Data Management

Resources for developing PIER Plans and DMPs with KBase as a collaborator.

Current language will be adjusted as these plans and guidance evolve.

Resources for Promoting Inclusion and Equity in Research (PIER) Plans

As required for Genomic Science Program Science Focus Areas and Funding Opportunity Announcement solicitations and invitations for research funding from the Department of Energy Office of Science.

Recruitment Strategy for Promoting Inclusive and Equitable Research

If you need resources for building a diverse team and expanding collaborations to promote equity and inclusion within your proposal, the following programs are available.

DOE-sponsored and collaborating National Lab programs:

Department of Energy’s Office of Science (DOE-SC) Workforce Development for Teachers and Scientists (WDTS) programs (https://science.osti.gov/wdts)
LBNL
- Workforce Development and Education (https://education.lbl.gov/internships/)
- K12 STEM Education and Outreach (https://k12education.lbl.gov/)
ORNL: Educational Programs (https://education.ornl.gov/)
ANL: Educational Programs and Outreach (https://www.anl.gov/education)
BNL: Workforce Development and Science Education (https://www.bnl.gov/education/)

KBase supported and affiliated programs:

KBase Educators supports and collaborates with educators and students at approximately 30 Minority-Serving Institutions in the US and in 19 countries across 6 continents.
Regularly hosts summer high school, undergraduate, and graduate interns.
Involved with the NSF Research Experience for Undergraduates National Summer Undergraduate Research Project (NSURP; https://nsurp.org/).

Example text: KBase supports inclusion and equity in research, working with a diverse user community. The KBase Educators program supports and collaborates with educators and students at approximately 30 Minority-Serving Institutions in the US and in 19 countries across 6 continents. The team regularly hosts high school, undergraduate, and graduate interns. KBase is also involved with the NSF Research Experience for Undergraduates National Summer Undergraduate Research Project (NSURP; https://nsurp.org/), a remote program built to support underrepresented STEM college and university students.

Creating and Sustaining an Inclusive, Safe, and Professional Environment

We recommend referring to your home-institution programs for resources on Diversity, Equity, and Inclusion training, including bias and mentoring.

Example language for proposals that include KBase staff or support the KBase community:

KBase provides equitable, inclusive, and holistic professional development opportunities for staff and researchers at any career level and any level of expertise. KBase enables researchers, educators, and students alike to grow their research, share and publish their discoveries, and network with the broader systems biology community. KBase also supports equitable access to data science training and high performance computing, without the prerequisite of knowing how to code. This enables KBase to support a more inclusive and diverse community of individuals, including the KBase Educators (https://www.kbase.us/engage/educators/).
KBase adheres to a Code of Conduct (https://www.kbase.us/kbase-code-of-conduct/) that provides a welcoming and supportive environment for both our team and our user community in an effort to recognize that people bring diverse life histories and experiences, and that everyone’s contribution has value. All KBase staff are encouraged to participate in their lab’s DEI-related training and events.

Examples of programs and events can be found on respective Lab sites:

LBNL: https://diversity.lbl.gov/
ORNL: https://diversity.ornl.gov/
ANL: https://www.anl.gov/diversity-and-inclusion
BNL: https://www.bnl.gov/diversity/

Data Management Plans (DMPs)

Required for all publishable data, metadata, and software from research funded by the the Genomic Science Program (https://genomicscience.energy.gov/datasharing/) and Department of Energy (https://www.energy.gov/datamanagement/doe-policy-digital-research-data-management).

Data Management Plans, or DMPs, should address how samples, data, software, and any other research products generated by the project will be accessed, shared, and preserved, and include ownership/responsibility considerations. These topics support the generation of Findable, Accessible, Interoperable, and Reusable (FAIR, Wilkinson et al. 2016) scientific research products. Quality metadata about the research products, especially samples, data, and the provenance on how each were generated, also support comparability and reproducibility. We recommend reviewing the 10 Simple Rules and Getting and Giving Credit for Data (Wood-Charlson et al. 2022) for additional details and resources.

For each topic, we have provided information and example text on how KBase adheres to community standards, enables sharing and public access, and fits into the broader architecture of DOE-funded resources that support a complete data lifecycle (Figure 1).

Fig. 1 Data and Analysis Ecosystem BER researchers and facilities produce a wealth of data for predictively understanding complex biological systems. To fully leverage this data, BSSD supports integrative computational and data science platforms to facilitate community access, analysis, and sharing of omics, imaging, and other data types. [Courtesy Lawrence Berkeley National Laboratory] (U.S. DOE. 2021. Biological Systems Science Division Strategic Plan, DOE/SC-0205. U.S. Department of Energy Office of Science (genomicscience.energy.gov/2021bssdstrategicplan/).

