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1 | 1 | # Data Use Policy |
2 | 2 |
|
3 | | -## Release with Attribution |
| 3 | +## Public Domain Data |
4 | 4 |
|
5 | | -We plan to make data from the Transportation Energy Resources from Renewable Agriculture Phenotyping Reference Platform \(TERRA-REF\) project available for use with attribution. |
6 | | - |
7 | | -Please consider engaging with team members to collaborate on new research with these data. You can learn more about our approach to co-authorship and also about planned research papers in the section [Manuscripts and Authorship Guidelines](manuscripts-and-authorship-guidelines.md). |
8 | | - |
9 | | -## Timing and of Data Releases |
10 | | - |
11 | | -We plan to release the data in stages. For access to unreleased data, please complete the [beta user application](https://terraref.org/beta) to access data that has not yet been fully processed or validated. |
| 5 | +Data will be released with a CC0 license, meaning that they are in the public domain. The CC0 license allows wide use of these data and while it does not legally bind users to acknowledge the source **data users are expected cite our data and research in publications, presentations, and other products.** |
12 | 6 |
|
13 | | -Any access to data prior to publication is granted with the understanding that the contributions and interests of the TERRA-REF team should be recognized and respected by the users of the data. The TERRA-REF team reserves the right to analyze and published its own data. Resource users should appropriately cite the source of the data and acknowledge the resource produces. The publication of the data, as suggested in the [TERRA-REF Authorship Guidelines](manuscripts-and-authorship-guidelines.md), should specify the collaborative nature of the project, and authorship is expected to include all those TERRA-REF team members contributing significantly to the work. |
| 7 | +The first release in 2020 included data from Seasons 4 and 6. This is available on [Dryad ](https://datadryad.org/stash/dataset/doi:10.5061/dryad.4b8gtht99)and [Globus](https://app.globus.org/file-manager?origin_id=e8feaff4-96cd-11ea-bf90-0e6cccbb0103&origin_path=%2F). |
14 | 8 |
|
15 | | -The **first data publication** in Spring 2020 will provide access to data from the Maricopa field site Seasons 4 and 6 \(on Dryad, citation forthcoming\). |
| 9 | +Data are in the public domain to enable broad and unrestricted re-use. However, any derived pubications should cite the dataset: |
16 | 10 |
|
17 | | -Planned **future releases** include Sorghum Season 9, data from experiments at Kansas State University, and data from the Danforth Indoor Phenotyping Facility. |
| 11 | +### Citing TERRA REF data: |
18 | 12 |
|
19 | | -Additional seasons can be requested as needed. We can provide the raw data and software required to process it. We can also collaborate with you to process the data, but this will typically require new funding sources. |
| 13 | +**Genomics, sensor, and phenotype data:** LeBauer, David et al. \(2020\), Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors, Dryad, Dataset, [https://doi.org/10.5061/dryad.4b8gtht99](https://doi.org/10.5061/dryad.4b8gtht99) |
20 | 14 |
|
21 | | -## Genomic Data |
| 15 | +**AZMet Weather Data \(available on Dryad\):** Brown, P. W., and B. Russell. 1996. “AZMET, the Arizona Meteorological Network. Arizona Cooperative Extension.” [https://cals.arizona.edu/AZMET/](https://cals.arizona.edu/AZMET/). |
22 | 16 |
|
23 | | -### Restrictions on dataset usage |
24 | | - |
25 | | -Genomic data for the _Sorghum bicolor_ Bioenergy Association Panel \(BAP\) from the TERRA-REF project is available pre-publication to maximize the community benefit of these resources. Use of the raw and processed data that is available should follow the principles of the [Fort Lauderdale Agreement](https://www.genome.gov/pages/research/wellcomereport0303.pdf) and the [Department of Energy's Joint Genome Institute \(JGI\) early release policies](http://genome.jgi.doe.gov/pages/data-usage-policy.jsf). |
| 17 | +**Data Processing Pipeline**: Burnette, Maxwell, et al. "TERRA-REF data processing infrastructure." Proceedings of the Practice and Experience on Advanced Research Computing. 2018. 1-7. [doi:10.1145/3219104.3219152](https://doi.org/10.1145/3219104.3219152) |
26 | 18 |
|
27 | | -By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by TERRA-REF and/or its collaborators of a comprehensive genome analysis \("Reserved Analyses"\). "Reserved analyses" include the identification of complete \(whole genome\) sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and whole-genome- or chromosome-scale comparisons with other species. The embargo on publication of Reserved Analyses by researchers outside of the TERRA-REF project is expected to extend until the publication of the results of the sequencing project is accepted. Scientific users are free to publish papers dealing with specific genes or small sets of genes using the sequence data. If these data are used for publication, the following acknowledgment should be included: 'These sequence data were produced by the US Department of Energy Transportation Energy Resources from Renewable Agriculture Phenotyping Reference Platform \(TERRA-REF\) Project'. These data may be freely downloaded and used by all who respect the restrictions in the previous paragraphs. The assembly and sequence data should not be redistributed or repackaged without permission from TERRA-REF. Any redistribution of the data during the embargo period should carry this notice: "The TERRA-REF project provides these data in good faith, but makes no warranty, expressed or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used. Once the sequence is moved to unreserved status, the data will be freely available for any subsequent use." |
