NMDC Data Use Policy
This work is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).
How to cite the NMDC:
E. M. Wood-Charlson, Anubhav, D. Auberry, H. Blanco, M. I. Borkum, Y. E. Corilo, K. W. Davenport, S. Deshpande, R. Devarakonda, M. Drake, W. D. Duncan, M. C. Flynn, D. Hays, B. Hu, M. Huntemann, P.-E. Li, M. Lipton, C.-C. Lo, D. Millard, K. Miller, P. D. Piehowski, S. Purvine, T. B. K. Reddy, M. Shakya, J. C. Sundaramurthi, P. Vangay, Y. Wei, B. E. Wilson, S. Canon, P. S. G. Chain, K. Fagnan, S. Martin, L. A. McCue, C. J. Mungall, N. J. Mouncey, M. E. Maxon, E. A. Eloe-Fadrosh, The National Microbiome Data Collaborative: enabling microbiome science. Nature Reviews Microbiology 18, 313-314 (2020). doi: 10.1038/s41579-020-0377-0
The data accessible on the National Microbiome Data Collaborative (NMDC) science gateway are contributed by NMDC Collaborators. The NMDC’s Data Policy is that all data and data contributors should be properly acknowledged in alignment with the FAIR (findable, accessible, interoperable, and reusable) data principles (Wilkinson, 2016) and in accordance with the Creative Commons with Attribution 4.0 International license.
Part A: NMDC Data Citations
Every data set and project in the NMDC is attributed to an NMDC Collaborator who chose to openly share their data with the global microbiome community. Proper citation of data sets discovered and accessed through the NMDC both supports reproducibility and provides important recognition of the NMDC data contributors through quantitative metrics on data reuse and impact of each contribution. To read more on data citations, please review the ESIP Data Citation Guidelines for Earth Science Data (https://doi.org/10.6084/m9.figshare.8441816.v1).
Citation elements include:
- Author: Person, people, or organization(s) responsible for the intellectual work to develop a data set.
- Public Release Date: When the source data was first made available for use.
- Title: Formal title of the data set. It is recommended that version information be independent of the title. Note this is the title of the data set, not the project or a related publication. It is important for the data set to have an identity and title of its own.
- Version ID: Careful versioning and documentation of version changes are central to enabling accurate citation. Data stewards need to track and clearly indicate precise versions as part of the citation for any version greater than 1. It may be appropriate to track major and minor versions.
- Repository: Name of the entity that holds, archives, publishes, prints, distributes, releases, issues, or produces the data. If citing processed data, this should also include a reference to the repository that holds the raw, source data.
- Resolvable Persistent Identifier(s): Unique identifier that provides the ability to access the data. If citing processed data, this should also include a reference to the identifier for the raw, source data. Not all data have Persistent Identifiers (PIDs) or can be digitally accessed, so an alternative method to access metadata, such as a URL or a physical address, can be provided instead.
- Access Date: Data can be dynamic and changeable in ways that are not always reflected in release dates and versions, so it is important to indicate when data were accessed.
Citing a single NMDC data set or project
A data citation captures the core concepts necessary to provide attribution and provenance. When citing a single data set or project accessed through the NMDC, please follow the below format(s):
Data set – source:
Wrighton, K. (2014) Deep subsurface shale carbon reservoir microbial communities from Ohio, USA – Utica-2 Time Series 2014_10_10 [Data set]. DOE Joint Genome Institute (PID). Accessed: 5 November 2020.
Data set – processed:
Wrighton, K. (2014) Deep subsurface shale carbon reservoir microbial communities from Ohio, USA – Utica-2 Time Series 2014_10_10 [Data set]. v2.0. DOE Joint Genome Institute (PID); NMDC (PID). Accessed: 5 November 2020.
Wrighton, K. (2014). Microbial controls on biogeochemical cycling in deep subsurface shale carbon reservoirs [Data set]. DOE Joint Genome Institute (https://doi.org/10.25585/1487763). Accessed: 5 November 2020.
Citing more than one NMDC data set or project
The NMDC science gateway enables the discovery and recombination of diverse data sets across projects. Each unique combination of data can be captured for citation and publication, enabling downstream attribution and reproducibility. The NMDC is able to issue a Collection DOI, through the U.S. Department of Energy Office of Scientific and Technical Information (OSTI), that appropriately cites each data set and/or project represented in the new analysis/study. The collection DOI refers to an NMDC landing page that can be provided as part of a data availability statement for a journal publication or report.
Jones, J. (2020) Title [Data set]. NMDC (PID).
Part B: NMDC Data Contributions
The NMDC supports open science and FAIR data principles. By contributing to the NMDC, your data become discoverable and accessible to the broader microbiome community. Data are processed through the standardized NMDC workflows with predefined parameters so that samples collected at different times and across diverse projects are analysed exactly the same enabling cross-studies comparable to each other.
During the NMDC pilot, direct contributions of data have been restricted to enable rapid, iterative feature-driven design, focused on metagenome, metatranscriptome, metaproteome, and metabolomic data. All data in the NMDC are associated with curated sample metadata. The NMDC has identified required metadata, based on the Genomic Standards Consortium MIxS packages. Finally, data in the NMDC adheres to the Creative Commons Attribution 4.0 License for data usage rights.
If you are interested in working with the NMDC and believe you have data that meet these requirements, please contact the NMDC team (firstname.lastname@example.org).
Part C: UC Berkeley Lab Data Contributor License Agreement
In order to clarify the intellectual property rights granted with respect to any contributions from any person or entity (“Contribution“), The Regents of the University of California, Department of Energy contract-operators of the Ernest Orlando Lawrence Berkeley National Laboratory (“Berkeley Lab”) must have a Contributor License Agreement (the “Agreement“) agreed to by each contributor. The license granted hereunder is for your protection as a contributor as well as for the protection of Berkeley Lab; it does not change your rights to use your own Contributions for any other purpose.
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