Samples and data

Describe the types of samples that will be generated; the protocols, tools, and instruments used to generate data; and any analysis the data will undergo. Include descriptions (size, format, frequency, etc) of any existing or planned datasets.

Samples

While not a sample repository, KBase does support community standards used to describe sample metadata. Examples include: International Geo/General Sample Number (IGSN) – a community-standard persistent identifier for physical samples, and NCBI Biosamples (see documentation on KBase samples for more information). For microbiome-specific samples, we recommend also reviewing the National Microbiome Data Collaborative’s DMP page on “Microbiome Community Standards & Repositories.”

Example text: KBase supports samples by storing sample metadata that adheres to community standards (or robust user-defined descriptors of samples where standards have not yet been established) and making it available for comparative analyses and exploration in the KBase platform.

Data

KBase supports a wide range of data types and file formats related to systems biology research, including genomes, annotations, metagenomes, expression, protein-protein interactions, models of organismal and community metabolism, gene regulation, and sample metadata. See links for a complete list of KBase data types and file formats and KBase Data Sources.

Example text: All curated data can be uploaded (and downloaded) using standardized file formats. Data will be integrated into KBase for open-access data sharing, and reproducible analysis through Narratives. Any Narrative used to share results and/or generated for publication will be assigned a DOI and cited in the publication’s reference section. All data contributed to KBase are immediately tracked for reuse within the KBase provenance architecture. KBase provides views and copies/download statistics for all Narratives with a DOI, which demonstrates the broader impact of the data through its use by others.

Software

KBase supports open source software and best practices as a resource developed to provide public access to cutting-edge software tools relevant to the mission of the Department of Energy Office of Science. It also provides a means for users to share their data and optimized software workflows. All KBase code is available in the KBase Github repository, as a community-standard, open source platform for making software and code widely available.

Example text: All software tools described are open source and will be freely available through KBase and Github, including the KBase GitHub repository. Documentation will be provided to users to empower adoption for their research studies. All software housed within KBase is developed under open source licenses (e.g., the MIT Open Source License). Impact of developer contributions are tracked as the number of Narratives a tool has been used in and how many times it has been run. In addition, all KBase Apps are cited within the Narrative and automatically linked to any downstream Narrative DOIs generated when a user is publishing their research.

Access, sharing, and preservation

KBase is free and open to anyone able to access a web browser and create an account. Data and analysis workflows can be made accessible outside the KBase login by creating a “static” HTML snapshot of the Narrative. Full access (e.g., add data, run tools, or download) requires viewers to create an account, as that supports provenance and reuse tracking.Therefore, it is recommended to provide sufficient documentation in the Narrative such that readers can explore your results prior to being asked to login.

A specific version of a KBase Narrative can be saved and assigned a DOI, by request. The Narrative DOI. The default reuse policy for Narratives with a DOI is a Creative Commons CC0 license, allowing unlimited reuse. Narrative authors may request a CC-BY-4.0 license (reuse with attribution) for a Narrative as an analysis workflow, but all data within the Narrative remain CC0.

All KBase user data are backed up to the Amazon S3 cloud services, ensuring that the full system could be restored if necessary. If KBase were to no longer be supported, KBase has a partnership with the California Digital Library to migrate all data associated with a Narrative with a DOI to Dryad for long-term access and storage.

Example text: Access, sharing, and preservation of data will be maintained through KBase’s existing functionality of daily backups to Google S3. By request, datasets can be assigned a DOI with a CC0 license. Relevant metadata will be included in the DOI landing page and full accessibility will be available within the KBase Narrative environment. As necessary, KBase will preserve all data and metadata associated with a DOI in a repository affiliated with the California Digital Library for long-term access and storage.

Ownership and responsibilities

The DMP should ensure that roles and responsibilities are accounted for and it is clear how the requirements for data management will be met. It should also be clear how responsibilities will be transferred if personnel leave the project. In KBase, the creator of a Narrative or Organization is permanently assigned. However, full administrative privileges can be granted (and revoked for) to other KBase users.

Example text: Primary ownership of data and organizations in KBase will be coordinated by (name/position). In the event (name/position) is no longer on the project, the administration of these resources will pass to (second name/position).

KBase also supports bioinformaticians to contribute code and analysis tools to the KBase open source project. Community developers are trained in the KBase software development kit (SDK) and supported throughout the KBase software release process. It is expected that community developers maintain and update their code as necessary.

Example text: KBase supports community developers to incorporate their software into the KBase open source project. By doing so, community developers agree to follow best practices, and maintain and update their code as necessary.

How to cite KBase: Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018; 36: 566. doi: 10.1038/nbt.4163

How to cite the KBase DMP: Arkin AP, et al. DOE Systems Biology Knowledgebase (KBase) Data Management Plan. DMPTool. 2024. doi: 10.48321/D13BA96b4d