Data Usage Policy
In 2009 the Toronto International Data Release Workshop agreed on a policy statement about prepublication data sharing (Nature 461, 168-170). Prepublication data release was recommended for genetic association studies involving "genomewide association analysis of thousands of samples", among other kinds of studies.
Accordingly, many of the datasets in T3 are being made available prior to publication of a global analysis by the data producers. Guidelines for appropriate sharing of these data are given in the excerpt from the Toronto Statement below.
Producers' information about specific datasets
| Description | Source | Datasets | Publication plan | Date in T3 | Unrestricted as of |
|---|---|---|---|---|---|
| Founders Panel | Kevin Smith | UMN Founders Trial, UMN Preliminary Yield Trial, UMN Variety Trial | A publication describing the agronomic, end-use quality, and abiotic and biotic stress tolerance is planned, with associated GWAS and genomic selection investigations. This data is made publicly available courtesy of the oat breeders who generated it. | April 2018 | April 2020 |
| Collaborative Oat Research Enterprise (CORE) 6K SNP array genotypes | Kathy Klos, Nick Tinker, Eric Jackson | CORE_2010_Infinium | The Plant Genome "first look" | 2014 | January 2016 |
| Collaborative Oat Research Enterprise (CORE) GBS data | Kathy Klos, Nick Tinker, Eric Jackson | CORE_2014_GBS | The Plant Genome "first look" | April 2015 | January 2016 |
| Collaborative Oat Research Enterprise (CORE) phenotype data | Nick Tinker, Eric Jackson | The CORE AFRI109 Panel, CORE Spring Panel and the CORE Winter Panel. | Planned analysis and publication of GWAS foundation papers by the CORE group following publication of consensus map, LD and diversity study. | 2014 | TBA at publication date |
| A high-density consensus map enhanced with additional SNPs and Haplotype-based loci called using Haplotag (Tinker et al., 2016). GBS loci were validated using 4657 diverse hexaploid oat lines as the training population and were placed on the oat consensus map (Chaffin et al. 2016). The placement was done by using 9 mapping populations that were components of the original consensus map as well as the GBS training population. | Nick Tinker, Wubishet A. Bekele | Expanded Oat Consensus Map (2016) | A publication describing the quality and attributes of marker placement, as well as an overall assessment of Haplotag software and haplotype-based genetic analysis of oat data is in preparation. | February 2016 | TBA at publication date |
| North American Public Oat Genotyping Initiative (POGI) | POGI Genotype Experiment Panel | This data is made publicly available courtesy of the oat breeders and geneticists who generated it. If you wish to use the data for publication, please contact the T3 curator to coordinate with others developing publication plans. | March 2016 | March 2016 |
Toronto Statement
Data producers should state their intentions and enable analyses of their data by:
- Informing data users about the data being generated, data standards and quality, planned analyses, timelines, and relevant contact information, ideally through publication of a citable marker paper near the start of the project or by provision of a citable URL at the project or funding-agency website
- Providing relevant metadata (e.g., questionnaires, phenotypes, environmental conditions, and laboratory methods) that will assist other researchers in reproducing and/or independently analyzing the data, while protecting interests of individuals enrolled in studies focusing on humans
- Ensuring that research participants are informed that their data will be shared with other scientists in the research community
- Publishing their initial global analyses, as stated in the marker paper or citable URL, in a timely fashion
- Creating databases designed to archive all data (including underlying raw data) in an easily retrievable form and facilitate usage of both pre-processed and processed data
Data analysts/users should freely analyse released prepublication data and act responsibly in publishing analyses of those data by:
- Respecting the scientific etiquette that allows data producers to publish the first global analyses of their data set
- Reading the citable document associated with the project
- Accurately and completely citing the source of prepublication data, including the version of the data set (if appropriate)
- Being aware that released prepublication data may be associated with quality issues that will be later rectified by the data producers
- Contacting the data producers to discuss publication plans in the case of overlap between planned analyses
- Ensuring that use of data does not harm research participants and is in conformity with ethical approvals
- Scientific journal editors should engage the research community about issues related to prepublication data release and provide guidance to authors and reviewers on the third-party use of prepublication data in manuscripts