1KSA Terms of Use
Data Access, Use and Publication by the Sample Contributor
The 1KSA project stores all sequencing data (pod5, FASTQ, and fasta files) on the Data Intensive Research Initiative of South Africa (DIRISA), a secure data storage platform of The National Integrated Cyber Infrastructure System (NICIS). You, the sample contributor, will receive a copy of your data and are free to use and re-analyse it (nonexclusively) for three years.
The 1KSA project acknowledges that a great deal of controversy exists over access and benefit sharing of digital sequence information (DSI). The 1KSA project has aimed through these terms of use to provide a middle path through the DSI controversy, providing an “as open as possible, as closed as necessary” approach.
For any species with no anticipated economic value beyond the development of tools for conservation (“1KSA conservation species”), the sample contributor will be expected to upload the files to the European Nucleotide Archive (ENA) within three years of receipt and/or publication of the species card on the 1KSA web page, using “1KSA project - Species Name” as the sample title and “1KSA - Nanopore sequencing and draft genome assembly of Species Name” as the project description. ENA allows for an embargo period of a year to the open release of this data.
Release of the embargo at the time of publication of the genome assembly will be expected. For any species with anticipated or any potential economic value and/or indigenous or traditional knowledge (“1KSA bioeconomy species”), the sample contributor is expected to engage with all stakeholders (for example, indigenous knowledge holders, their institution’s technology transfer oTice, intellectual property consultants) prior to publication and uploading the 1KSA genome assembly data to ENA (as detailed in the section above, for “1KSA conservation species”).
If the sample contributor wishes to embargo the release of the data beyond the three year period, they must request permission from the 1KSA-Data Access Committee (1KSA-DAC) in writing (1KSA@diplomics.org.za), providing reasons for this. If the sample contributor does not publish or upload the data to ENA within the three year period or apply for an embargo on the release of the data, the 1KSA project may upload the fastq and fasta files to ENA after three years using the project tags described above. Pod5 files are currently not accepted by ENA but will be included once/if ENA adds this functionality.
1KSA encourages publications in Open Access Journals and publication of a preprint in bioRxiv. Publications must cite the ENA accession numbers described above, make use of the Acknowledgement statement (see below) and must be checked by the 1KSA Data Access Committee (1KSA-DAC) prior to publication.
Data Access, Use and Publication by other scientists
The 1KSA-DAC committee also reviews requests for access to the pod5, fastq and fasta files. This includes collaborators of the sample contributor. Within the first three years of sequencing, the sample contributor will be consulted. Data will be made available under the conditions of a detailed Data Transfer Agreement (DTA) between the 1KSA project and the scientist requesting access to the data.
Open Science
We encourage you to follow Open Science and Open Data principles by sharing your research results openly. This includes popular science articles, GitHub repositories, etc.
Acknowledgements
Please acknowledge the 1KSA project, DIPLOMICS, the Centre for High Performance Computing (CHPC), DIRISA, and the Department of Science, Technology and Innovation (DSTI) in all presentations and publications using your data.
The following acknowledgement statement can be used:
“The authors acknowledge draft genome sequencing provided by the 1KSA project (www.1KSA.org.za) with support provided by DIPLOMICS through the South African Department of Science, Technology and Innovation’s South African Research Infrastructure Roadmap (SARIR). The National Integrated Cyber Infrastructure System (NICIS) is acknowledged for 1KSA data management and curation through the Data Intensive Research Initiative of South Africa (DIRISA) and for 1KSA draft genome analysis using the Centre High Performance Computer (CHPC)”
Reporting and Publicity
DIPLOMICS will request information about your research progress, such as publications, funding obtained, and trained students, to which you must comply. DIPLOMICS will also publicise the sequencing of your samples in reports and media channels.
Intellectual Property and Benefit Sharing
You (the sample contributor) and/or your institution own any intellectual property (IP) developed from the draft genome assembly, such as patents or inventions. However, we recognise that South Africa’s biodiversity is a national resource, and the 1KSA project was funded by the Department of Science, Technology and Innovation (DSTI) through the SARIR programme and DIPLOMICS.
To share the benefits of this research, a portion of any royalties earned from commercially valuable IP will be contributed to the 1KSA Education Program. This program, established by DIPLOMICS, aims to promote biodiversity genomics education in South Africa. You and/or your institution are responsible for tracking and reporting any commercially valuable IP to the 1KSA-DAC and contributing to the education program as needed.
This also applies to scientists who have downloaded the 1KSA data sets from the INSDC or have obtained the data through the 1KSA-DAC and used these data sets to generate IP resulting in the sale of a product or payment of commercial royalites.