without a signed MTA) or data produced for a VarGoats Associated Project will be submitted by INRA and Génoscope to the Archives without any hold until publication date, thus allowing the data to be publicly available immediately after successful archive submission and useful to the community as soon as possible.

The VarGoats Working Groups will turn the raw data into primary and integrated analysis results. Primary analysis results consist of sample level analysis such as alignment to a reference genome and generation of vcf files or running existing tools for CNV detection. Integrated analysis results represent analyses performed within the working groups, using either existing tools or new methods and that should lead to publications in Scientific journals.

The majority of these analysis results will not be archived before publication but VarGoats recognizes the need to share them within the Scientific Consortium. Initially all files that are not archived will be shared between VarGoats participants in Private Shared Storage hosted at Genotoul. Any individual who signs up to VarGoats Working Groups and agrees to the Toronto principles will be allowed access to this. It means that this individual:

  • respects the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.
  • will not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published, submitted to the public data repositories, or, a clear information is displayed on the VarGoats website.
  • will Contact the VarGoats steering committee to discuss any publication plans that utilize this data to avoid the overlap of any planned analyses.
  • will cite accurately and completely the prepublication data, including any applicable version.
  • understands that this data as accessed is precompetitive and is not patentable in its present state.

There will be metadata files in the private data sharing area, which make credit for different datasets as clear as possible.

VarGoats expects to make multiple releases each year. A data release will involve declaring a data freeze and copying all files associated with that data freeze from the Private Shared Storage to the public FTP site. In the first instance these data freezes will contain the primary analysis results. As VarGoats's analyses progress, the data freeze will be expanded to include integrative analysis too. The data freeze process will be coordinated by the VarGoats Steering Committee and will be based on consultation with VarGoats Participants. VarGoats will also aim to release all data associated with a paper before publication even if it lies outside this standard freeze cycle. The Public Data will be available to the whole community.

All VarGoats Public Data is released under Fort Lauderdale principles. The VarGoats website, data portal and FTP site will all have clear data reuse statements on them.

When considering VarGoats Internal Data, if one VarGoats participant wishes to publish using data generated from samples provided by another VarGoats Participant they should first contact the sample provider and clarify the participant's publication strategy. Collaboration is for everyone's benefit and is strongly encouraged. The VarGoats Steering Committee commits to report to journal editors and the laboratories involved any event that disregards the rights of data creators (including biological measurements as well as analysis of such measurements).

All VarGoats Participants can and will continue to do experimental and analysis work outside of VarGoats and the other data generated is not required to meet the same data sharing expectations.

Only VarGoats data can be distributed through the private storage and public FTP site.

References

  1. Toronto International Data Release Workshop: Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets .
  2. Fort Lauderdale principles: Reaffirmation and Extension of NHGRI Rapid Data Release Policies: Large-scale Sequencing and Other Community Resource Projects .


Approved by the VarGoats Steering Committee on 2017/12/05

Coordination

Gwenola Tosser-Klopp

Wenguang Zhang