| 19 | +## Software and Algorithms |
28 | 20 |
|
29 | | -We prefer that potential users of these sequence data contact the individuals listed under Contacts with their plans to ensure that proposed usage of sequence data are not considered Reserved Analyses. |
| 21 | +For algorithms, we intend to release via BSD 3 clause or MIT / BSD compatible license. Algorithms are available on GitHub in the terraref organization: [github.com/terraref](https://github.com/terraref) and have been archived on Zenodo \(see [https://zenodo.org/search?q=terraref](https://zenodo.org/search?page=1&size=20&q=terraref)\). |
30 | 22 |
|
31 | | -## Software and Algorithms |
| 23 | +Citations for Individual Software and Documentation Components are listed in the [references](../references.md#software) section and can be browsed on [Zenodo](https://zenodo.org/search?page=1&size=20&q=terraref). |
32 | 24 |
|
33 | | -For algorithms, we intend to release via BSD 3 clause or MIT / BSD compatible license. Algorithms are available on GitHub in the terraref organization: github.com/terraref. Algorithms have been versioned and released on Zenodo \(see [https://zenodo.org/search?q=terraref](https://zenodo.org/search?page=1&size=20&q=terraref)\). |
| 25 | +## Unpublished Data |
34 | 26 |
|
35 | | -## Images, Phenotypes, and Other Raw Data |
| 27 | +We plan to make data from the Transportation Energy Resources from Renewable Agriculture Phenotyping Reference Platform \(TERRA-REF\) project available for use with attribution. |
36 | 28 |
|
37 | | -For other raw data, such as phenotypic data and associated metadata, we intend to release data under [CC0: Creative Commons with No Rights Reserved - Public Domain\)](https://creativecommons.org/share-your-work/public-domain/cc0/). This follows the requirements of [Dryad](https://datadryad.org) where the data will be published, and you can learn more about the motivation for putting data in the public domain [on their blog](https://blog.datadryad.org/2011/10/05/why-does-dryad-use-cc0/); briefly: the CC0 license allows wide use of these data and while it does not legally bind users to acknowledge the source **data users are expected cite our data and research in publications, presentations, and other products.** |
| 29 | +Please consider engaging with team members to collaborate on new research with these data. You can learn more about our approach to co-authorship and also about planned research papers in the section [Manuscripts and Authorship Guidelines](manuscripts-and-authorship-guidelines.md). |
38 | 30 |
|
39 | | -## Citing Data and Software |
| 31 | +### Timing of Future Data Releases |
40 | 32 |
|
41 | | -**Images, Phenotypes, Genomics, and other Data: Dryad Citation TBD** |
| 33 | +Any access to data prior to publication is granted with the understanding that the contributions and interests of the TERRA-REF team should be recognized and respected by the users of the data. The TERRA-REF team reserves the right to analyze and published its own data. Resource users should appropriately cite the source of the data and acknowledge the resource produces. The publication of the data, as suggested in the [TERRA-REF Authorship Guidelines](manuscripts-and-authorship-guidelines.md), should specify the collaborative nature of the project, and authorship is expected to include all those TERRA-REF team members contributing significantly to the work. |
42 | 34 |
|
43 | | -**Data Processing Pipeline**: Burnette, Maxwell, et al. "TERRA-REF data processing infrastructure." Proceedings of the Practice and Experience on Advanced Research Computing. 2018. 1-7. [doi:10.1145/3219104.3219152](https://doi.org/10.1145/3219104.3219152) |
| 35 | +Planned **future releases** include Sorghum Season 9, data from experiments at Kansas State University, and data from the Danforth Indoor Phenotyping Facility. |
44 | 36 |
|
45 | | -Individual Software and Documentation Components can be found on Zenodo: [https://zenodo.org/search?page=1&size=20&q=terraref](https://zenodo.org/search?page=1&size=20&q=terraref) |
| 37 | +Additional seasons can be requested as needed. We can provide the raw data and software required to process it. We can also collaborate with you to process the data, but this will typically require new funding sources. |
46 | 38 |
|
47 | 39 | ## Contacts |
48 | 40 |
|
49 | 41 | * Todd Mockler, Project/Genomics Lead \(email: tmockler@danforthcenter.org\) |
50 | | -* David LeBauer, Computing Pipeline Lead \(email: dlebauer@email.arizona.edu\) |
| 42 | +* David LeBauer, Computing Pipeline Lead \(email: dlebauer@arizona.edu\) |
51 | 43 | * Nadia Shakoor, Project Director \(email: nshakoor@danforthcenter.org\) |
52 | 44 |
|
| 45 | +See also [Contact Information](../#contact-info-and-more) in the Introduction. |
| 46 | + |
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